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Conserved domains on  [gi|16131539|ref|NP_418125|]
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DNA-binding transcriptional activator UhpA [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

response regulator transcription factor UhpA( domain architecture ID 11484674)

two-component system rresponse regulator transcription factor UhpA binds DNA upon phosphorylation and functions as transcriptional regulator, as part of the UhpABC signaling cascade that controls expression of the hexose phosphate transporter UhpT

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10360 PRK10360
transcriptional regulator UhpA;
1-196 2.82e-149

transcriptional regulator UhpA;


:

Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 411.68  E-value: 2.82e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSV 80
Cdd:PRK10360   1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAA 160
Cdd:PRK10360  81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAA 160

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 16131539  161 ELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW 196
Cdd:PRK10360 161 ELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW 196
 
Name Accession Description Interval E-value
PRK10360 PRK10360
transcriptional regulator UhpA;
1-196 2.82e-149

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 411.68  E-value: 2.82e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSV 80
Cdd:PRK10360   1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAA 160
Cdd:PRK10360  81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAA 160

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 16131539  161 ELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW 196
Cdd:PRK10360 161 ELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW 196
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 3-193 2.86e-42

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 140.62  E-value: 2.86e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLLGLEpDLQVVAeFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMATIMLS 79
Cdd:COG4566   1 TVYIVDDDEAVRDSLAFLLESA-GLRVET-FASAEAFLAALDPDRPGCLLLDVRMPGMSGLELqeeLAARGSPLPVIFLT 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAVHT-VATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEI 158
Cdd:COG4566  79 GHGDVPMAVRAMKAGAVDFLEKPFDDQALLDAVRRaLARDRARRAERARRAELRARLASLTPREREVLDLVVAGLSNKQI 158

                       170       180       190
                ....*....|....*....|....*....|....*
gi 16131539 159 AAELGLSPKTVHVHRANLMEKLGVSNDVELARRMF 193
Cdd:COG4566 159 ARELGISPRTVEVHRANVMEKLGARSLAELVRLAL 193
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 4-116 2.31e-41

phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family response regulators; The NarL family is one of the more abundant families of DNA-binding response regulators (RRs). Members of the NarL family contain a REC domain and a helix-turn-helix (HTH) DNA-binding output domain, with a majority of members containing a LuxR-type HTH domain. They function as transcriptional regulators. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381090 [Multi-domain]  Cd Length: 117  Bit Score: 135.72  E-value: 2.31e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLSV 80
Cdd:cd17535   1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRrypDLKVIVLTA 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 16131539  81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVA 116
Cdd:cd17535  81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 4-112 1.93e-29

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: 104.93  E-value: 1.93e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539     4 VALIDDHLIVRSGFAQLLGLEPdlQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMATIMLSV 80
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEG--YVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIrrrDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 16131539    81 HDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 136-191 8.52e-23

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 86.43  E-value: 8.52e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 16131539    136 DPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARR 191
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
tetrathio_RR NF040749
tetrathionate respiration response regulator TtrR;
50-192 4.03e-19

tetrathionate respiration response regulator TtrR;


Pssm-ID: 468713 [Multi-domain]  Cd Length: 191  Bit Score: 80.48  E-value: 4.03e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   50 VCICDISMPDISGLELLSQLPK---GMATIMLSVH-DSPALVEQaLNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPD 125
Cdd:NF040749  46 VVLLDMRMPGLDGHQVHQALREqgsTLAVVFLTGHgDVPMAVEQ-MKLGAVDFLQKPVSAAPLQAALERALAVSAAAFER 124

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16131539  126 IAIKLasgRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRM 192
Cdd:NF040749 125 HQIRQ---RYQSLTPKEREIAGLVVQGLMNREIAEALNIAVRTVEVHRARVMEKMAAGSLAELVSQL 188
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 138-180 1.58e-04

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


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 40.41  E-value: 1.58e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 16131539   138 LTKRERQVAE-KLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180
Cdd:TIGR02937 111 LPEREREVLVlRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK10360 PRK10360
transcriptional regulator UhpA;
1-196 2.82e-149

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 411.68  E-value: 2.82e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSV 80
Cdd:PRK10360   1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAA 160
Cdd:PRK10360  81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAA 160

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 16131539  161 ELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW 196
Cdd:PRK10360 161 ELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW 196
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 3-193 2.86e-42

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 140.62  E-value: 2.86e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLLGLEpDLQVVAeFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMATIMLS 79
Cdd:COG4566   1 TVYIVDDDEAVRDSLAFLLESA-GLRVET-FASAEAFLAALDPDRPGCLLLDVRMPGMSGLELqeeLAARGSPLPVIFLT 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAVHT-VATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEI 158
Cdd:COG4566  79 GHGDVPMAVRAMKAGAVDFLEKPFDDQALLDAVRRaLARDRARRAERARRAELRARLASLTPREREVLDLVVAGLSNKQI 158

                       170       180       190
                ....*....|....*....|....*....|....*
gi 16131539 159 AAELGLSPKTVHVHRANLMEKLGVSNDVELARRMF 193
Cdd:COG4566 159 ARELGISPRTVEVHRANVMEKLGARSLAELVRLAL 193
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 4-116 2.31e-41

phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family response regulators; The NarL family is one of the more abundant families of DNA-binding response regulators (RRs). Members of the NarL family contain a REC domain and a helix-turn-helix (HTH) DNA-binding output domain, with a majority of members containing a LuxR-type HTH domain. They function as transcriptional regulators. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381090 [Multi-domain]  Cd Length: 117  Bit Score: 135.72  E-value: 2.31e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLSV 80
Cdd:cd17535   1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRrypDLKVIVLTA 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 16131539  81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVA 116
Cdd:cd17535  81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116
PRK09483 PRK09483
response regulator; Provisional
 1-190 3.71e-41

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 138.32  E-value: 3.71e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIM 77
Cdd:PRK09483   1 MINVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRytpDVKIIM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDP--------LTKRERQVAEKL 149
Cdd:PRK09483  81 LTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQQMALSQIEPatenpfasLSERELQIMLMI 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 16131539  150 AQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELAR 190
Cdd:PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTH 201
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 3-189 2.21e-38

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 131.30  E-value: 2.21e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    3 TVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL-PKGMAT--IMLS 79
Cdd:PRK10651   8 TILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLrEKSLSGriVVFS 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASG-RQDP---------LTKRERQVAEKL 149
Cdd:PRK10651  88 VSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLAASlRANRatterdvnqLTPRERDILKLI 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 16131539  150 AQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELA 189
Cdd:PRK10651 168 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAA 207
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 1-191 2.30e-37

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 125.77  E-value: 2.30e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLpkgmatimlsv 80
Cdd:COG2197   1 MIRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL----------- 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  81 hdspalveqalnagargflskrcspdeliaavhtvatggcyltpdiaiklasgrqdpLTKRERQVAEKLAQGMAVKEIAA 160
Cdd:COG2197  70 ---------------------------------------------------------LTPREREVLRLLAEGLSNKEIAE 92

                       170       180       190
                ....*....|....*....|....*....|.
gi 16131539 161 ELGLSPKTVHVHRANLMEKLGVSNDVELARR 191
Cdd:COG2197  93 RLGISERTVKTHVSNILRKLGVRNRTELVLL 123
fixJ PRK09390
response regulator FixJ; Provisional
 3-190 1.54e-31

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 113.17  E-value: 1.54e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    3 TVALIDDHLIVRSGFAQLLGLEpDLQVVAeFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLP---KGMATIMLS 79
Cdd:PRK09390   5 VVHVVDDDEAMRDSLAFLLDSA-GFEVRL-FESAQAFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKargSPLPVIVMT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTV------ATGGCYLTPDIAIKLASgrqdpLTKRERQVAEKLAQGM 153
Cdd:PRK09390  83 GHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERAlaqapeAAKSEAVAADIRARIAS-----LSERERQVMDGLVAGL 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 16131539  154 AVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELAR 190
Cdd:PRK09390 158 SNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVR 194
PRK15369 PRK15369
two component system response regulator;
2-192 9.58e-30

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 109.01  E-value: 9.58e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIML 78
Cdd:PRK15369   4 YKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQrwpAMNILVL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   79 SVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDI-------AIKLASGRQDPLTKRERQVAEKLAQ 151
Cdd:PRK15369  84 TARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPALnreailaLLNADDTNPPLLTPRERQILKLITE 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 16131539  152 GMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL---ARRM 192
Cdd:PRK15369 164 GYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELlnwARRL 207
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 4-112 1.93e-29

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: 104.93  E-value: 1.93e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539     4 VALIDDHLIVRSGFAQLLGLEPdlQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMATIMLSV 80
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEG--YVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIrrrDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 16131539    81 HDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
4-186 6.35e-29

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 106.86  E-value: 6.35e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    4 VALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT---IMLSV 80
Cdd:PRK10403   9 VLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTaqiIILTV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDI-----AIKLASGRQDP---LTKRERQVAEKLAQG 152
Cdd:PRK10403  89 SDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVnqylrEREMFGAEEDPfsvLTERELDVLHELAQG 168

                        170       180       190
                 ....*....|....*....|....*....|....
gi 16131539  153 MAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDV 186
Cdd:PRK10403 169 LSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRV 202
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
3-188 2.64e-25

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 97.25  E-value: 2.64e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    3 TVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLS---QLPKGMATIMLS 79
Cdd:PRK09935   5 SVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKrikQIQSTVKVLFLS 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQD-------PLTKRERQVAEKLAQG 152
Cdd:PRK09935  85 SKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNYIKSNKCStnsstdtVLSNREVTILRYLVSG 164

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 16131539  153 MAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
Cdd:PRK09935 165 LSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVEL 200
GerE pfam00196
Bacterial regulatory proteins, luxR family;
136-192 5.30e-23

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 86.87  E-value: 5.30e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 16131539   136 DPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRM 192
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 136-191 8.52e-23

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 86.43  E-value: 8.52e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 16131539    136 DPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARR 191
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
3-188 6.68e-22

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 88.41  E-value: 6.68e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    3 TVALIDDHLIVRSGFAQLLgLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT---IMLS 79
Cdd:PRK09958   2 NAIIIDDHPLAIAAIRNLL-IKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSgiiIIVS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYL-----TPDIAIKLASGRQDPLTKRERQVAEKLAQGMA 154
Cdd:PRK09958  81 AKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFpfslnRFVGSLTSDQQKLDSLSKQEISVMRYILDGKD 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 16131539  155 VKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
Cdd:PRK09958 161 NNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDL 194
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 1-181 2.01e-21

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: 86.93  E-value: 2.01e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   1 MITVALIDDHLIVRSGFAQLLGLEpDLQVVaEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMATIM 77
Cdd:COG0745   1 MPRILVVEDDPDIRELLADALERE-GYEVD-TAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLrarPSDIPIIM 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVA--------TGGCYLTPDIAIKLASGRQDPLTKRERQVAEKL 149
Cdd:COG0745  79 LTARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALLrrraaevlRVGDLLDLAAREVTRDGEPVELTPKEFRLLELL 158

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 16131539 150 AQ--GMAV------KEIAAELGLSPKTVHVHRANLMEKLG 181
Cdd:COG0745 159 MRnpGRVVsreqllEEVWGYDYGDDRTVDVHISRLRKKLE 198
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 1-115 3.30e-21

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: 89.64  E-value: 3.30e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   1 MITVALIDDHLIVRSGFAQLLGLEpDLQVVaEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMATIM 77
Cdd:COG2204   2 MARILVVDDDPDIRRLLKELLERA-GYEVE-TAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELralDPDLPVIL 79

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 16131539  78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTV 115
Cdd:COG2204  80 LTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERA 117
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 138-194 1.42e-20

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


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 80.66  E-value: 1.42e-20
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 16131539 138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFD 194
Cdd:cd06170   1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 4-115 1.54e-20

phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of Bacillus subtilis DesR, Streptococcus pneumoniae response regulator spr1814, and similar proteins, all containing an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. DesR is a response regulator that, together with its cognate sensor kinase DesK, comprises a two-component regulatory system that controls membrane fluidity. Phosphorylation of the REC domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381157 [Multi-domain]  Cd Length: 117  Bit Score: 82.32  E-value: 1.54e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLSV 80
Cdd:cd19930   1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREelpDTKVLIVTT 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 16131539  81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTV 115
Cdd:cd19930  81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTV 115
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 6-101 4.85e-20

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: 80.59  E-value: 4.85e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   6 LIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMATIMLSVHD 82
Cdd:COG4753   4 IVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIrelDPDTKIIILSGYS 83

                        90
                ....*....|....*....
gi 16131539  83 SPALVEQALNAGARGFLSK 101
Cdd:COG4753  84 DFEYAQEAIKLGADDYLLK 102
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 131-191 9.99e-20

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


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 78.85  E-value: 9.99e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16131539 131 ASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARR 191
Cdd:COG5905   6 STSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVW 66
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 2-188 1.02e-19

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 82.96  E-value: 1.02e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMP-DI--SGLELLSQLPK---GMAT 75
Cdd:PRK10840   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPgDKygDGITLIKYIKRhfpSLSI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   76 IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYlTPDIAIKL-----ASGRQD-PLTKRERQVAEKL 149
Cdd:PRK10840  84 IVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKF-TPESVSRLlekisAGGYGDkRLSPKESEVLRLF 162

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 16131539  150 AQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
Cdd:PRK10840 163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIAL 201
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 4-113 3.92e-19

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: 79.07  E-value: 3.92e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEpDLQVVAeFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLSV 80
Cdd:cd17549   1 VLLVDDDADVREALQQTLELA-GFRVRA-FADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIREldpDLPVILITG 78

                        90       100       110
                ....*....|....*....|....*....|....
gi 16131539  81 H-DSPALVeQALNAGARGFLSKRCSPDELIAAVH 113
Cdd:cd17549  79 HgDVPMAV-EAMRAGAYDFLEKPFDPERLLDVVR 111
tetrathio_RR NF040749
tetrathionate respiration response regulator TtrR;
50-192 4.03e-19

tetrathionate respiration response regulator TtrR;


Pssm-ID: 468713 [Multi-domain]  Cd Length: 191  Bit Score: 80.48  E-value: 4.03e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   50 VCICDISMPDISGLELLSQLPK---GMATIMLSVH-DSPALVEQaLNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPD 125
Cdd:NF040749  46 VVLLDMRMPGLDGHQVHQALREqgsTLAVVFLTGHgDVPMAVEQ-MKLGAVDFLQKPVSAAPLQAALERALAVSAAAFER 124

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16131539  126 IAIKLasgRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRM 192
Cdd:NF040749 125 HQIRQ---RYQSLTPKEREIAGLVVQGLMNREIAEALNIAVRTVEVHRARVMEKMAAGSLAELVSQL 188
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 1-112 6.59e-19

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 81.02  E-value: 6.59e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKG---MATIM 77
Cdd:COG3279   1 MMKILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELdppPPIIF 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 16131539  78 LSVHDSPALveQALNAGARGFLSKRCSPDELIAAV 112
Cdd:COG3279  81 TTAYDEYAL--EAFEVNAVDYLLKPIDEERLAKAL 113
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 4-117 6.89e-19

phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate/nitrite response regulator protein NarL contains an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. Escherichia coli NarL activates the expression of the nitrate reductase (narGHJI) and formate dehydrogenase-N (fdnGHI) operons, and represses the transcription of the fumarate reductase (frdABCD) operon in response to a nitrate/nitrite induction signal. Phosphorylation of the NarL REC domain releases the C-terminal HTH output domain that subsequently binds specific DNA promoter sites to repress or activate gene expression. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381158 [Multi-domain]  Cd Length: 117  Bit Score: 78.16  E-value: 6.89e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL-PKGMAT--IMLSV 80
Cdd:cd19931   1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALrEEGVSAriVILTV 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 16131539  81 HDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVAT 117
Cdd:cd19931  81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQAAS 117
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 3-115 2.26e-18

Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms];


Pssm-ID: 442663 [Multi-domain]  Cd Length: 224  Bit Score: 79.44  E-value: 2.26e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLLGLEpDLQVVaEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL-----PKGMATIM 77
Cdd:COG3437   8 TVLIVDDDPENLELLRQLLRTL-GYDVV-TAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLradpsTRDIPVIF 85

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 16131539  78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTV 115
Cdd:COG3437  86 LTALADPEDRERALEAGADDYLTKPFDPEELLARVRNA 123
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 1-154 6.85e-18

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: 77.26  E-value: 6.85e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   1 MITVALIDDHLIVRSGFAQLLGlEPDLQVVaEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMAT-- 75
Cdd:COG3706   1 PARILVVDDDPTNRKLLRRLLE-AAGYEVV-EAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLradPRTADIpi 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  76 IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVA-TGG---CYLTPDIAIKLAsgrqdpltkreRQVAEKLAQ 151
Cdd:COG3706  79 IFLTALDDEEDRARALEAGADDYLTKPFDPEELLARVDLVArYGGeefAILLPGTDLEGA-----------LAVAERIRE 147


                ...
gi 16131539 152 GMA 154
Cdd:COG3706 148 AVA 150
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-112 6.88e-18

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 76.16  E-value: 6.88e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMATIM 77
Cdd:COG4565   3 MIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELrarGPDVDVIV 82

                        90       100       110
                ....*....|....*....|....*....|....*
gi 16131539  78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:COG4565  83 ITAARDPETVREALRAGVVDYLIKPFTFERLREAL 117
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 1-115 1.62e-17

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: 74.89  E-value: 1.62e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   1 MITVALIDDHLIVRSGFAQLL---GLEpdlqvVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMA 74
Cdd:COG0784   5 GKRILVVDDNPDNRELLRRLLerlGYE-----VTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIralPRLPD 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 16131539  75 T--IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTV 115
Cdd:COG0784  80 IpiIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRL 122
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 6-101 1.95e-17

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: 73.80  E-value: 1.95e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   6 LIDDHLIVRSGFAQLLglEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMATIMLSVHD 82
Cdd:cd00156   2 IVDDDPAIRELLKSLL--EREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLrelPPDIPVIVLTAKA 79

                        90
                ....*....|....*....
gi 16131539  83 SPALVEQALNAGARGFLSK 101
Cdd:cd00156  80 DEEDAVRALELGADDYLVK 98
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 6-116 1.10e-15

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: 69.67  E-value: 1.10e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   6 LIDDHLIVRSGFAQLL-GLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMATIMLSVH 81
Cdd:cd17536   3 IVDDEPLIREGLKKLIdWEELGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELiekIRELYPDIKIIILSGY 82

                        90       100       110
                ....*....|....*....|....*....|....*
gi 16131539  82 DSPALVEQALNAGARGFLSKRCSPDELIAAVHTVA 116
Cdd:cd17536  83 DDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAK 117
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
134-191 3.64e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 70.17  E-value: 3.64e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 16131539 134 RQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARR 191
Cdd:COG2771 124 RAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVAL 181
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-112 3.19e-13

Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding antiterminator (ANTAR) domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 442921 [Multi-domain]  Cd Length: 194  Bit Score: 64.98  E-value: 3.19e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   1 MITVALIDDHLIVRSGFAQLLgLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL--PKGMATIML 78
Cdd:COG3707   3 GLRVLVVDDEPLRRADLREGL-REAGYEVVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQIseERPAPVILL 81

                        90       100       110
                ....*....|....*....|....*....|....
gi 16131539  79 SVHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:COG3707  82 TAYSDPELIERALEAGVSAYLVKPLDPEDLLPAL 115
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 3-112 8.06e-12

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: 59.53  E-value: 8.06e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLL---GLEpdlqvVAEFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMATI 76
Cdd:cd17537   2 TVYVVDDDEAVRDSLAFLLrsvGLA-----VKTFTSASAFLAAAPPDQPGCLVLDVRMPGMSGLELqdeLLARGSNIPII 76

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 16131539  77 MLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd17537  77 FITGHGDVPMAVEAMKAGAVDFLEKPFRDQVLLDAI 112
REC_CheY4-like cd17562
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ...
 30-115 1.78e-11

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY4 and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381110 [Multi-domain]  Cd Length: 118  Bit Score: 58.47  E-value: 1.78e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  30 VAEFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMAT--IMLSVHDSPALVEQALNAGARGFLSKRCS 104
Cdd:cd17562  27 VVEAADGRDALSKAQSKKFDLIITDQNMPNMDGIELikeLRKLPAYKFTpiLMLTTESSDEKKQEGKAAGATGWLVKPFD 106

                        90
                ....*....|.
gi 16131539 105 PDELIAAVHTV 115
Cdd:cd17562 107 PEQLLEVVKKV 117
REC_HupR-like cd17569
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ...
 2-113 2.54e-11

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar domains; This family is composed of mostly uncharacterized response regulators with similarity to the REC domains of response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It contains an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. Members of this family contain a REC domain and various output domains including the cyclase homology domain (CHD) and the c-di-GMP phosphodiesterase domains, HD-GYP and EAL. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381113 [Multi-domain]  Cd Length: 118  Bit Score: 58.18  E-value: 2.54e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   2 ITVALIDDHLIVRSGFAQLLGLEPdlQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL----PKgMATIM 77
Cdd:cd17569   1 PTILLVDDEPNILKALKRLLRREG--YEVLTATSGEEALEILKQEPVDVVISDQRMPGMDGAELLKRVreryPD-TVRIL 77

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 16131539  78 LSVHDSPALVEQALNAGA-RGFLSKRCSPDELIAAVH 113
Cdd:cd17569  78 LTGYADLDAAIEAINEGEiYRFLTKPWDDEELKETIR 114
REC_2_DhkD-like cd17580
second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal ...
 4-112 1.48e-10

second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal transduction histidine kinase D and similar domains; Dictyostelium discoideum hybrid signal transduction histidine kinase D (DhkD) is a large protein that contains two histidine kinase (HK) and two REC domains on the intracellular side of a single pass transmembrane domain, and extracellular PAS and PAC domains that likely are involved in ligand binding. This model represents the second REC domain and similar domains. DhkD activates the cAMP phosphodiesterase RegA to ensure proper prestalk and prespore patterning, tip formation, and the vertical elongation of the mound into a finger, in Dictyostelium discoideum. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381118 [Multi-domain]  Cd Length: 112  Bit Score: 55.93  E-value: 1.48e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLglEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMAT--IML 78
Cdd:cd17580   1 ILVVDDNEDAAEMLALLL--ELEGAEVTTAHSGEEALEAAQRFRPDVILSDIGMPGMDGYELarrLRELPWLANTpaIAL 78

                        90       100       110
                ....*....|....*....|....*....|....
gi 16131539  79 SVHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd17580  79 TGYGQPEDRERALEAGFDAHLVKPVDPDELIELI 112
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 3-113 1.67e-10

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator RpfG and similar proteins; Cyclic di-GMP phosphodiesterase response regulator RpfG, together with sensory/regulatory protein RpfC, constitute a two-component system implicated in sensing and responding to the diffusible signal factor (DSF) that is essential for cell-cell signaling. RpfC is a hybrid sensor/histidine kinase that phosphorylates and activates RpfG, which degrades cyclic di-GMP to GMP, leading to the activation of Clp, a global transcriptional regulator that regulates a large set of genes in the DSF pathway. RpfG contains a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381103 [Multi-domain]  Cd Length: 118  Bit Score: 55.91  E-value: 1.67e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLLGLEPDLQVVAeFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL--PKGMAT---IM 77
Cdd:cd17551   2 RILIVDDNPTNLLLLEALLRSAGYLEVVS-FTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLraLPGLEDvpiVM 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 16131539  78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVH 113
Cdd:cd17551  81 ITADTDREVRLRALEAGATDFLTKPFDPVELLARVR 116
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 2-115 2.14e-10

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: 55.75  E-value: 2.14e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   2 ITVALIDDHLIVRSGFAQLLgLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIML 78
Cdd:cd17542   1 KKVLIVDDAAFMRMMLKDIL-TKAGYEVVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKidpNAKVIMC 79

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 16131539  79 SVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTV 115
Cdd:cd17542  80 SAMGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKV 116
PRK11697 PRK11697
two-component system response regulator BtsR;
1-69 1.53e-09

two-component system response regulator BtsR;


Pssm-ID: 236956 [Multi-domain]  Cd Length: 238  Bit Score: 55.62  E-value: 1.53e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16131539    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL 69
Cdd:PRK11697   1 MIKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPRISGLELVGML 69
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
130-191 3.32e-09

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 53.94  E-value: 3.32e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16131539 130 LASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARR 191
Cdd:COG2909 115 ALRALGDREEALAALRRRLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVAR 176
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 4-112 3.84e-09

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: 52.15  E-value: 3.84e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMATIMLSV 80
Cdd:cd17532   1 ALIVDDEPLAREELRYLLEEHPDIEIVGEAENGEEALEAIEELKPDVVFLDIQMPGLDGLELakkLSKLAKPPLIVFVTA 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 16131539  81 HDSPALveQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd17532  81 YDEYAV--EAFELNAVDYLLKPFSEERLAEAL 110
REC_hyHK_CKI1_RcsC-like cd17546
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...
 4-112 4.88e-09

phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators similar to Arabidopsis thaliana CKI1 and Escherichia coli RcsC; This family is composed of hybrid sensor histidine kinases/response regulators that are sensor histidine kinases (HKs) fused with a REC domain, similar to the sensor histidine kinase CKI1 from Arabidopsis thaliana, which is involved in multi-step phosphorelay (MSP) signaling that mediates responses to a variety of important stimuli in plants. MSP involves a signal being transferred from HKs via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. The CKI1 REC domain specifically interacts with the downstream signaling protein AHP2, AHP3 and AHP5. The plant MSP system has evolved from the prokaryotic two-component system (TCS), which allows organisms to sense and respond to changes in environmental conditions. This family also includes bacterial hybrid sensor HKs such as Escherichia coli RcsC, which is a component of the Rcs signalling pathway that controls a variety of physiological functions like capsule synthesis, cell division, and motility. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381099 [Multi-domain]  Cd Length: 113  Bit Score: 52.09  E-value: 4.88e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLL---GLEpdlqvVAEFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMAT-- 75
Cdd:cd17546   1 VLVVDDNPVNRKVLKKLLeklGYE-----VDVAENGQEALELLKEEPFDLVLMDLQMPVMDGLEAtrrIRELEGGGRRtp 75

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 16131539  76 -IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd17546  76 iIALTANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 2-101 1.16e-08

phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate methylesterase CheB and similar chemotaxis proteins; Methylesterase CheB is a chemotaxis response regulator with an N-terminal REC domain and a C-terminal methylesterase domain. Chemotaxis is a behavior known in motile bacteria that directs their movement in response to chemical gradients. CheB is a phosphorylation-activated response regulator involved in the reversible modification of bacterial chemotaxis receptors. It catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins) by CheR. The CheB REC domain packs against the active site of the C-terminal domain and inhibits methylesterase activity by directly restricting access to the active site. Also included in this family is chemotaxis response regulator CheY, which contains a stand-alone REC domain, and an uncharacterized subfamily composed of proteins containing an N-terminal REC domain and a C-terminal CheY-P phosphatase (CheC) domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381096 [Multi-domain]  Cd Length: 125  Bit Score: 51.24  E-value: 1.16e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLpkgMAT-----I 76
Cdd:cd17541   1 IRVLIVDDSAVMRKLLSRILESDPDIEVVGTARDGEEALEKIKELKPDVITLDIEMPVMDGLEALRRI---MAErptpvV 77

                        90       100
                ....*....|....*....|....*..
gi 16131539  77 MLSVHDSP--ALVEQALNAGARGFLSK 101
Cdd:cd17541  78 MVSSLTEEgaEITLEALELGAVDFIAK 104
REC_Rcp-like cd17557
phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and ...
 3-115 1.51e-08

phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and similar domains; This family is composed of response regulators (RRs) that are members of phytochrome-associated, light-sensing two-component signal transduction pathways such as Synechocystis sp. Rcp1, Tolypothrix sp. RcpA, and Agrobacterium tumefaciens bacteriophytochrome response regulator AtBRR. They are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. Also included in this family us Methanosaeta harundinacea methanogenesis regulatory protein FilR2, also a stand-alone RR. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381108 [Multi-domain]  Cd Length: 129  Bit Score: 50.88  E-value: 1.51e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDH----LIVRSGFAQLlGLEPDLQVVaefGSGREALAGLPGRGVQVC-------ICDISMPDISGLELLSQL-- 69
Cdd:cd17557   1 TILLVEDNpgdaELIQEAFKEA-GVPNELHVV---RDGEEALDFLRGEGEYADaprpdliLLDLNMPRMDGFEVLREIka 76

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 16131539  70 -P--KGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTV 115
Cdd:cd17557  77 dPdlRRIPVVVLTTSDAEEDIERAYELGANSYIVKPVDFEEFVEAIRSL 125
REC_HupR cd17596
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of ...
 3-112 2.06e-08

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of this subfamily are response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It belongs to the nitrogen regulatory protein C (NtrC) family of response regulators, which activate transcription by RNA polymerase (RNAP) in response to a change in the environment. HupR is an unusual member of this family as it activates transcription when unphosphorylated, and transcription is inhibited by phosphorylation. Proteins in this subfamily contain an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381127 [Multi-domain]  Cd Length: 133  Bit Score: 50.83  E-value: 2.06e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHliVRSGFAQLLGLEPDLQVVAEfGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL----PKGMATIML 78
Cdd:cd17596   2 TILVVDDE--VRSLEALRRTLEEDFDVLTA-ASAEEALAILEEEWVQVILCDQRMPGTTGVEFLKEVrerwPEVVRIIIS 78

                        90       100       110
                ....*....|....*....|....*....|....
gi 16131539  79 SVHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd17596  79 GYTDSEDIIAGINEAGIYQYLTKPWHPDQLLLTV 112
REC_2_GGDEF cd17544
second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This ...
 2-108 5.33e-08

second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This family is composed of uncharacterized PleD-like response regulators that contain two N-terminal REC domains and a C-terminal diguanylate cyclase output domain with the characteristic GGDEF motif at the active site. Unlike PleD which contains a REC-like adaptor domain, the second REC domain of these uncharacterized GGDEF domain proteins, described in this model, contains characteristic metal-binding and active site residues. PleD response regulators are global regulators of cell metabolism in some important human pathogens. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381098 [Multi-domain]  Cd Length: 122  Bit Score: 49.44  E-value: 5.33e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   2 ITVALIDDHLIVRSGFAQLLGLEpDLQVVaEFGSGREALAGL---PGrgVQVCICDISMPDISGLELLSQLPKG-----M 73
Cdd:cd17544   1 IKVLVVDDSATSRNHLRALLRRH-NFQVL-EAANGQEALEVLeqhPD--IKLVITDYNMPEMDGFELVREIRKKysrdqL 76

                        90       100       110
                ....*....|....*....|....*....|....*
gi 16131539  74 ATIMLSVHDSPALVEQALNAGARGFLSKRCSPDEL 108
Cdd:cd17544  77 AIIGISASGDNALSARFIKAGANDFLTKPFLPEEF 111
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 4-114 9.18e-07

phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes Mycobacterium tuberculosis PdtaR, also called Rv1626, and similar proteins containing a REC domain and an ANTAR (AmiR and NasR transcription antitermination regulators) RNA-binding output domain. PdtaR is a response regulator that acts at the level of transcriptional antitermination and is a member of the PdtaR/PdtaS two-component regulatory system. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381159 [Multi-domain]  Cd Length: 118  Bit Score: 45.87  E-value: 9.18e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGlEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMA--TIMLSVH 81
Cdd:cd19932   3 VLIAEDEALIRMDLREMLE-EAGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSENIapIVLLTAY 81

                        90       100       110
                ....*....|....*....|....*....|...
gi 16131539  82 DSPALVEQALNAGARGFLSKRCSPDELIAAVHT 114
Cdd:cd19932  82 SQQDLVERAKEAGAMAYLVKPFSESDLIPAIEM 114
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 30-108 1.35e-06

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY3, Escherichia coli CheY, and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381150 [Multi-domain]  Cd Length: 119  Bit Score: 45.41  E-value: 1.35e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  30 VAEFGSGREALAGLPGRGVQVCICDISMPDISGLELL------SQLpKGMATIMLSVHDSPALVEQALNAGARGFLSKRC 103
Cdd:cd19923  28 VEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLktiradGAL-SHLPVLMVTAEAKKENVIAAAQAGVNNYIVKPF 106


                ....*
gi 16131539 104 SPDEL 108
Cdd:cd19923 107 TAATL 111
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 6-116 1.42e-06

phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This subfamily contains various OmpR family response regulators including PmrA, BasR, QseB, tctD, and RssB, which are components of two-component regulatory systems (TCSs). The PmrA/PmrB TCS controls transcription of genes that are involved in lipopolysaccharide modification in the outer membrane of bacteria, increasing bacterial resistance to host-derived antimicrobial peptides. The BasS/BasR TCS functions as an iron- and zinc-sensing transcription regulator. The QseB/QseC TCS activates the flagella regulon by activating transcription of FlhDC. The RssA/RssB TCS regulates swarming behavior in Serratia marcescens. OmpR family DNA-binding response regulators contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381139 [Multi-domain]  Cd Length: 115  Bit Score: 45.17  E-value: 1.42e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   6 LIDDHLIVRSGFAQLLGLEPDlqVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK-GMAT--IMLSVHD 82
Cdd:cd17624   3 LVEDDALLGDGLKTGLRKAGY--AVDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRqGQSLpvLILTARD 80

                        90       100       110
                ....*....|....*....|....*....|....
gi 16131539  83 SPALVEQALNAGARGFLSKRCSPDELIAAVHTVA 116
Cdd:cd17624  81 GVDDRVAGLDAGADDYLVKPFALEELLARLRALL 114
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 62-188 1.50e-06

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 46.66  E-value: 1.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   62 GLELLSQLPKG---MATIMLSVHDSPA-LVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDP 137
Cdd:PRK11475  55 GLSCLTELAIKfprMRRLVIADDDIEArLIGSLSPSPLDGVLSKASTLEILQQELFLSLNGVRQATDRLNNQWYINQSRM 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 16131539  138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
Cdd:PRK11475 135 LSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGL 185
REC_NtrC1-like cd17572
phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex ...
 4-112 1.77e-06

phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex aeolicus and similar NtrC family response regulators; NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include Aquifex aeolicus NtrC1 and Vibrio quorum-sensing signal integrator LuxO. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381114 [Multi-domain]  Cd Length: 121  Bit Score: 45.27  E-value: 1.77e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEP-DLQVVAefgSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKG---MATIMLS 79
Cdd:cd17572   1 VLLVEDSPSLAALYQEYLSDEGyKVTHVE---TGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERslpTSVIVIT 77

                        90       100       110
                ....*....|....*....|....*....|...
gi 16131539  80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd17572  78 AHGSVDIAVEAMRLGAYDFLEKPFDADRLRVTV 110
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 30-113 3.34e-06

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: 44.41  E-value: 3.34e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  30 VAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLSVHdspALVEQALNA---GARGFLSKRC 103
Cdd:cd17550  25 VDTAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEkypDLPVIMISGH---GTIETAVKAtklGAYDFIEKPL 101

                        90
                ....*....|
gi 16131539 104 SPDELIAAVH 113
Cdd:cd17550 102 SLDRLLLTIE 111
REC smart00448
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...
 2-58 5.83e-06

cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.


Pssm-ID: 214668 [Multi-domain]  Cd Length: 55  Bit Score: 42.17  E-value: 5.83e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 16131539      2 ITVALIDDHLIVRSGFAQLLGLEPDlqVVAEFGSGREALAGLPGRGVQVCICDISMP 58
Cdd:smart00448   1 MRILVVDDDPLLRELLKALLEKEGY--EVDEATDGEEALELLKEEKPDLILLDIMMP 55
PRK10100 PRK10100
transcriptional regulator CsgD;
108-184 7.10e-06

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 44.86  E-value: 7.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  108 LIAAVHTVATGGCYLTPDIAIKLA---------SGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLME 178
Cdd:PRK10100 117 VVNGLQGVLRGECYFTQKLASYLIthsgnyrynSTESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFK 196


                 ....*.
gi 16131539  179 KLGVSN 184
Cdd:PRK10100 197 KIAVKN 202
REC_hyHK cd17598
phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase ...
 36-118 7.38e-06

phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase/response regulators; Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase/response regulators contain all the elements of a classical TCS in a single polypeptide chain. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381128 [Multi-domain]  Cd Length: 118  Bit Score: 43.47  E-value: 7.38e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  36 GREALAGLPGRGVQVCICDISMPDISGLELLSQLP-----KGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIA 110
Cdd:cd17598  31 GREALAMLAEHRPTLVISDIVMPEMDGYELCRKIKsdpdlKDIPVILLTTLSDPRDVIRGLECGADNFITKPYDEKYLLS 110


                ....*...
gi 16131539 111 AVHTVATG 118
Cdd:cd17598 111 RIKYILVN 118
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 3-112 8.41e-06

phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; DNA-binding transcriptional regulator NtrC is also called nitrogen regulation protein NR(I) or nitrogen regulator I (NRI). It contains an N-terminal receiver (REC) domain, followed by a sigma-54 interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. It is part of the two-component regulatory system NtrB/NtrC, which controls expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. DNA-binding response regulator NtrC is phosphorylated by NtrB; phosphorylation of the N-terminal REC domain activates the central sigma-54 interaction domain and leads to the transcriptional activation from promoters that require sigma(54)-containing RNA polymerase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381146 [Multi-domain]  Cd Length: 116  Bit Score: 43.03  E-value: 8.41e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLLGLEpDLQVVAeFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLS 79
Cdd:cd19919   2 TVWIVDDDSSIRWVLERALAGA-GLTVTS-FENAQEALAALASSQPDVLISDIRMPGMDGLALLAQIKQrhpDLPVIIMT 79

                        90       100       110
                ....*....|....*....|....*....|...
gi 16131539  80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd19919  80 AHSDLDSAVSAYQGGAFEYLPKPFDIDEAVALV 112
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 30-101 1.07e-05

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: 42.39  E-value: 1.07e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16131539  30 VAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT---IMLSVHDSPALVEQALNAGARGFLSK 101
Cdd:cd17574  24 VDTAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGSDipiIMLTAKDEEEDKVLGLELGADDYITK 98
REC_typeB_ARR-like cd17584
phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and ...
 30-108 1.08e-05

phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and similar domains; Type-B ARRs (Arabidopsis response regulators) are a class of MYB-type transcription factors that act as major players in the transcriptional activation of cytokinin-responsive genes. They directly regulate the expression of type-A ARR genes and other downstream target genes. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Cytokinin signaling involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-B ARRs contain a receiver (REC) domain and a large C-terminal extension that has characteristics of an effector or output domain, with a Myb-like DNA binding domain referred to as the GARP domain. The GARP domain is a motif specific to plant transcription factors. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381121 [Multi-domain]  Cd Length: 115  Bit Score: 43.00  E-value: 1.08e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  30 VAEFGSGREALAGL--PGRGVQVCICDISMPDISGLELLSQLPKGM--ATIMLSVHDSPALVEQALNAGARGFLSKRCSP 105
Cdd:cd17584  25 VTTCTDAEEALSMLreNKDEFDLVITDVHMPDMDGFEFLELIRLEMdlPVIMMSADGSTSTVMKGLAHGACDYLLKPVSI 104


                ...
gi 16131539 106 DEL 108
Cdd:cd17584 105 EDL 107
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
134-192 2.19e-05

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 44.16  E-value: 2.19e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 16131539  134 RQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVElARRM 192
Cdd:PRK04841 835 RTSPLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQE-AVQH 892
PRK15115 PRK15115
response regulator GlrR; Provisional
 6-112 2.31e-05

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 44.06  E-value: 2.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    6 LIDDHlivrSGFAQLLG--LEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLSV 80
Cdd:PRK15115  10 LVDDD----PGLLKLLGmrLTSEGYSVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKvqpGMPVIILTA 85

                         90       100       110
                 ....*....|....*....|....*....|..
gi 16131539   81 HDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:PRK15115  86 HGSIPDAVAATQQGVFSFLTKPVDRDALYKAI 117
PRK00742 PRK00742
chemotaxis-specific protein-glutamate methyltransferase CheB;
1-116 2.40e-05

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 234828 [Multi-domain]  Cd Length: 354  Bit Score: 43.99  E-value: 2.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL----PkgMATI 76
Cdd:PRK00742   3 KIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKImrlrP--TPVV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 16131539   77 MLSvhdspALVE-------QALNAGARGFLSKRCSP---------DELIAAVHTVA 116
Cdd:PRK00742  81 MVS-----SLTErgaeitlRALELGAVDFVTKPFLGislgmdeykEELAEKVRAAA 131
REC_RssB-like cd17555
phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ...
 3-101 2.41e-05

phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; Pseudomonas aeruginosa RssB is an orphan atypical response regulator containing a REC domain and a PP2C-type protein phosphatase output domain. Its function is still unknown. Escherichia RssB, which is not included in this subfamily, is a ClpX adaptor protein which alters ClpX specificity by mediating a specific interaction between ClpX and the substrates such as RpoS, an RNA polymerase sigma factor. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381107 [Multi-domain]  Cd Length: 116  Bit Score: 41.80  E-value: 2.41e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLLglEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLS 79
Cdd:cd17555   2 TILVIDDDEVVRESIAAYL--EDSGFQVLQAADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKespDTPVIVVS 79

                        90       100
                ....*....|....*....|..
gi 16131539  80 VHDSPALVEQALNAGARGFLSK 101
Cdd:cd17555  80 GAGVMSDAVEALRLGAWDYLTK 101
REC_RocR cd17530
phosphoacceptor receiver (REC) domain of response regulator RocR; The response regulator RocR ...
 3-110 3.42e-05

phosphoacceptor receiver (REC) domain of response regulator RocR; The response regulator RocR from some pathogens contains an N-terminal phosphoreceiver (REC) domain and a C-terminal EAL domain that possesses c-di-GMP specific phosphodiesterase activity. The RocR REC domain is phosphorylated and modulates its EAL domain enzymatic activity, regulating the local level of c-di-GMP. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381086 [Multi-domain]  Cd Length: 123  Bit Score: 41.66  E-value: 3.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLLG-LEPDlqVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLP---KGMATIML 78
Cdd:cd17530   2 RVLVLDDDPFQCMMAATILEdLGPG--NVDEADDGREALVILLCNAPDIIICDLKMPDMDGIEFLRHLAeshSNAAVILM 79

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 16131539  79 SVHDSPALVEQALNAGARGF-----LSKRCSPDELIA 110
Cdd:cd17530  80 SGLDGGILESAETLAGANGLnllgtLSKPFSPEELTE 116
PRK10693 PRK10693
two-component system response regulator RssB;
31-101 3.92e-05

two-component system response regulator RssB;


Pssm-ID: 182652 [Multi-domain]  Cd Length: 303  Bit Score: 43.06  E-value: 3.92e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16131539   31 AEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLP-KGMAT--IMLSVHDSPALVEQALNAGARGFLSK 101
Cdd:PRK10693   1 VLAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRnRGDQTpvLVISATENMADIAKALRLGVQDVLLK 74
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 3-113 4.33e-05

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: 42.21  E-value: 4.33e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDhlivRSGFAQLLG--LEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMATIM 77
Cdd:COG4567   6 SLLLVDD----DEAFARVLAraLERRGFEVTTAASVEEALALLEQAPPDYAVLDLRLGDGSGLDLieaLRERDPDARIVV 81

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 16131539  78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVH 113
Cdd:COG4567  82 LTGYASIATAVEAIKLGADDYLAKPADADDLLAALE 117
REC_CheC-like cd17593
phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC ...
 2-113 5.15e-05

phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC domain; This subfamily is composed of uncharacterized proteins containing an N-terminal REC domain and a C-terminal CheC domain that may function as the output/effector domain of a response regulator. CheC is a CheY-P phosphatase, affecting the level of phosphorylated CheY which controls the sense of flagella rotation and determine swimming behavior of chemotactic bacteria. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381124 [Multi-domain]  Cd Length: 117  Bit Score: 40.98  E-value: 5.15e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   2 ITVALIDDHLIVRSGFAQLLGlePDLQVVAEFGS-GREALAGLPGRGVQVCICDISMPDISGLELLSQLPK-GMAT--IM 77
Cdd:cd17593   1 MKVLICDDSSMARKQLARALP--ADWDVEITFAEnGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVeQLETkvIV 78

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 16131539  78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVH 113
Cdd:cd17593  79 VSGDVQPEAKERVLELGALAFLKKPFDPEKLAQLLE 114
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 2-101 5.42e-05

phosphoacceptor receiver (REC) domain of citrate family two-component system response regulators; This family includes Lactobacillus paracasei MaeR, Escherichia coli DcuR and DpiA, Klebsiella pneumoniae CitB, as well as Bacillus DctR, MalR, and CitT. These are all response regulators of two-component systems (TCSs) from the citrate family, and are involved in the transcriptional regulation of genes associated with L-malate catabolism (MaeRK), citrate-specific fermentation (DpiAB, CitAB), plasmid inheritance (DpiAB), anaerobic fumarate respiratory system (DcuRS), and malate transport/utilization (MalKR). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381152 [Multi-domain]  Cd Length: 118  Bit Score: 41.08  E-value: 5.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT---IML 78
Cdd:cd19925   1 INVLIVEDDPMVAEIHRAYVEQVPGFTVIGTAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDvdvIVV 80

                        90       100
                ....*....|....*....|...
gi 16131539  79 SVHDSPALVEQALNAGARGFLSK 101
Cdd:cd19925  81 TAANDVETVREALRLGVVDYLIK 103
REC_OmpR_ChvI-like cd19936
phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; ...
 4-101 5.68e-05

phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; Sinorhizobium meliloti ChvI is part of the ExoS/ChvI two-component regulatory system (TCS) that is required for nitrogen-fixing symbiosis and exopolysaccharide synthesis. ExoS/ChvI also play important roles in regulating biofilm formation, motility, nutrient utilization, and the viability of free-living bacteria. ChvI belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381163 [Multi-domain]  Cd Length: 99  Bit Score: 40.51  E-value: 5.68e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAqlLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK--GMATIMLSVH 81
Cdd:cd19936   1 IALVDDDRNILTSVS--MALEAEGFSVETYTDGASALDGLNARPPDLAILDIKMPRMDGMELLQRLRQksTLPVIFLTSK 78

                        90       100
                ....*....|....*....|
gi 16131539  82 DSPALVEQALNAGARGFLSK 101
Cdd:cd19936  79 DDEIDEVFGLRMGADDYITK 98
REC_OmpR_KdpE-like cd17620
phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a ...
 29-101 6.18e-05

phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a component of the KdpD/KdpE two-component system (TCS) and is activated when histidine kinase KdpD senses a drop in external K+ concentration or upshift in ionic osmolarity, resulting in the expression of a heterooligomeric transporter KdpFABC. In addition, the KdpD/KdpE TCS is also an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. KdpE is a member of the OmpR family of DNA-binding response regulators that contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381135 [Multi-domain]  Cd Length: 99  Bit Score: 40.23  E-value: 6.18e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16131539  29 VVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT--IMLSVHDSPALVEQALNAGARGFLSK 101
Cdd:cd17620  24 RVFEAETGQEGLLEAATRKPDLIILDLGLPDMDGLEVIRRLREWSAVpvIVLSARDEESDKIAALDAGADDYLTK 98
REC_PatA-like cd17602
phosphoacceptor receiver (REC) domain of PatA and similar domains; Nostoc sp. (or Anabaena sp.) ...
 39-101 9.00e-05

phosphoacceptor receiver (REC) domain of PatA and similar domains; Nostoc sp. (or Anabaena sp.) PatA is necessary for proper patterning of heterocysts along filaments. PatA contains phosphoacceptor REC domain at its C-terminus and an N-terminal PATAN (PatA N-terminus) domain, which was proposed in a bioinformatics study to mediate protein-protein interactions. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Some members of this group may have an inactive REC domain, lacking canonical metal-binding and active site residues.


Pssm-ID: 381129 [Multi-domain]  Cd Length: 102  Bit Score: 40.04  E-value: 9.00e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  39 ALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMA-----TIMLSVHDspALVEQALN--AGARGFLSK 101
Cdd:cd17602  34 ALTTLLNSKPDLILIDIDMPDLDGYELCSLLRKSSAlkdtpIIMLTGKD--GLVDRIRAkmAGASGYLTK 101
REC_WspR-like cd17575
phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The ...
 2-110 1.02e-04

phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The GGDEF response regulator WspR is part of the Wsp system that is homologous to chemotaxis systems and also includes the membrane-bound receptor protein WspA. In response to growth on surfaces, WspR is phosphorylated by the Wsp signal transduction complex and is activated, functioning as a diguanylate cyclase (DGC) that catalyzes c-di-GMP synthesis. WspR is a hybrid response regulator-diguanylate cyclase, containing an N-terminal REC domain and a C-terminal GGDEF domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381117 [Multi-domain]  Cd Length: 128  Bit Score: 40.47  E-value: 1.02e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   2 ITVALIDDHLIVRSGFAQLLGLEPDlqVVAEFGSG-REALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT----- 75
Cdd:cd17575   1 IMVLLVDDQAIIGEAVRRALADEED--IDFHYCSDpTEAIEVASQIKPTVILQDLVMPGVDGLTLVRFFRANPATrdipi 78

                        90       100       110
                ....*....|....*....|....*....|....*
gi 16131539  76 IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIA 110
Cdd:cd17575  79 IVLSTKEEPEVKSEAFALGANDYLVKLPDKIELVA 113
REC_OmpR_CpxR cd17623
phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is ...
 4-110 1.04e-04

phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is part of the CpxA/CpxR two-component regulatory system that mediates envelope stress responses that is key for virulence and antibiotic resistance in several Gram negative pathogens. CpxR is a transcription factor/response regulator that controls the expression of numerous genes, including those of the classical porins OmpF and OmpC. It belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381138 [Multi-domain]  Cd Length: 115  Bit Score: 39.98  E-value: 1.04e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEP-DLQVVAEFGSGREALAGLPGRGVqvcICDISMPDISGLELLSQLPKG--MATIMLSV 80
Cdd:cd17623   1 ILLIDDDRELTELLTEYLEMEGfNVRAAHDGEQGLAALLEGSPDLV---VLDVMLPKMNGLDVLKELRKTsqVPVLMLTA 77

                        90       100       110
                ....*....|....*....|....*....|
gi 16131539  81 HDSPALVEQALNAGARGFLSKRCSPDELIA 110
Cdd:cd17623  78 RGDDIDRILGLELGADDYLPKPFNPRELVA 107
REC_OmpR_PrrA-like cd17627
phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ...
 4-112 1.37e-04

phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The Mycobacterium tuberculosis PrrA is part of the PrrA/PrrB two-component system (TCS) that has been implicated in early intracellular multiplication and is essential for viability. Also included in this subfamily is Mycobacterium tuberculosis MprA, part of the MprAB TCS that regulates EspR, a key regulator of the ESX-1 secretion system, and is required for establishment and maintenance of persistent infection in a tissue- and stage-specific fashion. PrrA and MprA belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381142 [Multi-domain]  Cd Length: 116  Bit Score: 39.67  E-value: 1.37e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLLGLEP-DLQVVAEfgsGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATI---MLS 79
Cdd:cd17627   1 ILVVDDDRAVRESLRRSLRFEGyEVETAVD---GAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLRAAGNDLpilVLT 77

                        90       100       110
                ....*....|....*....|....*....|...
gi 16131539  80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd17627  78 ARDSVSDRVAGLDAGADDYLVKPFALEELLARV 110
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 138-180 1.58e-04

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


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 40.41  E-value: 1.58e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 16131539   138 LTKRERQVAE-KLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180
Cdd:TIGR02937 111 LPEREREVLVlRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
REC_D1_PleD-like cd17538
first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ...
 3-101 1.60e-04

first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar domains; PleD contains a REC domain (D1) with the phosphorylatable aspartate, a REC-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes D1 of PleD and similar domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381093 [Multi-domain]  Cd Length: 104  Bit Score: 39.40  E-value: 1.60e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLLGLEpDLQVVaEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT-----IM 77
Cdd:cd17538   1 KILVVDDEPANRELLEALLSAE-GYEVL-TADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLKEDPETrhipvIM 78

                        90       100
                ....*....|....*....|....
gi 16131539  78 LSVHDSPALVEQALNAGARGFLSK 101
Cdd:cd17538  79 ITALDDREDRIRGLEAGADDFLSK 102
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 138-181 5.49e-04

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 39.21  E-value: 5.49e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 16131539 138 LTKRERQVAE-KLAQGMAVKEIAAELGLSPKTV--HVHRA--NLMEKLG 181
Cdd:COG1595 128 LPPRQREVLVlRYLEGLSYAEIAEILGISEGTVksRLSRArkKLREALE 176
REC_Spo0A cd17561
phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the ...
 2-101 5.73e-04

phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the phosphorelay system in the early stage of spore formation. It may be an element of the effector pathway responsible for the activation of sporulation genes in response to nutritional stress and may act in the with sigma factor spo0H to control the expression of some genes that are critical to the sporulation process. Spo0A contains a regulatory N-terminal REC domain and a C-terminal DNA-binding transcription activation domain as its effector/output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381109 [Multi-domain]  Cd Length: 108  Bit Score: 37.97  E-value: 5.73e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL--------PKgm 73
Cdd:cd17561   2 IKVLIADDNREFVQLLEEYLNSQPDMEVVGVAHNGQEALELIEEKEPDVLLLDIIMPHLDGIGVLEKLrrmrlekrPK-- 79

                        90       100
                ....*....|....*....|....*...
gi 16131539  74 aTIMLSVHDSPALVEQALNAGARGFLSK 101
Cdd:cd17561  80 -IIMLTAFGQEDITQRAVELGASYYILK 106
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 129-175 6.93e-04

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 39.45  E-value: 6.93e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 16131539 129 KLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVH--VHRAN 175
Cdd:COG3415  15 KLLRKTKDAREARRLRAVLLLAEGLSVREIAERLGVSRSTVYrwLKRYR 63
REC_PilR cd19926
phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR ...
 37-101 7.25e-04

phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR and similar proteins; Pseudomonas aeruginosa PilR is the response regulator of the PilS/PilR two-component regulatory system (PilSR TCS) that acts in conjunction with sigma-54 to regulate the expression of type 4 pilus (T4P) major subunit PilA. In addition, the PilSR TCS regulates flagellum-dependent swimming motility and pilus-dependent twitching motility. PilR contains an N-terminal REC domain, a central sigma-54 interaction domain, and a C-terminal Fis-type helix-turn-helix DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381153 [Multi-domain]  Cd Length: 100  Bit Score: 37.52  E-value: 7.25e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16131539  37 REALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMATIMLSVHDSPALVEQALNAGARGFLSK 101
Cdd:cd19926  32 KEARELLASEPYDLCLTDMRLPDGSGLELvqhIQQRLPQTPVAVITAYGSLDTAIEALKAGAFDFLTK 99
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 31-113 7.50e-04

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 39.47  E-value: 7.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   31 AEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL----PKGMATIMLSVHDSPALVeQALNAGARGFLSKRCSPD 106
Cdd:PRK10923  31 TTFENGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIkqrhPMLPVIIMTAHSDLDAAV-SAYQQGAFDYLPKPFDID 109


                 ....*..
gi 16131539  107 ELIAAVH 113
Cdd:PRK10923 110 EAVALVE 116
REC_CheV-like cd19924
phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This ...
 4-101 9.05e-04

phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This subfamily includes the REC domains of Bacillus subtilis chemotaxis protein CheV, Myxococcus xanthus gliding motility regulatory protein FrzE, and similar proteins. CheV is a hybrid protein with an N-terminal CheW-like domain and a C-terminal CheY-like REC domain. The CheV pathway is one of three systems employed by B. subtilis for sensory adaptation that contribute to chemotaxis. It is involved in the transmission of sensory signals from chemoreceptors to flagellar motors. Together with CheW, it is involved in the coupling of methyl-accepting chemoreceptors to the central two-component histidine kinase CheA. FrzE is a hybrid sensor histidine kinase/response regulator that is part of the Frz pathway that controls cell reversal frequency to support directional motility during swarming and fruiting body formation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381151 [Multi-domain]  Cd Length: 111  Bit Score: 37.36  E-value: 9.05e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   4 VALIDDHLIVRSGFAQLL---GLEpdlqvVAEFGSGREALAGLPGRGVQ---------VCICDISMPDISGLELLSQL-- 69
Cdd:cd19924   1 ILVVDDSPTARKQLRDLLknlGFE-----IAEAVDGEEALNKLENLAKEgndlskeldLIITDIEMPKMDGYELTFELrd 75

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 16131539  70 -PKgMATIMLSVH---DSPALVEQALNAGARGFLSK 101
Cdd:cd19924  76 dPR-LANIPVILNsslSGEFSRARGKKVGADAYLAK 110
REC_OmpR_BsPhoP-like cd19937
phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus ...
 30-115 1.12e-03

phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus subtilis PhoP (BsPhoP) is part of the PhoPR two-component system that participates in a signal transduction network that controls adaptation of the bacteria to phosphate deficiency by regulating (activating or repressing) genes of the Pho regulon upon phosphorylation by PhoR. When activated, PhoPR directs expression of phosphate scavenging enzymes, lowers synthesis of the phosphate-rich wall teichoic acid (WTA) and initiates synthesis of teichuronic acid, a non-phosphate containing replacement anionic polymer. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381164 [Multi-domain]  Cd Length: 116  Bit Score: 37.25  E-value: 1.12e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  30 VAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL-----PKGMATIMLSVHDSPALVEQALNAGARGFLSKRCS 104
Cdd:cd19937  24 VVTAYDGEEALKRAKDEKPDLIILDLMLPGIDGLEVCRILrsdpkTSSIPIIMLTAKGEEFDKVLGLELGADDYITKPFS 103

                        90
                ....*....|.
gi 16131539 105 PDELIAAVHTV 115
Cdd:cd19937 104 PRELLARVKAV 114
REC_OmpR_MtPhoP-like cd17615
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ...
 30-115 1.34e-03

phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; Mycobacterium tuberculosis PhoP (MtPhoP) is part of the PhoP/PhoR two-component system that is involved in phosphate control by stimulating expression of genes involved in scavenging, transport and mobilization of phosphate, and repressing the utilization of nitrogen sources. Also included in this subfamily is Mycobacterium tuberculosis transcriptional regulatory protein TcrX, part of the two-component regulatory system TcrY/TcrX that may be involved in virulence. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381131 [Multi-domain]  Cd Length: 118  Bit Score: 36.95  E-value: 1.34e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  30 VAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLSVHDSPALVEQALNAGARGFLSKRCSPD 106
Cdd:cd17615  26 VETAADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRAdgpDVPVLFLTAKDSVEDRIAGLTAGGDDYVTKPFSLE 105


                ....*....
gi 16131539 107 ELIAAVHTV 115
Cdd:cd17615 106 EVVARLRAL 114
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 151-180 1.39e-03

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


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 37.54  E-value: 1.39e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 16131539   151 QGMAVKEIAAELGLSPKTVHVHRANLMEKL 180
Cdd:TIGR02985 128 EGLSNKEIAEELGISVKTVEYHITKALKFL 157
HTH_Tnp_ISL3 pfam13542
Helix-turn-helix domain of transposase family ISL3;
139-170 1.50e-03

Helix-turn-helix domain of transposase family ISL3;


Pssm-ID: 463915 [Multi-domain]  Cd Length: 51  Bit Score: 35.52  E-value: 1.50e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 16131539   139 TKRERQVAEKLAQGMAVKEIAAELGLSPKTVH 170
Cdd:pfam13542  13 TLRFEAYILELLLEMSVKAVARLLGVSWTTVW 44
PRK11083 PRK11083
DNA-binding response regulator CreB; Provisional
 33-115 1.78e-03

DNA-binding response regulator CreB; Provisional


Pssm-ID: 236838 [Multi-domain]  Cd Length: 228  Bit Score: 38.02  E-value: 1.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   33 FGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL---PKGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELI 109
Cdd:PRK11083  33 FERGLPALDKLRQQPPDLVILDVGLPDISGFELCRQLlafHPALPVIFLTARSDEVDRLVGLEIGADDYVAKPFSPREVA 112


                 ....*.
gi 16131539  110 AAVHTV 115
Cdd:PRK11083 113 ARVRTI 118
REC_DC-like cd17534
phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ...
 28-112 1.95e-03

phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; This groups includes a modulated diguanylate cyclase containing a PAS sensor domain from Desulfovibrio desulfuricans G20. Members of this group contain N-terminal REC domains and various output domains including the GGDEF, histidine kinase, and helix-turn-helix (HTH) DNA binding domains. Also included in this family is Mycobacterium tuberculosis PdtaR, a transcriptional antiterminator that contains a REC domain and an ANTAR RNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381089 [Multi-domain]  Cd Length: 117  Bit Score: 36.62  E-value: 1.95e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  28 QVVAEFGSGREALAGLPGRGVQVCICDISMP-DISGLELLSQLPKGMAT--IMLSVHDSPALVEQALNAGARGFLSKRCS 104
Cdd:cd17534  26 EVVGIADSGEEAIELAEENKPDLILMDINLKgDMDGIEAAREIREKFDIpvIFLTAYSDEETLERAKETNPYGYLVKPFN 105


                ....*...
gi 16131539 105 PDELIAAV 112
Cdd:cd17534 106 ERELKAAI 113
REC_DivK-like cd17548
phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ...
 30-112 2.27e-03

phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus DivK is an essential response regulator that is involved in the complex phosphorelay pathways controlling both cell division and motility. It localizes cell cycle regulators to specific poles of the cell during division. DivK contains a stand-alone REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381100 [Multi-domain]  Cd Length: 115  Bit Score: 36.36  E-value: 2.27e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539  30 VAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATimlsvHDSP--ALV--------EQALNAGARGFL 99
Cdd:cd17548  26 VLEAADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKEDPAT-----RDIPviALTayamkgdrEKILEAGCDGYI 100

                        90
                ....*....|...
gi 16131539 100 SKRCSPDELIAAV 112
Cdd:cd17548 101 SKPIDTREFLETV 113
psREC_PRR cd17582
pseudo receiver domain of pseudo-response regulators; In Arabidopsis, five pseudo-response ...
 30-101 2.54e-03

pseudo receiver domain of pseudo-response regulators; In Arabidopsis, five pseudo-response regulators (PRRs), also called APRRs, comprise a core group of clock components that controls the pace of the central oscillator of the circadian clock, an endogenous time-keeping mechanism that enables organisms to adapt to external daily cycles. The coordinated sequential expression of PRR9 (APRR9), PRR7 (APRR7), PRR5 (APRR5), PRR3 (APRR3), and PRR1 (APRR1) results in circadian waves that may be at the basis of the endogenous circadian clock. PRRs contain an N-terminal pseudo receiver (psREC) domain that resembles the receiver domain of a two-component response regulator, but lacks an aspartate residue that accepts a phosphoryl group from the sensor kinase, and a CCT motif at the C-terminus that contains a putative nuclear localization signal. The psREC domain is involved in protein-protein interactions.


Pssm-ID: 381120 [Multi-domain]  Cd Length: 104  Bit Score: 36.22  E-value: 2.54e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16131539  30 VAEFGSGREALAGLPGRG--VQVCICDISMPDISGLELLSQLP-----KGMATIMLSVHDSPALVEQALNAGARGFLSK 101
Cdd:cd17582  25 VTAASDGLQAWDVLEDEQneIDLILTEVDLPVSSGFKLLSYIMrhkicKNIPVIMMSSQDSVGVVFKCLSKGAADYLVK 103
REC_CpdR_CckA-like cd18160
phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; ...
 3-101 2.95e-03

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: 35.94  E-value: 2.95e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQllGLEPDLQVVAEFGSGREALAGLP-GRGVQVCICDISMPDISGLELLSQLPK---GMATIML 78
Cdd:cd18160   1 TILLADDEPSVRKFIVT--TLKKAGYAVTEAESGAEALEKLQqGKDIDIVVTDIVMPEMDGIELAREARKidpDVKILFI 78

                        90       100
                ....*....|....*....|...
gi 16131539  79 SVHDSPALVEQALNAGARGFLSK 101
Cdd:cd18160  79 SGGAAAAPELLSDAVGDNATLKK 101
REC_OmpR_DrrD-like cd17625
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...
 36-110 3.15e-03

phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a OmpR/PhoB homolog from Thermotoga maritima whose function is not yet known. This subfamily also includes Streptococcus agalactiae transcriptional regulatory protein DltR, part of the DltS/DltR two-component system (TCS), and Pseudomonas aeruginosa transcriptional activator protein PfeR, part of the PfeR/PfeS TCS, which activates expression of the ferric enterobactin receptor. The DltS/DltR TCS regulates the expression of the dlt operon, which comprises four genes (dltA, dltB, dltC, and dltD) that catalyze the incorporation of D-alanine residues into the lipoteichoic acids. Members of this subfamily belong to the OmpR/PhoB family, which comprises of two domains, an N-terminal receiver domain and a C-terminal DNA-binding winged helix-turn-helix effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381140 [Multi-domain]  Cd Length: 115  Bit Score: 36.04  E-value: 3.15e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16131539  36 GREALAGLPGRGVQVCICDISMPDISGLELLSQLPK-GMAT--IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIA 110
Cdd:cd17625  30 GEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREeGIETpvLLLTALDAVEDRVKGLDLGADDYLPKPFSLAELLA 107
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
30-108 3.22e-03

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 37.70  E-value: 3.22e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   30 VAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQ---LPKGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPD 106
Cdd:PRK10365  32 VALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEikaLNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFD 111


                 ..
gi 16131539  107 EL 108
Cdd:PRK10365 112 NL 113
HTH_23 pfam13384
Homeodomain-like domain;
137-175 3.25e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 34.55  E-value: 3.25e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 16131539   137 PLTKRER-QVAEKLAQGMAVKEIAAELGLSPKTVH--VHRAN 175
Cdd:pfam13384   1 SARERRRaRALLLLAEGLSVKEIAELLGVSRRTVYrwLKRYN 42
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 3-111 3.43e-03

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: 35.88  E-value: 3.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   3 TVALIDDHLIVRSGFAQLL---GLEpdlqvVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATI 76
Cdd:cd17563   2 SLLLVDDDEVFAERLARALerrGFE-----VETAHSVEEALALAREEKPDYAVLDLRLGGDSGLDLIPPLRAlqpDARIV 76

                        90       100       110
                ....*....|....*....|....*....|....*
gi 16131539  77 MLSVHDSPALVEQALNAGARGFLSKRCSPDELIAA 111
Cdd:cd17563  77 VLTGYASIATAVEAIKLGADDYLAKPADADEILAA 111
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 138-174 3.65e-03

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 34.35  E-value: 3.65e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 16131539   138 LTKRERQV-AEKLAQGMAVKEIAAELGLSPKTV--HVHRA 174
Cdd:pfam08281  11 LPPRQREVfLLRYLEGLSYAEIAELLGISEGTVksRLSRA 50
Terminase_5 pfam06056
Putative ATPase subunit of terminase (gpP-like); This family of proteins are annotated as ...
 142-170 3.71e-03

Putative ATPase subunit of terminase (gpP-like); This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.


Pssm-ID: 428745 [Multi-domain]  Cd Length: 58  Bit Score: 34.67  E-value: 3.71e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 16131539   142 ERQVAEKLA-QGMAVKEIAAELGLSPKTVH 170
Cdd:pfam06056   2 VRRQARFLYwQGYRPAEIAEMLGLKEATVY 31
REC_RR468-like cd17552
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and ...
 6-112 4.02e-03

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and similar domains; Thermotoga maritima RR468 (encoded by gene TM0468) is the cognate response regulator (RR) of the class I histidine kinase HK853 (product of gene TM0853). HK853/RR468 comprise a two-component system (TCS) that couples environmental stimuli to adaptive responses. This subfamily also includes Fremyella diplosiphon complementary adaptation response regulator homolog RcaF, a small RR that is involved in four-step phosphorelays of the complementary chromatic adaptation (CCA) system that occurs in many cyanobacteria. Both RR468 and RcaF are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381104 [Multi-domain]  Cd Length: 121  Bit Score: 35.60  E-value: 4.02e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   6 LIDDHLIVRSgFAQL-LGLEPDLQVVAEfGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT-----IMLS 79
Cdd:cd17552   6 VIDDEEDIRE-VVQAcLEKLAGWEVLTA-SSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKLQANPETqsipvILLT 83

                        90       100       110
                ....*....|....*....|....*....|...
gi 16131539  80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAV 112
Cdd:cd17552  84 AKAQPSDRQRFASLGVAGVIAKPFDPLTLAEQI 116
COG1777 COG1777
Predicted transcriptional regulator, ArsR family [Transcription];
143-191 4.28e-03

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441383  Cd Length: 113  Bit Score: 35.78  E-value: 4.28e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 16131539 143 RQVAEKLAQG-MAVKEIAAELGLSPKTVHVH-----RANLMEKLGVSNDVELARR 191
Cdd:COG1777  20 RRILALLSEEpAYVSELARELGVSRQAVYKHlrkleEAGLVESYREGREDGRARK 74
PRK10188 PRK10188
transcriptional regulator SdiA;
138-189 4.39e-03

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 36.69  E-value: 4.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 16131539  138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELA 189
Cdd:PRK10188 180 FSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIA 231
REC_OmpR_PhoB cd17618
phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The ...
 54-115 4.42e-03

phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The transcription factor PhoB is a component of the PhoR/PhoB two-component system, a key regulatory protein network that facilitates response to inorganic phosphate (Pi) starvation conditions by turning on the phosphate (pho) regulon whose products are involved in phosphorus uptake and metabolism. PhoB is a member of the OmpR family of DNA-binding response regulators that contains REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381133 [Multi-domain]  Cd Length: 118  Bit Score: 35.69  E-value: 4.42e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16131539  54 DISMPDISGLELLSQLPKGMAT-----IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTV 115
Cdd:cd17618  51 DWMLPGGSGIQFIRRLKRDEMTrdipiIMLTARGEEEDKVRGLEAGADDYITKPFSPRELVARIKAV 117
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
3-108 5.48e-03

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 36.75  E-value: 5.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    3 TVALIDDHLIVRSGFAQLLGLEpDLQVVAEfGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLS 79
Cdd:PRK11361   6 RILIVDDEDNVRRMLSTAFALQ-GFETHCA-NNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRShetRTPVILMT 83

                         90       100
                 ....*....|....*....|....*....
gi 16131539   80 VHDSPALVEQALNAGARGFLSKRCSPDEL 108
Cdd:PRK11361  84 AYAEVETAVEALRCGAFDYVIKPFDLDEL 112
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 34-69 6.37e-03

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: 35.27  E-value: 6.37e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 16131539  34 GSGREALAGLPGRGVQVCICDISMPDISGLELLSQL 69
Cdd:cd17554  31 GNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKI 66
pleD PRK09581
response regulator PleD; Reviewed
 35-112 6.90e-03

response regulator PleD; Reviewed


Pssm-ID: 236577 [Multi-domain]  Cd Length: 457  Bit Score: 36.42  E-value: 6.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539   35 SGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMAT-----IMLSVHDSPALVEQALNAGARGFLSKRCSPDELI 109
Cdd:PRK09581  34 SGAEAIAICEREQPDIILLDVMMPGMDGFEVCRRLKSDPATthipvVMVTALDDPEDRVRGLEAGADDFLTKPINDVALF 113


                 ...
gi 16131539  110 AAV 112
Cdd:PRK09581 114 ARV 116
PRK15479 PRK15479
transcriptional regulator TctD;
50-110 7.20e-03

transcriptional regulator TctD;


Pssm-ID: 185376 [Multi-domain]  Cd Length: 221  Bit Score: 36.24  E-value: 7.20e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16131539   50 VCICDISMPDISGLELLSQLPK---GMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIA 110
Cdd:PRK15479  47 LAVLDINMPGMDGLEVLQRLRKrgqTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEELDA 110
PRK10610 PRK10610
chemotaxis protein CheY;
6-101 8.29e-03

chemotaxis protein CheY;


Pssm-ID: 170568 [Multi-domain]  Cd Length: 129  Bit Score: 34.95  E-value: 8.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131539    6 LIDDHLIVRSGFAQLLGlEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK--GMATI---MLSV 80
Cdd:PRK10610  10 VVDDFSTMRRIVRNLLK-ELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRAdgAMSALpvlMVTA 88

                         90       100
                 ....*....|....*....|.
gi 16131539   81 HDSPALVEQALNAGARGFLSK 101
Cdd:PRK10610  89 EAKKENIIAAAQAGASGYVVK 109
 
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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