MULTISPECIES: substrate-binding domain-containing protein [Bacteroides]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| PBP1_sensor_kinase-like | cd06308 | periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ... |
27-295 | 5.20e-135 | |||||
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail. : Pssm-ID: 380531 [Multi-domain] Cd Length: 268 Bit Score: 405.39 E-value: 5.20e-135
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| BaeS | COG0642 | Signal transduction histidine kinase [Signal transduction mechanisms]; |
387-641 | 1.58e-63 | |||||
Signal transduction histidine kinase [Signal transduction mechanisms]; : Pssm-ID: 440407 [Multi-domain] Cd Length: 328 Bit Score: 217.85 E-value: 1.58e-63
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| OmpR | COG0745 | DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ... |
708-909 | 1.51e-41 | |||||
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription]; : Pssm-ID: 440508 [Multi-domain] Cd Length: 204 Bit Score: 151.26 E-value: 1.51e-41
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| AraC | COG2207 | AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; |
870-954 | 3.45e-25 | |||||
AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; : Pssm-ID: 441809 [Multi-domain] Cd Length: 258 Bit Score: 106.02 E-value: 3.45e-25
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
357-415 | 1.59e-04 | |||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; : Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 45.28 E-value: 1.59e-04
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| Name | Accession | Description | Interval | E-value | |||||||
| PBP1_sensor_kinase-like | cd06308 | periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ... |
27-295 | 5.20e-135 | |||||||
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail. Pssm-ID: 380531 [Multi-domain] Cd Length: 268 Bit Score: 405.39 E-value: 5.20e-135
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| RbsB | COG1879 | ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ... |
2-300 | 4.12e-81 | |||||||
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism]; Pssm-ID: 441483 [Multi-domain] Cd Length: 307 Bit Score: 265.25 E-value: 4.12e-81
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| BaeS | COG0642 | Signal transduction histidine kinase [Signal transduction mechanisms]; |
387-641 | 1.58e-63 | |||||||
Signal transduction histidine kinase [Signal transduction mechanisms]; Pssm-ID: 440407 [Multi-domain] Cd Length: 328 Bit Score: 217.85 E-value: 1.58e-63
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| Peripla_BP_4 | pfam13407 | Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ... |
34-283 | 3.67e-48 | |||||||
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognizes fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 433182 [Multi-domain] Cd Length: 259 Bit Score: 172.11 E-value: 3.67e-48
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| OmpR | COG0745 | DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ... |
708-909 | 1.51e-41 | |||||||
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription]; Pssm-ID: 440508 [Multi-domain] Cd Length: 204 Bit Score: 151.26 E-value: 1.51e-41
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| PRK15347 | PRK15347 | two component system sensor kinase; |
388-813 | 5.63e-40 | |||||||
two component system sensor kinase; Pssm-ID: 237951 [Multi-domain] Cd Length: 921 Bit Score: 160.19 E-value: 5.63e-40
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| REC_D1_PleD-like | cd17538 | first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ... |
711-812 | 2.36e-35 | |||||||
first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar domains; PleD contains a REC domain (D1) with the phosphorylatable aspartate, a REC-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes D1 of PleD and similar domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381093 [Multi-domain] Cd Length: 104 Bit Score: 129.54 E-value: 2.36e-35
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| HATPase_c | smart00387 | Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
530-641 | 1.25e-32 | |||||||
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 121.99 E-value: 1.25e-32
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| HATPase_EvgS-ArcB-TorS-like | cd16922 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases, many are hybrid ... |
535-640 | 2.36e-30 | |||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases, many are hybrid sensor histidine kinases, similar to Escherichia coli EvgS, ArcB, TorS, BarA, RcsC; This family contains the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinases (HKs), including the following Escherichia coli HKs: EvgS, a HK of the EvgS-EvgA two-component system (TCS) that confers acid resistance; ArcB, a HK of the ArcB-ArcA TCS that modulates the expression of numerous genes in response to respiratory growth conditions; TorS, a HK of the TorS-TorR TCS which is involved in the anaerobic utilization of trimethylamine-N-oxide; BarA, a HK of the BarA-UvrY TCS involved in the regulation of carbon metabolism; and RcsC, a HK of the RcsB-RcsC TCS which regulates the expression of the capsule operon and of the cell division gene ftsZ. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), with most having accessory sensor domain(s) such as GAF, PAS and CHASE; many are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. Pssm-ID: 340399 [Multi-domain] Cd Length: 110 Bit Score: 115.67 E-value: 2.36e-30
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| HATPase_c | pfam02518 | Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
530-642 | 4.52e-28 | |||||||
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. Pssm-ID: 460579 [Multi-domain] Cd Length: 109 Bit Score: 108.99 E-value: 4.52e-28
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| Response_reg | pfam00072 | Response regulator receiver domain; This domain receives the signal from the sensor partner in ... |
711-822 | 5.91e-28 | |||||||
Response regulator receiver domain; This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. Pssm-ID: 395025 [Multi-domain] Cd Length: 111 Bit Score: 108.78 E-value: 5.91e-28
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| pleD | PRK09581 | response regulator PleD; Reviewed |
711-832 | 2.65e-27 | |||||||
response regulator PleD; Reviewed Pssm-ID: 236577 [Multi-domain] Cd Length: 457 Bit Score: 116.54 E-value: 2.65e-27
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| AraC | COG2207 | AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; |
870-954 | 3.45e-25 | |||||||
AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; Pssm-ID: 441809 [Multi-domain] Cd Length: 258 Bit Score: 106.02 E-value: 3.45e-25
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| HTH_ARAC | smart00342 | helix_turn_helix, arabinose operon control protein; |
869-952 | 5.73e-24 | |||||||
helix_turn_helix, arabinose operon control protein; Pssm-ID: 197666 [Multi-domain] Cd Length: 84 Bit Score: 96.47 E-value: 5.73e-24
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| cztS_silS_copS | TIGR01386 | heavy metal sensor kinase; Members of this family contain a sensor histidine kinase domain ... |
367-639 | 9.27e-24 | |||||||
heavy metal sensor kinase; Members of this family contain a sensor histidine kinase domain (pfam00512) and a domain found in bacterial signal proteins (pfam00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Pssm-ID: 273593 [Multi-domain] Cd Length: 457 Bit Score: 105.55 E-value: 9.27e-24
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| PRK10653 | PRK10653 | ribose ABC transporter substrate-binding protein RbsB; |
65-261 | 9.86e-24 | |||||||
ribose ABC transporter substrate-binding protein RbsB; Pssm-ID: 182620 [Multi-domain] Cd Length: 295 Bit Score: 102.48 E-value: 9.86e-24
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| HTH_18 | pfam12833 | Helix-turn-helix domain; |
875-954 | 5.52e-22 | |||||||
Helix-turn-helix domain; Pssm-ID: 432818 [Multi-domain] Cd Length: 81 Bit Score: 90.73 E-value: 5.52e-22
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| BaeS_SmeS | NF012163 | sensor histidine kinase efflux regulator BaeS; |
391-639 | 2.75e-18 | |||||||
sensor histidine kinase efflux regulator BaeS; Pssm-ID: 411086 [Multi-domain] Cd Length: 457 Bit Score: 88.73 E-value: 2.75e-18
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| REC | smart00448 | cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ... |
711-762 | 7.44e-12 | |||||||
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues. Pssm-ID: 214668 [Multi-domain] Cd Length: 55 Bit Score: 61.05 E-value: 7.44e-12
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| spore_0_A | TIGR02875 | sporulation transcription factor Spo0A; Spo0A, the stage 0 sporulation protein A, is a ... |
711-824 | 1.36e-10 | |||||||
sporulation transcription factor Spo0A; Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species. [Cellular processes, Sporulation and germination] Pssm-ID: 131922 [Multi-domain] Cd Length: 262 Bit Score: 62.89 E-value: 1.36e-10
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| PRK13503 | PRK13503 | HTH-type transcriptional activator RhaS; |
873-951 | 4.83e-10 | |||||||
HTH-type transcriptional activator RhaS; Pssm-ID: 184094 [Multi-domain] Cd Length: 278 Bit Score: 61.62 E-value: 4.83e-10
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
357-415 | 1.59e-04 | |||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 45.28 E-value: 1.59e-04
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
357-415 | 7.29e-04 | |||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 40.29 E-value: 7.29e-04
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| Atg16_CCD | cd22887 | Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family ... |
356-406 | 5.31e-03 | |||||||
Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins. Pssm-ID: 439196 [Multi-domain] Cd Length: 91 Bit Score: 37.16 E-value: 5.31e-03
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| Name | Accession | Description | Interval | E-value | ||||||||
| PBP1_sensor_kinase-like | cd06308 | periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ... |
27-295 | 5.20e-135 | ||||||||
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail. Pssm-ID: 380531 [Multi-domain] Cd Length: 268 Bit Score: 405.39 E-value: 5.20e-135
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| RbsB | COG1879 | ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ... |
2-300 | 4.12e-81 | ||||||||
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism]; Pssm-ID: 441483 [Multi-domain] Cd Length: 307 Bit Score: 265.25 E-value: 4.12e-81
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| PBP1_ABC_sugar_binding-like | cd01536 | periplasmic sugar-binding domain of active transport systems that are members of the type 1 ... |
27-294 | 1.78e-74 | ||||||||
periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily; Periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2) receptors such as LsrB and LuxP which are highly homologous to periplasmic pentose/hexose sugar-binding proteins. Pssm-ID: 380478 [Multi-domain] Cd Length: 268 Bit Score: 245.55 E-value: 1.78e-74
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| PBP1_galactofuranose_YtfQ-like | cd06309 | periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ... |
27-300 | 7.09e-64 | ||||||||
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally. Pssm-ID: 380532 [Multi-domain] Cd Length: 285 Bit Score: 217.09 E-value: 7.09e-64
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| BaeS | COG0642 | Signal transduction histidine kinase [Signal transduction mechanisms]; |
387-641 | 1.58e-63 | ||||||||
Signal transduction histidine kinase [Signal transduction mechanisms]; Pssm-ID: 440407 [Multi-domain] Cd Length: 328 Bit Score: 217.85 E-value: 1.58e-63
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| KdpD | COG2205 | K+-sensing histidine kinase KdpD [Signal transduction mechanisms]; |
403-642 | 2.37e-61 | ||||||||
K+-sensing histidine kinase KdpD [Signal transduction mechanisms]; Pssm-ID: 441807 [Multi-domain] Cd Length: 239 Bit Score: 208.61 E-value: 2.37e-61
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| WalK | COG5002 | Sensor histidine kinase WalK [Signal transduction mechanisms]; |
385-640 | 1.85e-58 | ||||||||
Sensor histidine kinase WalK [Signal transduction mechanisms]; Pssm-ID: 444026 [Multi-domain] Cd Length: 390 Bit Score: 205.94 E-value: 1.85e-58
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| PBP1_ribose_binding | cd06323 | periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ... |
55-261 | 7.51e-53 | ||||||||
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis D-ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group belong to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability. Pssm-ID: 380546 [Multi-domain] Cd Length: 268 Bit Score: 185.96 E-value: 7.51e-53
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| PBP1_ABC_sugar_binding-like | cd19996 | monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ... |
36-299 | 3.59e-52 | ||||||||
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. Pssm-ID: 380651 [Multi-domain] Cd Length: 302 Bit Score: 185.14 E-value: 3.59e-52
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| Peripla_BP_4 | pfam13407 | Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ... |
34-283 | 3.67e-48 | ||||||||
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognizes fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 433182 [Multi-domain] Cd Length: 259 Bit Score: 172.11 E-value: 3.67e-48
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| PBP1_ABC_IbpA-like | cd19968 | periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The ... |
42-290 | 3.41e-47 | ||||||||
periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by an ABC transporter that consists of the PBP IbpA, the transmembrane permease IatP, and the ABC IatA. IbpA shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. Pssm-ID: 380623 [Multi-domain] Cd Length: 271 Bit Score: 169.87 E-value: 3.41e-47
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| PBP1_ABC_ThpA_XypA | cd06313 | periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ... |
27-300 | 2.36e-46 | ||||||||
periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group includes periplasmic D-threitol-binding protein ThpA and xylitol/L-sorbitol-binding protein XypA, which are part of sugar ABC-type transport systems. Both ThpA and XypA share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. Pssm-ID: 380536 [Multi-domain] Cd Length: 277 Bit Score: 167.45 E-value: 2.36e-46
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| PBP1_rhizopine_binding-like | cd06301 | periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to ... |
28-261 | 1.36e-44 | ||||||||
periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily. Pssm-ID: 380524 [Multi-domain] Cd Length: 272 Bit Score: 162.40 E-value: 1.36e-44
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| PBP1_ABC_sugar_binding-like | cd19972 | monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ... |
54-295 | 4.26e-44 | ||||||||
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380627 [Multi-domain] Cd Length: 269 Bit Score: 160.68 E-value: 4.26e-44
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| PBP1_ABC_sugar_binding-like | cd19971 | monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ... |
42-292 | 3.16e-43 | ||||||||
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380626 [Multi-domain] Cd Length: 267 Bit Score: 158.13 E-value: 3.16e-43
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| PBP1_ABC_sugar_binding-like | cd06311 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ... |
62-239 | 8.25e-43 | ||||||||
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380534 [Multi-domain] Cd Length: 270 Bit Score: 157.14 E-value: 8.25e-43
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| OmpR | COG0745 | DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ... |
708-909 | 1.51e-41 | ||||||||
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription]; Pssm-ID: 440508 [Multi-domain] Cd Length: 204 Bit Score: 151.26 E-value: 1.51e-41
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| PRK15347 | PRK15347 | two component system sensor kinase; |
388-813 | 5.63e-40 | ||||||||
two component system sensor kinase; Pssm-ID: 237951 [Multi-domain] Cd Length: 921 Bit Score: 160.19 E-value: 5.63e-40
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| PBP1_ABC_D-talitol-like | cd06318 | periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; ... |
28-299 | 6.29e-40 | ||||||||
periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380541 [Multi-domain] Cd Length: 282 Bit Score: 149.10 E-value: 6.29e-40
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| PleD | COG3706 | Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ... |
708-821 | 8.28e-40 | ||||||||
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate cyclase (GGDEF) domain [Signal transduction mechanisms, Transcription]; Pssm-ID: 442920 [Multi-domain] Cd Length: 179 Bit Score: 145.44 E-value: 8.28e-40
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| RpfG | COG3437 | Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ... |
705-833 | 9.73e-40 | ||||||||
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms]; Pssm-ID: 442663 [Multi-domain] Cd Length: 224 Bit Score: 146.85 E-value: 9.73e-40
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| PRK09959 | PRK09959 | acid-sensing system histidine kinase EvgS; |
383-831 | 3.00e-38 | ||||||||
acid-sensing system histidine kinase EvgS; Pssm-ID: 182169 [Multi-domain] Cd Length: 1197 Bit Score: 155.28 E-value: 3.00e-38
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| PBP1_TmRBP-like | cd19967 | D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ... |
55-281 | 7.14e-38 | ||||||||
D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ribose binding protein (ttRBP); Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability. Pssm-ID: 380622 [Multi-domain] Cd Length: 272 Bit Score: 142.85 E-value: 7.14e-38
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| PBP1_ABC_sugar_binding-like | cd19999 | monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ... |
27-232 | 1.02e-36 | ||||||||
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. Pssm-ID: 380654 [Multi-domain] Cd Length: 313 Bit Score: 140.91 E-value: 1.02e-36
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| PBP1_ABC_sugar_binding-like | cd06322 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ... |
54-244 | 1.05e-36 | ||||||||
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380545 [Multi-domain] Cd Length: 270 Bit Score: 139.72 E-value: 1.05e-36
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| CheY | COG0784 | CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ... |
705-830 | 1.82e-36 | ||||||||
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator Spo0F [Signal transduction mechanisms]; Pssm-ID: 440547 [Multi-domain] Cd Length: 128 Bit Score: 133.82 E-value: 1.82e-36
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| PBP1_tmGBP | cd06314 | periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and ... |
55-296 | 1.87e-36 | ||||||||
periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs; Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are members of the type 1 periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP). Pssm-ID: 380537 [Multi-domain] Cd Length: 271 Bit Score: 138.87 E-value: 1.87e-36
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| PBP1_allose_binding | cd06320 | periplasmic allose-binding domain of bacterial transport systems that function as a primary ... |
55-300 | 4.02e-36 | ||||||||
periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis; Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Pssm-ID: 380543 [Multi-domain] Cd Length: 283 Bit Score: 138.16 E-value: 4.02e-36
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| PBP1_ABC_sugar_binding-like | cd06321 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ... |
55-244 | 9.22e-36 | ||||||||
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380544 [Multi-domain] Cd Length: 270 Bit Score: 136.65 E-value: 9.22e-36
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| PBP1_ABC_xylose_binding-like | cd19992 | periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ... |
27-242 | 1.36e-35 | ||||||||
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380647 [Multi-domain] Cd Length: 284 Bit Score: 136.95 E-value: 1.36e-35
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| REC_D1_PleD-like | cd17538 | first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ... |
711-812 | 2.36e-35 | ||||||||
first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar domains; PleD contains a REC domain (D1) with the phosphorylatable aspartate, a REC-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes D1 of PleD and similar domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381093 [Multi-domain] Cd Length: 104 Bit Score: 129.54 E-value: 2.36e-35
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| PRK11091 | PRK11091 | aerobic respiration control sensor protein ArcB; Provisional |
387-889 | 2.83e-34 | ||||||||
aerobic respiration control sensor protein ArcB; Provisional Pssm-ID: 236842 [Multi-domain] Cd Length: 779 Bit Score: 141.23 E-value: 2.83e-34
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| COG4251 | COG4251 | Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal ... |
376-641 | 3.59e-34 | ||||||||
Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Pssm-ID: 443393 [Multi-domain] Cd Length: 503 Bit Score: 137.99 E-value: 3.59e-34
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| PBP1_ABC_sugar_binding-like | cd19969 | monosaccharide ABC transporter substrate binding protein; Periplasmic sugar-binding domain of ... |
55-261 | 1.22e-33 | ||||||||
monosaccharide ABC transporter substrate binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380624 [Multi-domain] Cd Length: 278 Bit Score: 130.92 E-value: 1.22e-33
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| REC_PA4781-like | cd19920 | phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar ... |
711-812 | 1.64e-33 | ||||||||
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar domains; Pseudomonas aeruginosa cyclic di-GMP phosphodiesterase PA4781 contains an N-terminal REC domain and a C-terminal catalytic HD-GYP domain, characteristics of RpfG family response regulators. PA4781 is involved in cyclic di-3',5'-GMP (c-di-GMP) hydrolysis/degradation in a two-step reaction via the linear intermediate pGpG to produce GMP. Its unphosphorylated REC domain prevents accessibility of c-di-GMP to the active site. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381147 [Multi-domain] Cd Length: 103 Bit Score: 124.55 E-value: 1.64e-33
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| REC_OmpR | cd17574 | phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ... |
712-811 | 5.40e-33 | ||||||||
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins are one of the most widespread transcriptional regulators. OmpR family members contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domain. They are involved in the control of environmental stress tolerance (such as the oxidative, osmotic and acid stress response), motility, virulence, outer membrane biogenesis and other processes. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381116 [Multi-domain] Cd Length: 99 Bit Score: 122.90 E-value: 5.40e-33
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| PBP1_ABC_sugar_binding-like | cd06300 | periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are ... |
27-300 | 8.87e-33 | ||||||||
periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. Pssm-ID: 380523 [Multi-domain] Cd Length: 302 Bit Score: 128.98 E-value: 8.87e-33
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| PBP1_ABC_sugar_binding-like | cd20004 | monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ... |
55-242 | 9.60e-33 | ||||||||
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380659 [Multi-domain] Cd Length: 273 Bit Score: 128.12 E-value: 9.60e-33
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| PBP1_ABC_sugar_binding-like | cd20006 | monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ... |
65-297 | 1.08e-32 | ||||||||
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380661 [Multi-domain] Cd Length: 274 Bit Score: 128.10 E-value: 1.08e-32
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| HATPase_c | smart00387 | Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
530-641 | 1.25e-32 | ||||||||
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 121.99 E-value: 1.25e-32
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| XylF | COG4213 | ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism] ... |
45-296 | 3.28e-32 | ||||||||
ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]; Pssm-ID: 443359 [Multi-domain] Cd Length: 310 Bit Score: 127.56 E-value: 3.28e-32
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| PBP1_ABC_sugar_binding-like | cd06310 | monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ... |
55-242 | 1.98e-31 | ||||||||
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380533 [Multi-domain] Cd Length: 272 Bit Score: 124.38 E-value: 1.98e-31
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| COG4191 | COG4191 | Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal ... |
375-641 | 5.95e-31 | ||||||||
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Pssm-ID: 443345 [Multi-domain] Cd Length: 361 Bit Score: 125.30 E-value: 5.95e-31
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| PBP1_ABC_sugar_binding-like | cd19970 | monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ... |
70-244 | 8.62e-31 | ||||||||
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380625 [Multi-domain] Cd Length: 275 Bit Score: 122.74 E-value: 8.62e-31
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| REC_OmpR_BsPhoP-like | cd19937 | phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus ... |
712-825 | 1.16e-30 | ||||||||
phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus subtilis PhoP (BsPhoP) is part of the PhoPR two-component system that participates in a signal transduction network that controls adaptation of the bacteria to phosphate deficiency by regulating (activating or repressing) genes of the Pho regulon upon phosphorylation by PhoR. When activated, PhoPR directs expression of phosphate scavenging enzymes, lowers synthesis of the phosphate-rich wall teichoic acid (WTA) and initiates synthesis of teichuronic acid, a non-phosphate containing replacement anionic polymer. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381164 [Multi-domain] Cd Length: 116 Bit Score: 116.60 E-value: 1.16e-30
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| HATPase_EvgS-ArcB-TorS-like | cd16922 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases, many are hybrid ... |
535-640 | 2.36e-30 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases, many are hybrid sensor histidine kinases, similar to Escherichia coli EvgS, ArcB, TorS, BarA, RcsC; This family contains the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinases (HKs), including the following Escherichia coli HKs: EvgS, a HK of the EvgS-EvgA two-component system (TCS) that confers acid resistance; ArcB, a HK of the ArcB-ArcA TCS that modulates the expression of numerous genes in response to respiratory growth conditions; TorS, a HK of the TorS-TorR TCS which is involved in the anaerobic utilization of trimethylamine-N-oxide; BarA, a HK of the BarA-UvrY TCS involved in the regulation of carbon metabolism; and RcsC, a HK of the RcsB-RcsC TCS which regulates the expression of the capsule operon and of the cell division gene ftsZ. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), with most having accessory sensor domain(s) such as GAF, PAS and CHASE; many are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. Pssm-ID: 340399 [Multi-domain] Cd Length: 110 Bit Score: 115.67 E-value: 2.36e-30
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| REC_Ycf29 | cd19927 | phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a ... |
711-811 | 2.57e-30 | ||||||||
phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a probable response regulator of a two-component system (TCS), typically consisting a sensor and a response regulator, that functions in adaptation to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Ycf29 contains an N-terminal REC domain and a LuxR-type helix-turn-helix DNA-binding output domain. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381154 [Multi-domain] Cd Length: 102 Bit Score: 115.17 E-value: 2.57e-30
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| REC_OmpR_PhoB | cd17618 | phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The ... |
711-822 | 3.34e-30 | ||||||||
phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The transcription factor PhoB is a component of the PhoR/PhoB two-component system, a key regulatory protein network that facilitates response to inorganic phosphate (Pi) starvation conditions by turning on the phosphate (pho) regulon whose products are involved in phosphorus uptake and metabolism. PhoB is a member of the OmpR family of DNA-binding response regulators that contains REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381133 [Multi-domain] Cd Length: 118 Bit Score: 115.42 E-value: 3.34e-30
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| PBP1_ABC_sugar_binding-like | cd06319 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ... |
55-261 | 9.85e-30 | ||||||||
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380542 [Multi-domain] Cd Length: 278 Bit Score: 119.77 E-value: 9.85e-30
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| NtrB | COG3852 | Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms]; |
387-640 | 1.27e-29 | ||||||||
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms]; Pssm-ID: 443061 [Multi-domain] Cd Length: 361 Bit Score: 121.49 E-value: 1.27e-29
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| NtrY | COG5000 | Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ... |
425-641 | 1.46e-29 | ||||||||
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Pssm-ID: 444024 [Multi-domain] Cd Length: 422 Bit Score: 122.76 E-value: 1.46e-29
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| PBP1_ABC_sugar_binding-like | cd06324 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ... |
55-317 | 3.47e-29 | ||||||||
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380547 [Multi-domain] Cd Length: 317 Bit Score: 119.25 E-value: 3.47e-29
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| PBP1_ABC_xylose_binding | cd19991 | D-xylose binding periplasmic protein; Periplasmic xylose-binding component of the ABC-type ... |
55-242 | 1.31e-28 | ||||||||
D-xylose binding periplasmic protein; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380646 [Multi-domain] Cd Length: 284 Bit Score: 116.57 E-value: 1.31e-28
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| PRK09835 | PRK09835 | Cu(+)/Ag(+) sensor histidine kinase; |
421-639 | 2.80e-28 | ||||||||
Cu(+)/Ag(+) sensor histidine kinase; Pssm-ID: 182101 [Multi-domain] Cd Length: 482 Bit Score: 119.88 E-value: 2.80e-28
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| REC_DivK-like | cd17548 | phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ... |
711-822 | 4.25e-28 | ||||||||
phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus DivK is an essential response regulator that is involved in the complex phosphorelay pathways controlling both cell division and motility. It localizes cell cycle regulators to specific poles of the cell during division. DivK contains a stand-alone REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381100 [Multi-domain] Cd Length: 115 Bit Score: 109.55 E-value: 4.25e-28
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| HATPase_c | pfam02518 | Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
530-642 | 4.52e-28 | ||||||||
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. Pssm-ID: 460579 [Multi-domain] Cd Length: 109 Bit Score: 108.99 E-value: 4.52e-28
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| REC | cd00156 | phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ... |
712-811 | 5.50e-28 | ||||||||
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs); Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381085 [Multi-domain] Cd Length: 99 Bit Score: 108.47 E-value: 5.50e-28
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| Response_reg | pfam00072 | Response regulator receiver domain; This domain receives the signal from the sensor partner in ... |
711-822 | 5.91e-28 | ||||||||
Response regulator receiver domain; This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. Pssm-ID: 395025 [Multi-domain] Cd Length: 111 Bit Score: 108.78 E-value: 5.91e-28
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| PRK11107 | PRK11107 | hybrid sensory histidine kinase BarA; Provisional |
413-811 | 6.27e-28 | ||||||||
hybrid sensory histidine kinase BarA; Provisional Pssm-ID: 236848 [Multi-domain] Cd Length: 919 Bit Score: 121.49 E-value: 6.27e-28
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| HATPase_TutC-TodS-like | cd16925 | Histidine kinase-like ATPase domain of hybrid sensor histidine kinases similar to Pseudomonas ... |
531-639 | 6.81e-28 | ||||||||
Histidine kinase-like ATPase domain of hybrid sensor histidine kinases similar to Pseudomonas putida TodS and Thauera aromatica TutC; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinase (HKs) such Pseudomonas putida TodS HK of the TodS-TodT two-component regulatory system (TCS) which controls the expression of a toluene degradation pathway. Thauera aromatica TutC may be part of a TCS that is involved in anaerobic toluene metabolism. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), PAS sensor domain(s) and a REC domain. Pssm-ID: 340402 [Multi-domain] Cd Length: 110 Bit Score: 108.73 E-value: 6.81e-28
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| REC_OmpR_PrrA-like | cd17627 | phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ... |
711-830 | 8.79e-28 | ||||||||
phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The Mycobacterium tuberculosis PrrA is part of the PrrA/PrrB two-component system (TCS) that has been implicated in early intracellular multiplication and is essential for viability. Also included in this subfamily is Mycobacterium tuberculosis MprA, part of the MprAB TCS that regulates EspR, a key regulator of the ESX-1 secretion system, and is required for establishment and maintenance of persistent infection in a tissue- and stage-specific fashion. PrrA and MprA belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381142 [Multi-domain] Cd Length: 116 Bit Score: 108.62 E-value: 8.79e-28
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| PBP1_methylthioribose_binding-like | cd06305 | similar to methylthioribose-binding protein of ABC-type transport systems that belong to a ... |
27-244 | 9.61e-28 | ||||||||
similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily; Proteins similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380528 [Multi-domain] Cd Length: 273 Bit Score: 113.54 E-value: 9.61e-28
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| PBP1_ABC_xylose_binding-like | cd01538 | periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong ... |
28-242 | 1.23e-27 | ||||||||
periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily; Periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380480 [Multi-domain] Cd Length: 283 Bit Score: 113.67 E-value: 1.23e-27
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| REC_RR468-like | cd17552 | phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and ... |
710-824 | 2.43e-27 | ||||||||
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and similar domains; Thermotoga maritima RR468 (encoded by gene TM0468) is the cognate response regulator (RR) of the class I histidine kinase HK853 (product of gene TM0853). HK853/RR468 comprise a two-component system (TCS) that couples environmental stimuli to adaptive responses. This subfamily also includes Fremyella diplosiphon complementary adaptation response regulator homolog RcaF, a small RR that is involved in four-step phosphorelays of the complementary chromatic adaptation (CCA) system that occurs in many cyanobacteria. Both RR468 and RcaF are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381104 [Multi-domain] Cd Length: 121 Bit Score: 107.25 E-value: 2.43e-27
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| pleD | PRK09581 | response regulator PleD; Reviewed |
711-832 | 2.65e-27 | ||||||||
response regulator PleD; Reviewed Pssm-ID: 236577 [Multi-domain] Cd Length: 457 Bit Score: 116.54 E-value: 2.65e-27
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| PBP1_ABC_sugar_binding-like | cd20008 | monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ... |
49-295 | 4.38e-27 | ||||||||
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380663 [Multi-domain] Cd Length: 277 Bit Score: 111.94 E-value: 4.38e-27
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| REC_hyHK | cd17598 | phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase ... |
711-825 | 9.05e-27 | ||||||||
phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase/response regulators; Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase/response regulators contain all the elements of a classical TCS in a single polypeptide chain. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381128 [Multi-domain] Cd Length: 118 Bit Score: 105.87 E-value: 9.05e-27
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| AtoC | COG2204 | DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ... |
707-833 | 1.70e-26 | ||||||||
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains [Signal transduction mechanisms]; Pssm-ID: 441806 [Multi-domain] Cd Length: 418 Bit Score: 113.52 E-value: 1.70e-26
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| PBP1_ABC_sugar_binding-like | cd06317 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ... |
54-299 | 1.87e-26 | ||||||||
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380540 [Multi-domain] Cd Length: 281 Bit Score: 110.16 E-value: 1.87e-26
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| PRK10841 | PRK10841 | two-component system sensor histidine kinase RcsC; |
394-813 | 2.56e-26 | ||||||||
two-component system sensor histidine kinase RcsC; Pssm-ID: 182772 [Multi-domain] Cd Length: 924 Bit Score: 116.23 E-value: 2.56e-26
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| PBP1_ABC_sugar_binding-like | cd19997 | monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ... |
37-299 | 3.50e-26 | ||||||||
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. Pssm-ID: 380652 [Multi-domain] Cd Length: 305 Bit Score: 110.07 E-value: 3.50e-26
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| REC_OmpR_DrrD-like | cd17625 | phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ... |
712-830 | 1.30e-25 | ||||||||
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a OmpR/PhoB homolog from Thermotoga maritima whose function is not yet known. This subfamily also includes Streptococcus agalactiae transcriptional regulatory protein DltR, part of the DltS/DltR two-component system (TCS), and Pseudomonas aeruginosa transcriptional activator protein PfeR, part of the PfeR/PfeS TCS, which activates expression of the ferric enterobactin receptor. The DltS/DltR TCS regulates the expression of the dlt operon, which comprises four genes (dltA, dltB, dltC, and dltD) that catalyze the incorporation of D-alanine residues into the lipoteichoic acids. Members of this subfamily belong to the OmpR/PhoB family, which comprises of two domains, an N-terminal receiver domain and a C-terminal DNA-binding winged helix-turn-helix effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381140 [Multi-domain] Cd Length: 115 Bit Score: 102.30 E-value: 1.30e-25
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| KinE | COG5809 | Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ... |
425-649 | 1.47e-25 | ||||||||
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]; Pssm-ID: 444511 [Multi-domain] Cd Length: 489 Bit Score: 111.60 E-value: 1.47e-25
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| PBP1_ABC_sugar_binding-like | cd20007 | monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ... |
78-296 | 2.19e-25 | ||||||||
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380662 [Multi-domain] Cd Length: 271 Bit Score: 106.55 E-value: 2.19e-25
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| REC_NarL-like | cd17535 | phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ... |
711-822 | 2.95e-25 | ||||||||
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family response regulators; The NarL family is one of the more abundant families of DNA-binding response regulators (RRs). Members of the NarL family contain a REC domain and a helix-turn-helix (HTH) DNA-binding output domain, with a majority of members containing a LuxR-type HTH domain. They function as transcriptional regulators. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381090 [Multi-domain] Cd Length: 117 Bit Score: 101.43 E-value: 2.95e-25
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| AraC | COG2207 | AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; |
870-954 | 3.45e-25 | ||||||||
AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; Pssm-ID: 441809 [Multi-domain] Cd Length: 258 Bit Score: 106.02 E-value: 3.45e-25
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| REC_OmpR_MtPhoP-like | cd17615 | phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ... |
711-830 | 1.07e-24 | ||||||||
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; Mycobacterium tuberculosis PhoP (MtPhoP) is part of the PhoP/PhoR two-component system that is involved in phosphate control by stimulating expression of genes involved in scavenging, transport and mobilization of phosphate, and repressing the utilization of nitrogen sources. Also included in this subfamily is Mycobacterium tuberculosis transcriptional regulatory protein TcrX, part of the two-component regulatory system TcrY/TcrX that may be involved in virulence. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381131 [Multi-domain] Cd Length: 118 Bit Score: 99.73 E-value: 1.07e-24
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| PBP1_ABC_sugar_binding-like | cd19973 | monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ... |
41-261 | 1.27e-24 | ||||||||
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2) receptors such as LsrB and LuxP which are highly homologous to periplasmic pentose/hexose sugar-binding proteins. Pssm-ID: 380628 [Multi-domain] Cd Length: 285 Bit Score: 104.86 E-value: 1.27e-24
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| PBP1_ABC_sugar_binding-like | cd19998 | monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ... |
56-304 | 2.64e-24 | ||||||||
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. Pssm-ID: 380653 [Multi-domain] Cd Length: 302 Bit Score: 104.29 E-value: 2.64e-24
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| PRK11360 | PRK11360 | two-component system sensor histidine kinase AtoS; |
387-640 | 3.38e-24 | ||||||||
two-component system sensor histidine kinase AtoS; Pssm-ID: 236901 [Multi-domain] Cd Length: 607 Bit Score: 108.52 E-value: 3.38e-24
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| HTH_ARAC | smart00342 | helix_turn_helix, arabinose operon control protein; |
869-952 | 5.73e-24 | ||||||||
helix_turn_helix, arabinose operon control protein; Pssm-ID: 197666 [Multi-domain] Cd Length: 84 Bit Score: 96.47 E-value: 5.73e-24
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| REC_CheY4-like | cd17562 | phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ... |
711-825 | 6.08e-24 | ||||||||
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY4 and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381110 [Multi-domain] Cd Length: 118 Bit Score: 97.76 E-value: 6.08e-24
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| cztS_silS_copS | TIGR01386 | heavy metal sensor kinase; Members of this family contain a sensor histidine kinase domain ... |
367-639 | 9.27e-24 | ||||||||
heavy metal sensor kinase; Members of this family contain a sensor histidine kinase domain (pfam00512) and a domain found in bacterial signal proteins (pfam00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Pssm-ID: 273593 [Multi-domain] Cd Length: 457 Bit Score: 105.55 E-value: 9.27e-24
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| PRK10653 | PRK10653 | ribose ABC transporter substrate-binding protein RbsB; |
65-261 | 9.86e-24 | ||||||||
ribose ABC transporter substrate-binding protein RbsB; Pssm-ID: 182620 [Multi-domain] Cd Length: 295 Bit Score: 102.48 E-value: 9.86e-24
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| REC_hyHK_CKI1_RcsC-like | cd17546 | phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ... |
711-819 | 1.08e-23 | ||||||||
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators similar to Arabidopsis thaliana CKI1 and Escherichia coli RcsC; This family is composed of hybrid sensor histidine kinases/response regulators that are sensor histidine kinases (HKs) fused with a REC domain, similar to the sensor histidine kinase CKI1 from Arabidopsis thaliana, which is involved in multi-step phosphorelay (MSP) signaling that mediates responses to a variety of important stimuli in plants. MSP involves a signal being transferred from HKs via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. The CKI1 REC domain specifically interacts with the downstream signaling protein AHP2, AHP3 and AHP5. The plant MSP system has evolved from the prokaryotic two-component system (TCS), which allows organisms to sense and respond to changes in environmental conditions. This family also includes bacterial hybrid sensor HKs such as Escherichia coli RcsC, which is a component of the Rcs signalling pathway that controls a variety of physiological functions like capsule synthesis, cell division, and motility. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381099 [Multi-domain] Cd Length: 113 Bit Score: 96.77 E-value: 1.08e-23
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| PBP1_GGBP | cd01539 | periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and ... |
44-289 | 1.42e-23 | ||||||||
periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380481 [Multi-domain] Cd Length: 302 Bit Score: 102.28 E-value: 1.42e-23
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| PBP1_ABC_xylose_binding-like | cd19995 | periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ... |
55-296 | 1.89e-23 | ||||||||
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380650 [Multi-domain] Cd Length: 294 Bit Score: 101.60 E-value: 1.89e-23
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| phoR | PRK11006 | phosphate regulon sensor histidine kinase PhoR; |
409-639 | 2.05e-23 | ||||||||
phosphate regulon sensor histidine kinase PhoR; Pssm-ID: 182895 [Multi-domain] Cd Length: 430 Bit Score: 104.32 E-value: 2.05e-23
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| REC_OmpR_CusR-like | cd19935 | phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; ... |
711-811 | 2.40e-23 | ||||||||
phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; Escherichia coli CusR is part of the CusS/CusR two-component system (TCS) that is involved in response to copper and silver. Other members of this subfamily include Escherichia coli PcoR, Pseudomonas syringae CopR, and Streptomyces coelicolor CutR, which are all transcriptional regulatory proteins and components of TCSs that regulate genes involved in copper resistance and/or metabolism. member of the subfamily is Escherichia coli HprR (hydrogen peroxide response regulator), previously called YdeW, which is part of the HprSR (or YedVW) TCS involved in stress response to hydrogen peroxide, as well as Cupriavidus metallidurans CzcR, which is part of the CzcS/CzcR TCS involved in the control of cobalt, zinc, and cadmium homeostasis. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381162 [Multi-domain] Cd Length: 100 Bit Score: 95.20 E-value: 2.40e-23
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| YesN | COG4753 | Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ... |
711-811 | 3.12e-23 | ||||||||
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding domains [Signal transduction mechanisms, Transcription]; Pssm-ID: 443786 [Multi-domain] Cd Length: 103 Bit Score: 94.84 E-value: 3.12e-23
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| PurR | COG1609 | DNA-binding transcriptional regulator, LacI/PurR family [Transcription]; |
45-241 | 3.20e-23 | ||||||||
DNA-binding transcriptional regulator, LacI/PurR family [Transcription]; Pssm-ID: 441217 [Multi-domain] Cd Length: 335 Bit Score: 101.81 E-value: 3.20e-23
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| orf27 | CHL00148 | Ycf27; Reviewed |
706-825 | 9.95e-23 | ||||||||
Ycf27; Reviewed Pssm-ID: 214376 [Multi-domain] Cd Length: 240 Bit Score: 98.25 E-value: 9.95e-23
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| REC_OmpR_CpxR | cd17623 | phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is ... |
711-822 | 2.24e-22 | ||||||||
phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is part of the CpxA/CpxR two-component regulatory system that mediates envelope stress responses that is key for virulence and antibiotic resistance in several Gram negative pathogens. CpxR is a transcription factor/response regulator that controls the expression of numerous genes, including those of the classical porins OmpF and OmpC. It belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381138 [Multi-domain] Cd Length: 115 Bit Score: 93.14 E-value: 2.24e-22
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| PBP1_TorT-like | cd06306 | TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor ... |
55-295 | 2.30e-22 | ||||||||
TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria; TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type 1 periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport. Pssm-ID: 380529 [Multi-domain] Cd Length: 269 Bit Score: 98.04 E-value: 2.30e-22
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| PRK09701 | PRK09701 | D-allose transporter substrate-binding protein; |
2-244 | 2.45e-22 | ||||||||
D-allose transporter substrate-binding protein; Pssm-ID: 182037 [Multi-domain] Cd Length: 311 Bit Score: 98.79 E-value: 2.45e-22
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| REC_OmpR_PmrA-like | cd17624 | phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ... |
711-825 | 4.04e-22 | ||||||||
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This subfamily contains various OmpR family response regulators including PmrA, BasR, QseB, tctD, and RssB, which are components of two-component regulatory systems (TCSs). The PmrA/PmrB TCS controls transcription of genes that are involved in lipopolysaccharide modification in the outer membrane of bacteria, increasing bacterial resistance to host-derived antimicrobial peptides. The BasS/BasR TCS functions as an iron- and zinc-sensing transcription regulator. The QseB/QseC TCS activates the flagella regulon by activating transcription of FlhDC. The RssA/RssB TCS regulates swarming behavior in Serratia marcescens. OmpR family DNA-binding response regulators contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381139 [Multi-domain] Cd Length: 115 Bit Score: 92.16 E-value: 4.04e-22
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| CitA | COG3290 | Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction ... |
504-639 | 5.23e-22 | ||||||||
Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction mechanisms]; Pssm-ID: 442519 [Multi-domain] Cd Length: 389 Bit Score: 99.54 E-value: 5.23e-22
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| HTH_18 | pfam12833 | Helix-turn-helix domain; |
875-954 | 5.52e-22 | ||||||||
Helix-turn-helix domain; Pssm-ID: 432818 [Multi-domain] Cd Length: 81 Bit Score: 90.73 E-value: 5.52e-22
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| REC_OmpR_EcPhoP-like | cd19934 | phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; ... |
711-830 | 6.38e-22 | ||||||||
phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; Escherichia coli PhoP (EcPhoP) is part of the PhoQ/PhoP two-component system (TCS) that regulates virulence genes and plays an essential role in the response of the bacteria to the environment of their mammalian hosts, sensing several stimuli such as extracellular magnesium limitation, low pH, the presence of cationic antimicrobial peptides, and osmotic upshift. This subfamily also includes Brucella suis FeuP, part of the FeuPQ TCS that is involved in the regulation of iron uptake, and Microchaete diplosiphon RcaC, which is required for chromatic adaptation. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381161 [Multi-domain] Cd Length: 117 Bit Score: 91.96 E-value: 6.38e-22
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| PBP1_ABC_xylose_binding-like | cd19993 | periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ... |
37-242 | 7.28e-22 | ||||||||
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380648 [Multi-domain] Cd Length: 287 Bit Score: 96.78 E-value: 7.28e-22
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| PRK11517 | PRK11517 | DNA-binding response regulator HprR; |
711-828 | 7.40e-22 | ||||||||
DNA-binding response regulator HprR; Pssm-ID: 183172 [Multi-domain] Cd Length: 223 Bit Score: 95.35 E-value: 7.40e-22
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| PBP1_LacI_sugar_binding-like | cd06267 | ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ... |
45-244 | 9.08e-22 | ||||||||
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily; Ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain. Pssm-ID: 380491 [Multi-domain] Cd Length: 264 Bit Score: 96.05 E-value: 9.08e-22
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| PBP1_ChvE | cd19994 | periplasmic sugar binding protein ChvE that interacts with a bacterial two-component signaling ... |
27-242 | 9.77e-22 | ||||||||
periplasmic sugar binding protein ChvE that interacts with a bacterial two-component signaling system; Periplasmic aldose-monosaccharides binding protein ChvE that belongs to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380649 [Multi-domain] Cd Length: 304 Bit Score: 96.93 E-value: 9.77e-22
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| REC_RpfG-like | cd17551 | phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ... |
711-824 | 3.02e-21 | ||||||||
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator RpfG and similar proteins; Cyclic di-GMP phosphodiesterase response regulator RpfG, together with sensory/regulatory protein RpfC, constitute a two-component system implicated in sensing and responding to the diffusible signal factor (DSF) that is essential for cell-cell signaling. RpfC is a hybrid sensor/histidine kinase that phosphorylates and activates RpfG, which degrades cyclic di-GMP to GMP, leading to the activation of Clp, a global transcriptional regulator that regulates a large set of genes in the DSF pathway. RpfG contains a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381103 [Multi-domain] Cd Length: 118 Bit Score: 89.81 E-value: 3.02e-21
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| CitB | COG4565 | DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ... |
707-833 | 3.52e-21 | ||||||||
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal transduction mechanisms]; Pssm-ID: 443622 [Multi-domain] Cd Length: 138 Bit Score: 90.41 E-value: 3.52e-21
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| Spo0F | COG5803 | Stage 0 sporulation initiation response regulator Spo0F [Cell cycle control, cell division, ... |
711-825 | 4.07e-21 | ||||||||
Stage 0 sporulation initiation response regulator Spo0F [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]; Pssm-ID: 444505 [Multi-domain] Cd Length: 119 Bit Score: 89.47 E-value: 4.07e-21
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| HATPase_VanS-like | cd16923 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-639 | 4.32e-21 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Enterococcus faecium VanS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Enterococcus faecium VanS HK of the VanS-VanR two-component regulatory system (TCS) which activates the transcription of vanH, vanA and vanX vancomycin resistance genes. It also contains Ecoli YedV and PcoS, probable members of YedW-YedV TCS and PcoS-PcoR TCS, repectively. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); most also have a HAMP sensor domain. Pssm-ID: 340400 [Multi-domain] Cd Length: 102 Bit Score: 88.98 E-value: 4.32e-21
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| REC_OmpR_KdpE-like | cd17620 | phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a ... |
711-811 | 4.44e-21 | ||||||||
phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a component of the KdpD/KdpE two-component system (TCS) and is activated when histidine kinase KdpD senses a drop in external K+ concentration or upshift in ionic osmolarity, resulting in the expression of a heterooligomeric transporter KdpFABC. In addition, the KdpD/KdpE TCS is also an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. KdpE is a member of the OmpR family of DNA-binding response regulators that contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381135 [Multi-domain] Cd Length: 99 Bit Score: 88.76 E-value: 4.44e-21
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| PBP1_ABC_sugar_binding-like | cd20005 | monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ... |
54-242 | 7.14e-21 | ||||||||
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380660 [Multi-domain] Cd Length: 274 Bit Score: 93.46 E-value: 7.14e-21
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| ompR | PRK09468 | osmolarity response regulator; Provisional |
711-822 | 9.11e-21 | ||||||||
osmolarity response regulator; Provisional Pssm-ID: 181883 [Multi-domain] Cd Length: 239 Bit Score: 92.34 E-value: 9.11e-21
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| REC_OmpR_BfmR-like | cd19939 | phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators; ... |
711-825 | 1.37e-20 | ||||||||
phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators; Acinetobacter baumannii BfmR is part of the BfmR/S two-component system that functions as the master regulator of biofilm initiation. BfmR confers resistance to complement-mediated bactericidal activity, independent of capsular polysaccharide, and also increases resistance to the clinically important antimicrobials meropenem and colistin, making it a potential antimicrobial target. Its inhibition would have the dual benefit of significantly decreasing in vivo survival and increasing sensitivity to selected antimicrobials. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381166 [Multi-domain] Cd Length: 116 Bit Score: 87.81 E-value: 1.37e-20
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| REC_OmpR_YycF-like | cd17614 | phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF ... |
711-825 | 1.41e-20 | ||||||||
phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF appears to play an important role in cell wall integrity in a wide range of gram-positive bacteria, and may also modulate cell membrane integrity. It functions as part of a phosphotransfer system that ultimately controls the levels of competence within the bacteria. YycF belongs to the OmpR family of response regulators, which are characterized by a REC domain and a winged helix-turn-helix effector domain involved in DNA binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381130 [Multi-domain] Cd Length: 115 Bit Score: 87.86 E-value: 1.41e-20
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| PRK09303 | PRK09303 | histidine kinase; |
368-640 | 1.89e-20 | ||||||||
histidine kinase; Pssm-ID: 236462 [Multi-domain] Cd Length: 380 Bit Score: 94.63 E-value: 1.89e-20
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| REC_OmpR_BaeR-like | cd19938 | phosphoacceptor receiver (REC) domain of BaeR-like OmpR family response regulators; BaeR is ... |
711-825 | 2.32e-20 | ||||||||
phosphoacceptor receiver (REC) domain of BaeR-like OmpR family response regulators; BaeR is part of the BaeSR two-component system that is involved in regulating genes that confer multidrug and metal resistance. In Salmonella, BaeSR induces AcrD and MdtABC drug efflux systems, increasing multidrug and metal resistance. In Escherichia coli, BaeR stimulates multidrug resistance via mdtABC (multidrug transporter ABC, formerly known as yegMNO) genes, which encode a resistance-nodulation-cell division (RND) drug efflux system. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381165 [Multi-domain] Cd Length: 114 Bit Score: 87.43 E-value: 2.32e-20
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| REC_Rcp-like | cd17557 | phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and ... |
711-826 | 3.16e-20 | ||||||||
phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and similar domains; This family is composed of response regulators (RRs) that are members of phytochrome-associated, light-sensing two-component signal transduction pathways such as Synechocystis sp. Rcp1, Tolypothrix sp. RcpA, and Agrobacterium tumefaciens bacteriophytochrome response regulator AtBRR. They are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. Also included in this family us Methanosaeta harundinacea methanogenesis regulatory protein FilR2, also a stand-alone RR. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381108 [Multi-domain] Cd Length: 129 Bit Score: 87.47 E-value: 3.16e-20
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| REC_OmpR_MtrA-like | cd17626 | phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is ... |
711-822 | 3.98e-20 | ||||||||
phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is part of MtrA/MtrB (or MtrAB), a highly conserved two-component system (TCS) implicated in the regulation of cell division in the actinobacteria. In unicellular Mycobacterium tuberculosis, MtrAB coordinates DNA replication with cell division and regulates the transcription of resuscitation-promoting factor B. In filamentous Streptomyces venezuelae, it links antibiotic production to sporulation. MtrA belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381141 [Multi-domain] Cd Length: 115 Bit Score: 86.75 E-value: 3.98e-20
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| REC_YesN-like | cd17536 | phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ... |
711-826 | 7.52e-20 | ||||||||
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response regulators; This family is composed of uncharacterized response regulators that contain a REC domain and a AraC family helix-turn-helix (HTH) DNA-binding output domain, including Bacillus subtilis uncharacterized transcriptional regulatory protein YesN and Staphylococcus aureus uncharacterized response regulatory protein SAR0214. YesN is a member of the two-component regulatory system YesM/YesN and SAR0214 is a member of the probable two-component regulatory system SAR0215/SAR0214. Also included in this family is the AlgR-like group of LytTR/AlgR family response, which includes Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR and Bacillus subtilis sensory transduction protein LytT, among others. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381091 [Multi-domain] Cd Length: 121 Bit Score: 85.85 E-value: 7.52e-20
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| PBP1_ABC_sugar_binding-like | cd06312 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ... |
54-245 | 1.38e-19 | ||||||||
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380535 [Multi-domain] Cd Length: 272 Bit Score: 89.98 E-value: 1.38e-19
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| PBP1_ABC_sugar_binding-like | cd19965 | monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; ... |
78-279 | 1.83e-19 | ||||||||
monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380620 [Multi-domain] Cd Length: 272 Bit Score: 89.25 E-value: 1.83e-19
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| PBP1_MalI-like | cd06289 | ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia ... |
44-244 | 3.38e-19 | ||||||||
ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380512 [Multi-domain] Cd Length: 268 Bit Score: 88.39 E-value: 3.38e-19
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| REC_2_DhkD-like | cd17580 | second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal ... |
711-819 | 3.46e-19 | ||||||||
second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal transduction histidine kinase D and similar domains; Dictyostelium discoideum hybrid signal transduction histidine kinase D (DhkD) is a large protein that contains two histidine kinase (HK) and two REC domains on the intracellular side of a single pass transmembrane domain, and extracellular PAS and PAC domains that likely are involved in ligand binding. This model represents the second REC domain and similar domains. DhkD activates the cAMP phosphodiesterase RegA to ensure proper prestalk and prespore patterning, tip formation, and the vertical elongation of the mound into a finger, in Dictyostelium discoideum. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381118 [Multi-domain] Cd Length: 112 Bit Score: 83.66 E-value: 3.46e-19
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| REC_OmpR_kpRstA-like | cd17622 | phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; ... |
711-825 | 4.23e-19 | ||||||||
phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; Klebsiella pneumoniae RstA (kpRstA) is part of the RstA/RstB two-component regulatory system that may play a regulatory role in virulence. It belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381137 [Multi-domain] Cd Length: 116 Bit Score: 83.58 E-value: 4.23e-19
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| PBP1_Qymf-like | cd06291 | ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ... |
65-241 | 5.44e-19 | ||||||||
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380514 [Multi-domain] Cd Length: 264 Bit Score: 87.96 E-value: 5.44e-19
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| PBP1_LsrB_Quorum_Sensing-like | cd06302 | periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium ... |
66-244 | 7.87e-19 | ||||||||
periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs; Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. Pssm-ID: 380525 [Multi-domain] Cd Length: 296 Bit Score: 88.07 E-value: 7.87e-19
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| PRK10161 | PRK10161 | phosphate response regulator transcription factor PhoB; |
711-849 | 8.08e-19 | ||||||||
phosphate response regulator transcription factor PhoB; Pssm-ID: 182277 [Multi-domain] Cd Length: 229 Bit Score: 86.70 E-value: 8.08e-19
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| PRK11466 | PRK11466 | hybrid sensory histidine kinase TorS; Provisional |
358-641 | 1.92e-18 | ||||||||
hybrid sensory histidine kinase TorS; Provisional Pssm-ID: 236914 [Multi-domain] Cd Length: 914 Bit Score: 91.12 E-value: 1.92e-18
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| BaeS_SmeS | NF012163 | sensor histidine kinase efflux regulator BaeS; |
391-639 | 2.75e-18 | ||||||||
sensor histidine kinase efflux regulator BaeS; Pssm-ID: 411086 [Multi-domain] Cd Length: 457 Bit Score: 88.73 E-value: 2.75e-18
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| PRK10529 | PRK10529 | DNA-binding transcriptional activator KdpE; Provisional |
711-833 | 3.37e-18 | ||||||||
DNA-binding transcriptional activator KdpE; Provisional Pssm-ID: 182522 [Multi-domain] Cd Length: 225 Bit Score: 84.47 E-value: 3.37e-18
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| PRK11100 | PRK11100 | sensory histidine kinase CreC; Provisional |
427-640 | 3.55e-18 | ||||||||
sensory histidine kinase CreC; Provisional Pssm-ID: 236846 [Multi-domain] Cd Length: 475 Bit Score: 88.75 E-value: 3.55e-18
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| GlxA | COG4977 | Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ... |
859-950 | 9.00e-18 | ||||||||
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Pssm-ID: 444002 [Multi-domain] Cd Length: 318 Bit Score: 85.21 E-value: 9.00e-18
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| REC_CheY | cd17542 | phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ... |
711-824 | 1.28e-17 | ||||||||
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response regulator CheY contains a stand-alone REC domain. Chemotaxis is a behavior known for motile bacteria that directs their movement in response to chemical gradients. CheY is involved in transmitting sensory signals from chemoreceptors to the flagellar motors. Phosphorylated CheY interacts with the flagella switch components FliM and FliY, which causes counterclockwise rotation of the flagella, resulting in smooth swimming. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381097 [Multi-domain] Cd Length: 117 Bit Score: 79.63 E-value: 1.28e-17
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| PRK11083 | PRK11083 | DNA-binding response regulator CreB; Provisional |
707-834 | 2.22e-17 | ||||||||
DNA-binding response regulator CreB; Provisional Pssm-ID: 236838 [Multi-domain] Cd Length: 228 Bit Score: 82.32 E-value: 2.22e-17
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| PRK10490 | PRK10490 | sensor protein KdpD; Provisional |
377-642 | 2.23e-17 | ||||||||
sensor protein KdpD; Provisional Pssm-ID: 236701 [Multi-domain] Cd Length: 895 Bit Score: 87.40 E-value: 2.23e-17
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| PBP1_LacI-like | cd06285 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
49-244 | 2.92e-17 | ||||||||
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380508 [Multi-domain] Cd Length: 269 Bit Score: 83.04 E-value: 2.92e-17
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| AmiR | COG3707 | Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ... |
711-833 | 2.98e-17 | ||||||||
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding antiterminator (ANTAR) domains [Signal transduction mechanisms, Transcription]; Pssm-ID: 442921 [Multi-domain] Cd Length: 194 Bit Score: 80.77 E-value: 2.98e-17
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| REC_CheY_CheY3 | cd19923 | phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ... |
711-817 | 3.05e-17 | ||||||||
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY3, Escherichia coli CheY, and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381150 [Multi-domain] Cd Length: 119 Bit Score: 78.53 E-value: 3.05e-17
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| HATPase_DpiB-CitA-like | cd16915 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
541-639 | 5.17e-17 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli K-12 DpiB, DcuS, and Bacillus subtilis CitS, DctS, and YufL; This family includes histidine kinase-like ATPase domains of Escherichia coli K-12 DpiB and DcuS, and Bacillus subtilis CitS, DctS and MalK histidine kinases (HKs) all of which are two component transduction systems (TCSs). E. coli K-12 DpiB (also known as CitA) is the histidine kinase (HK) of DpiA-DpiB, a two-component signal transduction system (TCS) required for the expression of citrate-specific fermentation genes and genes involved in plasmid inheritance. E. coli K-12 DcuS (also known as YjdH) is the HK of DcuS-DcuR, a TCS that in the presence of the extracellular C4-dicarboxlates, activates the expression of the genes of anaerobic fumarate respiration and of aerobic C4-dicarboxylate uptake. CitS is the HK of Bacillus subtilis CitS-CitT, a TCS which regulates expression of CitM, the Mg-citrate transporter. Bacillus subtilis DctS forms a tripartite sensor unit (DctS/DctA/DctB) for sensing C4 dicarboxylates. Bacillus subtilis MalK (also known as YfuL) is the HK of MalK-MalR (YufL-YufM) a TCS which regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization of malate in minimal medium. Proteins having this DpiB-CitA-like HATPase domain generally have sensor domains such as Cache and PAS, and a histidine kinase A (HisKA)-like SpoOB-type, alpha-helical domain. Pssm-ID: 340392 [Multi-domain] Cd Length: 104 Bit Score: 77.33 E-value: 5.17e-17
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| REC_PdtaR-like | cd19932 | phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ... |
711-819 | 6.36e-17 | ||||||||
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes Mycobacterium tuberculosis PdtaR, also called Rv1626, and similar proteins containing a REC domain and an ANTAR (AmiR and NasR transcription antitermination regulators) RNA-binding output domain. PdtaR is a response regulator that acts at the level of transcriptional antitermination and is a member of the PdtaR/PdtaS two-component regulatory system. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381159 [Multi-domain] Cd Length: 118 Bit Score: 77.45 E-value: 6.36e-17
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| HATPase_AtoS-like | cd16943 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
533-640 | 7.51e-17 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli K-12 AtoS; This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs) such as Escherichia coli AtoS, an HK of the AtoS-AtoC TCS. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some have accessory domains such as HAMP or PAS sensor domains or CBS-pair domains. Pssm-ID: 340419 [Multi-domain] Cd Length: 105 Bit Score: 77.08 E-value: 7.51e-17
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| REC_NtrX-like | cd17550 | phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ... |
711-826 | 8.93e-17 | ||||||||
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and similar proteins; NtrX is part of the two-component regulatory system NtrY/NtrX that is involved in the activation of nitrogen assimilatory genes such as Gln. It is phosphorylated by the histidine kinase NtrY and interacts with sigma-54. NtrX is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. NtrC family response regulators are sigma54-dependent transcriptional activators. Also included in this subfamily is Aquifex aeolicus NtrC4. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381102 [Multi-domain] Cd Length: 115 Bit Score: 77.15 E-value: 8.93e-17
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| PRK10710 | PRK10710 | DNA-binding transcriptional regulator BaeR; Provisional |
705-833 | 9.94e-17 | ||||||||
DNA-binding transcriptional regulator BaeR; Provisional Pssm-ID: 182665 [Multi-domain] Cd Length: 240 Bit Score: 80.50 E-value: 9.94e-17
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| PBP1_ABC_sugar_binding-like | cd06316 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ... |
55-232 | 1.23e-16 | ||||||||
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380539 [Multi-domain] Cd Length: 294 Bit Score: 81.52 E-value: 1.23e-16
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| HATPase_BasS-like | cd16940 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
541-638 | 1.25e-16 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli BasS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) similar to Escherichia coli BasS HK of the BasS-BasR two-component regulatory system (TCS). Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some contain a HAMP sensory domain, while some an N-terminal two-component sensor kinase domain. Pssm-ID: 340417 [Multi-domain] Cd Length: 113 Bit Score: 76.68 E-value: 1.25e-16
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| REC_OmpR_ArcA_TorR-like | cd17619 | phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators; ... |
709-823 | 2.03e-16 | ||||||||
phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators; This subfamily includes Escherichia coli TorR and ArcA, both OmpR family response regulators that mediate adaptation to changes in various respiratory growth conditions. The TorS-TorR two-component system (TCS) is responsible for the tight regulation of the torCAD operon, which encodes the trimethylamine N-oxide (TMAO) reductase respiratory system in response to anaerobic conditions and the presence of TMAO. The ArcA-ArcB TCS is involved in cell growth during anaerobiosis. ArcA is a global regulator that controls more than 30 operons involved in redox regulation (the Arc modulon). OmpR family DNA-binding response regulators are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381134 [Multi-domain] Cd Length: 113 Bit Score: 75.89 E-value: 2.03e-16
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| HATPase_YcbM-like | cd16947 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
521-638 | 2.24e-16 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis YcbM; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis YcbM, a HK of the two-component system YcbM-YcbL. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA). Pssm-ID: 340423 [Multi-domain] Cd Length: 125 Bit Score: 76.40 E-value: 2.24e-16
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| REC_DctD-like | cd17549 | phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ... |
711-833 | 4.21e-16 | ||||||||
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and similar proteins; C4-dicarboxylic acid transport protein D (DctD) is part of the two-component regulatory system DctB/DctD, which regulates C4-dicarboxylate transport via regulation of expression of the dctPQM operon and dctA. It is an activator of sigma(54)-RNA polymerase holoenzyme that uses the energy released from ATP hydrolysis to stimulate the isomerization of a closed promoter complex to an open complex capable of initiating transcription. DctD is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381101 [Multi-domain] Cd Length: 130 Bit Score: 75.60 E-value: 4.21e-16
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| HATPase_EcPhoR-like | cd16952 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
541-639 | 4.27e-16 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli PhoR; This family includes histidine kinase-like ATPase (HATPase) domain of two-component sensor histidine kinases similar to Escherichia coli or Vibrio cholera PhoR, the histidine kinase (HK) of PhoB-PhoR a two-component signal transduction system (TCS) involved in phosphate regulation. PhoR monitors extracellular inorganic phosphate (Pi) availability and PhoB, the response regulator, regulates transcription of genes of the phosphate regulon. PhoR is a bifunctional histidine autokinase/phospho-PhoB phosphatase; in phosphate deficiency, it autophosphorylates and Pi is transferred to PhoB, and when environmental Pi is abundant, it removes the phosphoryl group from phosphorylated PhoB. Other roles of PhoB-PhoR TCS have been described, including motility, biofilm formation, intestinal colonization, and virulence in V. cholera. E.coli PhoR and Bacillus subtilis PhoR (whose HATPase domain belongs to a different family) sense very different signals in each bacterium. In E. coli the PhoR signal comes from phosphate transport mediated by the PstSCAB2 phosphate transporter and the PhoU chaperone-like protein while in B. subtilis, the PhoR activation signal comes from wall teichoic acid (WTA) metabolism. Pssm-ID: 340428 [Multi-domain] Cd Length: 108 Bit Score: 74.93 E-value: 4.27e-16
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| PRK10364 | PRK10364 | two-component system sensor histidine kinase ZraS; |
509-640 | 4.80e-16 | ||||||||
two-component system sensor histidine kinase ZraS; Pssm-ID: 236674 [Multi-domain] Cd Length: 457 Bit Score: 81.76 E-value: 4.80e-16
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| PBP1_repressor_sugar_binding-like | cd01537 | Ligand-binding domain of the LacI-GalR family of transcription regulators and the ... |
27-244 | 5.27e-16 | ||||||||
Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems; Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type 1 periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type 1, which has six beta strands, and type 2, which has five beta strands. These two distinct structural arrangements may have originated from a common ancestor. Pssm-ID: 380479 [Multi-domain] Cd Length: 265 Bit Score: 79.21 E-value: 5.27e-16
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| REC_CheV-like | cd19924 | phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This ... |
711-811 | 5.42e-16 | ||||||||
phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This subfamily includes the REC domains of Bacillus subtilis chemotaxis protein CheV, Myxococcus xanthus gliding motility regulatory protein FrzE, and similar proteins. CheV is a hybrid protein with an N-terminal CheW-like domain and a C-terminal CheY-like REC domain. The CheV pathway is one of three systems employed by B. subtilis for sensory adaptation that contribute to chemotaxis. It is involved in the transmission of sensory signals from chemoreceptors to flagellar motors. Together with CheW, it is involved in the coupling of methyl-accepting chemoreceptors to the central two-component histidine kinase CheA. FrzE is a hybrid sensor histidine kinase/response regulator that is part of the Frz pathway that controls cell reversal frequency to support directional motility during swarming and fruiting body formation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381151 [Multi-domain] Cd Length: 111 Bit Score: 74.72 E-value: 5.42e-16
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| PRK09836 | PRK09836 | DNA-binding transcriptional activator CusR; Provisional |
711-825 | 6.42e-16 | ||||||||
DNA-binding transcriptional activator CusR; Provisional Pssm-ID: 182102 [Multi-domain] Cd Length: 227 Bit Score: 78.04 E-value: 6.42e-16
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| PRK13837 | PRK13837 | two-component system VirA-like sensor kinase; |
394-653 | 6.98e-16 | ||||||||
two-component system VirA-like sensor kinase; Pssm-ID: 237526 [Multi-domain] Cd Length: 828 Bit Score: 82.42 E-value: 6.98e-16
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| REC_OmpR_CtrA | cd17616 | phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is ... |
711-825 | 7.14e-16 | ||||||||
phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is part of the CckA-ChpT-CtrA phosphorelay that is conserved in alphaproteobacteria and is important in orchestrating the cell cycle, polar development, and flagellar biogenesis. CtrA is the master regulator of flagella synthesis genes and also regulates genes involved in the cell cycle, exopolysaccharide synthesis, and cyclic-di-GMP signaling. CtrA is active as a transcription factor when phosphorylated. It is a member of the OmpR family of DNA-binding response regulators, characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381132 [Multi-domain] Cd Length: 114 Bit Score: 74.37 E-value: 7.14e-16
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| REC_NtrC | cd19919 | phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ... |
711-812 | 1.13e-15 | ||||||||
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; DNA-binding transcriptional regulator NtrC is also called nitrogen regulation protein NR(I) or nitrogen regulator I (NRI). It contains an N-terminal receiver (REC) domain, followed by a sigma-54 interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. It is part of the two-component regulatory system NtrB/NtrC, which controls expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. DNA-binding response regulator NtrC is phosphorylated by NtrB; phosphorylation of the N-terminal REC domain activates the central sigma-54 interaction domain and leads to the transcriptional activation from promoters that require sigma(54)-containing RNA polymerase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381146 [Multi-domain] Cd Length: 116 Bit Score: 73.85 E-value: 1.13e-15
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| REC_DC-like | cd17534 | phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ... |
711-819 | 1.78e-15 | ||||||||
phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; This groups includes a modulated diguanylate cyclase containing a PAS sensor domain from Desulfovibrio desulfuricans G20. Members of this group contain N-terminal REC domains and various output domains including the GGDEF, histidine kinase, and helix-turn-helix (HTH) DNA binding domains. Also included in this family is Mycobacterium tuberculosis PdtaR, a transcriptional antiterminator that contains a REC domain and an ANTAR RNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381089 [Multi-domain] Cd Length: 117 Bit Score: 73.21 E-value: 1.78e-15
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| FixJ | COG4566 | DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ... |
710-830 | 1.86e-15 | ||||||||
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription]; Pssm-ID: 443623 [Multi-domain] Cd Length: 196 Bit Score: 75.91 E-value: 1.86e-15
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| PRK10549 | PRK10549 | two-component system sensor histidine kinase BaeS; |
406-642 | 2.18e-15 | ||||||||
two-component system sensor histidine kinase BaeS; Pssm-ID: 182539 [Multi-domain] Cd Length: 466 Bit Score: 80.06 E-value: 2.18e-15
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| PRK10955 | PRK10955 | envelope stress response regulator transcription factor CpxR; |
711-825 | 5.51e-15 | ||||||||
envelope stress response regulator transcription factor CpxR; Pssm-ID: 182864 [Multi-domain] Cd Length: 232 Bit Score: 75.22 E-value: 5.51e-15
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| LytT | COG3279 | DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ... |
711-833 | 5.68e-15 | ||||||||
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction mechanisms]; Pssm-ID: 442510 [Multi-domain] Cd Length: 235 Bit Score: 75.24 E-value: 5.68e-15
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| REC_OmpR_VirG | cd17594 | phosphoacceptor receiver (REC) domain of VirG-like OmpR family response regulators; VirG is ... |
711-822 | 6.83e-15 | ||||||||
phosphoacceptor receiver (REC) domain of VirG-like OmpR family response regulators; VirG is part of the VirA/VirG two-component system that regulates the expression of virulence (vir) genes. The histidine kinase VirA senses a phenolic wound response signal, undergoes autophosphorylation, and phosphorelays to the VirG response regulator, which induces transcription of the vir regulon. VirG belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381125 [Multi-domain] Cd Length: 113 Bit Score: 71.71 E-value: 6.83e-15
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| REC_CheB-like | cd17541 | phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ... |
711-826 | 1.06e-14 | ||||||||
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate methylesterase CheB and similar chemotaxis proteins; Methylesterase CheB is a chemotaxis response regulator with an N-terminal REC domain and a C-terminal methylesterase domain. Chemotaxis is a behavior known in motile bacteria that directs their movement in response to chemical gradients. CheB is a phosphorylation-activated response regulator involved in the reversible modification of bacterial chemotaxis receptors. It catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins) by CheR. The CheB REC domain packs against the active site of the C-terminal domain and inhibits methylesterase activity by directly restricting access to the active site. Also included in this family is chemotaxis response regulator CheY, which contains a stand-alone REC domain, and an uncharacterized subfamily composed of proteins containing an N-terminal REC domain and a C-terminal CheY-P phosphatase (CheC) domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381096 [Multi-domain] Cd Length: 125 Bit Score: 71.27 E-value: 1.06e-14
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| REC_OmpR_ChvI-like | cd19936 | phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; ... |
711-811 | 1.38e-14 | ||||||||
phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; Sinorhizobium meliloti ChvI is part of the ExoS/ChvI two-component regulatory system (TCS) that is required for nitrogen-fixing symbiosis and exopolysaccharide synthesis. ExoS/ChvI also play important roles in regulating biofilm formation, motility, nutrient utilization, and the viability of free-living bacteria. ChvI belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381163 [Multi-domain] Cd Length: 99 Bit Score: 70.17 E-value: 1.38e-14
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| REC_TrrA-like | cd17554 | phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ... |
711-824 | 1.49e-14 | ||||||||
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and similar domains; Thermotoga maritima contains a two-component signal transduction system (TCS) composed of the ThkA sensory histidine kinase (HK) and its cognate response regulator (RR) TrrA; the specific function of the system is unknown. TCSs couple environmental stimuli to adaptive responses. TrrA is a stand-alone RR containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381106 [Multi-domain] Cd Length: 113 Bit Score: 70.71 E-value: 1.49e-14
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| PRK10766 | PRK10766 | two-component system response regulator TorR; |
710-825 | 1.53e-14 | ||||||||
two-component system response regulator TorR; Pssm-ID: 182711 [Multi-domain] Cd Length: 221 Bit Score: 73.92 E-value: 1.53e-14
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| Peripla_BP_1 | pfam00532 | Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ... |
34-261 | 4.62e-14 | ||||||||
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356). Pssm-ID: 395423 [Multi-domain] Cd Length: 281 Bit Score: 73.70 E-value: 4.62e-14
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| REC_2_GGDEF | cd17544 | second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This ... |
711-824 | 5.21e-14 | ||||||||
second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This family is composed of uncharacterized PleD-like response regulators that contain two N-terminal REC domains and a C-terminal diguanylate cyclase output domain with the characteristic GGDEF motif at the active site. Unlike PleD which contains a REC-like adaptor domain, the second REC domain of these uncharacterized GGDEF domain proteins, described in this model, contains characteristic metal-binding and active site residues. PleD response regulators are global regulators of cell metabolism in some important human pathogens. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381098 [Multi-domain] Cd Length: 122 Bit Score: 69.47 E-value: 5.21e-14
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| AdaA | COG2169 | Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ... |
852-956 | 5.32e-14 | ||||||||
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair]; Pssm-ID: 441772 [Multi-domain] Cd Length: 358 Bit Score: 74.70 E-value: 5.32e-14
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| PBP1_sugar_binding | cd06307 | periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ... |
52-239 | 5.77e-14 | ||||||||
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes. Pssm-ID: 380530 [Multi-domain] Cd Length: 275 Bit Score: 73.36 E-value: 5.77e-14
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| HATPase_BaeS-like | cd16946 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
531-639 | 9.85e-14 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli BasS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) similar to Escherichia coli BaeS HK of the BaeS/BaeR two-component regulatory system (TCS), which responds to envelope stress. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), and a HAMP sensory domain. Pssm-ID: 340422 [Multi-domain] Cd Length: 109 Bit Score: 68.26 E-value: 9.85e-14
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| HATPase_SpaK_NisK-like | cd16975 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
531-636 | 1.30e-13 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis SpaK and Lactococcus lactis NisK; This family includes histidine kinase-like ATPase (HATPase) domain of two-component sensor histidine kinases similar to Bacillus subtilis SpaK and Lactococcus lactis NisK. SpaK is the histidine kinase (HK) of the SpaK-SpaR two-component regulatory system (TCS), which is involved in the regulation of the biosynthesis of lantibiotic subtilin. NisK is the HK of the NisK-NisR TCS, which is involved in the regulation of the biosynthesis of lantibiotic nisin. SpaK and NisK may function as membrane-associated protein kinases that phosphorylate SpaR and NisR, respectively, in response to environmental signals. Pssm-ID: 340434 [Multi-domain] Cd Length: 107 Bit Score: 67.87 E-value: 1.30e-13
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| HATPase_FilI-like | cd16921 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-639 | 1.45e-13 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Methanosaeta harundinacea FilI and some hybrid sensor histidine kinases; This family includes FilI, the histidine kinase (HK) component of FilI-FilRs, a two-component signal transduction system (TCS) of the methanogenic archaeon, Methanosaeta harundinacea, which is involved in regulating methanogenesis. The cytoplasmic HK core consists of a C-terminal HK-like ATPase domain (represented here) and a histidine kinase dimerization and phosphoacceptor domain (HisKA) domain, which, in FilI, are coupled to CHASE, HAMP, PAS, and GAF sensor domains. FilI-FilRs catalyzes the phosphotransfer between FilI (HK) and FilRs (FilR1 and FilR2, response regulators) of the TCS. TCSs are predicted to be of bacterial origin, and acquired by archaea by horizontal gene transfer. This model also includes related HATPase domains such as that of Synechocystis sp. PCC6803 phytochrome-like protein Cph1. Proteins having this HATPase domain and HisKA domain also have accessory sensor domains such as CHASE, GAF, HAMP and PAS; some are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. Pssm-ID: 340398 [Multi-domain] Cd Length: 105 Bit Score: 67.74 E-value: 1.45e-13
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| Periplasmic_Binding_Protein_type1 | cd01391 | Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ... |
28-244 | 1.53e-13 | ||||||||
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold. Pssm-ID: 380477 [Multi-domain] Cd Length: 280 Bit Score: 72.30 E-value: 1.53e-13
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| PBP1_sucrose_transcription_regulator | cd06288 | ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members ... |
65-231 | 2.47e-13 | ||||||||
ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380511 [Multi-domain] Cd Length: 268 Bit Score: 71.04 E-value: 2.47e-13
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| PBP1_LacI-like | cd06278 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
82-230 | 2.73e-13 | ||||||||
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380501 [Multi-domain] Cd Length: 266 Bit Score: 71.03 E-value: 2.73e-13
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| REC_RssB-like | cd17555 | phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ... |
709-811 | 2.84e-13 | ||||||||
phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; Pseudomonas aeruginosa RssB is an orphan atypical response regulator containing a REC domain and a PP2C-type protein phosphatase output domain. Its function is still unknown. Escherichia RssB, which is not included in this subfamily, is a ClpX adaptor protein which alters ClpX specificity by mediating a specific interaction between ClpX and the substrates such as RpoS, an RNA polymerase sigma factor. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381107 [Multi-domain] Cd Length: 116 Bit Score: 67.23 E-value: 2.84e-13
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| PRK10610 | PRK10610 | chemotaxis protein CheY; |
712-817 | 3.79e-13 | ||||||||
chemotaxis protein CheY; Pssm-ID: 170568 [Multi-domain] Cd Length: 129 Bit Score: 67.31 E-value: 3.79e-13
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| HATPase_CreC-like | cd16945 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-624 | 4.03e-13 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli CreC; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Escherichia coli CreC of the CreC-CreB two-component regulatory system (TCS) involved in catabolic regulation. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), and accessory sensory domain(s) such as HAMP, CACHE or PAS. Pssm-ID: 340421 [Multi-domain] Cd Length: 106 Bit Score: 66.33 E-value: 4.03e-13
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| PRK13557 | PRK13557 | histidine kinase; Provisional |
425-826 | 4.70e-13 | ||||||||
histidine kinase; Provisional Pssm-ID: 237425 [Multi-domain] Cd Length: 540 Bit Score: 72.78 E-value: 4.70e-13
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| PRK15479 | PRK15479 | transcriptional regulator TctD; |
711-926 | 7.94e-13 | ||||||||
transcriptional regulator TctD; Pssm-ID: 185376 [Multi-domain] Cd Length: 221 Bit Score: 68.59 E-value: 7.94e-13
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| Spo0A | COG5801 | Stage 0 sporulation initiation regulator Spo0A (response regulator, REC-HTH domains) [Cell ... |
711-824 | 9.16e-13 | ||||||||
Stage 0 sporulation initiation regulator Spo0A (response regulator, REC-HTH domains) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]; Pssm-ID: 444503 [Multi-domain] Cd Length: 264 Bit Score: 69.44 E-value: 9.16e-13
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| PRK15395 | PRK15395 | galactose/glucose ABC transporter substrate-binding protein MglB; |
1-283 | 9.18e-13 | ||||||||
galactose/glucose ABC transporter substrate-binding protein MglB; Pssm-ID: 185293 [Multi-domain] Cd Length: 330 Bit Score: 70.53 E-value: 9.18e-13
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| REC_OmpR_NsrR-like | cd18159 | phosphoacceptor receiver (REC) domain of Streptococcus agalactiae NsrR-like OmpR family ... |
711-825 | 1.43e-12 | ||||||||
phosphoacceptor receiver (REC) domain of Streptococcus agalactiae NsrR-like OmpR family response regulators; Streptococcus agalactiae NsrR is a lantibiotic resistance-associated response regulator and is part of the nisin resistance operon. It is a member of the NsrRK two-component system (TCS) that is involved in the regulation of lantibiotic resistance genes such as a membrane-associated lipoprotein of LanI, and the nsr gene cluster which encodes for the resistance protein NSR and the ABC transporter NsrFP, both conferring resistance against nisin. This subfamily also includes Staphylococcus epidermidis GraR, part of the GraR/GraS TCS involved in resistance against cationic antimicrobial peptides, and Bacillus subtilis BceR, part of the BceS/BceR TCS involved in the regulation of bacitracin resistance. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381143 [Multi-domain] Cd Length: 113 Bit Score: 65.00 E-value: 1.43e-12
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| PRK10651 | PRK10651 | transcriptional regulator NarL; Provisional |
711-822 | 1.50e-12 | ||||||||
transcriptional regulator NarL; Provisional Pssm-ID: 182619 [Multi-domain] Cd Length: 216 Bit Score: 67.75 E-value: 1.50e-12
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| REC_NarL | cd19931 | phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ... |
711-823 | 2.32e-12 | ||||||||
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate/nitrite response regulator protein NarL contains an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. Escherichia coli NarL activates the expression of the nitrate reductase (narGHJI) and formate dehydrogenase-N (fdnGHI) operons, and represses the transcription of the fumarate reductase (frdABCD) operon in response to a nitrate/nitrite induction signal. Phosphorylation of the NarL REC domain releases the C-terminal HTH output domain that subsequently binds specific DNA promoter sites to repress or activate gene expression. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381158 [Multi-domain] Cd Length: 117 Bit Score: 64.68 E-value: 2.32e-12
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| PRK10643 | PRK10643 | two-component system response regulator PmrA; |
753-828 | 3.88e-12 | ||||||||
two-component system response regulator PmrA; Pssm-ID: 182612 [Multi-domain] Cd Length: 222 Bit Score: 66.60 E-value: 3.88e-12
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| CitB | COG2197 | DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ... |
711-773 | 4.55e-12 | ||||||||
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription]; Pssm-ID: 441799 [Multi-domain] Cd Length: 131 Bit Score: 64.14 E-value: 4.55e-12
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| REC_OmpR_RegX3-like | cd17621 | phosphoacceptor receiver (REC) domain of RegX3-like OmpR family response regulators; RegX3 is ... |
711-811 | 4.58e-12 | ||||||||
phosphoacceptor receiver (REC) domain of RegX3-like OmpR family response regulators; RegX3 is a member of the SenX3-RegX3 two-component system that is involved in phosphate-sensing signal transduction. Phosphorylated RegX3 functions as a transcriptional activator of phoA. It induces transcription in phosphate limiting environment and also controls expression of several critical metabolic enzymes in aerobic condition. RegX3 belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381136 [Multi-domain] Cd Length: 99 Bit Score: 62.99 E-value: 4.58e-12
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| PRK10604 | PRK10604 | sensor protein RstB; Provisional |
406-640 | 6.90e-12 | ||||||||
sensor protein RstB; Provisional Pssm-ID: 236724 [Multi-domain] Cd Length: 433 Bit Score: 68.86 E-value: 6.90e-12
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| HATPase_BvrS-ChvG-like | cd16953 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-639 | 7.09e-12 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Brucella abortus BvrS and Sinorhizobium meliloti ChvG; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Brucella abortus BvrS of the BvrR-BvrS two-component regulatory system (TCS), which controls cell invasion and intracellular survival, as well as Sinorhizobium meliloti and Agrobacterium tumefaciens ChvG of the ChvI-ChvG TCS necessary for endosymbiosis and pathogenicity in plants. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), an accessory HAMP sensor domain, a periplasmic stimulus-sensing domain, and some also have a sensor N-terminal transmembrane domain. Pssm-ID: 340429 [Multi-domain] Cd Length: 110 Bit Score: 62.98 E-value: 7.09e-12
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| REC | smart00448 | cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ... |
711-762 | 7.44e-12 | ||||||||
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues. Pssm-ID: 214668 [Multi-domain] Cd Length: 55 Bit Score: 61.05 E-value: 7.44e-12
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| KinA | COG5805 | Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ... |
509-641 | 8.80e-12 | ||||||||
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]; Pssm-ID: 444507 [Multi-domain] Cd Length: 496 Bit Score: 68.60 E-value: 8.80e-12
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| PRK11173 | PRK11173 | two-component response regulator; Provisional |
709-825 | 9.90e-12 | ||||||||
two-component response regulator; Provisional Pssm-ID: 183013 [Multi-domain] Cd Length: 237 Bit Score: 65.81 E-value: 9.90e-12
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| REC_LytTR_AlgR-like | cd17532 | phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ... |
711-822 | 1.38e-11 | ||||||||
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AlgR-like group of LytTR/AlgR family response regulators are Streptococcus agalactiae sensory transduction protein LytR, Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR, Bacillus subtilis sensory transduction protein LytT, and Escherichia coli transcriptional regulatory protein BtsR, which are members of two-component regulatory systems. LytR and LytT are components of regulatory systems that regulate genes involved in cell wall metabolism. AlgR positively regulates the algD gene, which codes for a GDP-mannose dehydrogenase, a key enzyme in the alginate biosynthesis pathway. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381087 [Multi-domain] Cd Length: 118 Bit Score: 62.17 E-value: 1.38e-11
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| PBP1_LsrB_Quorum_Sensing-like | cd20001 | ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; ... |
30-283 | 1.66e-11 | ||||||||
ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; Ligand-binding protein LsrB-like of a transport system, similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. Pssm-ID: 380656 Cd Length: 296 Bit Score: 66.15 E-value: 1.66e-11
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| PBP1_LsrB_Quorum_Sensing | cd20003 | ligand-binding protein LsrB of ABC transporter periplasmic binding protein; Periplasmic ... |
69-240 | 2.03e-11 | ||||||||
ligand-binding protein LsrB of ABC transporter periplasmic binding protein; Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. Pssm-ID: 380658 Cd Length: 298 Bit Score: 66.15 E-value: 2.03e-11
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| PRK00742 | PRK00742 | chemotaxis-specific protein-glutamate methyltransferase CheB; |
711-833 | 2.22e-11 | ||||||||
chemotaxis-specific protein-glutamate methyltransferase CheB; Pssm-ID: 234828 [Multi-domain] Cd Length: 354 Bit Score: 66.33 E-value: 2.22e-11
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| HATPase_TmoS-FixL-DctS-like | cd16920 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-639 | 2.26e-11 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Rhizobium meliloti FixL, and Rhodobacter capsulatus DctS; includes hybrid sensor histidine kinase similar to Pseudomonas mendocina TmoS; This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs), such as Pseudomonas mendocina TmoS HK of the TmoS-TmoT TCS, which controls the expression of the toluene-4-monooxygenase pathway, Rhizobium meliloti FixL HK of the FixL-FixJ TCS, which regulates the expression of the genes related to nitrogen fixation in the root nodule in response to O(2) levels, and Rhodobacter capsulatus DctS of the DctS-DctR TCS, which controls synthesis of the high-affinity C4-dicarboxylate transport system. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and PAS sensor domain(s); many are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. Pssm-ID: 340397 [Multi-domain] Cd Length: 104 Bit Score: 61.26 E-value: 2.26e-11
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| PRK10755 | PRK10755 | two-component system sensor histidine kinase PmrB; |
404-639 | 2.56e-11 | ||||||||
two-component system sensor histidine kinase PmrB; Pssm-ID: 236751 [Multi-domain] Cd Length: 356 Bit Score: 66.14 E-value: 2.56e-11
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| PBP1_ABC_sugar_binding-like | cd19966 | monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; ... |
55-276 | 2.94e-11 | ||||||||
monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Pssm-ID: 380621 [Multi-domain] Cd Length: 278 Bit Score: 65.04 E-value: 2.94e-11
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| HATPase_CckA-like | cd16919 | Histidine kinase-like ATPase domain of two-component sensor hybrid histidine kinases, similar ... |
535-639 | 3.07e-11 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor hybrid histidine kinases, similar to Brucella abortus 2308 CckA; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinase (HKs) similar to Brucella abortus 2308 CckA, which is a component of an essential protein phosphorelay that regulates expression of genes required for growth, division, and intracellular survival; phosphoryl transfer initiates from the sensor kinase CckA and proceeds via the ChpT phosphotransferase to two regulatory substrates: the DNA-binding response regulator CtrA and the phospho-receiver protein CpdR. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), a REC signal receiver domain, and some contain PAS or PAS and GAF sensor domain(s). Pssm-ID: 340396 [Multi-domain] Cd Length: 116 Bit Score: 61.24 E-value: 3.07e-11
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| HisKA | pfam00512 | His Kinase A (phospho-acceptor) domain; dimerization and phospho-acceptor domain of histidine ... |
417-483 | 3.79e-11 | ||||||||
His Kinase A (phospho-acceptor) domain; dimerization and phospho-acceptor domain of histidine kinases. Pssm-ID: 459839 [Multi-domain] Cd Length: 66 Bit Score: 59.53 E-value: 3.79e-11
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| PRK10337 | PRK10337 | sensor protein QseC; Provisional |
365-636 | 5.47e-11 | ||||||||
sensor protein QseC; Provisional Pssm-ID: 182388 [Multi-domain] Cd Length: 449 Bit Score: 65.83 E-value: 5.47e-11
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| REC_NtrC1-like | cd17572 | phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex ... |
711-833 | 5.61e-11 | ||||||||
phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex aeolicus and similar NtrC family response regulators; NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include Aquifex aeolicus NtrC1 and Vibrio quorum-sensing signal integrator LuxO. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381114 [Multi-domain] Cd Length: 121 Bit Score: 60.67 E-value: 5.61e-11
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| PBP1_CatR-like | cd06296 | ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in ... |
54-244 | 6.39e-11 | ||||||||
ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation; This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380519 [Multi-domain] Cd Length: 270 Bit Score: 64.22 E-value: 6.39e-11
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| KinB | COG5806 | Sporulation sensor histidine kinase B [Cell cycle control, cell division, chromosome ... |
398-640 | 6.47e-11 | ||||||||
Sporulation sensor histidine kinase B [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]; Pssm-ID: 444508 [Multi-domain] Cd Length: 412 Bit Score: 65.66 E-value: 6.47e-11
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| REC_FixJ | cd17537 | phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ... |
711-822 | 7.45e-11 | ||||||||
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response regulators contain an N-terminal receiver domain (REC) and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. The Sinorhizobium meliloti two-component system FixL/FixJ regulates nitrogen fixation in response to oxygen during symbiosis. Under microaerobic conditions, the kinase FixL phosphorylates the response regulator FixJ resulting in the regulation of nitrogen fixation genes such as nifA and fixK. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381092 [Multi-domain] Cd Length: 116 Bit Score: 60.30 E-value: 7.45e-11
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| PBP1_LacI-like | cd06280 | ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ... |
55-244 | 7.90e-11 | ||||||||
ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Pssm-ID: 380503 [Multi-domain] Cd Length: 266 Bit Score: 63.82 E-value: 7.90e-11
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| PBP1_LacI-like | cd06299 | ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum ... |
44-244 | 1.24e-10 | ||||||||
ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum produces significant amounts of L-glutamate directly from cheap sugar and ammonia; This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380522 [Multi-domain] Cd Length: 268 Bit Score: 63.07 E-value: 1.24e-10
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| spore_0_A | TIGR02875 | sporulation transcription factor Spo0A; Spo0A, the stage 0 sporulation protein A, is a ... |
711-824 | 1.36e-10 | ||||||||
sporulation transcription factor Spo0A; Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species. [Cellular processes, Sporulation and germination] Pssm-ID: 131922 [Multi-domain] Cd Length: 262 Bit Score: 62.89 E-value: 1.36e-10
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| HATPase_BceS-YxdK-YvcQ-like | cd16948 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
542-639 | 1.37e-10 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis BceS, YxdK, and Bacillus thuringiensis YvcQ; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis BceS and Bacillus thuringiensis YvcQ, the HKs of the two-component regulatory system (TCSs) BceS-BceR and YvcQ-YvcP, repsectively, which are both involved in regulating bacitracin resistance. It also includes the HATPase domain of YxdK, the HK of YxdK-YxdJ TCS involved in sensing antimicrobial compounds. Pssm-ID: 340424 [Multi-domain] Cd Length: 109 Bit Score: 59.22 E-value: 1.37e-10
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| PBP1_arabinose_binding | cd01540 | periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ... |
54-299 | 1.46e-10 | ||||||||
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily; Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such as LacI and GalR. Pssm-ID: 380482 [Multi-domain] Cd Length: 294 Bit Score: 63.46 E-value: 1.46e-10
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| psREC-like_D2_PleD | cd17539 | REC-like adaptor domain (D2) of response regulator PleD; PleD contains a REC domain (D1) with ... |
711-829 | 1.53e-10 | ||||||||
REC-like adaptor domain (D2) of response regulator PleD; PleD contains a REC domain (D1) with the phosphorylatable aspartate, a pseudo receiver (psREC)-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes the REC-like adaptor domain D2 of PleD, which is an inactive domain. Pssm-ID: 381094 [Multi-domain] Cd Length: 124 Bit Score: 59.63 E-value: 1.53e-10
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| HisKA | smart00388 | His Kinase A (phosphoacceptor) domain; Dimerisation and phosphoacceptor domain of histidine ... |
417-483 | 2.02e-10 | ||||||||
His Kinase A (phosphoacceptor) domain; Dimerisation and phosphoacceptor domain of histidine kinases. Pssm-ID: 214644 [Multi-domain] Cd Length: 66 Bit Score: 57.19 E-value: 2.02e-10
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| PBP1_EndR-like | cd19977 | periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its ... |
55-244 | 2.14e-10 | ||||||||
periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its close homologs; This group includes the ligand-binding domain of putative repressor of the endoglucanase operon from Paenibacillus polymyxa and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Pssm-ID: 380632 [Multi-domain] Cd Length: 264 Bit Score: 62.55 E-value: 2.14e-10
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| REC_hyHK_blue-like | cd18161 | phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators ... |
711-812 | 2.25e-10 | ||||||||
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators similar to Pseudomonas savastanoi blue-light-activated histidine kinase; Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase (HK)/response regulators contain all the elements of a classical TCS in a single polypeptide chain. Pseudomonas savastanoi blue-light-activated histidine kinase is a photosensitive HK and RR that is involved in increased bacterial virulence upon exposure to light. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381145 [Multi-domain] Cd Length: 102 Bit Score: 58.51 E-value: 2.25e-10
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| REC_Spo0F-like | cd17553 | phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone ... |
711-812 | 2.43e-10 | ||||||||
phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone response regulator containing only a REC domain with no output/effector domain, controls sporulation in Bacillus subtilis through the exchange of a phosphoryl group. Bacillus subtilis forms spores when conditions for growth become unfavorable. The initiation of sporulation is controlled by a phosphorelay (an expanded version of the two-component system) that consists of four main components: a histidine kinase (KinA), a secondary messenger (Spo0F), a phosphotransferase (Spo0B), and a transcription factor (Spo0A). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381105 [Multi-domain] Cd Length: 117 Bit Score: 58.72 E-value: 2.43e-10
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| REC_PatA-like | cd17602 | phosphoacceptor receiver (REC) domain of PatA and similar domains; Nostoc sp. (or Anabaena sp.) ... |
711-811 | 2.59e-10 | ||||||||
phosphoacceptor receiver (REC) domain of PatA and similar domains; Nostoc sp. (or Anabaena sp.) PatA is necessary for proper patterning of heterocysts along filaments. PatA contains phosphoacceptor REC domain at its C-terminus and an N-terminal PATAN (PatA N-terminus) domain, which was proposed in a bioinformatics study to mediate protein-protein interactions. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Some members of this group may have an inactive REC domain, lacking canonical metal-binding and active site residues. Pssm-ID: 381129 [Multi-domain] Cd Length: 102 Bit Score: 58.15 E-value: 2.59e-10
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| PBP1_PurR | cd06275 | ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ... |
45-230 | 2.82e-10 | ||||||||
ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380499 [Multi-domain] Cd Length: 269 Bit Score: 62.27 E-value: 2.82e-10
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| pleD | PRK09581 | response regulator PleD; Reviewed |
711-822 | 3.17e-10 | ||||||||
response regulator PleD; Reviewed Pssm-ID: 236577 [Multi-domain] Cd Length: 457 Bit Score: 63.38 E-value: 3.17e-10
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| xylF | PRK10355 | D-xylose ABC transporter substrate-binding protein; |
55-242 | 3.42e-10 | ||||||||
D-xylose ABC transporter substrate-binding protein; Pssm-ID: 182403 [Multi-domain] Cd Length: 330 Bit Score: 62.45 E-value: 3.42e-10
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| HATPase_CpxA-like | cd16949 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-639 | 3.62e-10 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli CpxA; This family includes the histidine kinase-like ATPase (HATPase) domains of two-component sensor histidine kinase (HKs) similar to Escherichia coli CpxA, HK of the CpxA-CpxR two-component regulatory system (TCS) which may function in acid stress and in cell wall stability. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and a HAMP sensor domain; some also contain a CpxA family periplasmic domain. Pssm-ID: 340425 [Multi-domain] Cd Length: 104 Bit Score: 57.72 E-value: 3.62e-10
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| PRK13503 | PRK13503 | HTH-type transcriptional activator RhaS; |
873-951 | 4.83e-10 | ||||||||
HTH-type transcriptional activator RhaS; Pssm-ID: 184094 [Multi-domain] Cd Length: 278 Bit Score: 61.62 E-value: 4.83e-10
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| REC_HupR-like | cd17569 | phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ... |
709-823 | 5.23e-10 | ||||||||
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar domains; This family is composed of mostly uncharacterized response regulators with similarity to the REC domains of response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It contains an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. Members of this family contain a REC domain and various output domains including the cyclase homology domain (CHD) and the c-di-GMP phosphodiesterase domains, HD-GYP and EAL. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381113 [Multi-domain] Cd Length: 118 Bit Score: 57.80 E-value: 5.23e-10
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| HATPase_EnvZ-like | cd16950 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-639 | 5.36e-10 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli EnvZ and Pseudomonas aeruginosa BfmS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Escherichia coli EnvZ of the EnvZ-OmpR two-component regulatory system (TCS), which functions in osmoregulation. It also contains the HATPase domain of Pseudomonas aeruginosa BfmS, the HK of the BfmSR TCS, which functions in the regulation of the rhl quorum-sensing system and bacterial virulence in P. aeruginosa. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and a HAMP sensor domain; some also contain a periplasmic domain. Pssm-ID: 340426 [Multi-domain] Cd Length: 101 Bit Score: 57.46 E-value: 5.36e-10
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| PRK10936 | PRK10936 | TMAO reductase system periplasmic protein TorT; Provisional |
69-211 | 5.70e-10 | ||||||||
TMAO reductase system periplasmic protein TorT; Provisional Pssm-ID: 236801 [Multi-domain] Cd Length: 343 Bit Score: 61.89 E-value: 5.70e-10
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| PRK10701 | PRK10701 | DNA-binding transcriptional regulator RstA; Provisional |
752-822 | 6.33e-10 | ||||||||
DNA-binding transcriptional regulator RstA; Provisional Pssm-ID: 236738 [Multi-domain] Cd Length: 240 Bit Score: 60.42 E-value: 6.33e-10
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| PBP1_AraR | cd01541 | ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a ... |
55-230 | 7.18e-10 | ||||||||
ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380483 [Multi-domain] Cd Length: 274 Bit Score: 61.03 E-value: 7.18e-10
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| PRK11361 | PRK11361 | acetoacetate metabolism transcriptional regulator AtoC; |
711-833 | 7.69e-10 | ||||||||
acetoacetate metabolism transcriptional regulator AtoC; Pssm-ID: 183099 [Multi-domain] Cd Length: 457 Bit Score: 62.17 E-value: 7.69e-10
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| PRK11086 | PRK11086 | sensory histidine kinase DcuS; Provisional |
509-641 | 7.91e-10 | ||||||||
sensory histidine kinase DcuS; Provisional Pssm-ID: 236839 [Multi-domain] Cd Length: 542 Bit Score: 62.62 E-value: 7.91e-10
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| COG4567 | COG4567 | DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ... |
706-822 | 8.53e-10 | ||||||||
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains [Signal transduction mechanisms, Transcription]; Pssm-ID: 443624 [Multi-domain] Cd Length: 177 Bit Score: 58.77 E-value: 8.53e-10
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| PBP1_LacI | cd01574 | ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of ... |
55-245 | 1.40e-09 | ||||||||
ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380488 [Multi-domain] Cd Length: 265 Bit Score: 59.90 E-value: 1.40e-09
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| REC_GlnL-like | cd17565 | phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar ... |
713-811 | 1.52e-09 | ||||||||
phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar proteins; Bacillus subtilis GlnL is part of the GlnK-GlnL (formerly YcbA-YcbB) two-component system that positively regulates the expression of the glsA-glnT (formerly ybgJ-ybgH) operon in response to glutamine. It contains a REC domain and a DNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381112 [Multi-domain] Cd Length: 103 Bit Score: 56.13 E-value: 1.52e-09
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| PBP1_DegA_Like | cd19976 | ligand-binding domain of putative DNA transcription regulators highly similar to that of the ... |
44-230 | 1.92e-09 | ||||||||
ligand-binding domain of putative DNA transcription regulators highly similar to that of the transcription regulator DegA; This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the transcription regulator DegA, which is involved in the control of degradation of Bacillus subtilis amidophosphoribosyltransferase (purF). This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Pssm-ID: 380631 [Multi-domain] Cd Length: 268 Bit Score: 59.57 E-value: 1.92e-09
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| REC_DesR-like | cd19930 | phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ... |
711-823 | 1.96e-09 | ||||||||
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of Bacillus subtilis DesR, Streptococcus pneumoniae response regulator spr1814, and similar proteins, all containing an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. DesR is a response regulator that, together with its cognate sensor kinase DesK, comprises a two-component regulatory system that controls membrane fluidity. Phosphorylation of the REC domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381157 [Multi-domain] Cd Length: 117 Bit Score: 56.13 E-value: 1.96e-09
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| HisKA | cd00082 | Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed ... |
421-479 | 2.75e-09 | ||||||||
Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes. Pssm-ID: 119399 [Multi-domain] Cd Length: 65 Bit Score: 54.14 E-value: 2.75e-09
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| REC_CpdR_CckA-like | cd18160 | phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; ... |
711-812 | 4.63e-09 | ||||||||
phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; Two-component systems (TCSs), consisting of a sensor and a response regulator, are used by bacteria to adapt to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis and membrane transport. Response regulators share the common phosphoacceptor REC domain and differ output domains such as DNA, RNA, ligand, and protein-binding, or enzymatic domain. CpdR is a stand-alone REC protein. CckA is a sensor histidine kinase containing N-terminal PAS domains and a C-terminal REC domain. CpdR and CckA are components of a regulatory phosphorelay system (composed of CckA, ChpT, CtrA and CpdR) that controls Brucella abortus cell growth, division, and intracellular survival inside mammalian host cells. CckA autophosphorylates in the presence of ATP and transfers a phosphoryl group to the conserved aspartic acid residue on its C-terminal REC domain, which is relayed to the ChpT phosphotransferase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381144 [Multi-domain] Cd Length: 103 Bit Score: 54.82 E-value: 4.63e-09
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| glnG | PRK10923 | nitrogen regulation protein NR(I); Provisional |
711-833 | 4.75e-09 | ||||||||
nitrogen regulation protein NR(I); Provisional Pssm-ID: 182842 [Multi-domain] Cd Length: 469 Bit Score: 59.88 E-value: 4.75e-09
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| HATPase_PhoQ-like | cd16954 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
508-636 | 5.59e-09 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli PhoQ and Providencia stuartii AarG; This family includes histidine kinase-like ATPase (HATPase) domain of two-component sensor histidine kinases similar to Escherichia coli PhoQ and Providencia stuartii AarG. PhoQ is the histidine kinase (HK) of the PhoP-PhoQ two-component regulatory system (TCS), which responds to the levels of Mg2+ and Ca2+, controls virulence, mediates the adaptation to Mg2+-limiting environments, and regulates numerous cellular activities. Providencia stuartii AarG is a putative sensor kinase which controls the expression of the 2'-N-acetyltransferase and an intrinsic multiple antibiotic resistance (Mar) response in Providencia stuartii. The AarG product is similar to PhoQ in that it is able to restore wild-type levels of resistance to a Salmonella typhimurium phoQ mutant. However, the expression of the 2'-N-acetyltransferase gene and of aarP (a gene encoding a transcriptional activator of 2'-N-acetyltransferase) are not significantly affected by the levels of Mg2+ or Ca2+. Most proteins in this group contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some have an accessory HAMP sensor domain, and some have an intracellular membrane -interaction PhoQ sensor domain. Pssm-ID: 340430 [Multi-domain] Cd Length: 135 Bit Score: 55.33 E-value: 5.59e-09
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| PRK10336 | PRK10336 | two-component system response regulator QseB; |
711-825 | 5.89e-09 | ||||||||
two-component system response regulator QseB; Pssm-ID: 182387 [Multi-domain] Cd Length: 219 Bit Score: 57.21 E-value: 5.89e-09
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| envZ | PRK09467 | osmolarity sensor protein; Provisional |
425-640 | 7.07e-09 | ||||||||
osmolarity sensor protein; Provisional Pssm-ID: 236531 [Multi-domain] Cd Length: 435 Bit Score: 59.15 E-value: 7.07e-09
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| PRK10816 | PRK10816 | two-component system response regulator PhoP; |
711-825 | 1.06e-08 | ||||||||
two-component system response regulator PhoP; Pssm-ID: 182755 [Multi-domain] Cd Length: 223 Bit Score: 56.67 E-value: 1.06e-08
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| HATPase_RstB-like | cd16939 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-640 | 1.09e-08 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Salmonella typhimurium RstB; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Salmonella typhimurium RstB HK of the RstA-RstB two-component regulatory system (TCS), which regulates expression of the constituents participating in pyrimidine metabolism and iron acquisition, and may be required for regulation of Salmonella motility and invasion. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), and a HAMP sensor domain. Pssm-ID: 340416 [Multi-domain] Cd Length: 104 Bit Score: 53.59 E-value: 1.09e-08
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| REC_Spo0A | cd17561 | phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the ... |
711-812 | 1.47e-08 | ||||||||
phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the phosphorelay system in the early stage of spore formation. It may be an element of the effector pathway responsible for the activation of sporulation genes in response to nutritional stress and may act in the with sigma factor spo0H to control the expression of some genes that are critical to the sporulation process. Spo0A contains a regulatory N-terminal REC domain and a C-terminal DNA-binding transcription activation domain as its effector/output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381109 [Multi-domain] Cd Length: 108 Bit Score: 53.38 E-value: 1.47e-08
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| HATPase_HupT_MifS-like | cd16976 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-638 | 1.56e-08 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Rhodobacter capsulatus HupT and Pseudomonas aeruginosa MifS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Rhodobacter capsulatus HupT of the HupT-HupR two-component regulatory system (TCS), which regulates the synthesis of HupSL, a membrane bound [NiFe]hydrogenase. It also contains the HATPase domain of Pseudomonas aeruginosa MifS, the HK of the MifS-MifR TCS, which may be involved in sensing alpha-ketoglutarate and regulating its transport and subsequent metabolism. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some also have a C-terminal PAS sensor domain. Pssm-ID: 340435 [Multi-domain] Cd Length: 102 Bit Score: 53.23 E-value: 1.56e-08
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| PRK10403 | PRK10403 | nitrate/nitrite response regulator protein NarP; |
711-822 | 1.91e-08 | ||||||||
nitrate/nitrite response regulator protein NarP; Pssm-ID: 182431 [Multi-domain] Cd Length: 215 Bit Score: 55.63 E-value: 1.91e-08
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| PRK10014 | PRK10014 | DNA-binding transcriptional repressor MalI; Provisional |
78-231 | 3.90e-08 | ||||||||
DNA-binding transcriptional repressor MalI; Provisional Pssm-ID: 182193 [Multi-domain] Cd Length: 342 Bit Score: 56.26 E-value: 3.90e-08
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| PBP1_LacI-like | cd06290 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
55-230 | 4.33e-08 | ||||||||
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380513 [Multi-domain] Cd Length: 267 Bit Score: 55.31 E-value: 4.33e-08
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| PRK13856 | PRK13856 | two-component response regulator VirG; Provisional |
711-822 | 4.84e-08 | ||||||||
two-component response regulator VirG; Provisional Pssm-ID: 172377 [Multi-domain] Cd Length: 241 Bit Score: 54.82 E-value: 4.84e-08
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| PBP1_TreR-like | cd01542 | ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a ... |
44-291 | 4.94e-08 | ||||||||
ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380484 [Multi-domain] Cd Length: 259 Bit Score: 55.19 E-value: 4.94e-08
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| PBP1_RegR_EndR_KdgR-like | cd06283 | ligand-binding domain of DNA transcription repressor RegR and other putative regulators such ... |
44-230 | 5.58e-08 | ||||||||
ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR; Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380506 [Multi-domain] Cd Length: 266 Bit Score: 55.25 E-value: 5.58e-08
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| fixJ | PRK09390 | response regulator FixJ; Provisional |
706-830 | 5.95e-08 | ||||||||
response regulator FixJ; Provisional Pssm-ID: 181815 [Multi-domain] Cd Length: 202 Bit Score: 53.85 E-value: 5.95e-08
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| REC_WspR-like | cd17575 | phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The ... |
711-833 | 6.13e-08 | ||||||||
phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The GGDEF response regulator WspR is part of the Wsp system that is homologous to chemotaxis systems and also includes the membrane-bound receptor protein WspA. In response to growth on surfaces, WspR is phosphorylated by the Wsp signal transduction complex and is activated, functioning as a diguanylate cyclase (DGC) that catalyzes c-di-GMP synthesis. WspR is a hybrid response regulator-diguanylate cyclase, containing an N-terminal REC domain and a C-terminal GGDEF domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381117 [Multi-domain] Cd Length: 128 Bit Score: 52.41 E-value: 6.13e-08
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| PRK10365 | PRK10365 | sigma-54-dependent response regulator transcription factor ZraR; |
711-812 | 7.70e-08 | ||||||||
sigma-54-dependent response regulator transcription factor ZraR; Pssm-ID: 182412 [Multi-domain] Cd Length: 441 Bit Score: 55.81 E-value: 7.70e-08
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| YesM | COG2972 | Sensor histidine kinase YesM [Signal transduction mechanisms]; |
542-642 | 7.91e-08 | ||||||||
Sensor histidine kinase YesM [Signal transduction mechanisms]; Pssm-ID: 442211 [Multi-domain] Cd Length: 445 Bit Score: 55.79 E-value: 7.91e-08
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| PBP1_GalS-like | cd06270 | ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory ... |
44-230 | 8.91e-08 | ||||||||
ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar binding of ABC-type transport systems. Pssm-ID: 380494 [Multi-domain] Cd Length: 266 Bit Score: 54.45 E-value: 8.91e-08
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| REC_RocR | cd17530 | phosphoacceptor receiver (REC) domain of response regulator RocR; The response regulator RocR ... |
711-819 | 9.54e-08 | ||||||||
phosphoacceptor receiver (REC) domain of response regulator RocR; The response regulator RocR from some pathogens contains an N-terminal phosphoreceiver (REC) domain and a C-terminal EAL domain that possesses c-di-GMP specific phosphodiesterase activity. The RocR REC domain is phosphorylated and modulates its EAL domain enzymatic activity, regulating the local level of c-di-GMP. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381086 [Multi-domain] Cd Length: 123 Bit Score: 51.67 E-value: 9.54e-08
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| PRK09685 | PRK09685 | DNA-binding transcriptional activator FeaR; Provisional |
856-954 | 1.34e-07 | ||||||||
DNA-binding transcriptional activator FeaR; Provisional Pssm-ID: 236612 [Multi-domain] Cd Length: 302 Bit Score: 54.27 E-value: 1.34e-07
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| REC_HupR | cd17596 | phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of ... |
709-831 | 1.63e-07 | ||||||||
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of this subfamily are response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It belongs to the nitrogen regulatory protein C (NtrC) family of response regulators, which activate transcription by RNA polymerase (RNAP) in response to a change in the environment. HupR is an unusual member of this family as it activates transcription when unphosphorylated, and transcription is inhibited by phosphorylation. Proteins in this subfamily contain an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381127 [Multi-domain] Cd Length: 133 Bit Score: 51.21 E-value: 1.63e-07
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| PRK15369 | PRK15369 | two component system response regulator; |
711-819 | 2.66e-07 | ||||||||
two component system response regulator; Pssm-ID: 185267 [Multi-domain] Cd Length: 211 Bit Score: 52.39 E-value: 2.66e-07
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| PRK12555 | PRK12555 | chemotaxis-specific protein-glutamate methyltransferase CheB; |
711-824 | 2.94e-07 | ||||||||
chemotaxis-specific protein-glutamate methyltransferase CheB; Pssm-ID: 237135 [Multi-domain] Cd Length: 337 Bit Score: 53.73 E-value: 2.94e-07
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| REC_HP-RR-like | cd17573 | phosphoacceptor receiver (REC) domain of orphan response regulator HP-RR and similar proteins; ... |
711-821 | 3.94e-07 | ||||||||
phosphoacceptor receiver (REC) domain of orphan response regulator HP-RR and similar proteins; Helicobacter pylori response regulator hp1043 (HP-RR) is an orphan response regulator which is phosphorylation-independent and is essential for growth. HP-RR functions as a cell growth-associated regulator in the absence of post-translational modification. Members of this subfamily contain REC and DNA-binding output domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381115 [Multi-domain] Cd Length: 110 Bit Score: 49.35 E-value: 3.94e-07
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| PBP1_GntR | cd01575 | ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of ... |
125-230 | 7.54e-07 | ||||||||
ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380489 [Multi-domain] Cd Length: 269 Bit Score: 51.73 E-value: 7.54e-07
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| PBP1_ABC_rhamnose | cd20000 | rhamnose ABC transporter substrate-binding protein; Rhamnose ABC transporter substrate-binding ... |
78-233 | 8.24e-07 | ||||||||
rhamnose ABC transporter substrate-binding protein; Rhamnose ABC transporter substrate-binding protein similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. Pssm-ID: 380655 Cd Length: 298 Bit Score: 51.87 E-value: 8.24e-07
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| PBP1_LacI-like | cd06293 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
49-244 | 8.76e-07 | ||||||||
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380516 [Multi-domain] Cd Length: 270 Bit Score: 51.50 E-value: 8.76e-07
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| PRK15186 | PRK15186 | AraC family transcriptional regulator; Provisional |
872-952 | 1.17e-06 | ||||||||
AraC family transcriptional regulator; Provisional Pssm-ID: 185108 [Multi-domain] Cd Length: 291 Bit Score: 51.22 E-value: 1.17e-06
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| PRK15115 | PRK15115 | response regulator GlrR; Provisional |
711-811 | 1.28e-06 | ||||||||
response regulator GlrR; Provisional Pssm-ID: 185070 [Multi-domain] Cd Length: 444 Bit Score: 52.15 E-value: 1.28e-06
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| REC_typeB_ARR-like | cd17584 | phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and ... |
711-813 | 2.34e-06 | ||||||||
phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and similar domains; Type-B ARRs (Arabidopsis response regulators) are a class of MYB-type transcription factors that act as major players in the transcriptional activation of cytokinin-responsive genes. They directly regulate the expression of type-A ARR genes and other downstream target genes. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Cytokinin signaling involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-B ARRs contain a receiver (REC) domain and a large C-terminal extension that has characteristics of an effector or output domain, with a Myb-like DNA binding domain referred to as the GARP domain. The GARP domain is a motif specific to plant transcription factors. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381121 [Multi-domain] Cd Length: 115 Bit Score: 47.24 E-value: 2.34e-06
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| PBP1_LacI-like | cd06284 | ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ... |
123-241 | 2.63e-06 | ||||||||
ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Pssm-ID: 380507 [Multi-domain] Cd Length: 267 Bit Score: 49.84 E-value: 2.63e-06
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| PRK10618 | PRK10618 | phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional |
401-641 | 2.77e-06 | ||||||||
phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional Pssm-ID: 236726 [Multi-domain] Cd Length: 894 Bit Score: 51.47 E-value: 2.77e-06
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| HTH_AraC | pfam00165 | Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ... |
915-953 | 3.23e-06 | ||||||||
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added. Pssm-ID: 425497 [Multi-domain] Cd Length: 42 Bit Score: 44.84 E-value: 3.23e-06
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| HATPase_Glnl-NtrB-like | cd16918 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
535-639 | 4.87e-06 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli GlnL (synonyms NtrB and NRII); This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs), similar to Escherichia coli GlnL/NtrB/NRII HK of the two-component regulatory system (TCS) GlnL/GlnG (NtrB-NtrC, or NRII-NRI), which regulates the transcription of genes encoding metabolic enzymes and permeases in response to carbon and nitrogen status in E. coli and related bacteria. Also included in this family are Rhodobacter capsulatus NtrB, Azospirillum brasilense NtrB, Vibrio alginolyticus NtrB, Rhizobium leguminosarum biovar phaseoli NtrB, and Herbaspirillum seropedicae NtrB. Escherichia coli GlnL/NtrB/NRII is both a kinase and a phosphatase, catalyzing the phosphorylation and dephosphorylation of GlnG/NtrC/NRI. The kinase and phosphatase activities of GlnL/NtrB/NRII are regulated by the PII signal transduction protein, which on binding to GlnL/NtrB/NRII, inhibits the kinase activity of GlnL/NtrB/NRII and activates the GlnL/NtrB/NRII phosphatase activity. Proteins having this HATPase domain also have a histidine kinase dimerization and phosphoacceptor domain (HisKA); some also contain PAS sensor domain(s). Pssm-ID: 340395 [Multi-domain] Cd Length: 109 Bit Score: 46.24 E-value: 4.87e-06
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| PRK10693 | PRK10693 | two-component system response regulator RssB; |
736-791 | 5.14e-06 | ||||||||
two-component system response regulator RssB; Pssm-ID: 182652 [Multi-domain] Cd Length: 303 Bit Score: 49.60 E-value: 5.14e-06
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| REC_RegA-like | cd17563 | phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ... |
711-819 | 7.58e-06 | ||||||||
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; Rhodobacter sphaeroides RegA, also called response regulator PrrA, is the DNA binding regulatory protein of a redox-responsive two-component regulatory system RegB/RegA that is involved in transactivating anaerobic expression of the photosynthetic apparatus. It contains a REC domain and a DNA-binding helix-turn-helix output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381111 [Multi-domain] Cd Length: 112 Bit Score: 45.90 E-value: 7.58e-06
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| REC_CheC-like | cd17593 | phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC ... |
711-819 | 7.87e-06 | ||||||||
phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC domain; This subfamily is composed of uncharacterized proteins containing an N-terminal REC domain and a C-terminal CheC domain that may function as the output/effector domain of a response regulator. CheC is a CheY-P phosphatase, affecting the level of phosphorylated CheY which controls the sense of flagella rotation and determine swimming behavior of chemotactic bacteria. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381124 [Multi-domain] Cd Length: 117 Bit Score: 45.99 E-value: 7.87e-06
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| PRK09958 | PRK09958 | acid-sensing system DNA-binding response regulator EvgA; |
712-810 | 8.14e-06 | ||||||||
acid-sensing system DNA-binding response regulator EvgA; Pssm-ID: 182168 [Multi-domain] Cd Length: 204 Bit Score: 47.58 E-value: 8.14e-06
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| PBP1_LacI-like | cd06282 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
46-232 | 9.32e-06 | ||||||||
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380505 [Multi-domain] Cd Length: 267 Bit Score: 48.43 E-value: 9.32e-06
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| PBP1_LuxPQ_Quorum_Sensing | cd06303 | periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi ... |
124-261 | 1.16e-05 | ||||||||
periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs; Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type 1 periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LuxPQ to control light production as well as its motility behavior. Pssm-ID: 380526 [Multi-domain] Cd Length: 320 Bit Score: 48.52 E-value: 1.16e-05
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| REC_citrate_TCS | cd19925 | phosphoacceptor receiver (REC) domain of citrate family two-component system response ... |
711-820 | 1.44e-05 | ||||||||
phosphoacceptor receiver (REC) domain of citrate family two-component system response regulators; This family includes Lactobacillus paracasei MaeR, Escherichia coli DcuR and DpiA, Klebsiella pneumoniae CitB, as well as Bacillus DctR, MalR, and CitT. These are all response regulators of two-component systems (TCSs) from the citrate family, and are involved in the transcriptional regulation of genes associated with L-malate catabolism (MaeRK), citrate-specific fermentation (DpiAB, CitAB), plasmid inheritance (DpiAB), anaerobic fumarate respiratory system (DcuRS), and malate transport/utilization (MalKR). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381152 [Multi-domain] Cd Length: 118 Bit Score: 45.31 E-value: 1.44e-05
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| PBP1_LacI-like | cd06273 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
66-244 | 1.60e-05 | ||||||||
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380497 [Multi-domain] Cd Length: 268 Bit Score: 47.50 E-value: 1.60e-05
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| COG3920 | COG3920 | Two-component sensor histidine kinase, HisKA and HATPase domains [Signal transduction ... |
542-641 | 1.82e-05 | ||||||||
Two-component sensor histidine kinase, HisKA and HATPase domains [Signal transduction mechanisms]; Pssm-ID: 443125 [Multi-domain] Cd Length: 495 Bit Score: 48.36 E-value: 1.82e-05
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| REC_ETR-like | cd19933 | phosphoacceptor receiver (REC) domain of plant ethylene receptors ETR1, ETR2, and EIN4, and ... |
711-813 | 1.83e-05 | ||||||||
phosphoacceptor receiver (REC) domain of plant ethylene receptors ETR1, ETR2, and EIN4, and similar proteins; Plant ethylene receptors contain N-terminal transmembrane domains that contain an ethylene binding site and also serve in localization of the receptor to the endoplasmic reticulum or the Golgi apparatus and a C-terminal histidine kinase (HK)-like domain. There are five ethylene receptors (ETR1, ERS1, ETR2, ERS2, and EIN4) in Arabidopsis thaliana. ETR1, ETR2, and EIN4 also contain REC domains C-terminal to the HK domain. ETR1 and ERS1 belong to subfamily 1, and have functional HK domains while ETR2, ERS2, and EIN4 belong to subfamily 2, and lack the necessary residues for HK activity and may function as serine/threonine kinases. The plant hormone ethylene plays an important role in plant growth and development. It regulates seed germination, seedling growth, leaf and petal abscission, fruit ripening, organ senescence, and pathogen responses. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381160 [Multi-domain] Cd Length: 117 Bit Score: 44.70 E-value: 1.83e-05
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| PBP1_LacI-like | cd06279 | ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium ... |
97-231 | 2.76e-05 | ||||||||
ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Pssm-ID: 380502 [Multi-domain] Cd Length: 284 Bit Score: 47.20 E-value: 2.76e-05
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| REC_typeA_ARR | cd17581 | phosphoacceptor receiver (REC) domain of type A Arabidopsis response regulators (ARRs) and ... |
711-811 | 3.70e-05 | ||||||||
phosphoacceptor receiver (REC) domain of type A Arabidopsis response regulators (ARRs) and similar proteins; Type-A response regulators of Arabidopsis (ARRs) are involved in cytokinin signaling, which involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Type-A ARRs function downstream of and are regulated by type-B ARRs, which are a class of MYB-type transcription factors. As primary cytokinin response genes, type-A ARRs act as redundant negative feedback regulators of cytokinin signaling by inactivating the phosphorelay. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-A ARRs are similar in domain structure to CheY, in that they lack a typical output domain and only contain a stand-alone receiver (REC) domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381119 [Multi-domain] Cd Length: 122 Bit Score: 44.28 E-value: 3.70e-05
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| dpiB | PRK15053 | sensor histidine kinase DpiB; Provisional |
505-639 | 6.17e-05 | ||||||||
sensor histidine kinase DpiB; Provisional Pssm-ID: 185013 [Multi-domain] Cd Length: 545 Bit Score: 46.75 E-value: 6.17e-05
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| PBP1_AglR-like | cd20010 | Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ... |
162-244 | 7.21e-05 | ||||||||
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and similar proteins; Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380665 [Multi-domain] Cd Length: 269 Bit Score: 45.62 E-value: 7.21e-05
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| PRK11697 | PRK11697 | two-component system response regulator BtsR; |
711-822 | 7.86e-05 | ||||||||
two-component system response regulator BtsR; Pssm-ID: 236956 [Multi-domain] Cd Length: 238 Bit Score: 45.22 E-value: 7.86e-05
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| PBP1_MalR-like | cd06294 | ligand-binding domain of maltose transcription regulator MalR which is a member of the ... |
97-230 | 9.40e-05 | ||||||||
ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors; This group includes the ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380517 [Multi-domain] Cd Length: 269 Bit Score: 45.27 E-value: 9.40e-05
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| PRK10572 | PRK10572 | arabinose operon transcriptional regulator AraC; |
868-954 | 9.43e-05 | ||||||||
arabinose operon transcriptional regulator AraC; Pssm-ID: 236717 [Multi-domain] Cd Length: 290 Bit Score: 45.35 E-value: 9.43e-05
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| PBP1_GalR | cd01544 | ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory ... |
98-241 | 9.46e-05 | ||||||||
ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism; Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar binding of ABC-type transport systems. Pssm-ID: 380486 [Multi-domain] Cd Length: 269 Bit Score: 45.21 E-value: 9.46e-05
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| HATPase_NtrY-like | cd16944 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
531-639 | 1.11e-04 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Azorhizobium caulinodans NtrY; This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs) such as Azorhizobium caulinodans ORS571 NtrY of the NtrY-NtrX TCS, which is involved in nitrogen fixation and metabolism. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and a HAMP sensor domain; some also have PAS sensor domains. Pssm-ID: 340420 [Multi-domain] Cd Length: 108 Bit Score: 42.52 E-value: 1.11e-04
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| REC_RcNtrC-like | cd19928 | phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C ... |
711-811 | 1.29e-04 | ||||||||
phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C (NtrC) and similar NtrC family response regulators; NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include NtrC, also called nitrogen regulator I (NRI), from Rhodobacter capsulatus, Azospirillum brasilense, and Azorhizobium caulinodans. NtrC is part of the NtrB/NtrC two-component system that controls the expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381155 [Multi-domain] Cd Length: 100 Bit Score: 42.11 E-value: 1.29e-04
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
357-415 | 1.59e-04 | ||||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 45.28 E-value: 1.59e-04
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| PRK15185 | PRK15185 | transcriptional regulator HilD; Provisional |
867-953 | 1.94e-04 | ||||||||
transcriptional regulator HilD; Provisional Pssm-ID: 185107 [Multi-domain] Cd Length: 309 Bit Score: 44.60 E-value: 1.94e-04
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| REC_PhyR | cd17540 | phosphoacceptor receiver (REC) domain of response regulator PhyR and similar proteins; PhyR is ... |
709-821 | 2.31e-04 | ||||||||
phosphoacceptor receiver (REC) domain of response regulator PhyR and similar proteins; PhyR is a hybrid stress regulator that contains an N-terminal sigma-like (SL) domain and a C-terminal REC domain. Phosphorylation of the REC domain is known to promote binding of the SL domain to an anti-sigma factor. PhyR thus functions as an anti-anti-sigma factor in its phosphorylated state. It is involved in the general stress response. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Pssm-ID: 381095 [Multi-domain] Cd Length: 117 Bit Score: 41.85 E-value: 2.31e-04
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| cpxA | PRK09470 | envelope stress sensor histidine kinase CpxA; |
411-625 | 2.31e-04 | ||||||||
envelope stress sensor histidine kinase CpxA; Pssm-ID: 236532 [Multi-domain] Cd Length: 461 Bit Score: 44.92 E-value: 2.31e-04
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| CwlO1 | COG3883 | Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ... |
363-414 | 2.41e-04 | ||||||||
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown]; Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 44.44 E-value: 2.41e-04
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| HATPase_CheA-like | cd16916 | Histidine kinase-like ATPase domain of the chemotaxis protein histidine kinase CheA, and some ... |
602-639 | 2.92e-04 | ||||||||
Histidine kinase-like ATPase domain of the chemotaxis protein histidine kinase CheA, and some hybrid sensor histidine kinases; This family includes the cytoplasmic histidine kinase (HK) CheA, a transmembrane receptor which, together with cytoplasmic adaptor protein (CheW), forms the lattice at the core of the chemosensory array that controls the cellular chemotaxis of motile bacteria and archaea. CheA forms a two-component signal transduction system (TCS) with the response regulator CheY. Proteins having this CheA-like HATPase domain generally also have a histidine-phosphotransfer domain, a histidine kinase homodimeric domain, and a regulatory domain; some are hybrid sensor histidine kinases as they contain a REC signal receiver domain. Pssm-ID: 340393 [Multi-domain] Cd Length: 178 Bit Score: 42.57 E-value: 2.92e-04
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
292-418 | 3.17e-04 | ||||||||
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 43.98 E-value: 3.17e-04
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| PBP1_SalR | cd01545 | ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of ... |
64-230 | 5.46e-04 | ||||||||
ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380487 [Multi-domain] Cd Length: 270 Bit Score: 42.93 E-value: 5.46e-04
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| PRK11303 | PRK11303 | catabolite repressor/activator; |
66-213 | 6.35e-04 | ||||||||
catabolite repressor/activator; Pssm-ID: 236897 [Multi-domain] Cd Length: 328 Bit Score: 42.94 E-value: 6.35e-04
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
357-415 | 7.29e-04 | ||||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 40.29 E-value: 7.29e-04
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
363-414 | 7.41e-04 | ||||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 42.97 E-value: 7.41e-04
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| PRK09483 | PRK09483 | response regulator; Provisional |
711-822 | 7.59e-04 | ||||||||
response regulator; Provisional Pssm-ID: 236538 [Multi-domain] Cd Length: 217 Bit Score: 42.02 E-value: 7.59e-04
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
364-418 | 1.02e-03 | ||||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 39.90 E-value: 1.02e-03
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| PBP1_LacI-like | cd06287 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
97-231 | 1.13e-03 | ||||||||
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380510 [Multi-domain] Cd Length: 268 Bit Score: 42.02 E-value: 1.13e-03
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
357-418 | 1.58e-03 | ||||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 41.81 E-value: 1.58e-03
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| DUF3584 | pfam12128 | Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. ... |
362-419 | 1.75e-03 | ||||||||
Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. Pssm-ID: 432349 [Multi-domain] Cd Length: 1191 Bit Score: 42.52 E-value: 1.75e-03
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| psREC_PRR | cd17582 | pseudo receiver domain of pseudo-response regulators; In Arabidopsis, five pseudo-response ... |
711-789 | 1.80e-03 | ||||||||
pseudo receiver domain of pseudo-response regulators; In Arabidopsis, five pseudo-response regulators (PRRs), also called APRRs, comprise a core group of clock components that controls the pace of the central oscillator of the circadian clock, an endogenous time-keeping mechanism that enables organisms to adapt to external daily cycles. The coordinated sequential expression of PRR9 (APRR9), PRR7 (APRR7), PRR5 (APRR5), PRR3 (APRR3), and PRR1 (APRR1) results in circadian waves that may be at the basis of the endogenous circadian clock. PRRs contain an N-terminal pseudo receiver (psREC) domain that resembles the receiver domain of a two-component response regulator, but lacks an aspartate residue that accepts a phosphoryl group from the sensor kinase, and a CCT motif at the C-terminus that contains a putative nuclear localization signal. The psREC domain is involved in protein-protein interactions. Pssm-ID: 381120 [Multi-domain] Cd Length: 104 Bit Score: 38.92 E-value: 1.80e-03
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| PRK10815 | PRK10815 | two-component system sensor histidine kinase PhoQ; |
541-626 | 1.83e-03 | ||||||||
two-component system sensor histidine kinase PhoQ; Pssm-ID: 182754 [Multi-domain] Cd Length: 485 Bit Score: 41.93 E-value: 1.83e-03
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| DDRGK | pfam09756 | DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and ... |
357-418 | 1.86e-03 | ||||||||
DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Pssm-ID: 370664 [Multi-domain] Cd Length: 188 Bit Score: 40.41 E-value: 1.86e-03
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| REC_TPR | cd17589 | phosphoacceptor receiver (REC) domain of uncharacterized tetratricopeptide repeat (TPR) ... |
711-821 | 1.92e-03 | ||||||||
phosphoacceptor receiver (REC) domain of uncharacterized tetratricopeptide repeat (TPR)-containing response regulators; Response regulators share the common phosphoacceptor REC domain and different output domains. This subfamily contains uncharacterized response regulators with TPR repeats as the effector or output domain, which might contain between 3 to 16 TPR repeats (each about 34 amino acids). TPR-containing proteins occur in all domains of life and the abundance of TPR-containing proteins in a bacterial proteome is not indicative of virulence. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Some members in this subfamily may contain inactive REC domains lacking canonical metal-binding and active site residues. Pssm-ID: 381123 [Multi-domain] Cd Length: 115 Bit Score: 39.17 E-value: 1.92e-03
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| PBP1_LacI-like | cd06281 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
62-241 | 2.13e-03 | ||||||||
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380504 [Multi-domain] Cd Length: 270 Bit Score: 41.07 E-value: 2.13e-03
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| ftrA | PRK09393 | transcriptional activator FtrA; Provisional |
869-954 | 2.24e-03 | ||||||||
transcriptional activator FtrA; Provisional Pssm-ID: 181818 [Multi-domain] Cd Length: 322 Bit Score: 41.10 E-value: 2.24e-03
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| PRK13501 | PRK13501 | HTH-type transcriptional activator RhaR; |
855-954 | 2.40e-03 | ||||||||
HTH-type transcriptional activator RhaR; Pssm-ID: 184092 [Multi-domain] Cd Length: 290 Bit Score: 41.04 E-value: 2.40e-03
|
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
362-414 | 2.73e-03 | ||||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 41.04 E-value: 2.73e-03
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| HATPase_AgrC-ComD-like | cd16935 | Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
504-638 | 2.96e-03 | ||||||||
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Staphylococcus aureus AgrC and Streptococcus pneumoniae ComD which are involved in quorum sensing; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) including Staphylococcus aureus AgrC which is an HK of the accessory gene regulator (agr) quorum sensing two-component regulatory system (TCS) AgrC-AgrA. The agr system plays a part in the transition from persistent to virulent phenotype. This family also includes Streptococcus pneumoniae ComD HK of the ComD-ComE TCS, involved in quorum sensing and genetic competence. Pssm-ID: 340412 [Multi-domain] Cd Length: 134 Bit Score: 38.71 E-value: 2.96e-03
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
360-413 | 3.60e-03 | ||||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 40.66 E-value: 3.60e-03
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
364-415 | 4.27e-03 | ||||||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 41.09 E-value: 4.27e-03
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| PRK09935 | PRK09935 | fimbriae biosynthesis transcriptional regulator FimZ; |
708-810 | 4.88e-03 | ||||||||
fimbriae biosynthesis transcriptional regulator FimZ; Pssm-ID: 182154 [Multi-domain] Cd Length: 210 Bit Score: 39.47 E-value: 4.88e-03
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| COG1340 | COG1340 | Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; |
367-414 | 5.01e-03 | ||||||||
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 39.89 E-value: 5.01e-03
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| Atg16_CCD | cd22887 | Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family ... |
356-406 | 5.31e-03 | ||||||||
Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins. Pssm-ID: 439196 [Multi-domain] Cd Length: 91 Bit Score: 37.16 E-value: 5.31e-03
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| PBP1_ABC_unchar_transporter | cd06325 | type 1 periplasmic ligand-binding domain of uncharacterized ABC-type transport systems ... |
56-147 | 5.46e-03 | ||||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC-type transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions; This group includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); its ligand specificity has not been determined experimentally. Pssm-ID: 380548 Cd Length: 282 Bit Score: 39.79 E-value: 5.46e-03
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| PRK09978 | PRK09978 | DNA-binding transcriptional regulator GadX; Provisional |
894-955 | 5.52e-03 | ||||||||
DNA-binding transcriptional regulator GadX; Provisional Pssm-ID: 137624 [Multi-domain] Cd Length: 274 Bit Score: 39.91 E-value: 5.52e-03
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| CREPT | pfam16566 | Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ... |
363-413 | 5.98e-03 | ||||||||
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours. Pssm-ID: 465181 [Multi-domain] Cd Length: 147 Bit Score: 38.37 E-value: 5.98e-03
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| Peripla_BP_3 | pfam13377 | Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ... |
154-230 | 6.70e-03 | ||||||||
Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognizes Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 433159 [Multi-domain] Cd Length: 160 Bit Score: 38.47 E-value: 6.70e-03
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| Atg16_CCD | cd22887 | Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family ... |
358-412 | 7.55e-03 | ||||||||
Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins. Pssm-ID: 439196 [Multi-domain] Cd Length: 91 Bit Score: 36.77 E-value: 7.55e-03
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| PspA | COG1842 | Phage shock protein A [Transcription, Signal transduction mechanisms]; |
367-414 | 7.64e-03 | ||||||||
Phage shock protein A [Transcription, Signal transduction mechanisms]; Pssm-ID: 441447 [Multi-domain] Cd Length: 217 Bit Score: 39.04 E-value: 7.64e-03
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
368-418 | 8.71e-03 | ||||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 39.90 E-value: 8.71e-03
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