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Conserved domains on  [gi|495186078|ref|WP_007910868|]
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MULTISPECIES: response regulator transcription factor [Pseudomonas]

Protein Classification

response regulator transcription factor( domain architecture ID 11450879)

response regulator transcription factor with a signal receiver (REC) domain and a LuxR family helix-turn-helix (HTH) domain that may be part of a two-component regulatory system; similar to Staphylococcus aureus response regulator VraR

CATH:  1.10.10.10
Gene Ontology:  GO:0000160|GO:0006355|GO:0003677
PubMed:  10966457
SCOP:  3001179

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 5-119 1.57e-32

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: 113.38  E-value: 1.57e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 495186078  85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAI 119
Cdd:cd17535   81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
GerE pfam00196
Bacterial regulatory proteins, luxR family;
140-196 1.22e-20

Bacterial regulatory proteins, luxR family;


:

Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 80.71  E-value: 1.22e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078  140 AALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
 
Name Accession Description Interval E-value
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 5-119 1.57e-32

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: 113.38  E-value: 1.57e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 495186078  85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAI 119
Cdd:cd17535   81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 3-193 4.40e-32

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 115.13  E-value: 4.40e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   3 CRIIIADDHPLFREAmLRTVQRLLPE-AVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIV 81
Cdd:PRK10651   7 ATILLIDDHPMLRTG-VKQLISMAPDiTVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLL---------PLETGAA-LTPRQQDVLR 151
Cdd:PRK10651  86 FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLaaslranraTTERDVNqLTPRERDILK 165

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 495186078 152 LIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRA-AAV 193
Cdd:PRK10651 166 LIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVeAAV 208
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-196 5.28e-29

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: 104.59  E-value: 5.28e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELrrrlprttlivvs 83
Cdd:COG2197    3 RVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL------------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  84 mvddeslisevmtagidgfigkniapdeigqailairegevlvkfapsgllpletgaaLTPRQQDVLRLIAQGKTNKEIA 163
Cdd:COG2197   70 ----------------------------------------------------------LTPREREVLRLLAEGLSNKEIA 91

                        170       180       190
                 ....*....|....*....|....*....|...
gi 495186078 164 RELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:COG2197   92 ERLGISERTVKTHVSNILRKLGVRNRTELVLLA 124
GerE pfam00196
Bacterial regulatory proteins, luxR family;
140-196 1.22e-20

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 80.71  E-value: 1.22e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078  140 AALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 140-196 1.63e-20

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 80.65  E-value: 1.63e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078   140 AALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 140-196 2.43e-20

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 80.77  E-value: 2.43e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078 140 AALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:COG5905   11 SLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWA 67
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 142-196 1.57e-19

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 77.96  E-value: 1.57e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 495186078 142 LTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYA 55
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 5-116 2.34e-16

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: 71.41  E-value: 2.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078    5 IIIADDHPLFREAMLRTVQRllPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEK--EGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 495186078   85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
141-196 5.39e-10

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 58.03  E-value: 5.39e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 495186078 141 ALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:PRK04841 838 PLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA 893
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 140-184 8.59e-06

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 44.09  E-value: 8.59e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 495186078  140 AALTPRQQDVLRL-IAQGKTNKEIARELDISPFTVRIHVSSLLRTL 184
Cdd:TIGR02985 112 EKLPEQCREIFILsRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157
 
Name Accession Description Interval E-value
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 5-119 1.57e-32

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: 113.38  E-value: 1.57e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 495186078  85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAI 119
Cdd:cd17535   81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 3-193 4.40e-32

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 115.13  E-value: 4.40e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   3 CRIIIADDHPLFREAmLRTVQRLLPE-AVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIV 81
Cdd:PRK10651   7 ATILLIDDHPMLRTG-VKQLISMAPDiTVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLL---------PLETGAA-LTPRQQDVLR 151
Cdd:PRK10651  86 FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLaaslranraTTERDVNqLTPRERDILK 165

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 495186078 152 LIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRA-AAV 193
Cdd:PRK10651 166 LIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVeAAV 208
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-196 5.28e-29

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: 104.59  E-value: 5.28e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELrrrlprttlivvs 83
Cdd:COG2197    3 RVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL------------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  84 mvddeslisevmtagidgfigkniapdeigqailairegevlvkfapsgllpletgaaLTPRQQDVLRLIAQGKTNKEIA 163
Cdd:COG2197   70 ----------------------------------------------------------LTPREREVLRLLAEGLSNKEIA 91

                        170       180       190
                 ....*....|....*....|....*....|...
gi 495186078 164 RELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:COG2197   92 ERLGISERTVKTHVSNILRKLGVRNRTELVLLA 124
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
4-192 4.49e-26

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 99.54  E-value: 4.49e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:PRK10403   8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  84 MVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREG---------EVLVKFAPSGLLPlETGAALTPRQQDVLRLIA 154
Cdd:PRK10403  88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGskvfservnQYLREREMFGAEE-DPFSVLTERELDVLHELA 166

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 495186078 155 QGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAA 192
Cdd:PRK10403 167 QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAA 204
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 6-199 5.90e-22

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: 88.23  E-value: 5.90e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   6 IIADDhplfrEAMLRTVQRLLpEAV---IEEAGDLDAVLALLPLGEPDTLILDLRFP---GLTCVSQLAELRRRLPrttL 79
Cdd:COG4566    4 IVDDD-----EAVRDSLAFLL-ESAglrVETFASAEAFLAALDPDRPGCLLLDVRMPgmsGLELQEELAARGSPLP---V 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  80 IVVSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLLPLETG-AALTPRQQDVLRLIAQGKT 158
Cdd:COG4566   75 IFLTGHGDVPMAVRAMKAGAVDFLEKPFDDQALLDAVRRALARDRARRAERARRAELRARlASLTPREREVLDLVVAGLS 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 495186078 159 NKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYAGTL 199
Cdd:COG4566  155 NKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLALAL 195
GerE pfam00196
Bacterial regulatory proteins, luxR family;
140-196 1.22e-20

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 80.71  E-value: 1.22e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078  140 AALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 140-196 1.63e-20

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 80.65  E-value: 1.63e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078   140 AALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 140-196 2.43e-20

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 80.77  E-value: 2.43e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078 140 AALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:COG5905   11 SLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWA 67
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 142-196 1.57e-19

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 77.96  E-value: 1.57e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 495186078 142 LTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYA 55
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 5-195 1.14e-18

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 80.26  E-value: 1.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTC---VSQLAELRRRLPRTTLIV 81
Cdd:PRK10840   6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYgdgITLIKYIKRHFPSLSIIV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEvlvKFAPSGLLPL-----ETG---AALTPRQQDVLRLI 153
Cdd:PRK10840  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGK---KFTPESVSRLlekisAGGygdKRLSPKESEVLRLF 162

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 495186078 154 AQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKY 195
Cdd:PRK10840 163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNY 204
PRK15369 PRK15369
two component system response regulator;
1-196 1.15e-18

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 80.12  E-value: 1.15e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   1 MTCRIIIADDHPLFREA---MLRTVQRLLpeaVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRT 77
Cdd:PRK15369   2 KNYKILLVDDHELIINGiknMLAPYPRYK---IVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAM 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  78 TLIVVSMVDDESLISEVMTAGIDGFIGKN-------------------IAPDEIGQAILAIREGEVlvkfapsgllplET 138
Cdd:PRK15369  79 NILVLTARQEEHMASRTLAAGALGYVLKKspqqillaaiqtvavgkryIDPALNREAILALLNADD------------TN 146

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495186078 139 GAALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:PRK15369 147 PPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWA 204
PRK10360 PRK10360
transcriptional regulator UhpA;
5-186 1.38e-17

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 76.94  E-value: 1.38e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVsqlaELRRRLPR-TTLIVVS 83
Cdd:PRK10360   4 VALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGL----ELLSQLPKgMATIMLS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  84 MVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREG------EVLVKFAPSGLLPLetgaalTPRQQDVLRLIAQGK 157
Cdd:PRK10360  80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGgcyltpDIAIKLASGRQDPL------TKRERQVAEKLAQGM 153

                        170       180
                 ....*....|....*....|....*....
gi 495186078 158 TNKEIARELDISPFTVRIHVSSLLRTLNV 186
Cdd:PRK10360 154 AVKEIAAELGLSPKTVHVHRANLMEKLGV 182
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 5-116 2.34e-16

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: 71.41  E-value: 2.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078    5 IIIADDHPLFREAMLRTVQRllPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEK--EGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 495186078   85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
6-188 4.38e-16

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 73.01  E-value: 4.38e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   6 IIADDHPLFREAmlrtVQRLLPEAVIEEAGDLD----AVLALLPLgEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIV 81
Cdd:PRK09958   4 IIIDDHPLAIAA----IRNLLIKNDIEILAELTeggsAVQRVETL-KPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIII 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGE-----VLVKFAPSGLLPLETGAALTPRQQDVLRLIAQG 156
Cdd:PRK09958  79 VSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYcyfpfSLNRFVGSLTSDQQKLDSLSKQEISVMRYILDG 158

                        170       180       190
                 ....*....|....*....|....*....|..
gi 495186078 157 KTNKEIARELDISPFTVRIHVSSLLRTLNVPS 188
Cdd:PRK09958 159 KDNNDIAEKMFISNKTVSTYKSRLMEKLECKS 190
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-121 3.01e-15

DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal transduction mechanisms];


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 69.23  E-value: 3.01e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   1 MTCRIIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLI 80
Cdd:COG4565    2 KMIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDVI 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 495186078  81 VVSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIRE 121
Cdd:COG4565   82 VITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLE 122
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
19-196 1.26e-14

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 69.01  E-value: 1.26e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  19 LRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSMVDDESLISEVMTAG 98
Cdd:COG2771    5 ALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLAL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  99 IDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLLPLETGAALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVS 178
Cdd:COG2771   85 LLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLK 164

                        170
                 ....*....|....*...
gi 495186078 179 SLLRTLNVPSRAAAVKYA 196
Cdd:COG2771  165 RIYRKLGVSSRAELVALA 182
PRK09483 PRK09483
response regulator; Provisional
 5-186 4.87e-13

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 65.13  E-value: 4.87e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:PRK09483   4 VLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIIMLTV 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGE-----------VLVKFAPSGLLPLETgaaLTPRQQDVLRLI 153
Cdd:PRK09483  84 HTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQryiasdiaqqmALSQIEPATENPFAS---LSERELQIMLMI 160

                        170       180       190
                 ....*....|....*....|....*....|...
gi 495186078 154 AQGKTNKEIARELDISPFTVRIHVSSLLRTLNV 186
Cdd:PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 4-105 1.52e-12

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: 60.94  E-value: 1.52e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILS 80

                         90       100
                 ....*....|....*....|..
gi 495186078  84 MVDDESLISEVMTAGIDGFIGK 105
Cdd:COG4753   81 GYSDFEYAQEAIKLGADDYLLK 102
fixJ PRK09390
response regulator FixJ; Provisional
 39-196 3.43e-12

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 62.33  E-value: 3.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  39 AVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAI-L 117
Cdd:PRK09390  38 AFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIeR 117

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495186078 118 AIREGEVLVKFAPSGLLPLETGAALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:PRK09390 118 ALAQAPEAAKSEAVAADIRARIASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMA 196
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
5-196 3.89e-12

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 62.59  E-value: 3.89e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:PRK09935   6 VIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSS 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGevlVKFAPSGLLPL------ETGAA----LTPRQQDVLRLIA 154
Cdd:PRK09935  86 KSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSG---YTFFPSETLNYiksnkcSTNSStdtvLSNREVTILRYLV 162

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 495186078 155 QGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:PRK09935 163 SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYA 204
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 4-155 1.02e-11

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: 62.67  E-value: 1.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLlpEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:COG2204    4 RILVVDDDPDIRRLLKELLERA--GYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLT 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495186078  84 MVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLLPLETGAALtprqQDVLRLIAQ 155
Cdd:COG2204   82 GYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRRLRRENAEDSGLIGRSPAM----QEVRRLIEK 149
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 5-117 3.66e-11

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: 57.74  E-value: 3.66e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:cd19931    1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTV 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 495186078  85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAIL 117
Cdd:cd19931   81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEALK 113
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 4-184 1.18e-10

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: 58.43  E-value: 1.18e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLlpEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:COG0745    3 RILVVEDDPDIRELLADALERE--GYEVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPIIMLT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  84 MVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLLPLETGAA--------LTPRQQDVLRLIAQ 155
Cdd:COG0745   81 ARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALLRRRAAEVLRVGDLLDLAAREVtrdgepveLTPKEFRLLELLMR 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495186078 156 GK----TNKEIAREL----DISPFTVRIHVSSLLRTL 184
Cdd:COG0745  161 NPgrvvSREQLLEEVwgydYGDDRTVDVHISRLRKKL 197
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 4-116 2.88e-10

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: 55.63  E-value: 2.88e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLlpEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRR--LPRTTLIV 81
Cdd:COG0784    7 RILVVDDNPDNRELLRRLLERL--GYEVTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALprLPDIPIIA 84

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:COG0784   85 LTAYADEEDRERALEAGADDYLTKPVDPEELLEAL 119
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
141-196 5.39e-10

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 58.03  E-value: 5.39e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 495186078 141 ALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:PRK04841 838 PLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA 893
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 7-105 8.10e-10

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: 53.77  E-value: 8.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   7 IADDHPLFREAMLRTVQRLlpEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSMVD 86
Cdd:cd00156    2 IVDDDPAIRELLKSLLERE--GYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAKA 79

                         90
                 ....*....|....*....
gi 495186078  87 DESLISEVMTAGIDGFIGK 105
Cdd:cd00156   80 DEEDAVRALELGADDYLVK 98
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 5-116 1.03e-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: 53.82  E-value: 1.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSM 84
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 495186078  85 VDDESLISEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:cd19930   81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAI 112
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
151-199 1.23e-09

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 55.10  E-value: 1.23e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 495186078 151 RLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYAGTL 199
Cdd:COG2909  132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARAREL 180
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 4-142 2.54e-09

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: 54.79  E-value: 2.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLlpEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRR--RLPRTTLIV 81
Cdd:COG3437    8 TVLIVDDDPENLELLRQLLRTL--GYDVVTAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRAdpSTRDIPVIF 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLLPLETGAAL 142
Cdd:COG3437   86 LTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALELRRLQRELDDLVLYLKLAAPL 146
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 2-122 2.76e-08

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: 51.45  E-value: 2.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   2 TCRIIIADDHPLFREAMLRTVQRLlpEAVIEEAGDLDAVLALLPLGEPDTLILDLRFP---GLTCVSQLaelrRRLPRTT 78
Cdd:COG3706    1 PARILVVDDDPTNRKLLRRLLEAA--GYEVVEAADGEEALELLQEHRPDLILLDLEMPdmdGLELCRRL----RADPRTA 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 495186078  79 ---LIVVSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAI-LAIREG 122
Cdd:COG3706   75 dipIIFLTALDDEEDRARALEAGADDYLTKPFDPEELLARVdLVARYG 122
REC_HupR cd17596
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of ...
 4-122 3.02e-08

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: 50.44  E-value: 3.02e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTvqrLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:cd17596    2 TILVVDDEVRSLEALRRT---LEEDFDVLTAASAEEALAILEEEWVQVILCDQRMPGTTGVEFLKEVRERWPEVVRIIIS 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 495186078  84 -MVDDESLISEVMTAGIDGFIGKNIAPDeigQAILAIREG 122
Cdd:cd17596   79 gYTDSEDIIAGINEAGIYQYLTKPWHPD---QLLLTVRNA 115
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 5-121 5.43e-08

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: 49.26  E-value: 5.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRL-LPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEeLGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIRELYPDIKIIILS 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 495186078  84 MVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIRE 121
Cdd:cd17536   81 GYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKE 118
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 4-120 1.08e-07

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: 49.96  E-value: 1.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPEaVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:COG3707    5 RVLVVDDEPLRRADLREGLREAGYE-VVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISEERPAPVILLTA 83

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 495186078  84 mVDDESLISEVMTAGIDGFIGKNIAPDEIGQAI-LAIR 120
Cdd:COG3707   84 -YSDPELIERALEAGVSAYLVKPLDPEDLLPALeLALA 120
PRK10100 PRK10100
transcriptional regulator CsgD;
140-196 2.74e-07

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 49.10  E-value: 2.74e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078 140 AALTPRQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:PRK10100 154 ALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWA 210
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 4-180 3.06e-07

DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction mechanisms];


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 49.04  E-value: 3.06e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:COG3279    3 KILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIFTT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  84 MVDDESLIS-EVmtAGIDgFIGKNIAPDEIGQAILAIRE-----GEVLVKFAPSGLLPLETGAALTP-RQQDVLRLIAQG 156
Cdd:COG3279   83 AYDEYALEAfEV--NAVD-YLLKPIDEERLAKALEKAKErleakAAAEASPEEKDRIFVKSGGKLVKiPLDDILYIEAEG 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 495186078 157 K---------------TNKEIARELDISPFtVRIHVSSL 180
Cdd:COG3279  160 NyvkihtkdkkylvrkTLKELEEKLPPKQF-FRVHRSYI 197
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 4-137 1.09e-06

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: 46.83  E-value: 1.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLlpEAVIEEAGDLDAVLALLPLGEPDTLILDLRFP---GLTCVsqlAELRRRLPRTTLI 80
Cdd:COG4567    6 SLLLVDDDEAFARVLARALERR--GFEVTTAASVEEALALLEQAPPDYAVLDLRLGdgsGLDLI---EALRERDPDARIV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078  81 VVSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLLPLE 137
Cdd:COG4567   81 VLTGYASIATAVEAIKLGADDYLAKPADADDLLAALERAEGDAPAPPENPMSLDRLE 137
PRK10188 PRK10188
transcriptional regulator SdiA;
123-196 1.44e-06

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 47.09  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078 123 EVLVKFAPSGLLPLETGAALTP------RQQDVLRLIAQGKTNKEIARELDISPFTVRIHVSSLLRTLNVPSRAAAVKYA 196
Cdd:PRK10188 155 QLLVRESLMALMRLEDEMVMTPemnfskREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYA 234
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 4-120 1.79e-06

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: 1.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:cd19925    2 NVLIVEDDPMVAEIHRAYVEQVPGFTVIGTAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDVIVVT 81

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 495186078  84 MVDDESLISEVMTAGIDGFIGKNIAPDEIGQAILAIR 120
Cdd:cd19925   82 AANDVETVREALRLGVVDYLIKPFTFERLRQRLERYR 118
REC_hyHK_CKI1_RcsC-like cd17546
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...
 5-116 4.12e-06

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: 44.00  E-value: 4.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEavIEEAGDLDAVLALLPLGEPDTLILDLRFP---GLTCVSQLAELRRRLPRTTLIV 81
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLLEKLGYE--VDVAENGQEALELLKEEPFDLVLMDLQMPvmdGLEATRRIRELEGGGRRTPIIA 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:cd17546   79 LTANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113
REC_CheC-like cd17593
phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC ...
 4-117 4.88e-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: 44.06  E-value: 4.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPeAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:cd17593    2 KVLICDDSSMARKQLARALPADWD-VEITFAENGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIVVS 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 495186078  84 M-VDDESlISEVMTAGIDGFIGKNIAPDEIGQAIL 117
Cdd:cd17593   81 GdVQPEA-KERVLELGALAFLKKPFDPEKLAQLLE 114
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 3-190 6.90e-06

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 44.74  E-value: 6.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   3 CRIIIADDHPLFREAMLRTvqrllpeavieeagDLDAVLALLPlgepdtlilDLRFPGLTCVSQLAELRRRLPRTTLIVv 82
Cdd:PRK11475  18 YKLHTFSSQSSFQDAMSRI--------------SFSAVIFSLS---------AMRSERREGLSCLTELAIKFPRMRRLV- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078  83 sMVDDES---LISEVMTAGIDGFIGKNIAPDEIGQAILAIREGEVLVKFAPSGLLPLETGAALTPRQQDVLRLIAQGKTN 159
Cdd:PRK11475  74 -IADDDIearLIGSLSPSPLDGVLSKASTLEILQQELFLSLNGVRQATDRLNNQWYINQSRMLSPTEREILRFMSRGYSM 152

                        170       180       190
                 ....*....|....*....|....*....|.
gi 495186078 160 KEIARELDISPFTVRIHVSSLLRTLNVPSRA 190
Cdd:PRK11475 153 PQIAEQLERNIKTIRAHKFNVMSKLGVSSDA 183
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 140-184 8.59e-06

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 44.09  E-value: 8.59e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 495186078  140 AALTPRQQDVLRL-IAQGKTNKEIARELDISPFTVRIHVSSLLRTL 184
Cdd:TIGR02985 112 EKLPEQCREIFILsRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 4-116 2.09e-05

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: 42.33  E-value: 2.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLLPEAvIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRR--RLPRTTLIV 81
Cdd:cd19923    2 KVLVVDDFSTMRRIIKNLLKELGFNN-VEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRAdgALSHLPVLM 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:cd19923   81 VTAEAKKENVIAAAQAGVNNYIVKPFTAATLKEKL 115
REC_GlnL-like cd17565
phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar ...
 49-107 2.54e-05

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: 41.49  E-value: 2.54e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 495186078  49 PDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVSMVDDESLISEVMTAGIDGFIGKNI 107
Cdd:cd17565   45 PDIVLIDLLMPGMDGIQLVRKLKDTGSNGKFIMISQVSDKEMIGKAYQAGIEFFINKPI 103
REC_RssB-like cd17555
phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ...
 4-83 3.63e-05

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: 41.42  E-value: 3.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLrtvqrllpeAVIE-------EAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPR 76
Cdd:cd17555    2 TILVIDDDEVVRESIA---------AYLEdsgfqvlQAADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKESPD 72


                 ....*..
gi 495186078  77 TTLIVVS 83
Cdd:cd17555   73 TPVIVVS 79
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 140-184 9.72e-05

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 41.13  E-value: 9.72e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 495186078 140 AALTPRQQDVLRLIA-QGKTNKEIARELDISPFTVRIHVSSLLRTL 184
Cdd:COG1595  126 ERLPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 140-184 1.27e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 40.79  E-value: 1.27e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 495186078  140 AALTPRQQDVLRLIA-QGKTNKEIARELDISPFTVRIHVSSLLRTL 184
Cdd:TIGR02937 109 EKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-173 2.53e-04

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 37.30  E-value: 2.53e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 495186078 141 ALTPRQQD-VLRLIAQGKTNKEIARELDISPFTV 173
Cdd:cd00569    5 KLTPEQIAeARRLLAAGESVAEIARELGVSRSTL 38
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 5-81 5.22e-04

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: 38.29  E-value: 5.22e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495186078   5 IIIADDHPLFREAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVsQLAELRRRLPRTTLIV 81
Cdd:cd17532    1 ALIVDDEPLAREELRYLLEEHPDIEIVGEAENGEEALEAIEELKPDVVFLDIQMPGLDGL-ELAKKLSKLAKPPLIV 76
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 4-116 7.19e-04

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: 37.78  E-value: 7.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAmLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:cd19932    2 RVLIAEDEALIRMD-LREMLEEAGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSENIAPIVLLTA 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 495186078  84 MVDDEsLISEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:cd19932   81 YSQQD-LVERAKEAGAMAYLVKPFSESDLIPAI 112
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 4-81 7.88e-04

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: 37.81  E-value: 7.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMLRTVQRLlpEAVIEEAGDLDAVLALLPLGEPDTLILDLRFP---GLTCVsqlAELRRRLPRTTLI 80
Cdd:cd17563    2 SLLLVDDDEVFAERLARALERR--GFEVETAHSVEEALALAREEKPDYAVLDLRLGgdsGLDLI---PPLRALQPDARIV 76


                 .
gi 495186078  81 V 81
Cdd:cd17563   77 V 77
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 4-116 7.97e-04

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: 37.59  E-value: 7.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPlfreamlrTVQRLLPEAVIEE------AGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRT 77
Cdd:cd17554    2 KILVVDDEE--------NIRELYKEELEDEgyevvtAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDL 73

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 495186078  78 TLIVVSMVDDESliSEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:cd17554   74 PVIICTAYSEYK--SDFSSWAADAYVVKSSDLTELKETI 110
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 140-178 8.91e-04

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 35.89  E-value: 8.91e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 495186078  140 AALTPRQQDVLRLIA-QGKTNKEIARELDISPFTVRIHVS 178
Cdd:pfam08281   9 EELPPRQREVFLLRYlEGLSYAEIAELLGISEGTVKSRLS 48
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
4-97 1.54e-03

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 38.68  E-value: 1.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREaMLRTVQRLLPEAVIEEAGDLDAvLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTLIVVS 83
Cdd:PRK11361   6 RILIVDDEDNVRR-MLSTAFALQGFETHCANNGRTA-LHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMT 83

                         90
                 ....*....|....
gi 495186078  84 MvddeslISEVMTA 97
Cdd:PRK11361  84 A------YAEVETA 91
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 4-111 1.80e-03

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: 36.65  E-value: 1.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFReAMLRTVQRLLPEAVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELRRRLPRTTL--IV 81
Cdd:cd17551    2 RILIVDDNPTNL-LLLEALLRSAGYLEVVSFTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGLEDVpiVM 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 495186078  82 VSMVDDESLISEVMTAGIDGFIGKNIAPDE 111
Cdd:cd17551   81 ITADTDREVRLRALEAGATDFLTKPFDPVE 110
REC_Spo0A cd17561
phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the ...
 4-105 2.83e-03

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: 36.05  E-value: 2.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREaMLRTVQRLLPE-AVIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVSQLAELR--RRLPRTTLI 80
Cdd:cd17561    3 KVLIADDNREFVQ-LLEEYLNSQPDmEVVGVAHNGQEALELIEEKEPDVLLLDIIMPHLDGIGVLEKLRrmRLEKRPKII 81

                         90       100
                 ....*....|....*....|....*
gi 495186078  81 VVSMVDDESLISEVMTAGIDGFIGK 105
Cdd:cd17561   82 MLTAFGQEDITQRAVELGASYYILK 106
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 145-174 2.88e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 34.49  E-value: 2.88e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 495186078  145 RQQDVLRLIAQGKTNKEIARELDISPFTVR 174
Cdd:pfam13518   1 ERLKIVLLALEGESIKEAARLFGISRSTVY 30
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
142-174 3.01e-03

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 37.89  E-value: 3.01e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 495186078 142 LTPRQ-QDVLRLIAQGKTNKEIARELDISPFTVR 174
Cdd:COG4584    2 LTMEQiREIRRLLREGLSIREIARELGISRNTVR 35
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 140-174 7.18e-03

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 33.62  E-value: 7.18e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 495186078 140 AALTPRQQDVLRLI-AQGKTNKEIARELDISPFTVR 174
Cdd:cd06171    9 DKLPEREREVILLRfGEGLSYEEIAEILGISRSTVR 44
REC_DivK-like cd17548
phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ...
 4-116 8.65e-03

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: 34.82  E-value: 8.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495186078   4 RIIIADDHPLFREAMlrtvqRLLPEA---VIEEAGDLDAVLALLPLGEPDTLILDLRFPGLTCVsQLAELRRRLPRTTLI 80
Cdd:cd17548    1 KILIVEDNPLNMKLA-----RDLLESagyEVLEAADGEEALEIARKEKPDLILMDIQLPGMDGL-EATRLLKEDPATRDI 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 495186078  81 VV------SMVDDEsliSEVMTAGIDGFIGKNIAPDEIGQAI 116
Cdd:cd17548   75 PVialtayAMKGDR---EKILEAGCDGYISKPIDTREFLETV 113
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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