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Conserved domains on  [gi|922015940|ref|WP_053299021|]
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MULTISPECIES: response regulator transcription factor [Burkholderia]

Protein Classification

response regulator transcription factor( domain architecture ID 11450879)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10840 super family cl32589
transcriptional regulator RcsB; Provisional
 1-202 4.74e-53

transcriptional regulator RcsB; Provisional


The actual alignment was detected with superfamily member PRK10840:

Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 169.63  E-value: 4.74e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   1 MNefSVRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGKYGDGQTLLSYLSRRF 80
Cdd:PRK10840   1 MN--NMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHF 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  81 PTLRYVTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIASLLERTeSAAG---ATLSKRETE 157
Cdd:PRK10840  79 PSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKI-SAGGygdKRLSPKESE 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 922015940 158 IVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELI 202
Cdd:PRK10840 158 VLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALL 202
 
Name Accession Description Interval E-value
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-202 4.74e-53

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 169.63  E-value: 4.74e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   1 MNefSVRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGKYGDGQTLLSYLSRRF 80
Cdd:PRK10840   1 MN--NMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHF 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  81 PTLRYVTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIASLLERTeSAAG---ATLSKRETE 157
Cdd:PRK10840  79 PSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKI-SAGGygdKRLSPKESE 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 922015940 158 IVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELI 202
Cdd:PRK10840 158 VLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALL 202
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 8-127 1.01e-25

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


Pssm-ID: 381090 [Multi-domain]  Cd Length: 117  Bit Score: 96.43  E-value: 1.01e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   8 VVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGkygDGQTLLSYLSRRFPTLRYVT 87
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGM---DGIEALRRLRRRYPDLKVIV 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 922015940  88 VTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHS 127
Cdd:cd17535   78 LTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVAA 117
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 6-203 1.26e-23

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: 91.49  E-value: 1.26e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   6 VRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGkygDGQTLLSYLsrrfptlry 85
Cdd:COG2197    2 IRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGM---DGLEALRRL--------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  86 vtvtmlnspavfralqelgvnsivsksdpmshliaaihaahsggrylsptiasllertesaagatLSKRETEIVRLFREG 165
Cdd:COG2197   70 -----------------------------------------------------------------LTPREREVLRLLAEG 84

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 922015940 166 YKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:COG2197   85 LSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVL 122
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 149-203 2.71e-15

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 67.55  E-value: 2.71e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 922015940   149 ATLSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVR 56
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 8-122 1.39e-12

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: 61.78  E-value: 1.39e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940    8 VVIADDHPVSVHGMKAALsampTIE--IVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPTLRY 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLL----EKEgyVVAEADDGKEALELLKEERPDLILLDINMPG---MDGLELLKRIRRRDPTTPV 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 922015940   86 VTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAI 122
Cdd:pfam00072  74 IILTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 149-193 3.58e-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: 39.64  E-value: 3.58e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 922015940  149 ATLSKRETEIVRL-FREGYKVTEIAEKLHRSKKTISAQKLAAMRKL 193
Cdd:TIGR02937 109 EKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-202 4.74e-53

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 169.63  E-value: 4.74e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   1 MNefSVRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGKYGDGQTLLSYLSRRF 80
Cdd:PRK10840   1 MN--NMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHF 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  81 PTLRYVTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIASLLERTeSAAG---ATLSKRETE 157
Cdd:PRK10840  79 PSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKI-SAGGygdKRLSPKESE 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 922015940 158 IVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELI 202
Cdd:PRK10840 158 VLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALL 202
PRK15369 PRK15369
two component system response regulator;
5-202 7.17e-27

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 102.08  E-value: 7.17e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   5 SVRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGkygDGQTLLSYLSRRFPTLR 84
Cdd:PRK15369   3 NYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGM---NGLDVIPQLHQRWPAMN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  85 YVTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTI-ASLLERTESAAGAT---LSKRETEIVR 160
Cdd:PRK15369  80 ILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPALnREAILALLNADDTNpplLTPRERQILK 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 922015940 161 LFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELI 202
Cdd:PRK15369 160 LITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 8-127 1.01e-25

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


Pssm-ID: 381090 [Multi-domain]  Cd Length: 117  Bit Score: 96.43  E-value: 1.01e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   8 VVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGkygDGQTLLSYLSRRFPTLRYVT 87
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGM---DGIEALRRLRRRYPDLKVIV 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 922015940  88 VTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHS 127
Cdd:cd17535   78 LTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVAA 117
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 6-203 1.26e-23

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: 91.49  E-value: 1.26e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   6 VRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGkygDGQTLLSYLsrrfptlry 85
Cdd:COG2197    2 IRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGM---DGLEALRRL--------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  86 vtvtmlnspavfralqelgvnsivsksdpmshliaaihaahsggrylsptiasllertesaagatLSKRETEIVRLFREG 165
Cdd:COG2197   70 -----------------------------------------------------------------LTPREREVLRLLAEG 84

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 922015940 166 YKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:COG2197   85 LSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVL 122
PRK10360 PRK10360
transcriptional regulator UhpA;
6-203 1.40e-20

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 85.41  E-value: 1.40e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   6 VRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkygdgQTLLSYLSRRFPTLRY 85
Cdd:PRK10360   2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPD------ISGLELLSQLPKGMAT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  86 VTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIASLLertesAAGAT--LSKRETEIVRLFR 163
Cdd:PRK10360  76 IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKL-----ASGRQdpLTKRERQVAEKLA 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 922015940 164 EGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:PRK10360 151 QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELAR 190
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
9-201 5.17e-18

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 78.78  E-value: 5.17e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   9 VIADDHPVSVHGMKAALSAMpTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGkygDGQTLLSYLSRRFPTLRYVTV 88
Cdd:PRK09958   4 IIIDDHPLAIAAIRNLLIKN-DIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGV---NGIQVLETLRKRQYSGIIIIV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  89 TMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRY----LSPTIASLLerTESAAGATLSKRETEIVRLFRE 164
Cdd:PRK09958  80 SAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYfpfsLNRFVGSLT--SDQQKLDSLSKQEISVMRYILD 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 922015940 165 GYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAEL 201
Cdd:PRK09958 158 GKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDL 194
PRK09483 PRK09483
response regulator; Provisional
 6-203 5.41e-17

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 76.30  E-value: 5.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   6 VRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPsGKYGDGQTllSYLSRRFPTLRY 85
Cdd:PRK09483   2 INVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMP-GIGGLEAT--RKILRYTPDVKI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  86 VTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIA-----SLLERTESAAGATLSKRETEIVR 160
Cdd:PRK09483  79 IMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAqqmalSQIEPATENPFASLSERELQIML 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 922015940 161 LFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:PRK09483 159 MITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTH 201
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
8-202 6.83e-17

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 75.68  E-value: 6.83e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   8 VVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSGkygDGQTLLsylsRRFPTLR-YV 86
Cdd:PRK09935   6 VIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGT---DGFTFL----KRIKQIQsTV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  87 TVTMLNSPA----VFRALQElGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIASLLERTESAAGAT----LSKRETEI 158
Cdd:PRK09935  79 KVLFLSSKSecfyAGRAIQA-GANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNYIKSNKCSTNSStdtvLSNREVTI 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 922015940 159 VRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELI 202
Cdd:PRK09935 158 LRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELI 201
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 151-203 2.11e-15

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: 67.94  E-value: 2.11e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 922015940 151 LSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVA 53
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 68-204 2.68e-15

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 71.31  E-value: 2.68e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  68 DGQTLLSYLSRRFPTL-RYVTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIASLLERTESA 146
Cdd:PRK11475  54 EGLSCLTELAIKFPRMrRLVIADDDIEARLIGSLSPSPLDGVLSKASTLEILQQELFLSLNGVRQATDRLNNQWYINQSR 133

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 922015940 147 agaTLSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIRA 204
Cdd:PRK11475 134 ---MLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLDA 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 149-203 2.71e-15

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 67.55  E-value: 2.71e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 922015940   149 ATLSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVR 56
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
7-197 2.80e-14

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 68.73  E-value: 2.80e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   7 RVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMpsgKYGDGQTLLSYLSRRFPTLRYV 86
Cdd:PRK10403   8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNM---KGMSGLDTLNALRRDGVTAQII 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  87 TVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTI-ASLLER----TESAAGATLSKRETEIVRL 161
Cdd:PRK10403  85 ILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVnQYLRERemfgAEEDPFSVLTERELDVLHE 164

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 922015940 162 FREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTS 197
Cdd:PRK10403 165 LAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 8-122 1.39e-12

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: 61.78  E-value: 1.39e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940    8 VVIADDHPVSVHGMKAALsampTIE--IVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPTLRY 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLL----EKEgyVVAEADDGKEALELLKEERPDLILLDINMPG---MDGLELLKRIRRRDPTTPV 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 922015940   86 VTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAI 122
Cdd:pfam00072  74 IILTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 1-200 4.19e-12

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 62.74  E-value: 4.19e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   1 MNEFSVRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRF 80
Cdd:PRK10651   2 SNQEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPG---MNGLETLDKLREKS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  81 PTLRYVTVTMLNSPA-VFRALQElGVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIASLL-------ERTESAAGATLS 152
Cdd:PRK10651  79 LSGRIVVFSVSNHEEdVVTALKR-GADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLaaslranRATTERDVNQLT 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 922015940 153 KRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAE 200
Cdd:PRK10651 158 PRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205
GerE pfam00196
Bacterial regulatory proteins, luxR family;
149-203 7.98e-11

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 55.67  E-value: 7.98e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 922015940  149 ATLSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVR 55
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 7-111 1.17e-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: 56.68  E-value: 1.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   7 RVVIADDHPVSVHGMKAALSAMPTIEIVAvTSDTTSLVDMLDAHACDVLVLDYVMPsgkYGDGQTLLSYLsRRFPTLRYV 86
Cdd:cd17551    2 RILIVDDNPTNLLLLEALLRSAGYLEVVS-FTDPREALAWCRENPPDLILLDYMMP---GMDGLEFIRRL-RALPGLEDV 76

                         90       100
                 ....*....|....*....|....*....
gi 922015940  87 TVTML---NSPAV-FRALqELGVNSIVSK 111
Cdd:cd17551   77 PIVMItadTDREVrLRAL-EAGATDFLTK 104
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
146-203 2.06e-10

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 57.84  E-value: 2.06e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 922015940 146 AAGATLSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIR 203
Cdd:COG2771  123 ARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVA 180
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 8-126 9.21e-10

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: 54.59  E-value: 9.21e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   8 VVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPsGKygDGQTLLSYLSRRFPTLRYVT 87
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMP-GR--TGLEVAAELREELPDTKVLI 77

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 922015940  88 VTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAAH 126
Cdd:cd19930   78 VTTFGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVH 116
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 7-125 1.31e-09

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 54.59  E-value: 1.31e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   7 RVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPTLRYV 86
Cdd:COG4565    5 RVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPD---GDGLELLRELRARGPDVDVI 81

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 922015940  87 TVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAA 125
Cdd:COG4565   82 VITAARDPETVREALRAGVVDYLIKPFTFERLREALERY 120
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 38-203 4.32e-09

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: 54.34  E-value: 4.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  38 SDTTSLVDMLDAHACDVLVLDYVMPSGkygDGQTLLSYLSRRFPTLRYV------TVTMlnspAVfRALQeLGVNSIVSK 111
Cdd:COG4566   30 ASAEAFLAALDPDRPGCLLLDVRMPGM---SGLELQEELAARGSPLPVIfltghgDVPM----AV-RAMK-AGAVDFLEK 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940 112 SDPMSHLIAAIHAAHSGGRylspTIASLLERTESAAG--ATLSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAA 189
Cdd:COG4566  101 PFDDQALLDAVRRALARDR----ARRAERARRAELRArlASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANV 176

                        170
                 ....*....|....
gi 922015940 190 MRKLGVTSDAELIR 203
Cdd:COG4566  177 MEKLGARSLAELVR 190
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 7-111 6.99e-09

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: 51.70  E-value: 6.99e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   7 RVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPTLRYV 86
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALELLEEHKPDLVITDINMPG---MDGLELLEAIRELDPDTKII 77

                         90       100
                 ....*....|....*....|....*
gi 922015940  87 TVTMLNSPAVFRALQELGVNSIVSK 111
Cdd:COG4753   78 ILSGYSDFEYAQEAIKLGADDYLLK 102
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 151-204 2.85e-08

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: 49.19  E-value: 2.85e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 922015940 151 LSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGVTSDAELIRA 204
Cdd:COG5905   13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVW 66
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 1-125 1.16e-07

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: 50.55  E-value: 1.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   1 MNEFS-VRVVIADDHPVSVHGMKAALSAMPtIEIVAVTSDTTSLvDMLDAHACDVLVLDYVMPsgkYGDGQTLLSYLsRR 79
Cdd:COG3437    1 MRTGQaPTVLIVDDDPENLELLRQLLRTLG-YDVVTAESGEEAL-ELLLEAPPDLILLDVRMP---GMDGFELLRLL-RA 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 922015940  80 FPTLRYVTVTML----NSPAVFRALqELGVNSIVSKSDPMSHLIAAIHAA 125
Cdd:COG3437   75 DPSTRDIPVIFLtalaDPEDRERAL-EAGADDYLTKPFDPEELLARVRNA 123
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 5-125 7.29e-07

CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator Spo0F [Signal transduction mechanisms];


Pssm-ID: 440547 [Multi-domain]  Cd Length: 128  Bit Score: 46.77  E-value: 7.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   5 SVRVVIADDHPVSVHGMKAALSAMPtIEIVAVtSDTTSLVDMLDAHACDVLVLDYVMPsgkYGDGQTLLSYL--SRRFPT 82
Cdd:COG0784    5 GKRILVVDDNPDNRELLRRLLERLG-YEVTTA-EDGAEALELLRAGPPDLILLDINMP---GMDGLELLRRIraLPRLPD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 922015940  83 LRYVTVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAA 125
Cdd:COG0784   80 IPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRL 122
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 10-111 1.87e-06

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: 44.91  E-value: 1.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  10 IADDHPVSVHGMKAALSAMPtiEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPTLRYVTVT 89
Cdd:cd00156    2 IVDDDPAIRELLKSLLEREG--YEVDTAADGEEALELLREERPDLVLLDLMMPG---MDGLELLRKLRELPPDIPVIVLT 76

                         90       100
                 ....*....|....*....|..
gi 922015940  90 MLNSPAVFRALQELGVNSIVSK 111
Cdd:cd00156   77 AKADEEDAVRALELGADDYLVK 98
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 7-64 2.63e-06

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 46.73  E-value: 2.63e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 922015940   7 RVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSG 64
Cdd:COG3279    3 KILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGL 60
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 7-125 4.13e-06

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: 46.50  E-value: 4.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   7 RVVIADDHPVSVHGMKAALSAMPtIEIVAVtSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPTLRYV 86
Cdd:COG2204    4 RILVVDDDPDIRRLLKELLERAG-YEVETA-ASGEEALALLREEPPDLVLLDLRMPG---MDGLELLRELRALDPDLPVI 78

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 922015940  87 TVTMLNSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAA 125
Cdd:COG2204   79 LLTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERA 117
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 6-111 4.63e-06

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: 44.30  E-value: 4.63e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   6 VRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPsgkyG-DGQTLLSYLSRRFPTLR 84
Cdd:cd17541    1 IRVLIVDDSAVMRKLLSRILESDPDIEVVGTARDGEEALEKIKELKPDVITLDIEMP----VmDGLEALRRIMAERPTPV 76

                         90       100
                 ....*....|....*....|....*....
gi 922015940  85 YV--TVTMLNSPAVFRALqELGVNSIVSK 111
Cdd:cd17541   77 VMvsSLTEEGAEITLEAL-ELGAVDFIAK 104
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 7-125 4.72e-06

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: 45.72  E-value: 4.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   7 RVVIADDHPVSVHGMKAALSAMPtIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPtlryV 86
Cdd:COG3707    5 RVLVVDDEPLRRADLREGLREAG-YEVVAEAADGEDAVELVRELKPDLVIVDIDMPD---RDGLEAARQISEERP----A 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 922015940  87 TVTML---NSPAVFRALQELGVNSIVSKSDPMSHLIAAIHAA 125
Cdd:COG3707   77 PVILLtaySDPELIERALEAGVSAYLVKPLDPEDLLPALELA 118
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 7-210 8.09e-06

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: 44.51  E-value: 8.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   7 RVVIADDHPVSVHGMKAALSAMpTIEIVAVTsDTTSLVDMLDAHACDVLVLDYVMPsgkYGDGQTLLSYLsRRFPTLRYV 86
Cdd:COG3706    3 RILVVDDDPTNRKLLRRLLEAA-GYEVVEAA-DGEEALELLQEHRPDLILLDLEMP---DMDGLELCRRL-RADPRTADI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  87 TVTML----NSPAVFRALqELGVNSIVSKSDPMSHLIAAIHAAhsgGRYLSPTIASLLERTESAAGATLSKRETEIVrlf 162
Cdd:COG3706   77 PIIFLtaldDEEDRARAL-EAGADDYLTKPFDPEELLARVDLV---ARYGGEEFAILLPGTDLEGALAVAERIREAV--- 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 922015940 163 regykvteiaEKLHRSKKTISaqklaamrkLGVTSDAELIRADGLPMA 210
Cdd:COG3706  150 ----------AELPSLRVTVS---------IGVAGDSLLKRADALYQA 178
REC_Spo0A cd17561
phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the ...
 6-91 1.41e-05

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: 42.60  E-value: 1.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   6 VRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPsgkYGDGQTLLSYLsRRFPTLRY 85
Cdd:cd17561    2 IKVLIADDNREFVQLLEEYLNSQPDMEVVGVAHNGQEALELIEEKEPDVLLLDIIMP---HLDGIGVLEKL-RRMRLEKR 77


                 ....*.
gi 922015940  86 VTVTML 91
Cdd:cd17561   78 PKIIML 83
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
150-183 7.40e-05

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 42.56  E-value: 7.40e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 922015940 150 TLSKREtEIVRLFREGYKVTEIAEKLHRSKKTIS 183
Cdd:COG2826    8 TLEERE-EIEALLKAGLSVREIARRLGRSPSTIS 40
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 7-162 1.00e-04

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: 41.87  E-value: 1.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   7 RVVIADDHPVSVHGMKAALSAmptiE--IVAVTSDTTSLVDMLDAHACDVLVLDYVMPsgkYGDGQTLLSYLSRRFPTLR 84
Cdd:COG0745    3 RILVVEDDPDIRELLADALER----EgyEVDTAADGEEALELLEEERPDLILLDLMLP---GMDGLEVCRRLRARPSDIP 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  85 YVTVTMLNSPAVFRALQELGVNSIVSKsdP--MSHLIAAIHAAHSGGRYLSPTIASLL---ERTESAAGAT--LSKRETE 157
Cdd:COG0745   76 IIMLTARDDEEDRVRGLEAGADDYLTK--PfdPEELLARIRALLRRRAAEVLRVGDLLdlaAREVTRDGEPveLTPKEFR 153


                 ....*
gi 922015940 158 IVRLF 162
Cdd:COG0745  154 LLELL 158
REC smart00448
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...
 7-62 1.32e-04

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: 38.70  E-value: 1.32e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 922015940     7 RVVIADDHPVSVHGMKAALSAMPtiEIVAVTSDTTSLVDMLDAHACDVLVLDYVMP 62
Cdd:smart00448   2 RILVVDDDPLLRELLKALLEKEG--YEVDEATDGEEALELLKEEKPDLILLDIMMP 55
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 8-89 1.40e-04

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AlgR-like group of LytTR/AlgR family response regulators are Streptococcus agalactiae sensory transduction protein LytR, Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR, Bacillus subtilis sensory transduction protein LytT, and Escherichia coli transcriptional regulatory protein BtsR, which are members of two-component regulatory systems. LytR and LytT are components of regulatory systems that regulate genes involved in cell wall metabolism. AlgR positively regulates the algD gene, which codes for a GDP-mannose dehydrogenase, a key enzyme in the alginate biosynthesis pathway. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381087 [Multi-domain]  Cd Length: 118  Bit Score: 40.21  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   8 VVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPTLRYVT 87
Cdd:cd17532    1 ALIVDDEPLAREELRYLLEEHPDIEIVGEAENGEEALEAIEELKPDVVFLDIQMPG---LDGLELAKKLSKLAKPPLIVF 77


                 ..
gi 922015940  88 VT 89
Cdd:cd17532   78 VT 79
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
115-204 1.55e-04

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 41.23  E-value: 1.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940 115 MSHLIAAIHAAHSGGRYLSPTIASLLERTESAAGATLSKReteivrLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLG 194
Cdd:COG2909   93 LALLERLLALAEAAGRLLLRALALRALGDREEALAALRRR------LLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLG 166

                         90
                 ....*....|
gi 922015940 195 VTSDAELIRA 204
Cdd:COG2909  167 VRSRTEAVAR 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 149-193 3.58e-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: 39.64  E-value: 3.58e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 922015940  149 ATLSKRETEIVRL-FREGYKVTEIAEKLHRSKKTISAQKLAAMRKL 193
Cdd:TIGR02937 109 EKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK10100 PRK10100
transcriptional regulator CsgD;
76-195 8.70e-04

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 39.08  E-value: 8.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940  76 LSRRFPTLRyvtVTMLNSPAVFrALQEL----GVNSIVSKSDPMSHLIAAIHAAHSGGRYLSPTIASLL------ERTES 145
Cdd:PRK10100  75 LSRKNNNIK---ILLLNTPEDY-PYREIenwpHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLithsgnYRYNS 150

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 922015940 146 AAGATLSKRETEIVRLFREGYKVTEIAEKLHRSKKTISAQKLAAMRKLGV 195
Cdd:PRK10100 151 TESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAV 200
HTH_5 pfam01022
Bacterial regulatory protein, arsR family; Members of this family contains a DNA binding ...
 157-195 8.83e-04

Bacterial regulatory protein, arsR family; Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.


Pssm-ID: 425993 [Multi-domain]  Cd Length: 45  Bit Score: 35.88  E-value: 8.83e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 922015940  157 EIVRLFREG-YKVTEIAEKLHRSKKTISAQkLAAMRKLGV 195
Cdd:pfam01022   6 KILKLLAEGeLCVCELAEELGLSQSTVSHH-LKKLREAGL 44
PRK00742 PRK00742
chemotaxis-specific protein-glutamate methyltransferase CheB;
6-62 1.04e-03

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 234828 [Multi-domain]  Cd Length: 354  Bit Score: 39.36  E-value: 1.04e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 922015940   6 VRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMP 62
Cdd:PRK00742   4 IRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMP 60
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 149-193 1.89e-03

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: 37.67  E-value: 1.89e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 922015940 149 ATLSKRETEIVRLFR-EGYKVTEIAEKLHRSKKTISAQKLAAMRKL 193
Cdd:COG1595  126 ERLPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 6-105 2.91e-03

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: 36.45  E-value: 2.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922015940   6 VRVVIADDHPVSVHGMKAALSAMPTIEIVAVTSDTTSLVDMLDAHACDVLVLDYVMPSgkyGDGQTLLSYLSRRFPTLRY 85
Cdd:cd19925    1 INVLIVEDDPMVAEIHRAYVEQVPGFTVIGTAGTGEEALKLLKERQPDLILLDIYLPD---GNGLDLLRELRAAGHDVDV 77

                         90       100
                 ....*....|....*....|
gi 922015940  86 VTVTMLNSPAVFRALQELGV 105
Cdd:cd19925   78 IVVTAANDVETVREALRLGV 97
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 150-183 3.15e-03

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


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 34.41  E-value: 3.15e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 922015940  150 TLSKREtEIVRLFREGYKVTEIAEKLHRSKKTIS 183
Cdd:pfam13936   6 SLEERE-EIARLLAEGLSLREIARRLGRSPSTIS 38
HTH_23 pfam13384
Homeodomain-like domain;
157-183 3.18e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 34.55  E-value: 3.18e-03
                          10        20
                  ....*....|....*....|....*..
gi 922015940  157 EIVRLFREGYKVTEIAEKLHRSKKTIS 183
Cdd:pfam13384   9 RALLLLAEGLSVKEIAELLGVSRRTVY 35
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
151-182 3.19e-03

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 37.20  E-value: 3.19e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 922015940 151 LSKRETEIVRLFREGYKVTEIAEKLHRSKKTI 182
Cdd:PRK08295 156 LSELEKEVLELYLDGKSYQEIAEELNRHVKSI 187
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 149-193 3.99e-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. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 34.33  E-value: 3.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 922015940  149 ATLSKRETEIVRL-FREGYKVTEIAEKLHRSKKTISAQKLAAMRKL 193
Cdd:pfam04545   3 ASLPPRERQVLVLrYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
157-195 8.47e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 33.72  E-value: 8.47e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 922015940   157 EIVRLFREG-YKVTEIAEKLHRSKKTISAQkLAAMRKLGV 195
Cdd:smart00418   1 KILKLLAEGeLCVCELAEILGLSQSTVSHH-LKKLREAGL 39
 
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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