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Conserved domains on  [gi|728887181|gb|AIY95576|]
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hypothetical protein QU35_19685 [Bacillus subtilis subsp. subtilis str. 168]

Protein Classification

sensor histidine kinase( domain architecture ID 11459466)

sensor histidine kinase, part of a two-component regulatory system, functions as a protein kinase that phosphorylates a target protein in response to a signal; may contain an N-terminal HAMP signaling domain

CATH:  3.30.565.10
EC:  2.7.13.3
Gene Ontology:  GO:0000155|GO:0004673|GO:0007165|GO:0005524|GO:0000156
PubMed:  10339418|11406410|10966457|8029829|18076326|11489844
SCOP:  4001957

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YesM COG2972
Sensor histidine kinase YesM [Signal transduction mechanisms];
8-260 8.47e-62

Sensor histidine kinase YesM [Signal transduction mechanisms];


:

Pssm-ID: 442211 [Multi-domain]  Cd Length: 445  Bit Score: 201.40  E-value: 8.47e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   8 SMVDLPVLIITAAI--IGHDKYKAFHAGAND-ILQKPYHYSEFMARIQNLI-MMKHTANQATRMEMAFLQSQIKPHFLYN 83
Cdd:COG2972  179 RSITRPIKRLKKAMkkVEKGDLVRLEVSGNDeIGILARSFNEMVERIKELIeEVYELELEKKEAELKALQAQINPHFLFN 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  84 VLNTIISLTHL-DIEKAREVTEEFTNYLRMSFdfQNTSAISSFRHELSIINSYLSIEKTRFSNRLEVLFDIDEDI-DFIL 161
Cdd:COG2972  259 TLNSIRWLAELeDPEEAEEMLEALSKLLRYSL--SKGDELVTLEEELELIKSYLEIQKLRFGDRLEVEIEIDEELlDLLI 336

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 162 PPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQsKNEYHIKVEDNGPGITPEKQIDLL----STDFDRSVGLKNINQRLK 237
Cdd:COG2972  337 PKLILQPLVENAIEHGIEPKEGGGTIRISIRKE-GDRLVITVEDNGVGMPEEKLEKLLeelsSKGEGRGIGLRNVRERLK 415

                        250       260
                 ....*....|....*....|....*
gi 728887181 238 HFCGSE--LMISSTPDAGTSVSMLI 260
Cdd:COG2972  416 LYYGEEygLEIESEPGEGTTVTIRI 440
 
Name Accession Description Interval E-value
YesM COG2972
Sensor histidine kinase YesM [Signal transduction mechanisms];
8-260 8.47e-62

Sensor histidine kinase YesM [Signal transduction mechanisms];


Pssm-ID: 442211 [Multi-domain]  Cd Length: 445  Bit Score: 201.40  E-value: 8.47e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   8 SMVDLPVLIITAAI--IGHDKYKAFHAGAND-ILQKPYHYSEFMARIQNLI-MMKHTANQATRMEMAFLQSQIKPHFLYN 83
Cdd:COG2972  179 RSITRPIKRLKKAMkkVEKGDLVRLEVSGNDeIGILARSFNEMVERIKELIeEVYELELEKKEAELKALQAQINPHFLFN 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  84 VLNTIISLTHL-DIEKAREVTEEFTNYLRMSFdfQNTSAISSFRHELSIINSYLSIEKTRFSNRLEVLFDIDEDI-DFIL 161
Cdd:COG2972  259 TLNSIRWLAELeDPEEAEEMLEALSKLLRYSL--SKGDELVTLEEELELIKSYLEIQKLRFGDRLEVEIEIDEELlDLLI 336

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 162 PPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQsKNEYHIKVEDNGPGITPEKQIDLL----STDFDRSVGLKNINQRLK 237
Cdd:COG2972  337 PKLILQPLVENAIEHGIEPKEGGGTIRISIRKE-GDRLVITVEDNGVGMPEEKLEKLLeelsSKGEGRGIGLRNVRERLK 415

                        250       260
                 ....*....|....*....|....*
gi 728887181 238 HFCGSE--LMISSTPDAGTSVSMLI 260
Cdd:COG2972  416 LYYGEEygLEIESEPGEGTTVTIRI 440
HATPase_YpdA-like cd16955
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 161-261 3.26e-50

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli YpdA; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Escherichia coli YpdA, a HK of the two-component system (TCS) YpdA-YpdB which is involved in a nutrient sensing regulatory network with YehU-YehT. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase), and some have a GAF sensor domain; some contain a DUF3816 domain; some are hybrid sensor histidine kinases as they also contain a REC signal receiver domain.


Pssm-ID: 340431 [Multi-domain]  Cd Length: 102  Bit Score: 160.70  E-value: 3.26e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 161 LPPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQSKNEYHIKVEDNGPGITPeKQIDLLSTD--FDRSVGLKNINQRLKH 238
Cdd:cd16955    1 IPKLMIQPLVENAIVHGIQEKKGKGVVKISVKKQLKNRLHIAVEDNGIGISP-KVIERVEQDemPGNKIGLLNVHQRLKL 79

                         90       100
                 ....*....|....*....|...
gi 728887181 239 FCGSELMISSTPDAGTSVSMLIH 261
Cdd:cd16955   80 GYGEGLHIRSRPDPGTLIAFYIP 102
His_kinase pfam06580
Histidine kinase; This family represents a region within bacterial histidine kinase enzymes. ...
 67-147 2.19e-25

Histidine kinase; This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain pfam02518 and/or pfam00672.


Pssm-ID: 461952 [Multi-domain]  Cd Length: 79  Bit Score: 95.97  E-value: 2.19e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   67 MEMAFLQSQIKPHFLYNVLNTIISLTHLDIEKAREVTEEFTNYLRMSFDfqNTSAISSFRHELSIINSYLSIEKTRFSNR 146
Cdd:pfam06580   1 AELKALQAQINPHFLFNTLNSISSLAIEDPEEAAEMILKLSDLLRYSLY--EGEELVTLEEELEFLENYLEIQKIRFGDR 78


                  .
gi 728887181  147 L 147
Cdd:pfam06580  79 L 79
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 165-263 1.28e-12

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 63.05  E-value: 1.28e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   165 MIQPLVENAVLHGVSkkrgGGWIKLTAKKQsKNEYHIKVEDNGPGITPEKQIDLL----STDFDRS------VGLKNINQ 234
Cdd:smart00387   9 VLSNLLDNAIKYTPE----GGRITVTLERD-GDHVEITVEDNGPGIPPEDLEKIFepffRTDKRSRkiggtgLGLSIVKK 83

                           90       100
                   ....*....|....*....|....*....
gi 728887181   235 RLKHFcGSELMISSTPDAGTSVSMLIHLA 263
Cdd:smart00387  84 LVELH-GGEISVESEPGGGTTFTITLPLE 111
PRK10816 PRK10816
two-component system response regulator PhoP;
4-89 1.16e-06

two-component system response regulator PhoP;


Pssm-ID: 182755 [Multi-domain]  Cd Length: 223  Bit Score: 48.20  E-value: 1.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   4 RERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLiMMKHT--ANQA----------TRMEMAF 71
Cdd:PRK10816  65 RWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQAL-MRRNSglASQVislppfqvdlSRRELSI 143

                         90
                 ....*....|....*....
gi 728887181  72 LQSQIK-PHFLYNVLNTII 89
Cdd:PRK10816 144 NDEVIKlTAFEYTIMETLI 162
top6b TIGR01052
DNA topoisomerase VI, B subunit; This model describes DNA topoisomerase VI, an archaeal type ...
 186-216 2.36e-03

DNA topoisomerase VI, B subunit; This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273417 [Multi-domain]  Cd Length: 488  Bit Score: 39.03  E-value: 2.36e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 728887181  186 WIKLTAKKQSKNEYHIKVEDNGPGItPEKQI 216
Cdd:TIGR01052  52 DIKVEIEKIGKDHYKVTVEDNGPGI-PEEYI 81
 
Name Accession Description Interval E-value
YesM COG2972
Sensor histidine kinase YesM [Signal transduction mechanisms];
8-260 8.47e-62

Sensor histidine kinase YesM [Signal transduction mechanisms];


Pssm-ID: 442211 [Multi-domain]  Cd Length: 445  Bit Score: 201.40  E-value: 8.47e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   8 SMVDLPVLIITAAI--IGHDKYKAFHAGAND-ILQKPYHYSEFMARIQNLI-MMKHTANQATRMEMAFLQSQIKPHFLYN 83
Cdd:COG2972  179 RSITRPIKRLKKAMkkVEKGDLVRLEVSGNDeIGILARSFNEMVERIKELIeEVYELELEKKEAELKALQAQINPHFLFN 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  84 VLNTIISLTHL-DIEKAREVTEEFTNYLRMSFdfQNTSAISSFRHELSIINSYLSIEKTRFSNRLEVLFDIDEDI-DFIL 161
Cdd:COG2972  259 TLNSIRWLAELeDPEEAEEMLEALSKLLRYSL--SKGDELVTLEEELELIKSYLEIQKLRFGDRLEVEIEIDEELlDLLI 336

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 162 PPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQsKNEYHIKVEDNGPGITPEKQIDLL----STDFDRSVGLKNINQRLK 237
Cdd:COG2972  337 PKLILQPLVENAIEHGIEPKEGGGTIRISIRKE-GDRLVITVEDNGVGMPEEKLEKLLeelsSKGEGRGIGLRNVRERLK 415

                        250       260
                 ....*....|....*....|....*
gi 728887181 238 HFCGSE--LMISSTPDAGTSVSMLI 260
Cdd:COG2972  416 LYYGEEygLEIESEPGEGTTVTIRI 440
LytS COG3275
Sensor histidine kinase, LytS/YehU family [Signal transduction mechanisms];
44-262 9.61e-59

Sensor histidine kinase, LytS/YehU family [Signal transduction mechanisms];


Pssm-ID: 442506 [Multi-domain]  Cd Length: 352  Bit Score: 190.85  E-value: 9.61e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  44 YSEFMARIQNLIMMKHTANQATRMEMAFLQSQIKPHFLYNVLNTIISLTHLDIEKAREVTEEFTNYLRMSFDFQNTSAIs 123
Cdd:COG3275  136 LALLLSLQEEELELEELEKELLEAELKALKAQINPHFLFNTLNSIYSLIREDPEKARELLLKLSDLLRYSLYESDKELV- 214

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 124 SFRHELSIINSYLSIEKTRFSNRLEVLFDIDEDIDFIL-PPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQsKNEYHIK 202
Cdd:COG3275  215 PLEEELEFLENYLELEKLRFGDRLQVEIDIDEELLDLLiPPLLLQPLVENAIKHGISSKEGGGTISISIEVE-GDRLVIE 293

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 728887181 203 VEDNGPGITPEKQIDllstdfDRSVGLKNINQRLKHFCGSE--LMISSTPDAGTSVSMLIHL 262
Cdd:COG3275  294 VENNGVGIQPKKKKK------GSGIGLKNVRERLELLYGDKysLEIESTDGGGTKVTLKIPL 349
HATPase_YpdA-like cd16955
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 161-261 3.26e-50

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli YpdA; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Escherichia coli YpdA, a HK of the two-component system (TCS) YpdA-YpdB which is involved in a nutrient sensing regulatory network with YehU-YehT. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase), and some have a GAF sensor domain; some contain a DUF3816 domain; some are hybrid sensor histidine kinases as they also contain a REC signal receiver domain.


Pssm-ID: 340431 [Multi-domain]  Cd Length: 102  Bit Score: 160.70  E-value: 3.26e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 161 LPPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQSKNEYHIKVEDNGPGITPeKQIDLLSTD--FDRSVGLKNINQRLKH 238
Cdd:cd16955    1 IPKLMIQPLVENAIVHGIQEKKGKGVVKISVKKQLKNRLHIAVEDNGIGISP-KVIERVEQDemPGNKIGLLNVHQRLKL 79

                         90       100
                 ....*....|....*....|...
gi 728887181 239 FCGSELMISSTPDAGTSVSMLIH 261
Cdd:cd16955   80 GYGEGLHIRSRPDPGTLIAFYIP 102
His_kinase pfam06580
Histidine kinase; This family represents a region within bacterial histidine kinase enzymes. ...
 67-147 2.19e-25

Histidine kinase; This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain pfam02518 and/or pfam00672.


Pssm-ID: 461952 [Multi-domain]  Cd Length: 79  Bit Score: 95.97  E-value: 2.19e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   67 MEMAFLQSQIKPHFLYNVLNTIISLTHLDIEKAREVTEEFTNYLRMSFDfqNTSAISSFRHELSIINSYLSIEKTRFSNR 146
Cdd:pfam06580   1 AELKALQAQINPHFLFNTLNSISSLAIEDPEEAAEMILKLSDLLRYSLY--EGEELVTLEEELEFLENYLEIQKIRFGDR 78


                  .
gi 728887181  147 L 147
Cdd:pfam06580  79 L 79
HATPase_YpdA-YehU-LytS-like cd16924
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 161-260 3.72e-21

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli YpdA, YehU, Bacillus subtilis LytS, and some hybrid sensor histidine kinases; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis LytS, a HK of the two-component system (TCS) LytS-LytR needed for growth on pyruvate, and Staphylococcus aureus LytS-LytR TCS involved in the adaptation of S. aureus to cationic antimicrobial peptides. It also includes the HATPase domains of Escherichia coli YpdA and YehU, HKs of YpdA-YpdB and YehU-YehTCSs, which are involved together in a nutrient sensing regulatory network. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase), some having accessory sensor domain(s) such as Cache, HAMP or GAF; some are hybrid sensor histidine kinases as they also contain a REC signal receiver domain.


Pssm-ID: 340401 [Multi-domain]  Cd Length: 103  Bit Score: 85.58  E-value: 3.72e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 161 LPPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQsKNEYHIKVEDNGPGITPekqiDLLST-----DFDRSVGLKNINQR 235
Cdd:cd16924    1 IPPFTLQPLVENAIQHGLSPLTDKGVVTISALKE-DNHVMIEVEDNGRGIDP----KVLNIlgkkpKEGNGIGLYNVHQR 75

                         90       100
                 ....*....|....*....|....*..
gi 728887181 236 LKHFCG--SELMISSTPDAGTSVSMLI 260
Cdd:cd16924   76 LILLFGedYGIHIASEPDKGTRITFTI 102
HATPase_YehU-like cd16956
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 161-258 3.24e-18

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli YehU; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) including Escherichia coli YehU, a HK of the two-component system (TCS) YehU-YehT which is involved in a nutrient sensing regulatory network. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase); some have a GAF sensor domain while some have a cupin domain.


Pssm-ID: 340432 [Multi-domain]  Cd Length: 101  Bit Score: 77.86  E-value: 3.24e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 161 LPPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQSkNEYHIKVEDNGPGITPEKQIDLLStDFDRSVGLKNINQRLKHFC 240
Cdd:cd16956    1 LPFLTLQPIVENAVKHGLSGLLDGGRVEITARLDG-QHLLLEVEDNGGGMDPDTLARILI-RSSNGLGLNLVDKRLRQAF 78

                         90       100
                 ....*....|....*....|
gi 728887181 241 GSE--LMISSTPDAGTSVSM 258
Cdd:cd16956   79 GNDygLDIECAPGEGTRITI 98
HATPase_LytS-like cd16957
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 161-260 2.85e-17

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis LytS and Staphylococcus aureus LytS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis LytS, a HK of the two-component system (TCS) LytS-LytR needed for growth on pyruvate, and Staphylococcus aureus LytS-LytR TCS involved in the adaptation of S. aureus to cationic antimicrobial peptides. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase), and a GAF sensor domain; most contain a DUF3816 domain.


Pssm-ID: 340433 [Multi-domain]  Cd Length: 106  Bit Score: 75.54  E-value: 2.85e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 161 LPPLMIQPLVENAVLHGVSKKRGGGWIKLTAKKQsKNEYHIKVEDNGPGITPEKQIDLLSTDFDRSVG----LKNINQRL 236
Cdd:cd16957    1 VPPFALQVLVENAIRHAFPKRKENNEVRVVVKKD-QHKVHVSVSDNGQGIPEERLDLLGKTTVTSEKGtgtaLENLNRRL 79

                         90       100
                 ....*....|....*....|....*.
gi 728887181 237 KHFCGSE--LMISSTPDAGTSVSMLI 260
Cdd:cd16957   80 IGLFGSEacLHIESEVHGGTEVWFVI 105
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 165-263 1.28e-12

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 63.05  E-value: 1.28e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   165 MIQPLVENAVLHGVSkkrgGGWIKLTAKKQsKNEYHIKVEDNGPGITPEKQIDLL----STDFDRS------VGLKNINQ 234
Cdd:smart00387   9 VLSNLLDNAIKYTPE----GGRITVTLERD-GDHVEITVEDNGPGIPPEDLEKIFepffRTDKRSRkiggtgLGLSIVKK 83

                           90       100
                   ....*....|....*....|....*....
gi 728887181   235 RLKHFcGSELMISSTPDAGTSVSMLIHLA 263
Cdd:smart00387  84 LVELH-GGEISVESEPGGGTTFTITLPLE 111
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 2-54 2.27e-11

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: 59.76  E-value: 2.27e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 728887181   2 KIRERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNL 54
Cdd:cd17551   66 RLRALPGLEDVPIVMITADTDREVRLRALEAGATDFLTKPFDPVELLARVRNL 118
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 165-264 9.30e-11

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: 57.76  E-value: 9.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  165 MIQPLVENAVLHgvSKKRGGGWIKLTAKkqskNEYHIKVEDNGPGITPEKqIDLLSTDFDRS---------VGLKNINQR 235
Cdd:pfam02518   9 VLSNLLDNALKH--AAKAGEITVTLSEG----GELTLTVEDNGIGIPPED-LPRIFEPFSTAdkrggggtgLGLSIVRKL 81

                          90       100
                  ....*....|....*....|....*....
gi 728887181  236 LKHFcGSELMISSTPDAGTSVSMLIHLAE 264
Cdd:pfam02518  82 VELL-GGTITVESEPGGGTTVTLTLPLAQ 109
CitA COG3290
Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction ...
 83-260 8.29e-10

Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction mechanisms];


Pssm-ID: 442519 [Multi-domain]  Cd Length: 389  Bit Score: 58.71  E-value: 8.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  83 NVLNTIISLTHL-DIEKARE-VTEEFTNYlrmsfdfQNTSAISSFRHELSIINSYLsIEKTRFSNRLEVLFDIDEDIDfi 160
Cdd:COG3290  202 NHLHTISGLLQLgEYDEALEyIDEISEEL-------QELIDSLLSRIGNPVLAALL-LGKAARARERGIDLTIDIDSD-- 271

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 161 LPPLMIQP---------LVENAVLHGVSKKRGGGWIKLTAKkQSKNEYHIKVEDNGPGITPEKQIDLLSTDF------DR 225
Cdd:COG3290  272 LPDLPLSDtdlvtilgnLLDNAIEAVEKLPEEERRVELSIR-DDGDELVIEVEDSGPGIPEELLEKIFERGFstklgeGR 350

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 728887181 226 SVGLKNINQRLKHfCGSELMISSTPDAGTSVSMLI 260
Cdd:COG3290  351 GLGLALVKQIVEK-YGGTIEVESEEGEGTVFTVRL 384
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 2-55 2.88e-08

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: 52.65  E-value: 2.88e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 728887181   2 KIRERFSmvDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:COG0745   66 RLRARPS--DIPIIMLTARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALL 117
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 2-51 4.43e-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: 51.83  E-value: 4.43e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 728887181   2 KIRERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARI 51
Cdd:COG3706   66 RLRADPRTADIPIIFLTALDDEEDRARALEAGADDYLTKPFDPEELLARV 115
REC_OmpR_EcPhoP-like cd19934
phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; ...
 4-55 5.46e-08

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: 50.36  E-value: 5.46e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 728887181   4 RERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd19934   63 RWRSEGRATPVLILTARDSWQDKVEGLDAGADDYLTKPFHIEELLARLRALI 114
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 2-59 7.44e-08

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: 51.70  E-value: 7.44e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 728887181   2 KIRERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLIMMKH 59
Cdd:COG3437   71 LLRADPSTRDIPVIFLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALELRR 128
REC_OmpR_DrrD-like cd17625
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...
 6-55 2.53e-07

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: 48.37  E-value: 2.53e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 728887181   6 RFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd17625   64 REEGIETPVLLLTALDAVEDRVKGLDLGADDYLPKPFSLAELLARIRALL 113
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 2-55 7.13e-07

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: 47.15  E-value: 7.13e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 728887181   2 KIRERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:COG0784   70 RIRALPRLPDIPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLL 123
PRK10816 PRK10816
two-component system response regulator PhoP;
4-89 1.16e-06

two-component system response regulator PhoP;


Pssm-ID: 182755 [Multi-domain]  Cd Length: 223  Bit Score: 48.20  E-value: 1.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181   4 RERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLiMMKHT--ANQA----------TRMEMAF 71
Cdd:PRK10816  65 RWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQAL-MRRNSglASQVislppfqvdlSRRELSI 143

                         90
                 ....*....|....*....
gi 728887181  72 LQSQIK-PHFLYNVLNTII 89
Cdd:PRK10816 144 NDEVIKlTAFEYTIMETLI 162
REC_OmpR_CtrA cd17616
phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is ...
 4-55 2.47e-06

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: 45.48  E-value: 2.47e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 728887181   4 RERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd17616   63 TLRLAKVKTPILILSGLADIEDKVKGLGFGADDYMTKPFHKDELVARIHAIV 114
BaeS COG0642
Signal transduction histidine kinase [Signal transduction mechanisms];
146-263 2.55e-06

Signal transduction histidine kinase [Signal transduction mechanisms];


Pssm-ID: 440407 [Multi-domain]  Cd Length: 328  Bit Score: 47.98  E-value: 2.55e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 146 RLEVLFDIDEDIDFIL-PPLMIQP----LVENAVLHGvskkRGGGWIKLTAKKQSkNEYHIKVEDNGPGITPEKQIDLL- 219
Cdd:COG0642  203 GIELELDLPDDLPTVRgDPDRLRQvllnLLSNAIKYT----PEGGTVTVSVRREG-DRVRISVEDTGPGIPPEDLERIFe 277

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 728887181 220 ------STDFDRSVGL-----KNINQRLkhfcGSELMISSTPDAGTSVSMLIHLA 263
Cdd:COG0642  278 pffrtdPSRRGGGTGLglaivKRIVELH----GGTIEVESEPGKGTTFTVTLPLA 328
envZ PRK09467
osmolarity sensor protein; Provisional
 95-216 2.72e-06

osmolarity sensor protein; Provisional


Pssm-ID: 236531 [Multi-domain]  Cd Length: 435  Bit Score: 47.98  E-value: 2.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  95 DIEKAREVTEEFTNYLR----MSFDFQNTSaissfrhelSIINSYLSIEktrfSNRlEVlfDIDEDIDFILPPLMIQP-- 168
Cdd:PRK09467 268 DIEECNAIIEQFIDYLRtgqeMPMEMADLN---------ALLGEVIAAE----SGY-ER--EIETALQPGPIEVPMNPia 331

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 728887181 169 -------LVENAVlhgvskKRGGGWIKLTAKkQSKNEYHIKVEDNGPGItPEKQI 216
Cdd:PRK09467 332 ikralanLVVNAA------RYGNGWIKVSSG-TEGKRAWFQVEDDGPGI-PPEQL 378
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 10-55 3.35e-06

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: 45.17  E-value: 3.35e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 728887181  10 VDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd17624   69 QSLPVLILTARDGVDDRVAGLDAGADDYLVKPFALEELLARLRALL 114
ComP COG4585
Signal transduction histidine kinase ComP [Signal transduction mechanisms];
147-260 3.73e-06

Signal transduction histidine kinase ComP [Signal transduction mechanisms];


Pssm-ID: 443642 [Multi-domain]  Cd Length: 252  Bit Score: 46.92  E-value: 3.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 147 LEVLFDIDEDIDFILPPL------MIQPLVENAVLHGvskkrGGG--WIKLTakkQSKNEYHIKVEDNGPGITPEKQIdl 218
Cdd:COG4585  142 IRVELDVDGDPDRLPPEVelalyrIVQEALTNALKHA-----GATrvTVTLE---VDDGELTLTVRDDGVGFDPEAAP-- 211

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 728887181 219 lstdfDRSVGLKNINQRLKHFCGsELMISSTPDAGTSVSMLI 260
Cdd:COG4585  212 -----GGGLGLRGMRERAEALGG-TLTIGSAPGGGTRVRATL 247
PRK10643 PRK10643
two-component system response regulator PmrA;
4-55 7.04e-06

two-component system response regulator PmrA;


Pssm-ID: 182612 [Multi-domain]  Cd Length: 222  Bit Score: 45.80  E-value: 7.04e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 728887181   4 RERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:PRK10643  65 RWRQKKYTLPVLILTARDTLEDRVAGLDVGADDYLVKPFALEELHARIRALI 116
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 2-69 8.89e-06

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 44.58  E-value: 8.89e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 728887181   2 KIRERFSmvDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLIMMKHTANQATRMEM 69
Cdd:COG4565   70 ELRARGP--DVDVIVITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLEYRRLLREDQEEDL 135
RsbW COG2172
Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms];
169-262 1.64e-05

Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms];


Pssm-ID: 441775 [Multi-domain]  Cd Length: 127  Bit Score: 43.36  E-value: 1.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 169 LVENAVLHGVsKKRGGGWIKLTAKkQSKNEYHIKVEDNGPGITPEKQIDLLSTDFDRSVGLKNInqrlKHFCgSELMISS 248
Cdd:COG2172   42 AVTNAVRHAY-GGDPDGPVEVELE-LDPDGLEIEVRDEGPGFDPEDLPDPYSTLAEGGRGLFLI----RRLM-DEVEYES 114

                         90
                 ....*....|....
gi 728887181 249 TPDaGTSVSMLIHL 262
Cdd:COG2172  115 DPG-GTTVRLVKRL 127
HATPase_UhpB-NarQ-NarX-like cd16917
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 165-258 1.71e-05

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli UhpB, NarQ and NarX, and Bacillus subtilis YdfH, YhcY and YfiJ; 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 UhpB, a HK of the UhpB-UhpA TCS, NarQ and NarX, HKs of the NarQ-NarP and NarX-NarL TCSs, respectively, and Bacillus YdfH, YhcY and YfiJ HKs, of the YdfH-YdfI, YhcY-YhcZ and YfiJ-YfiK TCSs, respectively. In addition, it includes Bacillus YxjM, ComP, LiaS and DesK, HKs of the YxjM-YxjML, ComP-ComA, LiaS-LiaR, DesR-DesK TCSs, respectively. Proteins having this HATPase domain have a histidine kinase dimerization and phosphoacceptor domain; some have accessory domains such as GAF, HAMP, PAS and MASE sensor domains.


Pssm-ID: 340394 [Multi-domain]  Cd Length: 87  Bit Score: 42.54  E-value: 1.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 165 MIQPLVENAVLHGvskkrGGG--WIKLTakkQSKNEYHIKVEDNGPGITPEkqidllSTDFDRSVGLKNINQRLKHfCGS 242
Cdd:cd16917    4 IVQEALTNALKHA-----GASrvRVTLS---YTADELTLTVVDDGVGFDGP------APPGGGGFGLLGMRERAEL-LGG 68

                         90
                 ....*....|....*.
gi 728887181 243 ELMISSTPDAGTSVSM 258
Cdd:cd16917   69 TLTIGSRPGGGTRVTA 84
WalK COG5002
Sensor histidine kinase WalK [Signal transduction mechanisms];
169-265 3.95e-05

Sensor histidine kinase WalK [Signal transduction mechanisms];


Pssm-ID: 444026 [Multi-domain]  Cd Length: 390  Bit Score: 44.54  E-value: 3.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 169 LVENAVLHGvskkRGGGWIKLTAKKQsKNEYHIKVEDNGPGItPEKQIDLLstdFDR-------------SVGL-----K 230
Cdd:COG5002  289 LLDNAIKYT----PEGGTITVSLREE-DDQVRISVRDTGIGI-PEEDLPRI---FERfyrvdksrsretgGTGLglaivK 359

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 728887181 231 NINQRlkHfcGSELMISSTPDAGTSVSMLIHLAET 265
Cdd:COG5002  360 HIVEA--H--GGRIWVESEPGKGTTFTITLPLARE 390
COG4191 COG4191
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal ...
 72-213 5.80e-05

Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms];


Pssm-ID: 443345 [Multi-domain]  Cd Length: 361  Bit Score: 44.02  E-value: 5.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  72 LQSQIKPHFLYNVLNTIISLthldIEKAREVTEEFTNYLRmsfdfQNTSAISSFR-HELsiINSYLSIEKTRF-SNRLEV 149
Cdd:COG4191  171 LEDEPDPEELREALERILEG----AERAAEIVRSLRAFSR-----RDEEEREPVDlNEL--IDEALELLRPRLkARGIEV 239

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 728887181 150 LFDIDEDidfiLPPLMIQP---------LVENAvLHGVSKKRGGgWIKLTAKkQSKNEYHIKVEDNGPGITPE 213
Cdd:COG4191  240 ELDLPPD----LPPVLGDPgqleqvllnLLINA-IDAMEEGEGG-RITISTR-REGDYVVISVRDNGPGIPPE 305
KdpD COG2205
K+-sensing histidine kinase KdpD [Signal transduction mechanisms];
144-265 1.10e-04

K+-sensing histidine kinase KdpD [Signal transduction mechanisms];


Pssm-ID: 441807 [Multi-domain]  Cd Length: 239  Bit Score: 42.59  E-value: 1.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 144 SNRLEVLFDIDEDIDFIL--PPLMIQ---PLVENAVLHGvskkRGGGWIKLTAKKQsKNEYHIKVEDNGPGITPEKQIDL 218
Cdd:COG2205  110 EKGIRLELDLPPELPLVYadPELLEQvlaNLLDNAIKYS----PPGGTITISARRE-GDGVRISVSDNGPGIPEEELERI 184

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 728887181 219 lstdFDR-----------SVGLK-NINQRLKHFCGSELMISSTPDAGTSVSMLIHLAET 265
Cdd:COG2205  185 ----FERfyrgdnsrgegGTGLGlAIVKRIVEAHGGTIWVESEPGGGTTFTVTLPLAES 239
PRK11517 PRK11517
DNA-binding response regulator HprR;
13-73 1.21e-04

DNA-binding response regulator HprR;


Pssm-ID: 183172 [Multi-domain]  Cd Length: 223  Bit Score: 42.19  E-value: 1.21e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728887181  13 PVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLIMMKHTANqaTRMEMAFLQ 73
Cdd:PRK11517  73 PVICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQHHALN--STLEISGLR 131
HATPase_EnvZ-like cd16950
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 169-225 1.44e-04

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: 40.12  E-value: 1.44e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 728887181 169 LVENAVLHGvskkrgGGWIKLtAKKQSKNEYHIKVEDNGPGITPEkQIDLLSTDFDR 225
Cdd:cd16950    8 LVDNALRYG------GGWVEV-SSDGEGNRTRIQVLDNGPGIAPE-EVDELFQPFYR 56
PRK15479 PRK15479
transcriptional regulator TctD;
11-55 1.59e-04

transcriptional regulator TctD;


Pssm-ID: 185376 [Multi-domain]  Cd Length: 221  Bit Score: 42.02  E-value: 1.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 728887181  11 DLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:PRK15479  72 TLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEELDARLRALL 116
HATPase_DpiB-CitA-like cd16915
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 165-260 1.78e-04

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: 39.96  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 165 MIQPLVENAVLHGVSKKRGGGWIKLTAKkQSKNEYHIKVEDNGPGITPEKQIDLLSTDF------DRSVGLKNInQRLKH 238
Cdd:cd16915    4 IVGNLIDNALDALAATGAPNKQVEVFLR-DEGDDLVIEVRDTGPGIAPELRDKVFERGVstkgqgERGIGLALV-RQSVE 81

                         90       100
                 ....*....|....*....|..
gi 728887181 239 FCGSELMISSTPDAGTSVSMLI 260
Cdd:cd16915   82 RLGGSITVESEPGGGTTFSIRI 103
REC_hyHK cd17598
phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase ...
 2-55 2.30e-04

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: 40.00  E-value: 2.30e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 728887181   2 KIRERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd17598   63 KIKSDPDLKDIPVILLTTLSDPRDVIRGLECGADNFITKPYDEKYLLSRIKYIL 116
REC_OmpR_PrrA-like cd17627
phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ...
 11-55 3.49e-04

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: 39.29  E-value: 3.49e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 728887181  11 DLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd17627   70 DLPILVLTARDSVSDRVAGLDAGADDYLVKPFALEELLARVRALL 114
HATPase_BasS-like cd16940
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 158-228 6.00e-04

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: 38.54  E-value: 6.00e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728887181 158 DFILPPLMIQPLVENAVLHGVSkkrgGGWIKLtaKKQSKNEYHIKVEDNGPGITPEKQiDLLSTDFDRSVG 228
Cdd:cd16940   10 DALLLFLLLRNLVDNAVRYSPQ----GSRVEI--KLSADDGAVIRVEDNGPGIDEEEL-EALFERFYRSDG 73
REC_OmpR_PhoB cd17618
phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The ...
 2-52 1.20e-03

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: 38.00  E-value: 1.20e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 728887181   2 KIRERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQ 52
Cdd:cd17618   65 RLKRDEMTRDIPIIMLTARGEEEDKVRGLEAGADDYITKPFSPRELVARIK 115
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 2-41 1.93e-03

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: 36.82  E-value: 1.93e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 728887181   2 KIRERFSmvDLPVLIITAAIIGHDKYKAFHAGANDILQKP 41
Cdd:cd00156   62 KLRELPP--DIPVIVLTAKADEEDAVRALELGADDYLVKP 99
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 2-52 2.05e-03

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: 37.13  E-value: 2.05e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 728887181    2 KIRERFSmvDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQ 52
Cdd:pfam00072  63 RIRRRDP--TTPVIILTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
PRK10529 PRK10529
DNA-binding transcriptional activator KdpE; Provisional
 12-64 2.16e-03

DNA-binding transcriptional activator KdpE; Provisional


Pssm-ID: 182522 [Multi-domain]  Cd Length: 225  Bit Score: 38.63  E-value: 2.16e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 728887181  12 LPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQnLIMMKHTANQA 64
Cdd:PRK10529  73 IPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLR-VALRRHSATPA 124
top6b TIGR01052
DNA topoisomerase VI, B subunit; This model describes DNA topoisomerase VI, an archaeal type ...
 186-216 2.36e-03

DNA topoisomerase VI, B subunit; This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273417 [Multi-domain]  Cd Length: 488  Bit Score: 39.03  E-value: 2.36e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 728887181  186 WIKLTAKKQSKNEYHIKVEDNGPGItPEKQI 216
Cdd:TIGR01052  52 DIKVEIEKIGKDHYKVTVEDNGPGI-PEEYI 81
REC_OmpR_MtPhoP-like cd17615
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ...
 4-55 2.41e-03

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: 36.95  E-value: 2.41e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 728887181   4 RERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd17615   64 RLRADGPDVPVLFLTAKDSVEDRIAGLTAGGDDYVTKPFSLEEVVARLRALL 115
HATPase_PhoQ-like cd16954
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 146-225 2.46e-03

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: 37.23  E-value: 2.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 146 RLEVLFDIDEDIDFILPP--LM--IQPLVENAVLHGVSkkrgggWIKLTAKKQSkNEYHIKVEDNGPGItPEKQIDLLst 221
Cdd:cd16954   18 GVSISLDISPELRFPGERndLMelLGNLLDNACKWCLE------FVEVTARQTD-GGLHLIVDDDGPGV-PESQRSKI-- 87


                 ....
gi 728887181 222 dFDR 225
Cdd:cd16954   88 -FQR 90
PRK15347 PRK15347
two component system sensor kinase;
185-266 3.24e-03

two component system sensor kinase;


Pssm-ID: 237951 [Multi-domain]  Cd Length: 921  Bit Score: 38.85  E-value: 3.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 185 GWIKLTAKKQsKNEYHIKVEDNGPGITPEKQIDLLsTDFDRS--------VGLKnINQRLKHFCGSELMISSTPDAGTSV 256
Cdd:PRK15347 532 GGIRLRVKRH-EQQLCFTVEDTGCGIDIQQQQQIF-TPFYQAdthsqgtgLGLT-IASSLAKMMGGELTLFSTPGVGSCF 608

                         90
                 ....*....|
gi 728887181 257 SMLIHLAETT 266
Cdd:PRK15347 609 SLVLPLNEYA 618
REC_OmpR_BfmR-like cd19939
phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators; ...
 2-55 3.52e-03

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: 36.58  E-value: 3.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 728887181   2 KIRERFsmvDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd19939   64 EVREHS---HVPILMLTARTEEMDRVLGLEMGADDYLCKPFSPRELLARVRALL 114
PRK09836 PRK09836
DNA-binding transcriptional activator CusR; Provisional
 12-55 3.61e-03

DNA-binding transcriptional activator CusR; Provisional


Pssm-ID: 182102 [Multi-domain]  Cd Length: 227  Bit Score: 37.98  E-value: 3.61e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 728887181  12 LPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:PRK09836  73 MPILLLTALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLL 116
HATPase_EcPhoR-like cd16952
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 169-260 3.71e-03

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: 36.41  E-value: 3.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 169 LVENAVLHgvskKRGGGWIKLTAKkQSKNEYHIKVEDNGPGITPEkQIDLLSTDFDR------------SVGLKNINQRL 236
Cdd:cd16952    8 LVSNAVKY----TPPSDTITVRWS-QEESGARLSVEDTGPGIPPE-HIPRLTERFYRvdiercrntggtGLGLAIVKHVM 81

                         90       100
                 ....*....|....*....|....
gi 728887181 237 KHFcGSELMISSTPDAGTSVSMLI 260
Cdd:cd16952   82 SRH-DARLLIASELGKGSRFTCLF 104
HATPase_TopVIB-like cd16933
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family ...
 186-216 3.84e-03

Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family includes the histidine kinase-like ATPase (HATPase) domain of the B subunit of topoisomerase VI (Topo VIB). Topo VI is a heterotetrameric complex composed of two TopVIA and two TopVIB subunits and is categorized as a type II B DNA topoisomerase. It is found in archaea and also in plants. Type II enzymes cleave both strands of a DNA duplex and pass a second duplex through the resulting break in an ATP-dependent mechanism. DNA cleavage by Topo VI generates two-nucleotide 5'-protruding ends.


Pssm-ID: 340410 [Multi-domain]  Cd Length: 203  Bit Score: 37.71  E-value: 3.84e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 728887181 186 WIKLTAKKQSKNEYHIKVEDNGPGItPEKQI 216
Cdd:cd16933   43 DIKVEIEEIGKDHYKVIVEDNGPGI-PEEQI 72
PRK11086 PRK11086
sensory histidine kinase DcuS; Provisional
 169-254 4.66e-03

sensory histidine kinase DcuS; Provisional


Pssm-ID: 236839 [Multi-domain]  Cd Length: 542  Bit Score: 38.36  E-value: 4.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 169 LVENAvLHGVSKKrGGGWIKLTAKKQSkNEYHIKVEDNGPGITPEKQIDLLSTDF-----DRSVGLKNINQRLKHFcGSE 243
Cdd:PRK11086 441 LIENA-LEAVGGE-EGGEISVSLHYRN-GWLHCEVSDDGPGIAPDEIDAIFDKGYstkgsNRGVGLYLVKQSVENL-GGS 516

                         90
                 ....*....|.
gi 728887181 244 LMISSTPDAGT 254
Cdd:PRK11086 517 IAVESEPGVGT 527
REC_OmpR_BaeR-like cd19938
phosphoacceptor receiver (REC) domain of BaeR-like OmpR family response regulators; BaeR is ...
 6-55 4.67e-03

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: 36.20  E-value: 4.67e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 728887181   6 RFSmvDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:cd19938   67 RFS--DVPIIMVTARVEEIDRLLGLELGADDYICKPYSPREVVARVKAIL 114
REC_D1_PleD-like cd17538
first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ...
 2-42 5.04e-03

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: 35.94  E-value: 5.04e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 728887181   2 KIRERFSMVDLPVLIITAAIIGHDKYKAFHAGANDILQKPY 42
Cdd:cd17538   64 RLKEDPETRHIPVIMITALDDREDRIRGLEAGADDFLSKPI 104
PRK14867 PRK14867
DNA topoisomerase VI subunit B; Provisional
 187-213 5.42e-03

DNA topoisomerase VI subunit B; Provisional


Pssm-ID: 237841 [Multi-domain]  Cd Length: 659  Bit Score: 38.26  E-value: 5.42e-03
                         10        20
                 ....*....|....*....|....*..
gi 728887181 187 IKLTAKKQSKNEYHIKVEDNGPGITPE 213
Cdd:PRK14867  61 IKVEIEKLGSDHYKVAVEDNGPGIPPE 87
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
138-259 5.43e-03

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 38.03  E-value: 5.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 138 IEKTRFSNRLEVLFDIDEDIDFIL--PPLMIQPLVeNAVLHGVSKKRGGGWIKLTAKKQSKNEYHIKVEDNGPGITPEkq 215
Cdd:PRK11360 472 FQTAGVQARVDFETELDNELPPIWadPELLKQVLL-NILINAVQAISARGKIRIRTWQYSDGQVAVSIEDNGCGIDPE-- 548

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 728887181 216 idLLSTDFD-------RSVGLK-NINQRLKHFCGSELMISSTPDAGTSVSML 259
Cdd:PRK11360 549 --LLKKIFDpffttkaKGTGLGlALSQRIINAHGGDIEVESEPGVGTTFTLY 598
COG4251 COG4251
Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal ...
 169-213 5.63e-03

Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms];


Pssm-ID: 443393 [Multi-domain]  Cd Length: 503  Bit Score: 37.84  E-value: 5.63e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 728887181 169 LVENAVLHgvSKKRGGGWIKLTAKkQSKNEYHIKVEDNGPGITPE 213
Cdd:COG4251  402 LISNAIKY--SRPGEPPRIEIGAE-REGGEWVFSVRDNGIGIDPE 443
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 2-55 6.04e-03

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: 37.64  E-value: 6.04e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 728887181   2 KIRERFSmvDLPVLIITAAIIGHDKYKAFHAGANDILQKPYHYSEFMARIQNLI 55
Cdd:COG2204   67 ELRALDP--DLPVILLTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERAL 118
COG3920 COG3920
Two-component sensor histidine kinase, HisKA and HATPase domains [Signal transduction ...
 83-266 6.27e-03

Two-component sensor histidine kinase, HisKA and HATPase domains [Signal transduction mechanisms];


Pssm-ID: 443125 [Multi-domain]  Cd Length: 495  Bit Score: 37.96  E-value: 6.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  83 NVLNTIISLTHL-----DIEKAREVTEEFTN----------YLRMSFDFQNTSAissfrHEL--SIINSYLSIEKTRfsn 145
Cdd:COG3920  308 NNLQVVSSLLRLqarraDDPEAREALEESQNriqalalvheLLYQSEDWEGVDL-----RDYlrELLEPLRDSYGGR--- 379

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181 146 RLEVLFDIDediDFILPP-------LMIQPLVENAVLHGvSKKRGGGWIKLTAKKQSkNEYHIKVEDNGPGITPEkqIDL 218
Cdd:COG3920  380 GIRIELDGP---DVELPAdaavplgLILNELVTNALKHA-FLSGEGGRIRVSWRRED-GRLRLTVSDNGVGLPED--VDP 452

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 728887181 219 LSTdfdRSVGLKNINQRLKHFCGSelmISSTPDAGTSVSMLIHLAETT 266
Cdd:COG3920  453 PAR---KGLGLRLIRALVRQLGGT---LELDRPEGTRVRITFPLAELA 494
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 85-213 8.66e-03

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: 37.25  E-value: 8.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728887181  85 LNTIISlthlDIEKAREVTEEFTNYLRMS-FDFQNTSAISSFRHELSIINSYLSIEKTRFSnrlevlFDIDEDIDFIL-- 161
Cdd:COG5000  245 LDTIIR----QVDRLKRIVDEFLDFARLPePQLEPVDLNELLREVLALYEPALKEKDIRLE------LDLDPDLPEVLad 314

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 728887181 162 PPLMIQP---LVENAVlHGVSkkrGGGWIKLTAKKQSkNEYHIKVEDNGPGITPE 213
Cdd:COG5000  315 RDQLEQVlinLLKNAI-EAIE---EGGEIEVSTRRED-GRVRIEVSDNGPGIPEE 364
COG1389 COG1389
DNA topoisomerase VI, subunit B [Replication, recombination and repair];
187-216 8.98e-03

DNA topoisomerase VI, subunit B [Replication, recombination and repair];


Pssm-ID: 440999 [Multi-domain]  Cd Length: 530  Bit Score: 37.12  E-value: 8.98e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 728887181 187 IKLTAKK-QSKNEYHIKVEDNGPGItPEKQI 216
Cdd:COG1389   60 IKVSIERvDGKDIYRVTVEDNGPGI-PPEQI 89
REC_2_GGDEF cd17544
second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This ...
 2-54 9.26e-03

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: 35.57  E-value: 9.26e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728887181   2 KIRERFSMVDLpvliitaAIIG---HDKY----KAFHAGANDILQKPYHYSEFMARI-QNL 54
Cdd:cd17544   66 EIRKKYSRDQL-------AIIGisaSGDNalsaRFIKAGANDFLTKPFLPEEFYCRVtQNL 119
PRK04184 PRK04184
DNA topoisomerase VI subunit B; Validated
 169-216 9.33e-03

DNA topoisomerase VI subunit B; Validated


Pssm-ID: 235246 [Multi-domain]  Cd Length: 535  Bit Score: 37.18  E-value: 9.33e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 728887181 169 LVENAV----LHGVSKkrgggWIKLTAKK--QSKNEYHIKVEDNGPGItPEKQI 216
Cdd:PRK04184  44 LVDNSLdaceEAGILP-----DIKIEIKRvdEGKDHYRVTVEDNGPGI-PPEEI 91
HATPase_CheA-like cd16916
Histidine kinase-like ATPase domain of the chemotaxis protein histidine kinase CheA, and some ...
 157-214 9.68e-03

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: 36.02  E-value: 9.68e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 728887181 157 IDFILPPLMiqPLVENAVLHGV--------SKKRGGGWIKLTAKkQSKNEYHIKVEDNGPGITPEK 214
Cdd:cd16916   36 LEKLADPLT--HLLRNAVDHGIeapeerlaAGKPPEGTITLRAE-HQGNQVVIEVSDDGRGIDREK 98
 
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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