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Conserved domains on  [gi|937116939|ref|WP_054554374|]
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MULTISPECIES: LuxR C-terminal-related transcriptional regulator [Pseudoalteromonas]

Protein Classification

response regulator transcription factor( domain architecture ID 1002138)

two-component system rresponse regulator transcription factor that consists of a receiver domain and a LuxR family DNA-binding domain

CATH:  3.40.50.2300|1.10.10.10
Gene Ontology:  GO:0003677|GO:0006355
SCOP:  4003632|4000720

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FixJ super family cl34778
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 53-183 1.62e-18

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


The actual alignment was detected with superfamily member COG4566:

Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 78.99  E-value: 1.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  53 LQKLTAQ--RLPVIVMTTQLDIQQLCDALQLGARGYIEA-FANKTVIEQVAETVNAGGIWLPGQLLSNLVGVLsgqainy 129
Cdd:COG4566   62 QEELAARgsPLPVIFLTGHGDVPMAVRAMKAGAVDFLEKpFDDQALLDAVRRALARDRARRAERARRAELRAR------- 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 937116939 130 phqcdLSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVR 183
Cdd:COG4566  135 -----LASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGAR 183
 
Name Accession Description Interval E-value
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 53-183 1.62e-18

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: 78.99  E-value: 1.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  53 LQKLTAQ--RLPVIVMTTQLDIQQLCDALQLGARGYIEA-FANKTVIEQVAETVNAGGIWLPGQLLSNLVGVLsgqainy 129
Cdd:COG4566   62 QEELAARgsPLPVIFLTGHGDVPMAVRAMKAGAVDFLEKpFDDQALLDAVRRALARDRARRAERARRAELRAR------- 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 937116939 130 phqcdLSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVR 183
Cdd:COG4566  135 -----LASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGAR 183
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 135-188 1.61e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 72.56  E-value: 1.61e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 937116939   135 LSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQL 188
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQA 54
GerE pfam00196
Bacterial regulatory proteins, luxR family;
136-188 5.99e-16

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 68.77  E-value: 5.99e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 937116939  136 SSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQL 188
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVEL 53
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 138-188 6.24e-14

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: 63.32  E-value: 6.24e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937116939 138 LTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQL 188
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQL 51
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 63-187 3.05e-12

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 62.74  E-value: 3.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  63 VIVMTTQLDIQQLCDALQLGARGYI------EAFANKtvIEQVAetvnAGGIWLPGQLLSNLVGVLSGQaiNYPHQCDLS 136
Cdd:PRK10651  83 IVVFSVSNHEEDVVTALKRGADGYLlkdmepEDLLKA--LQQAA----AGEMVLSEALTPVLAASLRAN--RATTERDVN 154

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937116939 137 SLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQ 187
Cdd:PRK10651 155 QLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 135-181 8.66e-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: 38.10  E-value: 8.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 937116939  135 LSSLTKREKQVVDEV-IKGATNKQVAQVLNITERTVKEHMSSIFHKLK 181
Cdd:TIGR02937 108 LEKLPEREREVLVLRyLEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
 
Name Accession Description Interval E-value
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 53-183 1.62e-18

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: 78.99  E-value: 1.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  53 LQKLTAQ--RLPVIVMTTQLDIQQLCDALQLGARGYIEA-FANKTVIEQVAETVNAGGIWLPGQLLSNLVGVLsgqainy 129
Cdd:COG4566   62 QEELAARgsPLPVIFLTGHGDVPMAVRAMKAGAVDFLEKpFDDQALLDAVRRALARDRARRAERARRAELRAR------- 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 937116939 130 phqcdLSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVR 183
Cdd:COG4566  135 -----LASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGAR 183
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 135-188 1.61e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 72.56  E-value: 1.61e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 937116939   135 LSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQL 188
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQA 54
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 138-195 7.37e-17

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: 73.00  E-value: 7.37e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 937116939 138 LTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQLMLAVKGH 195
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 136-191 8.67e-17

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: 71.53  E-value: 8.67e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 937116939 136 SSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQLMLA 191
Cdd:COG5905   11 SLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVW 66
GerE pfam00196
Bacterial regulatory proteins, luxR family;
136-188 5.99e-16

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 68.77  E-value: 5.99e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 937116939  136 SSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQL 188
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVEL 53
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
34-189 5.34e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 69.78  E-value: 5.34e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  34 LLADTLVWLLADSADWQVQLQKLTAQRLPVIVMTTQLDIQQLCDALQLGARGYIEAFANKTVIEQVAETVNAGGIWLPGQ 113
Cdd:COG2771   24 LLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAALLARLAA 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 937116939 114 LLSNLVGVLSGQAINYPHQCDLSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQLM 189
Cdd:COG2771  104 LLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELV 179
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 138-188 6.24e-14

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: 63.32  E-value: 6.24e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937116939 138 LTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQL 188
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQL 51
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 63-187 3.05e-12

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 62.74  E-value: 3.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  63 VIVMTTQLDIQQLCDALQLGARGYI------EAFANKtvIEQVAetvnAGGIWLPGQLLSNLVGVLSGQaiNYPHQCDLS 136
Cdd:PRK10651  83 IVVFSVSNHEEDVVTALKRGADGYLlkdmepEDLLKA--LQQAA----AGEMVLSEALTPVLAASLRAN--RATTERDVN 154

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937116939 137 SLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQ 187
Cdd:PRK10651 155 QLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
56-186 8.77e-12

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 61.41  E-value: 8.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  56 LTAQRLPVIVMTTQLDIQQLCDAlqlGARGYIeafANKTVIEQVAETVNAGgiwlpgqllSNLVGVLSGQAINYPHQCDL 135
Cdd:PRK10403  79 VTAQIIILTVSDASSDVFALIDA---GADGYL---LKDSDPEVLLEAIRAG---------AKGSKVFSERVNQYLREREM 143

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 937116939 136 --------SSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRM 186
Cdd:PRK10403 144 fgaeedpfSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRV 202
fixJ PRK09390
response regulator FixJ; Provisional
 53-181 9.82e-11

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 58.48  E-value: 9.82e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  53 LQKLTAQ--RLPVIVMTTQLDIQQLCDALQLGARGYIEA-FANKTVIEQVAETvnaggiwlpgqlLSNLVGVLSGQAINY 129
Cdd:PRK09390  66 LRRLKARgsPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKpFEDERLIGAIERA------------LAQAPEAAKSEAVAA 133

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937116939 130 PHQCDLSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLK 181
Cdd:PRK09390 134 DIRARIASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQ 185
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
149-193 2.04e-09

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 54.32  E-value: 2.04e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 937116939 149 VIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQLMLAVK 193
Cdd:COG2909  134 LAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARAR 178
PRK10100 PRK10100
transcriptional regulator CsgD;
133-187 3.02e-09

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 54.49  E-value: 3.02e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 937116939 133 CDLSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQ 187
Cdd:PRK10100 151 TESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQ 205
PRK15369 PRK15369
two component system response regulator;
59-189 4.66e-08

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 51.23  E-value: 4.66e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  59 QRLP---VIVMTTQLDIQQLCDALQLGARGYIEAFANKTVIEQVAETVNAGGIWLPGQLLSNLVGVLSGQAINYPhqcdl 135
Cdd:PRK15369  73 QRWPamnILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPALNREAILALLNADDTNP----- 147

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 937116939 136 SSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQLM 189
Cdd:PRK15369 148 PLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201
PRK10360 PRK10360
transcriptional regulator UhpA;
60-188 9.10e-08

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 49.98  E-value: 9.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  60 RLP---VIVMTTQLDIQQLCD-ALQLGARGYIEAFANKTVIEQVAETVNAGGIWLPGQLLSNLVgvlSGQAinyphqcdl 135
Cdd:PRK10360  68 QLPkgmATIMLSVHDSPALVEqALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLA---SGRQ--------- 135

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937116939 136 SSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQL 188
Cdd:PRK10360 136 DPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
78-195 2.00e-05

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 43.71  E-value: 2.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  78 ALQLGARGYIEAFANKTVIEQVAETVNAGGIWLPGQLLS--NLVGVLSGQAINYPhqcdlssLTKREKQVVDEVIKGATN 155
Cdd:PRK09935  95 AIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNyiKSNKCSTNSSTDTV-------LSNREVTILRYLVSGLSN 167

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 937116939 156 KQVAQVLNITERTVKEHMSSIFHKLKVRDRMQLMLAVKGH 195
Cdd:PRK09935 168 KEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLH 207
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 135-181 6.58e-05

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: 38.95  E-value: 6.58e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 937116939  135 LSSLTKREKQVVDEV-IKGATNKQVAQVLNITERTVKEHMSSIFHKLK 181
Cdd:pfam04545   2 LASLPPRERQVLVLRyGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 135-181 8.66e-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: 38.10  E-value: 8.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 937116939  135 LSSLTKREKQVVDEV-IKGATNKQVAQVLNITERTVKEHMSSIFHKLK 181
Cdd:TIGR02937 108 LEKLPEREREVLVLRyLEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 150-174 2.07e-03

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


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 37.16  E-value: 2.07e-03
                          10        20
                  ....*....|....*....|....*
gi 937116939  150 IKGATNKQVAQVLNITERTVKEHMS 174
Cdd:TIGR02985 127 FEGLSNKEIAEELGISVKTVEYHIT 151
PRK09483 PRK09483
response regulator; Provisional
 63-193 3.65e-03

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 37.01  E-value: 3.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  63 VIVMTTQLDIQQLCDALQLGARGYIEAFANKTVIEQVAETVNAGGIWLPGQLLSNLVgvLSgqAINYPHQCDLSSLTKRE 142
Cdd:PRK09483  78 IIMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQQMA--LS--QIEPATENPFASLSERE 153

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937116939 143 KQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQLM-LAVK 193
Cdd:PRK09483 154 LQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELThLAIR 205
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 135-181 4.21e-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: 36.51  E-value: 4.21e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 937116939 135 LSSLTKREKQVVDEV-IKGATNKQVAQVLNITERTVKEHMSSIFHKLK 181
Cdd:COG1595  125 LERLPPRQREVLVLRyLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
128-185 4.44e-03

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 37.23  E-value: 4.44e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 937116939 128 NYPHQCDLSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDR 185
Cdd:PRK04841 829 DVPELIRTSPLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHR 886
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
53-189 6.17e-03

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 36.03  E-value: 6.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116939  53 LQKLTAQRLP--VIVMTTQLDIQQLCDALQLGARGYIEAFANKTVIEQVAETVNAGGIWLPGQLLSNLVGVLSGQAinyp 130
Cdd:PRK09958  64 LETLRKRQYSgiIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFSLNRFVGSLTSDQQ---- 139

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 937116939 131 hqcDLSSLTKREKQVVDEVIKGATNKQVAQVLNITERTVKEHMSSIFHKLKVRDRMQLM 189
Cdd:PRK09958 140 ---KLDSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLY 195
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 60-87 8.62e-03

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: 34.80  E-value: 8.62e-03
                         10        20
                 ....*....|....*....|....*...
gi 937116939  60 RLPVIVMTTQLDIQQLCDALQLGARGYI 87
Cdd:cd17535   72 DLKVIVLTAHDDPEYVLRALKAGAAGYL 99
 
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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