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Conserved domains on  [gi|2540514736|ref|WP_296680088|]
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MULTISPECIES: GAF domain-containing protein [unclassified Thiothrix]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG4191 super family cl34736
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal ...
 685-965 2.40e-20

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


The actual alignment was detected with superfamily member COG4191:

Pssm-ID: 443345 [Multi-domain]  Cd Length: 361  Bit Score: 94.09  E-value: 2.40e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  685 LDLSFLSNIAAQVSGLLRSLELSETNRKLKDAIAnniELKKAQVKIAEQQHILSTSLLAQDLTHRINNSIGSISININQA 764
Cdd:COG4191     91 EALLLLLLAALDAEENAELEELERDITELERAEE---ELRELQEQLVQSEKLAALGELAAGIAHEINNPLAAILGNAELL 167

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  765 CRDIKNIMNIVD-DDSLQFTLDSLNDSNTMLEDL---AREtkkiSDDANQPVSVKQLLEKTLKQVRlgKRLDEMGINATL 840
Cdd:COG4191    168 RRRLEDEPDPEElREALERILEGAERAAEIVRSLrafSRR----DEEEREPVDLNELIDEALELLR--PRLKARGIEVEL 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  841 SIPDNLPSILAH----NRTLFNsfyaIIDNAADALREQhifqAEKRslyLSIEANQCQENIVITISDNGCSIPAGVKNHL 916
Cdd:COG4191    242 DLPPDLPPVLGDpgqlEQVLLN----LLINAIDAMEEG----EGGR---ITISTRREGDYVVISVRDNGPGIPPEVLERI 310

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2540514736  917 FEYGISTK----GTsGFGLWRANAVITALGGTIKYTDDIRTCVkTFTIALPIQ 965
Cdd:COG4191    311 FEPFFTTKpvgkGT-GLGLSISYGIVEKHGGRIEVESEPGGGT-TFTITLPLA 361
AtoC super family cl34427
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 983-1072 1.76e-09

DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG2204:

Pssm-ID: 441806 [Multi-domain]  Cd Length: 418  Bit Score: 61.13  E-value: 1.76e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKIIL 1062
Cdd:COG2204      7 VVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEP--PDLVLLDLRMP-----GMDGLELLRELRALDPDLPVIL 79

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:COG2204     80 LTGYGDVETA 89
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 557-698 6.61e-08

GAF domain; The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


:

Pssm-ID: 433019 [Multi-domain]  Cd Length: 137  Bit Score: 52.47  E-value: 6.61e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  557 LTRQGILEIAHRHIKEIMFGDNLYISLYDKHKQeisfpLIYVDGQPKEQAARIINPNALGRTEEIILTKKPLRHRTKAES 636
Cdd:pfam13185    2 ADLEELLDAVLEAAVELGASAVGFILLVDDDGR-----LAAWGGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAAD 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2540514736  637 KAWYDTPghgeFMGNHLASWIGVPIFSPDGIQGVIAAYHPNFDAiYSKLDLSFLSNIAAQVS 698
Cdd:pfam13185   77 PAKKGLP----AGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGA-FDEEDLELLELLAEQAA 133
 
Name Accession Description Interval E-value
COG4191 COG4191
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal ...
 685-965 2.40e-20

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


Pssm-ID: 443345 [Multi-domain]  Cd Length: 361  Bit Score: 94.09  E-value: 2.40e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  685 LDLSFLSNIAAQVSGLLRSLELSETNRKLKDAIAnniELKKAQVKIAEQQHILSTSLLAQDLTHRINNSIGSISININQA 764
Cdd:COG4191     91 EALLLLLLAALDAEENAELEELERDITELERAEE---ELRELQEQLVQSEKLAALGELAAGIAHEINNPLAAILGNAELL 167

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  765 CRDIKNIMNIVD-DDSLQFTLDSLNDSNTMLEDL---AREtkkiSDDANQPVSVKQLLEKTLKQVRlgKRLDEMGINATL 840
Cdd:COG4191    168 RRRLEDEPDPEElREALERILEGAERAAEIVRSLrafSRR----DEEEREPVDLNELIDEALELLR--PRLKARGIEVEL 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  841 SIPDNLPSILAH----NRTLFNsfyaIIDNAADALREQhifqAEKRslyLSIEANQCQENIVITISDNGCSIPAGVKNHL 916
Cdd:COG4191    242 DLPPDLPPVLGDpgqlEQVLLN----LLINAIDAMEEG----EGGR---ITISTRREGDYVVISVRDNGPGIPPEVLERI 310

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2540514736  917 FEYGISTK----GTsGFGLWRANAVITALGGTIKYTDDIRTCVkTFTIALPIQ 965
Cdd:COG4191    311 FEPFFTTKpvgkGT-GLGLSISYGIVEKHGGRIEVESEPGGGT-TFTITLPLA 361
HATPase_DpiB-CitA-like cd16915
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 863-963 9.25e-13

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: 65.39  E-value: 9.25e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  863 IIDNAADALREQHifQAEKRslyLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTKGTS--GFGLWRANAVITA 940
Cdd:cd16915      8 LIDNALDALAATG--APNKQ---VEVFLRDEGDDLVIEVRDTGPGIAPELRDKVFERGVSTKGQGerGIGLALVRQSVER 82

                           90       100
                   ....*....|....*....|...
gi 2540514736  941 LGGTIKYTDDIrTCVKTFTIALP 963
Cdd:cd16915     83 LGGSITVESEP-GGGTTFSIRIP 104
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
722-964 2.96e-10

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 64.22  E-value: 2.96e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  722 ELKKAQVKIAEQQHILSTSLLAQDLTHRINNSIGSIS--ININQACRDIK---NIMNIVDDDslqftLDSLNDSNTMLED 796
Cdd:PRK11360   373 ERKRLQRRVARQERLAALGELVAGVAHEIRNPLTAIRgyVQIWRQQTSDPpsqEYLSVVLRE-----VDRLNKVIDQLLE 447

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  797 LARETKKisddANQPVSVKQLLEKTLKQVRLGKRLDemGINATLSIPDNLPSILAHNRTLFNSFYAIIDNAadalreqhi 876
Cdd:PRK11360   448 FSRPRES----QWQPVSLNALVEEVLQLFQTAGVQA--RVDFETELDNELPPIWADPELLKQVLLNILINA--------- 512

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  877 FQAEKRSLYLSIEANQCQE-NIVITISDNGCSIPAGVKNHLFEYGISTKGT-SGFGLWRANAVITALGGTIkYTDDIRTC 954
Cdd:PRK11360   513 VQAISARGKIRIRTWQYSDgQVAVSIEDNGCGIDPELLKKIFDPFFTTKAKgTGLGLALSQRIINAHGGDI-EVESEPGV 591

                          250
                   ....*....|
gi 2540514736  955 VKTFTIALPI 964
Cdd:PRK11360   592 GTTFTLYLPI 601
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 863-965 3.72e-10

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


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 58.04  E-value: 3.72e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736   863 IIDNAADALREQHIfqaekrslyLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTKGTS------GFGLWRANA 936
Cdd:smart00387   13 LLDNAIKYTPEGGR---------ITVTLERDGDHVEITVEDNGPGIPPEDLEKIFEPFFRTDKRSrkiggtGLGLSIVKK 83

                            90       100       110
                    ....*....|....*....|....*....|.
gi 2540514736   937 VITALGGTIKYTDDIR--TcvkTFTIALPIQ 965
Cdd:smart00387   84 LVELHGGEISVESEPGggT---TFTITLPLE 111
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 983-1072 1.76e-09

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: 61.13  E-value: 1.76e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKIIL 1062
Cdd:COG2204      7 VVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEP--PDLVLLDLRMP-----GMDGLELLRELRALDPDLPVIL 79

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:COG2204     80 LTGYGDVETA 89
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 983-1072 2.52e-09

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: 55.31  E-value: 2.52e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKIIL 1062
Cdd:cd00156      2 IVDDDPAIRELLKSLLEREGYEVDTAADGEEALELLREER--PDLVLLDLMMP-----GMDGLELLRKLRELPPDIPVIV 74

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:cd00156     75 LTAKADEEDA 84
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 557-698 6.61e-08

GAF domain; The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433019 [Multi-domain]  Cd Length: 137  Bit Score: 52.47  E-value: 6.61e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  557 LTRQGILEIAHRHIKEIMFGDNLYISLYDKHKQeisfpLIYVDGQPKEQAARIINPNALGRTEEIILTKKPLRHRTKAES 636
Cdd:pfam13185    2 ADLEELLDAVLEAAVELGASAVGFILLVDDDGR-----LAAWGGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAAD 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2540514736  637 KAWYDTPghgeFMGNHLASWIGVPIFSPDGIQGVIAAYHPNFDAiYSKLDLSFLSNIAAQVS 698
Cdd:pfam13185   77 PAKKGLP----AGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGA-FDEEDLELLELLAEQAA 133
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 863-965 7.76e-08

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: 51.60  E-value: 7.76e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  863 IIDNAADalreqhiFQAEKRSLYLSIEANqcqENIVITISDNGCSIPAGVKNHLFE-----YGISTKGTsGFGLWRANAV 937
Cdd:pfam02518   13 LLDNALK-------HAAKAGEITVTLSEG---GELTLTVEDNGIGIPPEDLPRIFEpfstaDKRGGGGT-GLGLSIVRKL 81

                           90       100
                   ....*....|....*....|....*...
gi 2540514736  938 ITALGGTIKYTDDIRTcVKTFTIALPIQ 965
Cdd:pfam02518   82 VELLGGTITVESEPGG-GTTVTLTLPLA 108
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 983-1072 2.29e-06

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: 47.53  E-value: 2.29e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKIIL 1062
Cdd:pfam00072    3 IVDDDPLIRELLRQLLEKEGYVVAEADDGKEALELLKEER--PDLILLDINMP-----GMDGLELLKRIRRRDPTTPVII 75

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:pfam00072   76 LTAHGDEDDA 85
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
537-731 8.46e-06

Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 47.58  E-value: 8.46e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  537 RRFDILNQFSKEVAElkPDNLtrQGILEIAHRHIKEIMFGDNLYISLYDKHKQEISFpliyvdgqpkeQAARIINPNALG 616
Cdd:COG3605      1 EMLKALRRISEAVAS--ALDL--DEALDRIVRRIAEALGVDVCSIYLLDPDGGRLEL-----------RATEGLNPEAVG 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  617 RTE---------EIILTKKPLRHRTKAESKAWYDTPGHGEfmgNHLASWIGVPIFSPDGIQGVIAAYHPNfDAIYSKLDL 687
Cdd:COG3605     66 KVRlplgeglvgLVAERGEPLNLADAASHPRFKYFPETGE---EGFRSFLGVPIIRRGRVLGVLVVQSRE-PREFTEEEV 141

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 2540514736  688 SFLSNIAAQVSGLLRSLELS-ETNRKLKDAIANNIELKKAQVKIA 731
Cdd:COG3605    142 EFLVTLAAQLAEAIANAELLgELRAALAELSLAREEEREAAVEAA 186
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
983-1082 1.41e-03

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 42.53  E-value: 1.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLdatdgANLDGLGLISEVTKTNPSAKIIL 1062
Cdd:PRK11361     9 IVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIH--PDVVLMDIRM-----PEMDGIKALKEMRSHETRTPVIL 81

                           90       100
                   ....*....|....*....|....
gi 2540514736 1063 VTGYSAFADAY----DGKYNLLIE 1082
Cdd:PRK11361    82 MTAYAEVETAVealrCGAFDYVIK 105
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 562-711 1.46e-03

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 40.44  E-value: 1.46e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736   562 ILEIAHRHIKEIMFGDNLYISLYDkHKQEISFPLIYVDGQPKEQAARIInPNALGRTEEIILTKKPLR-HRTKAESKAWY 640
Cdd:smart00065    5 LLQTILEELRQLLGADRVLIYLVD-ENDRGELVLVAADGLTLPTLGIRF-PLDEGLAGRVAETGRPLNiPDVEADPLFAE 82

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2540514736   641 DTPGHGEFMGnhlaSWIGVPIFSPDGIQGVIAAYHPNFDAIYSKLDLSFLSNIAAQVSGLLRSLELSETNR 711
Cdd:smart00065   83 DLLGRYQGVR----SFLAVPLVADGELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEELR 149
 
Name Accession Description Interval E-value
COG4191 COG4191
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal ...
 685-965 2.40e-20

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


Pssm-ID: 443345 [Multi-domain]  Cd Length: 361  Bit Score: 94.09  E-value: 2.40e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  685 LDLSFLSNIAAQVSGLLRSLELSETNRKLKDAIAnniELKKAQVKIAEQQHILSTSLLAQDLTHRINNSIGSISININQA 764
Cdd:COG4191     91 EALLLLLLAALDAEENAELEELERDITELERAEE---ELRELQEQLVQSEKLAALGELAAGIAHEINNPLAAILGNAELL 167

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  765 CRDIKNIMNIVD-DDSLQFTLDSLNDSNTMLEDL---AREtkkiSDDANQPVSVKQLLEKTLKQVRlgKRLDEMGINATL 840
Cdd:COG4191    168 RRRLEDEPDPEElREALERILEGAERAAEIVRSLrafSRR----DEEEREPVDLNELIDEALELLR--PRLKARGIEVEL 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  841 SIPDNLPSILAH----NRTLFNsfyaIIDNAADALREQhifqAEKRslyLSIEANQCQENIVITISDNGCSIPAGVKNHL 916
Cdd:COG4191    242 DLPPDLPPVLGDpgqlEQVLLN----LLINAIDAMEEG----EGGR---ITISTRREGDYVVISVRDNGPGIPPEVLERI 310

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2540514736  917 FEYGISTK----GTsGFGLWRANAVITALGGTIKYTDDIRTCVkTFTIALPIQ 965
Cdd:COG4191    311 FEPFFTTKpvgkGT-GLGLSISYGIVEKHGGRIEVESEPGGGT-TFTITLPLA 361
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 742-966 7.71e-17

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: 84.24  E-value: 7.71e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  742 LAQDLTHRINNSIGSISININQACRDIKNIMNIVDDDSLQFT---LDSLNDSNTMLEDLARETKkISDDANQPVSVKQLL 818
Cdd:COG5000    204 LARRIAHEIKNPLTPIQLSAERLRRKLADKLEEDREDLERALdtiIRQVDRLKRIVDEFLDFAR-LPEPQLEPVDLNELL 282

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  819 EKTLKQVRlgKRLDEMGINATLSIPDNLPSILAhNRTLFNS-FYAIIDNAADALreqhifqAEKRSLYLSIEANQcqENI 897
Cdd:COG5000    283 REVLALYE--PALKEKDIRLELDLDPDLPEVLA-DRDQLEQvLINLLKNAIEAI-------EEGGEIEVSTRRED--GRV 350

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2540514736  898 VITISDNGCSIPAGVKNHLFEYGISTK--GTsGFGLWRANAVITALGGTIKYTD--DIRTCvktFTIALPIQD 966
Cdd:COG5000    351 RIEVSDNGPGIPEEVLERIFEPFFTTKpkGT-GLGLAIVKKIVEEHGGTIELESrpGGGTT---FTIRLPLAE 419
CitA COG3290
Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction ...
 827-966 3.46e-14

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


Pssm-ID: 442519 [Multi-domain]  Cd Length: 389  Bit Score: 75.66  E-value: 3.46e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  827 LGK--RLDEMGINATLSIPDNLPSILAHNRTLFNSFYAIIDNAADALREQhifQAEKRSLYLSIEANQcqENIVITISDN 904
Cdd:COG3290    251 LGKaaRARERGIDLTIDIDSDLPDLPLSDTDLVTILGNLLDNAIEAVEKL---PEEERRVELSIRDDG--DELVIEVEDS 325

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2540514736  905 GCSIPAGVKNHLFEYGISTK--GTSGFGLWRANAVITALGGTIKYTDDIRTCVkTFTIALPIQD 966
Cdd:COG3290    326 GPGIPEELLEKIFERGFSTKlgEGRGLGLALVKQIVEKYGGTIEVESEEGEGT-VFTVRLPKEG 388
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
722-964 3.76e-14

Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 75.27  E-value: 3.76e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  722 ELKKAQVKIAEQQHILSTSLLAQDLTHRINNSIGSISININQACRDiknimniVDDDSLQFTLDSLNDSNTMLEDLARE- 800
Cdd:COG3852    118 ERKRLERELRRAEKLAAVGELAAGLAHEIRNPLTGIRGAAQLLERE-------LPDDELREYTQLIIEEADRLNNLVDRl 190

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  801 --TKKISDDANQPVSVKQLLEKTLKQVRLGkrLDEmGINATLSIPDNLPSILAhNRT-----LFNsfyaIIDNAADALRE 873
Cdd:COG3852    191 lsFSRPRPPEREPVNLHEVLERVLELLRAE--APK-NIRIVRDYDPSLPEVLG-DPDqliqvLLN----LVRNAAEAMPE 262

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  874 QH--IFQAEKRSLyLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTKGT-SGFGLWRANAVITALGGTIKYT-- 948
Cdd:COG3852    263 GGtiTIRTRVERQ-VTLGGLRPRLYVRIEVIDNGPGIPEEILDRIFEPFFTTKEKgTGLGLAIVQKIVEQHGGTIEVEse 341

                          250
                   ....*....|....*.
gi 2540514736  949 DDIRTcvkTFTIALPI 964
Cdd:COG3852    342 PGKGT---TFRIYLPL 354
KdpD COG2205
K+-sensing histidine kinase KdpD [Signal transduction mechanisms];
722-966 3.06e-13

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


Pssm-ID: 441807 [Multi-domain]  Cd Length: 239  Bit Score: 70.71  E-value: 3.06e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  722 ELKKAQVKiAEQQHILSTSLLAqDLTHRINNSIGSISININQAcRDIKNIMNIVDDDSLQFTLDSLNDSNTMLEDL---A 798
Cdd:COG2205      1 ELEEALEE-LEELERLKSEFLA-NVSHELRTPLTSILGAAELL-LDEEDLSPEERRELLEIIRESAERLLRLIEDLldlS 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  799 R-ETKKISDDAnQPVSVKQLLEKTLKQVRLgkRLDEMGINATLSIPDNLPSILAHNRTLFNSFYAIIDNAAD-ALREQHI 876
Cdd:COG2205     78 RlESGKLSLEL-EPVDLAELLEEAVEELRP--LAEEKGIRLELDLPPELPLVYADPELLEQVLANLLDNAIKySPPGGTI 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  877 fqaekrslylSIEANQCQENIVITISDNGCSIPAGVKNHLFE-----YGISTKGTSGFGLWRANAVITALGGTIKY--TD 949
Cdd:COG2205    155 ----------TISARREGDGVRISVSDNGPGIPEEELERIFErfyrgDNSRGEGGTGLGLAIVKRIVEAHGGTIWVesEP 224

                          250
                   ....*....|....*..
gi 2540514736  950 DIRTcvkTFTIALPIQD 966
Cdd:COG2205    225 GGGT---TFTVTLPLAE 238
HATPase_DpiB-CitA-like cd16915
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 863-963 9.25e-13

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: 65.39  E-value: 9.25e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  863 IIDNAADALREQHifQAEKRslyLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTKGTS--GFGLWRANAVITA 940
Cdd:cd16915      8 LIDNALDALAATG--APNKQ---VEVFLRDEGDDLVIEVRDTGPGIAPELRDKVFERGVSTKGQGerGIGLALVRQSVER 82

                           90       100
                   ....*....|....*....|...
gi 2540514736  941 LGGTIKYTDDIrTCVKTFTIALP 963
Cdd:cd16915     83 LGGSITVESEP-GGGTTFSIRIP 104
BaeS COG0642
Signal transduction histidine kinase [Signal transduction mechanisms];
667-965 1.17e-12

Signal transduction histidine kinase [Signal transduction mechanisms];


Pssm-ID: 440407 [Multi-domain]  Cd Length: 328  Bit Score: 70.32  E-value: 1.17e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  667 IQGVIAAYHPNFDAIYSKLDLSFLSNIAAQVSGLLRSLELSETNRKLKDAIANNIELKKAQVKIAEQQHILSTSLLAqDL 746
Cdd:COG0642     39 ALLLLLLLLLLLLLLLALALLALLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLLLLEEANEAKSRFLA-NV 117

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  747 THRINNSIGSISININQACR----DIKNIMNIVDDDSLQftLDSLNDSntmLEDLARETKKISDDANQPVSVKQLLEKTL 822
Cdd:COG0642    118 SHELRTPLTAIRGYLELLLEeldeEQREYLETILRSADR--LLRLIND---LLDLSRLEAGKLELEPEPVDLAELLEEVV 192

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  823 KQVRLgkRLDEMGINATLSIPDNLPSILAhNRTLFNS-FYAIIDNAADALREQHifqaekrslYLSIEANQCQENIVITI 901
Cdd:COG0642    193 ELFRP--LAEEKGIELELDLPDDLPTVRG-DPDRLRQvLLNLLSNAIKYTPEGG---------TVTVSVRREGDRVRISV 260

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2540514736  902 SDNGCSIPAGVKNHLFEYGISTKGT-----SGFGLWRANAVITALGGTIKYTDDIRTCVkTFTIALPIQ 965
Cdd:COG0642    261 EDTGPGIPPEDLERIFEPFFRTDPSrrgggTGLGLAIVKRIVELHGGTIEVESEPGKGT-TFTVTLPLA 328
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
722-964 2.96e-10

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 64.22  E-value: 2.96e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  722 ELKKAQVKIAEQQHILSTSLLAQDLTHRINNSIGSIS--ININQACRDIK---NIMNIVDDDslqftLDSLNDSNTMLED 796
Cdd:PRK11360   373 ERKRLQRRVARQERLAALGELVAGVAHEIRNPLTAIRgyVQIWRQQTSDPpsqEYLSVVLRE-----VDRLNKVIDQLLE 447

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  797 LARETKKisddANQPVSVKQLLEKTLKQVRLGKRLDemGINATLSIPDNLPSILAHNRTLFNSFYAIIDNAadalreqhi 876
Cdd:PRK11360   448 FSRPRES----QWQPVSLNALVEEVLQLFQTAGVQA--RVDFETELDNELPPIWADPELLKQVLLNILINA--------- 512

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  877 FQAEKRSLYLSIEANQCQE-NIVITISDNGCSIPAGVKNHLFEYGISTKGT-SGFGLWRANAVITALGGTIkYTDDIRTC 954
Cdd:PRK11360   513 VQAISARGKIRIRTWQYSDgQVAVSIEDNGCGIDPELLKKIFDPFFTTKAKgTGLGLALSQRIINAHGGDI-EVESEPGV 591

                          250
                   ....*....|
gi 2540514736  955 VKTFTIALPI 964
Cdd:PRK11360   592 GTTFTLYLPI 601
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 863-965 3.72e-10

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


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 58.04  E-value: 3.72e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736   863 IIDNAADALREQHIfqaekrslyLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTKGTS------GFGLWRANA 936
Cdd:smart00387   13 LLDNAIKYTPEGGR---------ITVTLERDGDHVEITVEDNGPGIPPEDLEKIFEPFFRTDKRSrkiggtGLGLSIVKK 83

                            90       100       110
                    ....*....|....*....|....*....|.
gi 2540514736   937 VITALGGTIKYTDDIR--TcvkTFTIALPIQ 965
Cdd:smart00387   84 LVELHGGEISVESEPGggT---TFTITLPLE 111
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 983-1072 1.76e-09

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: 61.13  E-value: 1.76e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKIIL 1062
Cdd:COG2204      7 VVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEP--PDLVLLDLRMP-----GMDGLELLRELRALDPDLPVIL 79

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:COG2204     80 LTGYGDVETA 89
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 983-1072 2.52e-09

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: 55.31  E-value: 2.52e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKIIL 1062
Cdd:cd00156      2 IVDDDPAIRELLKSLLEREGYEVDTAADGEEALELLREER--PDLVLLDLMMP-----GMDGLELLRKLRELPPDIPVIV 74

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:cd00156     75 LTAKADEEDA 84
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 983-1072 3.39e-09

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: 55.53  E-value: 3.39e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdGANldGLGLISEVTKTNPSAKIIL 1062
Cdd:cd17563      5 LVDDDEVFAERLARALERRGFEVETAHSVEEALALAREEK--PDYAVLDLRLG---GDS--GLDLIPPLRALQPDARIVV 77

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:cd17563     78 LTGYASIATA 87
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 983-1098 6.36e-09

phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and similar proteins; NtrX is part of the two-component regulatory system NtrY/NtrX that is involved in the activation of nitrogen assimilatory genes such as Gln. It is phosphorylated by the histidine kinase NtrY and interacts with sigma-54. NtrX is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. NtrC family response regulators are sigma54-dependent transcriptional activators. Also included in this subfamily is Aquifex aeolicus NtrC4. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381102 [Multi-domain]  Cd Length: 115  Bit Score: 54.81  E-value: 6.36e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKIIL 1062
Cdd:cd17550      3 IVDDEEDIRESLSGILEDEGYEVDTAADGEEALKLIKERR--PDLVLLDIWLP-----DMDGLELLKEIKEKYPDLPVIM 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2540514736 1063 VTGYSAFAD--------AYDgkynlLIEK-ISGDGVILSKEKFFE 1098
Cdd:cd17550     76 ISGHGTIETavkatklgAYD-----FIEKpLSLDRLLLTIERALE 115
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 978-1073 1.50e-08

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: 53.76  E-value: 1.50e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  978 KKIaYILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKriKPSHVFLDISLdatdgANLDGLGLISEVTKTNPS 1057
Cdd:cd17554      1 KKI-LVVDDEENIRELYKEELEDEGYEVVTAGNGEEALEKLESE--DPDLVILDIKM-----PGMDGLETLRKIREKKPD 72

                           90       100
                   ....*....|....*....|....
gi 2540514736 1058 AKIILVTGYSAF--------ADAY 1073
Cdd:cd17554     73 LPVIICTAYSEYksdfsswaADAY 96
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 983-1072 1.85e-08

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: 55.31  E-value: 1.85e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatDGanlDGLGLISEVTKTNPSAKIIL 1062
Cdd:COG4567      9 LVDDDEAFARVLARALERRGFEVTTAASVEEALALLEQAP--PDYAVLDLRLG--DG---SGLDLIEALRERDPDARIVV 81

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:COG4567     82 LTGYASIATA 91
PRK11086 PRK11086
sensory histidine kinase DcuS; Provisional
 827-965 2.39e-08

sensory histidine kinase DcuS; Provisional


Pssm-ID: 236839 [Multi-domain]  Cd Length: 542  Bit Score: 58.00  E-value: 2.39e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  827 LGK--RLDEMGINATLS----IPDNLPSILAHnrTLFNSFYAIIDNAADALREQhifqaEKRSLYLSIEANQcqENIVIT 900
Cdd:PRK11086   401 LGKisRARELGITLIISedsqLPDSGDEDQVH--ELITILGNLIENALEAVGGE-----EGGEISVSLHYRN--GWLHCE 471

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2540514736  901 ISDNGCSIPAGVKNHLFEYGISTKGTS-GFGLWRANAVITALGGTIKYT--DDIRTcvkTFTIALPIQ 965
Cdd:PRK11086   472 VSDDGPGIAPDEIDAIFDKGYSTKGSNrGVGLYLVKQSVENLGGSIAVEsePGVGT---QFFVQIPWD 536
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 982-1072 3.89e-08

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: 52.08  E-value: 3.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  982 YILDDERSWRNIISRWLKELS--FEVKTSSNKEEMLAFLqdKRIKPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAK 1059
Cdd:COG4753      3 LIVDDEPLIREGLKRILEWEAgfEVVGEAENGEEALELL--EEHKPDLVITDINMP-----GMDGLELLEAIRELDPDTK 75

                           90
                   ....*....|...
gi 2540514736 1060 IILVTGYSAFADA 1072
Cdd:COG4753     76 IIILSGYSDFEYA 88
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 557-698 6.61e-08

GAF domain; The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433019 [Multi-domain]  Cd Length: 137  Bit Score: 52.47  E-value: 6.61e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  557 LTRQGILEIAHRHIKEIMFGDNLYISLYDKHKQeisfpLIYVDGQPKEQAARIINPNALGRTEEIILTKKPLRHRTKAES 636
Cdd:pfam13185    2 ADLEELLDAVLEAAVELGASAVGFILLVDDDGR-----LAAWGGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAAD 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2540514736  637 KAWYDTPghgeFMGNHLASWIGVPIFSPDGIQGVIAAYHPNFDAiYSKLDLSFLSNIAAQVS 698
Cdd:pfam13185   77 PAKKGLP----AGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGA-FDEEDLELLELLAEQAA 133
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 863-965 7.76e-08

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: 51.60  E-value: 7.76e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  863 IIDNAADalreqhiFQAEKRSLYLSIEANqcqENIVITISDNGCSIPAGVKNHLFE-----YGISTKGTsGFGLWRANAV 937
Cdd:pfam02518   13 LLDNALK-------HAAKAGEITVTLSEG---GELTLTVEDNGIGIPPEDLPRIFEpfstaDKRGGGGT-GLGLSIVRKL 81

                           90       100
                   ....*....|....*....|....*...
gi 2540514736  938 ITALGGTIKYTDDIRTcVKTFTIALPIQ 965
Cdd:pfam02518   82 VELLGGTITVESEPGG-GTTVTLTLPLA 108
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 981-1074 1.13e-07

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 54.05  E-value: 1.13e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  981 AYILDDERSWRNIISRWLKELSF--EVKTSSNKEEMLAFLQDKriKPSHVFLDISLdatdgANLDGLGLISEVTKTNPSA 1058
Cdd:COG3279      4 ILIVDDEPLARERLERLLEKYPDleVVGEASNGEEALELLEEH--KPDLVFLDIQM-----PGLDGFELARQLRELDPPP 76

                           90
                   ....*....|....*..
gi 2540514736 1059 KIILVTGYSAFA-DAYD 1074
Cdd:COG3279     77 PIIFTTAYDEYAlEAFE 93
GAF COG2203
GAF domain [Signal transduction mechanisms];
510-892 1.56e-07

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 55.58  E-value: 1.56e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  510 RAGGLTAKAIDEISNALAYRVVQFDRPRRFDILNQFSKEVAElkpdNLTRQGILEIAHRHIKEIMFGDNLYISLYDKHKQ 589
Cdd:COG2203    163 LVGQLAALAGLILDIARLLTQRARLELERLALLNEISQALRS----ALDLEELLQRILELAGELLGADRGAILLVDEDGG 238

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  590 EISfpLIYVDGQPKEQAARIinPNALGRTEEIILTKKPLRHRTKAESKAWYDTPgHGEFMGNHLASWIGVPIFSPDGIQG 669
Cdd:COG2203    239 ELE--LVAAPGLPEEELGRL--PLGEGLAGRALRTGEPVVVNDASTDPRFAPSL-RELLLALGIRSLLCVPLLVDGRLIG 313

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  670 VIAAYHPNFDAiYSKLDLSFLSNIAAQVSGllrSLELSETNRKLKDAIANNIELKKAQVKIAEQQHILSTSLLAQDLTHR 749
Cdd:COG2203    314 VLALYSKEPRA-FTEEDLELLEALADQAAI---AIERARLYEALEAALAALLQELALLRLLLDLELTLLRLRQLLLELLL 389

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  750 INNSIGSISININQACRDIKNIMNIVDDDSLQFTLDSLNDSNTMLEDLARETKKISDDANQPVSVKQLLEKTLKQVRLGK 829
Cdd:COG2203    390 ALLLLLSLLGAELLLLLLDAADLSGLLALEGLLLLDLLLLLLLLRRILLLRVLRRLLLGDEEGLVLLLALAELELLEILE 469

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2540514736  830 RLDEMGINATLSIPDNLPSILAHNRTLFNSFYAIIDNAADALREQHIFQAEKRSLYLSIEANQ 892
Cdd:COG2203    470 LLVLLAVILLALALLAALLLLLLLLLALLALSALAVLASLLLALLLLLLLLLLLLLLGLLAAL 532
dpiB PRK15053
sensor histidine kinase DpiB; Provisional
 829-963 3.23e-07

sensor histidine kinase DpiB; Provisional


Pssm-ID: 185013 [Multi-domain]  Cd Length: 545  Bit Score: 54.45  E-value: 3.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  829 KRLDEMGINATL-------SIPDNLPSilahnrtlfNSFYAIIDNAADalreqHIFQAEKRS--------LYLSIEANQc 893
Cdd:PRK15053   404 QRARELGLKMVIvpgsqlsQLPPGLDS---------TEFAAIVGNLLD-----NAFEASLRSdegnkiveLFLSDEGDD- 468

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2540514736  894 qenIVITISDNGCSIPAGVKNHLFEYGISTK----GTSGFGLWRANAVITALGGTIKYTDDiRTCVKTFTIALP 963
Cdd:PRK15053   469 ---VVIEVADQGCGVPESLRDKIFEQGVSTRadepGEHGIGLYLIASYVTRCGGVITLEDN-DPCGTLFSIFIP 538
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 981-1074 1.39e-06

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: 48.30  E-value: 1.39e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  981 AYILDDERSWRNIISRWLKELS--FEVKTSSNKEEMLAFLQDKriKPSHVFLDISLdatdgANLDGLGLISEVTKTNPSA 1058
Cdd:cd17532      1 ALIVDDEPLAREELRYLLEEHPdiEIVGEAENGEEALEAIEEL--KPDVVFLDIQM-----PGLDGLELAKKLSKLAKPP 73

                           90
                   ....*....|....*..
gi 2540514736 1059 KIILVTGYSAFA-DAYD 1074
Cdd:cd17532     74 LIVFVTAYDEYAvEAFE 90
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 983-1071 1.42e-06

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: 50.34  E-value: 1.42e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLdatdgANLDGLGLISEVTKTNPSAKIIL 1062
Cdd:COG0745      6 VVEDDPDIRELLADALEREGYEVDTAADGEEALELLEEER--PDLILLDLML-----PGMDGLEVCRRLRARPSDIPIIM 78


                   ....*....
gi 2540514736 1063 VTGYSAFAD 1071
Cdd:COG0745     79 LTARDDEED 87
WalK COG5002
Sensor histidine kinase WalK [Signal transduction mechanisms];
794-964 1.59e-06

Sensor histidine kinase WalK [Signal transduction mechanisms];


Pssm-ID: 444026 [Multi-domain]  Cd Length: 390  Bit Score: 51.86  E-value: 1.59e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  794 LEDLAR-ETKKISDDaNQPVSVKQLLEKTLKQVRLgkRLDEMGINATLSIPDNLPSILAhNRTLFNS-FYAIIDNAadaL 871
Cdd:COG5002    222 LLDLSRlESGELKLE-KEPVDLAELLEEVVEELRP--LAEEKGIELELDLPEDPLLVLG-DPDRLEQvLTNLLDNA---I 294

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  872 ReqhiFQAEKRSLYLSIEANQcqENIVITISDNGCSIPAGVKNHLFE--Y------GISTKGTsGFGLWRANAVITALGG 943
Cdd:COG5002    295 K----YTPEGGTITVSLREED--DQVRISVRDTGIGIPEEDLPRIFErfYrvdksrSRETGGT-GLGLAIVKHIVEAHGG 367

                          170       180
                   ....*....|....*....|...
gi 2540514736  944 TIKYTDDIR--TcvkTFTIALPI 964
Cdd:COG5002    368 RIWVESEPGkgT---TFTITLPL 387
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 983-1072 2.29e-06

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: 47.53  E-value: 2.29e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKIIL 1062
Cdd:pfam00072    3 IVDDDPLIRELLRQLLEKEGYVVAEADDGKEALELLKEER--PDLILLDINMP-----GMDGLELLKRIRRRDPTTPVII 75

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:pfam00072   76 LTAHGDEDDA 85
REC_RssB-like cd17555
phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ...
 983-1072 3.92e-06

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: 46.81  E-value: 3.92e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLdatdgANLDGLGLISEVTKTNPSAKIIL 1062
Cdd:cd17555      5 VIDDDEVVRESIAAYLEDSGFQVLQAADGRQGLELFRSEQ--PDLVLCDLRM-----PEMDGLEVLKQITKESPDTPVIV 77

                           90
                   ....*....|
gi 2540514736 1063 VTGYSAFADA 1072
Cdd:cd17555     78 VSGAGVMSDA 87
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 983-1073 8.40e-06

phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins are one of the most widespread transcriptional regulators. OmpR family members contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domain. They are involved in the control of environmental stress tolerance (such as the oxidative, osmotic and acid stress response), motility, virulence, outer membrane biogenesis and other processes. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381116 [Multi-domain]  Cd Length: 99  Bit Score: 45.48  E-value: 8.40e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKriKPSHVFLDISLdatdgANLDGLGLISEVTKTNPSAKIIL 1062
Cdd:cd17574      2 VVEDDEEIAELLSDYLEKEGYEVDTAADGEEALELAREE--QPDLIILDVML-----PGMDGFEVCRRLREKGSDIPIIM 74

                           90       100
                   ....*....|....*....|.
gi 2540514736 1063 VT----------GYSAFADAY 1073
Cdd:cd17574     75 LTakdeeedkvlGLELGADDY 95
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
537-731 8.46e-06

Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 47.58  E-value: 8.46e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  537 RRFDILNQFSKEVAElkPDNLtrQGILEIAHRHIKEIMFGDNLYISLYDKHKQEISFpliyvdgqpkeQAARIINPNALG 616
Cdd:COG3605      1 EMLKALRRISEAVAS--ALDL--DEALDRIVRRIAEALGVDVCSIYLLDPDGGRLEL-----------RATEGLNPEAVG 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  617 RTE---------EIILTKKPLRHRTKAESKAWYDTPGHGEfmgNHLASWIGVPIFSPDGIQGVIAAYHPNfDAIYSKLDL 687
Cdd:COG3605     66 KVRlplgeglvgLVAERGEPLNLADAASHPRFKYFPETGE---EGFRSFLGVPIIRRGRVLGVLVVQSRE-PREFTEEEV 141

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 2540514736  688 SFLSNIAAQVSGLLRSLELS-ETNRKLKDAIANNIELKKAQVKIA 731
Cdd:COG3605    142 EFLVTLAAQLAEAIANAELLgELRAALAELSLAREEEREAAVEAA 186
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 983-1072 2.05e-05

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: 45.23  E-value: 2.05e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEV--TKTNPSAKI 1060
Cdd:COG0784     10 VVDDNPDNRELLRRLLERLGYEVTTAEDGAEALELLRAGP--PDLILLDINMP-----GMDGLELLRRIraLPRLPDIPI 82

                           90
                   ....*....|..
gi 2540514736 1061 ILVTGYSAFADA 1072
Cdd:COG0784     83 IALTAYADEEDR 94
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 983-1070 2.10e-05

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: 45.02  E-value: 2.10e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISR---WlKELSFE-VKTSSNKEEMLAFLQDKriKPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSA 1058
Cdd:cd17536      3 IVDDEPLIREGLKKlidW-EELGFEvVGEAENGEEALELIEEH--KPDIVITDIRMP-----GMDGLELIEKIRELYPDI 74

                           90
                   ....*....|..
gi 2540514736 1059 KIILVTGYSAFA 1070
Cdd:cd17536     75 KIIILSGYDDFE 86
PRK10364 PRK10364
two-component system sensor histidine kinase ZraS;
785-964 2.11e-05

two-component system sensor histidine kinase ZraS;


Pssm-ID: 236674 [Multi-domain]  Cd Length: 457  Bit Score: 48.24  E-value: 2.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  785 DSLNDSNTMLEDLAREtkkiSDDANQPVSVKQLLEKTLKQVRLGKRldEMGINATLSIPDNLPSILAH----NRTLFNSF 860
Cdd:PRK10364   284 DRLNRVVSELLELVKP----THLALQAVDLNDLINHSLQLVSQDAN--SREIQLRFTANDTLPEIQADpdrlTQVLLNLY 357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  861 YaiidNAADALREQHIfqaekrslyLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTKGT-SGFGLWRANAVIT 939
Cdd:PRK10364   358 L----NAIQAIGQHGV---------ISVTASESGAGVKISVTDSGKGIAADQLEAIFTPYFTTKAEgTGLGLAVVHNIVE 424

                          170       180
                   ....*....|....*....|....*
gi 2540514736  940 ALGGTIKYTdDIRTCVKTFTIALPI 964
Cdd:PRK10364   425 QHGGTIQVA-SQEGKGATFTLWLPV 448
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 983-1067 4.64e-05

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: 45.28  E-value: 4.64e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQdkRIKPSHVFLDISLdatdgANLDGLGLISEVtKTNPSAK--- 1059
Cdd:COG3706      6 VVDDDPTNRKLLRRLLEAAGYEVVEAADGEEALELLQ--EHRPDLILLDLEM-----PDMDGLELCRRL-RADPRTAdip 77


                   ....*...
gi 2540514736 1060 IILVTGYS 1067
Cdd:COG3706     78 IIFLTALD 85
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 983-1064 5.45e-05

phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response regulator CheY contains a stand-alone REC domain. Chemotaxis is a behavior known for motile bacteria that directs their movement in response to chemical gradients. CheY is involved in transmitting sensory signals from chemoreceptors to the flagellar motors. Phosphorylated CheY interacts with the flagella switch components FliM and FliY, which causes counterclockwise rotation of the flagella, resulting in smooth swimming. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381097 [Multi-domain]  Cd Length: 117  Bit Score: 43.81  E-value: 5.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFE-VKTSSNKEEmlAFLQDKRIKPSHVFLDISLDATDGanldgLGLISEVTKTNPSAKII 1061
Cdd:cd17542      5 IVDDAAFMRMMLKDILTKAGYEvVGEAANGEE--AVEKYKELKPDLVTMDITMPEMDG-----IEALKEIKKIDPNAKVI 77


                   ...
gi 2540514736 1062 LVT 1064
Cdd:cd17542     78 MCS 80
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 982-1066 8.91e-05

phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response regulators contain an N-terminal receiver domain (REC) and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. The Sinorhizobium meliloti two-component system FixL/FixJ regulates nitrogen fixation in response to oxygen during symbiosis. Under microaerobic conditions, the kinase FixL phosphorylates the response regulator FixJ resulting in the regulation of nitrogen fixation genes such as nifA and fixK. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381092 [Multi-domain]  Cd Length: 116  Bit Score: 42.97  E-value: 8.91e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  982 YILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatdgaNLDGLGLISEVTKTNPSAKII 1061
Cdd:cd17537      4 YVVDDDEAVRDSLAFLLRSVGLAVKTFTSASAFLAAAPPDQ--PGCLVLDVRMP-----GMSGLELQDELLARGSNIPII 76


                   ....*
gi 2540514736 1062 LVTGY 1066
Cdd:cd17537     77 FITGH 81
YesM COG2972
Sensor histidine kinase YesM [Signal transduction mechanisms];
783-932 9.31e-05

Sensor histidine kinase YesM [Signal transduction mechanisms];


Pssm-ID: 442211 [Multi-domain]  Cd Length: 445  Bit Score: 46.16  E-value: 9.31e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  783 TLDSLN---------DSNTMLEDLARETKKISDDANQPVSVKQ---LLEK--TLKQVRLGKRLDemginATLSIPDNLPS 848
Cdd:COG2972    259 TLNSIRwlaeledpeEAEEMLEALSKLLRYSLSKGDELVTLEEeleLIKSylEIQKLRFGDRLE-----VEIEIDEELLD 333

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  849 ILAHNRTLFNsfyaIIDNAAdalreQHIFQAEKRSLYLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTKGTSG 928
Cdd:COG2972    334 LLIPKLILQP----LVENAI-----EHGIEPKEGGGTIRISIRKEGDRLVITVEDNGVGMPEEKLEKLLEELSSKGEGRG 404


                   ....
gi 2540514736  929 FGLW 932
Cdd:COG2972    405 IGLR 408
REC_CpdR_CckA-like cd18160
phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; ...
 983-1070 1.04e-04

phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; Two-component systems (TCSs), consisting of a sensor and a response regulator, are used by bacteria to adapt to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis and membrane transport. Response regulators share the common phosphoacceptor REC domain and differ output domains such as DNA, RNA, ligand, and protein-binding, or enzymatic domain. CpdR is a stand-alone REC protein. CckA is a sensor histidine kinase containing N-terminal PAS domains and a C-terminal REC domain. CpdR and CckA are components of a regulatory phosphorelay system (composed of CckA, ChpT, CtrA and CpdR) that controls Brucella abortus cell growth, division, and intracellular survival inside mammalian host cells. CckA autophosphorylates in the presence of ATP and transfers a phosphoryl group to the conserved aspartic acid residue on its C-terminal REC domain, which is relayed to the ChpT phosphotransferase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381144 [Multi-domain]  Cd Length: 103  Bit Score: 42.49  E-value: 1.04e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikpshvflDISLDATD--GANLDGLGLISEVTKTNPSAKI 1060
Cdd:cd18160      4 LADDEPSVRKFIVTTLKKAGYAVTEAESGAEALEKLQQGK--------DIDIVVTDivMPEMDGIELAREARKIDPDVKI 75

                           90
                   ....*....|
gi 2540514736 1061 ILVTGYSAFA 1070
Cdd:cd18160     76 LFISGGAAAA 85
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 983-1067 1.43e-04

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 43.03  E-value: 1.43e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSF--EVKTSSNKEEMLAFLQDKRikPSHVFLDISLDatDGanlDGLGLISEVTKTNPSAKI 1060
Cdd:COG4565      8 IVEDDPMVAELLRRYLERLPGfeVVGVASSGEEALALLAEHR--PDLILLDIYLP--DG---DGLELLRELRARGPDVDV 80


                   ....*..
gi 2540514736 1061 ILVTGYS 1067
Cdd:COG4565     81 IVITAAR 87
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 559-698 2.15e-04

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 42.47  E-value: 2.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  559 RQGILEIAHRHIKEIMFGDNLYISLYDKHkqeisfPLIYVDGQPKEQAARIINPnALGRTEEIILTKKPLRHRTKAESKA 638
Cdd:pfam01590    2 LEEILQTILEELRELLGADRCALYLPDAD------GLEYLPPGARWLKAAGLEI-PPGTGVTVLRTGRPLVVPDAAGDPR 74

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  639 WYDTPGHGEFMGnhLASWIGVPIFSPDGIQGVIAAYHPnfDAIYSKLDLSFLSNIAAQVS 698
Cdd:pfam01590   75 FLDPLLLLRNFG--IRSLLAVPIIDDGELLGVLVLHHP--RPPFTEEELELLEVLADQVA 130
HATPase_AtoS-like cd16943
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 853-964 2.28e-04

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli K-12 AtoS; This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs) such as Escherichia coli AtoS, an HK of the AtoS-AtoC TCS. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some have accessory domains such as HAMP or PAS sensor domains or CBS-pair domains.


Pssm-ID: 340419 [Multi-domain]  Cd Length: 105  Bit Score: 41.64  E-value: 2.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  853 NRTLFNsfyaIIDNAADALREqhifqaEKRslyLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTK----GTsG 928
Cdd:cd16943      5 NQVLLN----LLVNAAQAMEG------RGR---ITIRTWAHVDQVLIEVEDTGSGIDPEILGRIFDPFFTTKpvgeGT-G 70

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 2540514736  929 FGLWRANAVITALGGTIKytddIRTCV---KTFTIALPI 964
Cdd:cd16943     71 LGLSLSYRIIQKHGGTIR----VASVPgggTRFTIILPI 105
glnL PRK11073
nitrogen regulation protein NR(II);
810-964 3.09e-04

nitrogen regulation protein NR(II);


Pssm-ID: 182947 [Multi-domain]  Cd Length: 348  Bit Score: 44.30  E-value: 3.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  810 QPVSVKQLLEKTLKQVRLgkrldEMGINATLsIPDNLPSI--LAHN-----RTLFNsfyaIIDNAADALREQH--IFQAE 880
Cdd:PRK11073   195 VTESIHKVAERVVQLVSL-----ELPDNVRL-IRDYDPSLpeLAHDpdqieQVLLN----IVRNALQALGPEGgtITLRT 264

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  881 KRSLYLSIEANQCQENIVITISDNGCSIPAGVKNHLFEYGISTK-GTSGFGLWRANAVITALGGTIKYTD-DIRTcvkTF 958
Cdd:PRK11073   265 RTAFQLTLHGERYRLAARIDIEDNGPGIPPHLQDTLFYPMVSGReGGTGLGLSIARNLIDQHSGKIEFTSwPGHT---EF 341


                   ....*.
gi 2540514736  959 TIALPI 964
Cdd:PRK11073   342 SVYLPI 347
COG4251 COG4251
Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal ...
 776-945 5.56e-04

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


Pssm-ID: 443393 [Multi-domain]  Cd Length: 503  Bit Score: 44.01  E-value: 5.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  776 DDDSLQFtLDSLNDS----NTMLEDL---ARETKKisDDANQPVSVKQLLEKTLKQvrLGKRLDEMGinATLSIpDNLPS 848
Cdd:COG4251    316 DEEGREY-LERIRDAaermQALIDDLlaySRVGRQ--ELEFEPVDLNELLEEVLED--LEPRIEERG--AEIEV-GPLPT 387

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  849 ILAhNRTLFNS-FYAIIDNAAdalreqhIFQAEKRSLYLSIEANQCQENIVITISDNGCSIPAGVKNHLF---------- 917
Cdd:COG4251    388 VRG-DPTLLRQvFQNLISNAI-------KYSRPGEPPRIEIGAEREGGEWVFSVRDNGIGIDPEYAEKIFeifqrlhsrd 459

                          170       180       190
                   ....*....|....*....|....*....|
gi 2540514736  918 EYGistkGTsGFGLwrANA--VITALGGTI 945
Cdd:COG4251    460 EYE----GT-GIGL--AIVkkIVERHGGRI 482
HATPase_NtrY-like cd16944
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 863-949 8.26e-04

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Azorhizobium caulinodans NtrY; This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs) such as Azorhizobium caulinodans ORS571 NtrY of the NtrY-NtrX TCS, which is involved in nitrogen fixation and metabolism. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and a HAMP sensor domain; some also have PAS sensor domains.


Pssm-ID: 340420 [Multi-domain]  Cd Length: 108  Bit Score: 40.21  E-value: 8.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  863 IIDNAADALREQHIFQAEKRslyLSIEANQcQENIVITISDNGCSIPAGVKNHLFEYGIST--KGTsGFGLWRANAVITA 940
Cdd:cd16944     12 ILKNAAEAIEGRPSDVGEVR---IRVEADQ-DGRIVLIVCDNGKGFPREMRHRATEPYVTTrpKGT-GLGLAIVKKIMEE 86


                   ....*....
gi 2540514736  941 LGGTIKYTD 949
Cdd:cd16944     87 HGGRISLSN 95
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
983-1082 1.41e-03

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 42.53  E-value: 1.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQDKRikPSHVFLDISLdatdgANLDGLGLISEVTKTNPSAKIIL 1062
Cdd:PRK11361     9 IVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIH--PDVVLMDIRM-----PEMDGIKALKEMRSHETRTPVIL 81

                           90       100
                   ....*....|....*....|....
gi 2540514736 1063 VTGYSAFADAY----DGKYNLLIE 1082
Cdd:PRK11361    82 MTAYAEVETAVealrCGAFDYVIK 105
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 562-711 1.46e-03

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 40.44  E-value: 1.46e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736   562 ILEIAHRHIKEIMFGDNLYISLYDkHKQEISFPLIYVDGQPKEQAARIInPNALGRTEEIILTKKPLR-HRTKAESKAWY 640
Cdd:smart00065    5 LLQTILEELRQLLGADRVLIYLVD-ENDRGELVLVAADGLTLPTLGIRF-PLDEGLAGRVAETGRPLNiPDVEADPLFAE 82

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2540514736   641 DTPGHGEFMGnhlaSWIGVPIFSPDGIQGVIAAYHPNFDAIYSKLDLSFLSNIAAQVSGLLRSLELSETNR 711
Cdd:smart00065   83 DLLGRYQGVR----SFLAVPLVADGELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEELR 149
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 983-1066 1.71e-03

phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and similar proteins; C4-dicarboxylic acid transport protein D (DctD) is part of the two-component regulatory system DctB/DctD, which regulates C4-dicarboxylate transport via regulation of expression of the dctPQM operon and dctA. It is an activator of sigma(54)-RNA polymerase holoenzyme that uses the energy released from ATP hydrolysis to stimulate the isomerization of a closed promoter complex to an open complex capable of initiating transcription. DctD is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381101 [Multi-domain]  Cd Length: 130  Bit Score: 39.78  E-value: 1.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLkELS-FEVKTSSNKEEMLAFLQDKRikPSHVFLDISLDAtdganLDGLGLISEVTKTNPSAKII 1061
Cdd:cd17549      3 LVDDDADVREALQQTL-ELAgFRVRAFADAEEALAALSPDF--PGVVISDIRMPG-----MDGLELLAQIRELDPDLPVI 74


                   ....*
gi 2540514736 1062 LVTGY 1066
Cdd:cd17549     75 LITGH 79
PRK11644 PRK11644
signal transduction histidine-protein kinase/phosphatase UhpB;
685-963 1.74e-03

signal transduction histidine-protein kinase/phosphatase UhpB;


Pssm-ID: 236945 [Multi-domain]  Cd Length: 495  Bit Score: 42.27  E-value: 1.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  685 LDLsFLSNIAAQVSGLLRSL---ELSETNRKLKDAIANNIELKKAQVKIAEQqhilstslLAQDLTHRINNSIGSisiNI 761
Cdd:PRK11644   250 VDL-LLSLLAQSLTGLLLGAgiqRQRELNQSLQKELARNRHLAERLLETEES--------VRRDVARELHDEIGQ---TI 317

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  762 NqACRDIKNIMNIVDDDSLQF--------TLdSLNDSNTMLEDLARETKKISDDANQPVSVKQLL-EKTLKQ----VRLG 828
Cdd:PRK11644   318 T-AIRTQAGIIKRLAADNASVkqsaqlieQL-SLGVYDTVRRLLGRLRPRQLDDLTLEQAIRSLMrEMELEDrgivSHLD 395

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  829 KRLDEMGINATLSIpdnlpsilahnrTLFNSFYAIIDNAADALREQHIfqaekrslylSIEANQCQENIVITISDNGCSI 908
Cdd:PRK11644   396 WRIDESALSETQRV------------TLFRVCQEGLNNIVKHADASAV----------TLQGWQQDERLMLVIEDDGSGL 453

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2540514736  909 PAGvknhlfeygistKGTSGFGLWRANAVITALGGTIKYTDDIRTCVktfTIALP 963
Cdd:PRK11644   454 PPG------------SGQQGFGLRGMRERVTALGGTLTISCTHGTRL---SVSLP 493
REC_OmpR_MtPhoP-like cd17615
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ...
 983-1071 4.78e-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: 38.10  E-value: 4.78e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  983 ILDDERSWRNIISRWLKELSFEVKTSSNKEEMLAFLQdkRIKPSHVFLDISLdatdgANLDGLGLISEVTKTNPSAKIIL 1062
Cdd:cd17615      4 VVDDEPNITELLSMALRYEGWDVETAADGAEALAAAR--EFRPDAVVLDIML-----PDMDGLEVLRRLRADGPDVPVLF 76


                   ....*....
gi 2540514736 1063 VTGYSAFAD 1071
Cdd:cd17615     77 LTAKDSVED 85
COG3920 COG3920
Two-component sensor histidine kinase, HisKA and HATPase domains [Signal transduction ...
 886-969 5.70e-03

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


Pssm-ID: 443125 [Multi-domain]  Cd Length: 495  Bit Score: 40.66  E-value: 5.70e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  886 LSIEANQCQENIVITISDNGCSIPAGVknhlfeygiSTKGTSGFGLWRANAVITALGGTIKYTDDIRTCvktFTIALPIQ 965
Cdd:COG3920    424 IRVSWRREDGRLRLTVSDNGVGLPEDV---------DPPARKGLGLRLIRALVRQLGGTLELDRPEGTR---VRITFPLA 491


                   ....
gi 2540514736  966 DLKT 969
Cdd:COG3920    492 ELAA 495
HATPase_CckA-like cd16919
Histidine kinase-like ATPase domain of two-component sensor hybrid histidine kinases, similar ...
 866-946 7.03e-03

Histidine kinase-like ATPase domain of two-component sensor hybrid histidine kinases, similar to Brucella abortus 2308 CckA; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinase (HKs) similar to Brucella abortus 2308 CckA, which is a component of an essential protein phosphorelay that regulates expression of genes required for growth, division, and intracellular survival; phosphoryl transfer initiates from the sensor kinase CckA and proceeds via the ChpT phosphotransferase to two regulatory substrates: the DNA-binding response regulator CtrA and the phospho-receiver protein CpdR. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), a REC signal receiver domain, and some contain PAS or PAS and GAF sensor domain(s).


Pssm-ID: 340396 [Multi-domain]  Cd Length: 116  Bit Score: 37.74  E-value: 7.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  866 NAADALRE--QHIFQAEKRSLYLSIEANQCQ----ENIVITISDNGCSIPAGVKNHLFEYGISTKGT---SGFGLWRANA 936
Cdd:cd16919     11 NARDAMPEggRLTIETSNQRVDADYALNYRDlipgNYVCLEVSDTGSGMPAEVLRRAFEPFFTTKEVgkgTGLGLSMVYG 90

                           90
                   ....*....|
gi 2540514736  937 VITALGGTIK 946
Cdd:cd16919     91 FVKQSGGHLR 100
REC_LytTR_AgrA-like cd17533
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; ...
 982-1070 8.36e-03

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; 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 AgrA-like group of LytTR/AlgR family response regulators are Staphylococcus aureus accessory gene regulator protein A (AgrA) and Streptococcus pneumoniae response regulator ComE, which are members of two-component regulatory systems. AgrA is a global regulator that controls the synthesis of virulence factors and other exoproteins. ComE is part of the ComD-ComE system that is part of a quorum-sensing signaling pathway that controls the development of competence, a physiological state required for genetic transformation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381088 [Multi-domain]  Cd Length: 131  Bit Score: 37.60  E-value: 8.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2540514736  982 YILDDERSWRNIISRWLKELS------FEVKTSSNKEEMLAfLQDKRIKPSHVFLDISLDATDganLDGLGLISEVTKTN 1055
Cdd:cd17533      4 FILEDDKIQRVRLEEIIENILkienieYVIELTGKTEELLE-KIKERGKNGIYFLDIDIKMEE---KNGLEVAQKIRKYD 79

                           90
                   ....*....|....*
gi 2540514736 1056 PSAKIILVTGYSAFA 1070
Cdd:cd17533     80 PYAIIIFVTTHSEFA 94
 
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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