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Conserved domains on  [gi|1941185309|ref|WP_197033844|]
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response regulator transcription factor [Bradyrhizobium sp. URHD0069]

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

Gene Ontology:  GO:0006355|GO:0000160|GO:0003677
PubMed:  10966457

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 62-160 2.36e-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: 89.18  E-value: 2.36e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  62 ADASQIDAAIRAVSAG------LIVRVPDMmdAGFGAMREthghaLLTPRELEVLATLAEGMTNKAIARRLNISLHTVKF 135
Cdd:COG2197    31 GEAADGEEALELLEELrpdvvlLDIRMPGM--DGLEALRR-----LLTPREREVLRLLAEGLSNKEIAERLGISERTVKT 103

                          90       100
                  ....*....|....*....|....*
gi 1941185309 136 HIESLFRKLGARTRTEAVAKAAERR 160
Cdd:COG2197   104 HVSNILRKLGVRNRTELVLLALRLG 128
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 62-160 2.36e-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: 89.18  E-value: 2.36e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  62 ADASQIDAAIRAVSAG------LIVRVPDMmdAGFGAMREthghaLLTPRELEVLATLAEGMTNKAIARRLNISLHTVKF 135
Cdd:COG2197    31 GEAADGEEALELLEELrpdvvlLDIRMPGM--DGLEALRR-----LLTPREREVLRLLAEGLSNKEIAERLGISERTVKT 103

                          90       100
                  ....*....|....*....|....*
gi 1941185309 136 HIESLFRKLGARTRTEAVAKAAERR 160
Cdd:COG2197   104 HVSNILRKLGVRNRTELVLLALRLG 128
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 99-156 3.78e-23

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 86.43  E-value: 3.78e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1941185309   99 HALLTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKA 156
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 102-158 4.09e-21

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: 81.04  E-value: 4.09e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1941185309 102 LTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAAE 158
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
102-156 4.40e-19

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 76.08  E-value: 4.40e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1941185309 102 LTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKA 156
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 44-161 9.45e-16

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 71.21  E-value: 9.45e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  44 VVTLGGADYDLPGVLSRHADA--------SQIDAAIRAVSAGLIVRVPDMMDAGFGAMRE-----THGHALLTPRELEVL 110
Cdd:PRK10651   85 VFSVSNHEEDVVTALKRGADGyllkdmepEDLLKALQQAAAGEMVLSEALTPVLAASLRAnrattERDVNQLTPRERDIL 164

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1941185309 111 ATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAAERRR 161
Cdd:PRK10651  165 KLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERI 215
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 115-137 2.38e-05

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: 42.16  E-value: 2.38e-05
                          10        20
                  ....*....|....*....|...
gi 1941185309 115 EGMTNKAIARRLNISLHTVKFHI 137
Cdd:TIGR02985 128 EGLSNKEIAEELGISVKTVEYHI 150
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 62-160 2.36e-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: 89.18  E-value: 2.36e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  62 ADASQIDAAIRAVSAG------LIVRVPDMmdAGFGAMREthghaLLTPRELEVLATLAEGMTNKAIARRLNISLHTVKF 135
Cdd:COG2197    31 GEAADGEEALELLEELrpdvvlLDIRMPGM--DGLEALRR-----LLTPREREVLRLLAEGLSNKEIAERLGISERTVKT 103

                          90       100
                  ....*....|....*....|....*
gi 1941185309 136 HIESLFRKLGARTRTEAVAKAAERR 160
Cdd:COG2197   104 HVSNILRKLGVRNRTELVLLALRLG 128
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 99-156 3.78e-23

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 86.43  E-value: 3.78e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1941185309   99 HALLTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKA 156
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 96-160 6.34e-22

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: 83.86  E-value: 6.34e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1941185309  96 THGHALLTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAAERR 160
Cdd:COG5905     7 TSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLG 71
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 102-158 4.09e-21

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: 81.04  E-value: 4.09e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1941185309 102 LTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAAE 158
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
102-156 4.40e-19

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 76.08  E-value: 4.40e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1941185309 102 LTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKA 156
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 44-161 9.45e-16

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 71.21  E-value: 9.45e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  44 VVTLGGADYDLPGVLSRHADA--------SQIDAAIRAVSAGLIVRVPDMMDAGFGAMRE-----THGHALLTPRELEVL 110
Cdd:PRK10651   85 VFSVSNHEEDVVTALKRGADGyllkdmepEDLLKALQQAAAGEMVLSEALTPVLAASLRAnrattERDVNQLTPRERDIL 164

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1941185309 111 ATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAAERRR 161
Cdd:PRK10651  165 KLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERI 215
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
1-160 2.72e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 69.78  E-value: 2.72e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309   1 MDPLRRAALSRVVAEAGHIVVGAQDIADVVLADGDCLPGETRPVVTLGGADYDLPGVLSRHADASQIDAAIRAVSAGLIV 80
Cdd:COG2771    27 LLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAALLARLAALLL 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  81 RVPDMMDAGFGAMRETHGHALLTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAAERR 160
Cdd:COG2771   107 ALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALRLG 186
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 2-158 2.84e-15

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: 69.74  E-value: 2.84e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309   2 DPLRRAALSRVVAEAGHIVVG-----------AQDIADVVLADgDCLPGETRPVV--TLGGADYDLP-GVLSRHADasqI 67
Cdd:COG4566     8 DEAVRDSLAFLLESAGLRVETfasaeaflaalDPDRPGCLLLD-VRMPGMSGLELqeELAARGSPLPvIFLTGHGD---V 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  68 DAAIRAVSAG-------------LIVRVPDMMDAGFGAMRETHGH-------ALLTPRELEVLATLAEGMTNKAIARRLN 127
Cdd:COG4566    84 PMAVRAMKAGavdflekpfddqaLLDAVRRALARDRARRAERARRaelrarlASLTPREREVLDLVVAGLSNKQIARELG 163

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1941185309 128 ISLHTVKFHIESLFRKLGARTRTEAVAKAAE 158
Cdd:COG4566   164 ISPRTVEVHRANVMEKLGARSLAELVRLALA 194
PRK10100 PRK10100
transcriptional regulator CsgD;
100-162 5.43e-13

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 64.12  E-value: 5.43e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1941185309 100 ALLTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAAERRRH 162
Cdd:PRK10100  154 ALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDNLRR 216
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
113-159 1.11e-12

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 62.80  E-value: 1.11e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1941185309 113 LAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAAER 159
Cdd:COG2909   134 LAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARAREL 180
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
49-152 2.83e-12

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 62.18  E-value: 2.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  49 GADydlpGVLSRHADASQIDAAIRAVSAGLIV---RVPDMMDAGFGAMRETHGHALLTPRELEVLATLAEGMTNKAIARR 125
Cdd:PRK10403  102 GAD----GYLLKDSDPEVLLEAIRAGAKGSKVfseRVNQYLREREMFGAEEDPFSVLTERELDVLHELAQGLSNKQIASV 177

                          90       100
                  ....*....|....*....|....*..
gi 1941185309 126 LNISLHTVKFHIESLFRKLGARTRTEA 152
Cdd:PRK10403  178 LNISEQTVKVHIRNLLRKLNVRSRVAA 204
PRK15369 PRK15369
two component system response regulator;
69-151 2.33e-11

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 59.32  E-value: 2.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  69 AAIRAVSAGLIVRVP----DMMDAGFGAmrETHGHALLTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKL 144
Cdd:PRK15369  115 AAIQTVAVGKRYIDPalnrEAILALLNA--DDTNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192


                  ....*..
gi 1941185309 145 GARTRTE 151
Cdd:PRK15369  193 DVHKVAE 199
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
102-156 1.11e-08

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 53.02  E-value: 1.11e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1941185309 102 LTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKA 156
Cdd:PRK04841  839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA 893
PRK10360 PRK10360
transcriptional regulator UhpA;
56-151 2.60e-07

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 48.05  E-value: 2.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  56 GVLSRHADASQIDAAIRAVSAGLIVRVPDMmdagfgAMRETHGHA-LLTPRELEVLATLAEGMTNKAIARRLNISLHTVK 134
Cdd:PRK10360   97 GFLSKRCSPDELIAAVHTVATGGCYLTPDI------AIKLASGRQdPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVH 170

                          90
                  ....*....|....*..
gi 1941185309 135 FHIESLFRKLGARTRTE 151
Cdd:PRK10360  171 VHRANLMEKLGVSNDVE 187
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
56-158 9.86e-06

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 43.71  E-value: 9.86e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  56 GVLSRHADASQIDAAIRAVSAGLIVRVPDMMD--AGFGAMRETHGHALLTPRELEVLATLAEGMTNKAIARRLNISLHTV 133
Cdd:PRK09935  102 GFVSKCNDQNDIFHAVQMILSGYTFFPSETLNyiKSNKCSTNSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTV 181

                          90       100
                  ....*....|....*....|....*..
gi 1941185309 134 KFHIESLFRKLGARTRTEAV--AKAAE 158
Cdd:PRK09935  182 SAHKSNIYGKLGLHSIVELIdyAKLHE 208
fixJ PRK09390
response regulator FixJ; Provisional
 100-153 1.53e-05

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 43.07  E-value: 1.53e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1941185309 100 ALLTPRELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAV 153
Cdd:PRK09390  140 ASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELV 193
PRK10188 PRK10188
transcriptional regulator SdiA;
105-157 2.18e-05

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 43.24  E-value: 2.18e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1941185309 105 RELEVLATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGARTRTEAVAKAA 157
Cdd:PRK10188  183 REKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAA 235
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 115-137 2.38e-05

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: 42.16  E-value: 2.38e-05
                          10        20
                  ....*....|....*....|...
gi 1941185309 115 EGMTNKAIARRLNISLHTVKFHI 137
Cdd:TIGR02985 128 EGLSNKEIAEELGISVKTVEYHI 150
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 44-145 7.94e-04

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 38.28  E-value: 7.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  44 VVTLGGADYDLPGVLS-----RHADASQIDAAIRAVSAGlivrvpdmmdaGFGAMRethghalLTPRELEVLATLAEGMT 118
Cdd:PRK10840  106 IVLKQGAPTDLPKALAalqkgKKFTPESVSRLLEKISAG-----------GYGDKR-------LSPKESEVLRLFAEGFL 167

                          90       100
                  ....*....|....*....|....*..
gi 1941185309 119 NKAIARRLNISLHTVKFHIESLFRKLG 145
Cdd:PRK10840  168 VTEIAKKLNRSIKTISSQKKSAMMKLG 194
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 102-144 1.73e-03

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: 36.94  E-value: 1.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1941185309 102 LTPRELEVLaTLA--EGMTNKAIARRLNISLHTVKFHIESLFRKL 144
Cdd:TIGR02937 111 LPEREREVL-VLRylEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK06930 PRK06930
positive control sigma-like factor; Validated
 100-148 4.50e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 35.86  E-value: 4.50e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1941185309 100 ALLTPRELEV-LATLAEGMTNKAIARRLNISLHTVKFHIESLFRKLGART 148
Cdd:PRK06930  113 SVLTEREKEVyLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
106-140 5.38e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 33.56  E-value: 5.38e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1941185309 106 ELEVLATLAE--GMTNKAIARRLNISLHTVKFHIESL 140
Cdd:pfam13412   3 DRKILNLLQEnpRISQRELAERLGLSPSTVNRRLKRL 39
PRK09483 PRK09483
response regulator; Provisional
 56-145 9.23e-03

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 35.47  E-value: 9.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941185309  56 GVLSRHADASQIDAAIRAVSAGLIVRVPD----MMDAGFGAMRETHgHALLTPRELEVLATLAEGMTNKAIARRLNISLH 131
Cdd:PRK09483  100 GYLSKGAAPQEVVSAIRSVHSGQRYIASDiaqqMALSQIEPATENP-FASLSERELQIMLMITKGQKVNEISEQLNLSPK 178

                          90
                  ....*....|....
gi 1941185309 132 TVKFHIESLFRKLG 145
Cdd:PRK09483  179 TVNSYRYRMFSKLN 192
 
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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