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Conserved domains on  [gi|2104000529|ref|WP_224433497|]
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MULTISPECIES: response regulator transcription factor [Corynebacterium]

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
PRK10360 super family cl32505
transcriptional regulator UhpA;
35-209 7.73e-21

transcriptional regulator UhpA;


The actual alignment was detected with superfamily member PRK10360:

Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 86.95  E-value: 7.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  35 LLRVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLAdvGTDDR-LDVVVLDLRLADNSdpaqnvlSLELVTD--- 110
Cdd:PRK10360    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALA--GLPGRgVQVCICDISMPDIS-------GLELLSQlpk 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 111 --HVLILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGKGALTTEWASVVDS---DPlldsvdLSERQREV 185
Cdd:PRK10360   72 gmATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASgrqDP------LTKRERQV 145

                         170       180
                  ....*....|....*....|....
gi 2104000529 186 LELYASGESTKRVASMTGLTPNTV 209
Cdd:PRK10360  146 AEKLAQGMAVKEIAAELGLSPKTV 169
 
Name Accession Description Interval E-value
PRK10360 PRK10360
transcriptional regulator UhpA;
35-209 7.73e-21

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 86.95  E-value: 7.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  35 LLRVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLAdvGTDDR-LDVVVLDLRLADNSdpaqnvlSLELVTD--- 110
Cdd:PRK10360    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALA--GLPGRgVQVCICDISMPDIS-------GLELLSQlpk 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 111 --HVLILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGKGALTTEWASVVDS---DPlldsvdLSERQREV 185
Cdd:PRK10360   72 gmATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASgrqDP------LTKRERQV 145

                         170       180
                  ....*....|....*....|....
gi 2104000529 186 LELYASGESTKRVASMTGLTPNTV 209
Cdd:PRK10360  146 AEKLAQGMAVKEIAAELGLSPKTV 169
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 36-246 1.74e-15

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: 70.69  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  36 LRVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVgTDDRLDVVVLDLRLADNSDpaqnvlslelvtdhvlil 115
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELL-EELRPDVVLLDIRMPGMDG------------------ 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 116 ssaespylvrkavrtgvmgvvqksetpetiVSAVRLAalgkgalttewasvvdsdplldsvdLSERQREVLELYASGEST 195
Cdd:COG2197    63 ------------------------------LEALRRL-------------------------LTPREREVLRLLAEGLSN 87

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2104000529 196 KRVASMTGLTPNTVLDYLGRIRAKYAAAGRAenslnksEMYRLAQQDGYLP 246
Cdd:COG2197    88 KEIAERLGISERTVKTHVSNILRKLGVRNRT-------ELVLLALRLGLLD 131
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 38-153 1.97e-15

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: 70.23  E-value: 1.97e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  38 VAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVGTdDRLDVVVLDLRLadnsdPAQNVLSL--ELVTDH---- 111
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRE-LRPDVVLMDLSM-----PGMDGIEAlrRLRRRYpdlk 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2104000529 112 VLILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAA 153
Cdd:cd17535    75 VIVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116
GerE pfam00196
Bacterial regulatory proteins, luxR family;
178-227 1.01e-07

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 47.58  E-value: 1.01e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2104000529 178 LSERQREVLELYASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVE 52
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 176-227 3.93e-07

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 45.98  E-value: 3.93e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2104000529  176 VDLSERQREVLELYASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQ 53
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 178-219 2.19e-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: 2.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2104000529 178 LSERQREVLELYA-SGESTKRVASMTGLTPNTVLDYLGRIRAK 219
Cdd:TIGR02937 111 LPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKK 153
 
Name Accession Description Interval E-value
PRK10360 PRK10360
transcriptional regulator UhpA;
35-209 7.73e-21

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 86.95  E-value: 7.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  35 LLRVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLAdvGTDDR-LDVVVLDLRLADNSdpaqnvlSLELVTD--- 110
Cdd:PRK10360    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALA--GLPGRgVQVCICDISMPDIS-------GLELLSQlpk 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 111 --HVLILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGKGALTTEWASVVDS---DPlldsvdLSERQREV 185
Cdd:PRK10360   72 gmATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASgrqDP------LTKRERQV 145

                         170       180
                  ....*....|....*....|....
gi 2104000529 186 LELYASGESTKRVASMTGLTPNTV 209
Cdd:PRK10360  146 AEKLAQGMAVKEIAAELGLSPKTV 169
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 36-246 1.74e-15

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: 70.69  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  36 LRVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVgTDDRLDVVVLDLRLADNSDpaqnvlslelvtdhvlil 115
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELL-EELRPDVVLLDIRMPGMDG------------------ 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 116 ssaespylvrkavrtgvmgvvqksetpetiVSAVRLAalgkgalttewasvvdsdplldsvdLSERQREVLELYASGEST 195
Cdd:COG2197    63 ------------------------------LEALRRL-------------------------LTPREREVLRLLAEGLSN 87

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2104000529 196 KRVASMTGLTPNTVLDYLGRIRAKYAAAGRAenslnksEMYRLAQQDGYLP 246
Cdd:COG2197    88 KEIAERLGISERTVKTHVSNILRKLGVRNRT-------ELVLLALRLGLLD 131
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 38-153 1.97e-15

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: 70.23  E-value: 1.97e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  38 VAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVGTdDRLDVVVLDLRLadnsdPAQNVLSL--ELVTDH---- 111
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRE-LRPDVVLMDLSM-----PGMDGIEAlrRLRRRYpdlk 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2104000529 112 VLILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAA 153
Cdd:cd17535    75 VIVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
37-209 8.55e-11

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 59.87  E-value: 8.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  37 RVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVGTDDrLDVVVLDLRLADNSD-PAQNVLSLELVTDHVLIL 115
Cdd:PRK10403    8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLD-PDVILLDLNMKGMSGlDTLNALRRDGVTAQIIIL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 116 SSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGKGALTTEWASVVDSDPLLDSVD-----LSERQREVLELYA 190
Cdd:PRK10403   87 TVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREMFGAEEdpfsvLTERELDVLHELA 166

                         170
                  ....*....|....*....
gi 2104000529 191 SGESTKRVASMTGLTPNTV 209
Cdd:PRK10403  167 QGLSNKQIASVLNISEQTV 185
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
72-227 1.57e-10

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 58.61  E-value: 1.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  72 ELLADVGTDDRLDVVVLDLRLADNSDPAQNVLSLELVTDHVLILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRL 151
Cdd:COG2771    22 ALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAALLARL 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2104000529 152 AALGKGALTTEWASVVDSDPLLDSVDLSERQREVLELYASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:COG2771   102 AALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAE 177
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 37-209 3.53e-10

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 58.12  E-value: 3.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  37 RVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLAdVGTDDRLDVVVLDLRLAD-NSDPAQNVLSLELVTDHVLIL 115
Cdd:PRK10651    8 TILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIE-LAESLDPDLILLDLNMPGmNGLETLDKLREKSLSGRIVVF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 116 SSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGK----GALTTEWASVVDSDPLLDSVD---LSERQREVLEL 188
Cdd:PRK10651   87 SVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEmvlsEALTPVLAASLRANRATTERDvnqLTPRERDILKL 166

                         170       180
                  ....*....|....*....|.
gi 2104000529 189 YASGESTKRVASMTGLTPNTV 209
Cdd:PRK10651  167 IAQGLPNKMIARRLDITESTV 187
PRK15369 PRK15369
two component system response regulator;
36-209 6.42e-10

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 57.40  E-value: 6.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  36 LRVAAIDDHALTLQGLETLLSAEPDFELVG-----------CYQTVPelladvgtddrlDVVVLDLRLadnsdPAQNVLS 104
Cdd:PRK15369    4 YKILLVDDHELIINGIKNMLAPYPRYKIVGqvdnglevynaCRQLEP------------DIVILDLGL-----PGMNGLD 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 105 L---------ELvtdHVLILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGKG--------ALTTEWASVV 167
Cdd:PRK15369   67 VipqlhqrwpAM---NILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRyidpalnrEAILALLNAD 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2104000529 168 DSDPLLdsvdLSERQREVLELYASGESTKRVASMTGLTPNTV 209
Cdd:PRK15369  144 DTNPPL----LTPRERQILKLITEGYTNRDIAEQLSISIKTV 181
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 34-153 6.29e-08

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 50.35  E-value: 6.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  34 RLLRVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVGtDDRLDVVVLDLRLADnsdpaQNVLSL--ELVTDH 111
Cdd:COG4565     2 KMIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLA-EHRPDLILLDIYLPD-----GDGLELlrELRARG 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2104000529 112 ----VLILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAA 153
Cdd:COG4565    76 pdvdVIVITAARDPETVREALRAGVVDYLIKPFTFERLREALERYL 121
GerE pfam00196
Bacterial regulatory proteins, luxR family;
178-227 1.01e-07

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 47.58  E-value: 1.01e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2104000529 178 LSERQREVLELYASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVE 52
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 41-219 1.26e-07

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: 50.48  E-value: 1.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  41 IDDHALTLQGLETLLSAEpDFElVGCYQTVPELLADVgTDDRLDVVVLDLRLadnsdPAQNVLSL--ELVTDH----VLI 114
Cdd:COG4566     5 VDDDEAVRDSLAFLLESA-GLR-VETFASAEAFLAAL-DPDRPGCLLLDVRM-----PGMSGLELqeELAARGsplpVIF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 115 LSS-AESPyLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGKGALTTEWASVVDSDPLLDSvdLSERQREVLELYASGE 193
Cdd:COG4566    77 LTGhGDVP-MAVRAMKAGAVDFLEKPFDDQALLDAVRRALARDRARRAERARRAELRARLAS--LTPREREVLDLVVAGL 153

                         170       180
                  ....*....|....*....|....*.
gi 2104000529 194 STKRVASMTGLTPNTVLDYLGRIRAK 219
Cdd:COG4566   154 SNKQIARELGISPRTVEVHRANVMEK 179
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 178-227 1.73e-07

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: 46.76  E-value: 1.73e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2104000529 178 LSERQREVLELYASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQ 50
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 176-227 3.93e-07

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 45.98  E-value: 3.93e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2104000529  176 VDLSERQREVLELYASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQ 53
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 178-227 6.26e-07

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: 46.11  E-value: 6.26e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2104000529 178 LSERQREVLELYASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:COG5905    13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQ 62
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 36-94 4.59e-06

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 46.35  E-value: 4.59e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2104000529  36 LRVAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVgTDDRLDVVVLDLRLAD 94
Cdd:COG3279     2 MKILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELL-EEHKPDLVFLDIQMPG 59
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 42-150 3.21e-05

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: 42.26  E-value: 3.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  42 DDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVGTDdRLDVVVLDLRL--ADNSDPAQNVLSlELVTDHVLILSSAE 119
Cdd:cd19930     5 EDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKH-SPDVAILDIEMpgRTGLEVAAELRE-ELPDTKVLIVTTFG 82

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2104000529 120 SPYLVRKAVRTGVMGVVQKSETPETIVSAVR 150
Cdd:cd19930    83 RPGYFRRALAAGVDGYVLKDRPIEELADAIR 113
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 38-153 1.19e-04

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: 40.41  E-value: 1.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  38 VAAIDDHALTLQGLETLLSAEPDFELVGCYQTVPELLADVGTDDRlDVVVLDLRLAD-NSDPAQNVLSLELVTDHVLILS 116
Cdd:cd19931     1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDP-DLILLDLNMKGmSGLDTLKALREEGVSARIVILT 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2104000529 117 SAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAA 153
Cdd:cd19931    80 VSDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQAA 116
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 178-219 2.19e-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: 2.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2104000529 178 LSERQREVLELYA-SGESTKRVASMTGLTPNTVLDYLGRIRAK 219
Cdd:TIGR02937 111 LPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKK 153
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 38-150 2.47e-04

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: 39.44  E-value: 2.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  38 VAAIDDHALTLQGLETLLsAEPDFElVGCYQTVPELLADVGTDdRLDVVVLDLRLADNS--DPAQNVLSLELVTDhVLIL 115
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLL-EKEGYV-VAEADDGKEALELLKEE-RPDLILLDINMPGMDglELLKRIRRRDPTTP-VIIL 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2104000529 116 SSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVR 150
Cdd:pfam00072  77 TAHGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 178-219 4.99e-04

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 37.05  E-value: 4.99e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2104000529 178 LSERQREVLEL-YASGESTKRVASMTGLTPNTVLDYLGRIRAK 219
Cdd:pfam08281  11 LPPRQREVFLLrYLEGLSYAEIAELLGISEGTVKSRLSRARKK 53
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
38-227 8.45e-04

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 39.47  E-value: 8.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  38 VAAIDDHALTLQGLETLLSAEPDFELV---GCYQTVPELLADVGtddrLDVVVLDLRL--ADNSDPAQNVLSLELVTdHV 112
Cdd:PRK09935    6 VIIMDTHPIIRMSIEVLLQKNSELQIVlktDDYRITIDYLRTRP----VDLIIMDIDLpgTDGFTFLKRIKQIQSTV-KV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 113 LILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGKGALTTEWASVVDSDP----LLDSVDLSERQREVLEL 188
Cdd:PRK09935   81 LFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNYIKSNKcstnSSTDTVLSNREVTILRY 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2104000529 189 YASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:PRK09935  161 LVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVE 199
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 178-219 1.07e-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: 38.82  E-value: 1.07e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2104000529 178 LSERQREVLEL-YASGESTKRVASMTGLTPNTVLDYLGRIRAK 219
Cdd:COG1595   128 LPPRQREVLVLrYLEGLSYAEIAEILGISEGTVKSRLSRARKK 170
HTH_23 pfam13384
Homeodomain-like domain;
177-224 1.91e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.32  E-value: 1.91e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2104000529 177 DLSERQR-EVLELYASGESTKRVASMTGLTPNTVLdylgRIRAKYAAAG 224
Cdd:pfam13384   1 SARERRRaRALLLLAEGLSVKEIAELLGVSRRTVY----RWLKRYNEEG 45
PRK09483 PRK09483
response regulator; Provisional
 35-227 2.78e-03

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 37.78  E-value: 2.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  35 LLRVAAIDDHALTLQGLETLLSAEPDFELVGcyqtvpelLADVGTD-------DRLDVVVLDLRLadnsdPAQNVLS--- 104
Cdd:PRK09483    1 MINVLLVDDHELVRAGIRRILEDIKGIKVVG--------EACCGEDavkwcrtNAVDVVLMDMNM-----PGIGGLEatr 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529 105 --LELVTDHVLILSSA--ESPyLVRKAVRTGVMGVVQKSETPETIVSAVRLAALGKGALTTEWA--------SVVDSDPL 172
Cdd:PRK09483   68 kiLRYTPDVKIIMLTVhtENP-LPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAqqmalsqiEPATENPF 146

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2104000529 173 ldsVDLSERQREVLELYASGESTKRVASMTGLTPNTVLDYLGRIRAKYAAAGRAE 227
Cdd:PRK09483  147 ---ASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVE 198
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 37-162 4.47e-03

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


Pssm-ID: 441806 [Multi-domain]  Cd Length: 418  Bit Score: 38.02  E-value: 4.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2104000529  37 RVAAIDDHALTLQGLETLLSAEpDFELVGCyQTVPELLADVgTDDRLDVVVLDLRLADNSDPAqnVLSlELVTDH----V 112
Cdd:COG2204     4 RILVVDDDPDIRRLLKELLERA-GYEVETA-ASGEEALALL-REEPPDLVLLDLRMPGMDGLE--LLR-ELRALDpdlpV 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2104000529 113 LILSSAESPYLVRKAVRTGVMGVVQKSETPETIVSAVRlAALGKGALTTE 162
Cdd:COG2204    78 ILLTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVE-RALERRRLRRE 126
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 178-219 5.50e-03

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 34.39  E-value: 5.50e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2104000529 178 LSERQREVLEL-YASGESTKRVASMTGLTPNTVLDYLGRIRAK 219
Cdd:cd06171    11 LPEREREVILLrFGEGLSYEEIAEILGISRSTVRQRLHRALKK 53
 
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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