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Conserved domains on  [gi|446438425|ref|WP_000516280|]
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response regulator transcription factor [Escherichia coli]

Protein Classification

response regulator transcription factor( domain architecture ID 1013612)

two-component system response regulator transcription factor binds DNA upon phosphorylation and functions as transcriptional regulator

CATH:  3.40.50.2300
Gene Ontology:  GO:0000156|GO:0000160|GO:0003677|GO:0006355
PubMed:  31100988|10966457
SCOP:  4003632

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK15369 super family cl33127
two component system response regulator;
1-207 2.97e-38

two component system response regulator;


The actual alignment was detected with superfamily member PRK15369:

Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 131.35  E-value: 2.97e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   1 MGKIKIVVSDQQPFMIDGIIGFLGHYPDlYEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAH 80
Cdd:PRK15369   1 MKNYKILLVDDHELIINGIKNMLAPYPR-YKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  81 IITFVAKMPYIDSIKLLEAGAKGCVWKTSHPAKLNRAIDSISNGYTYFDSVhMDCEKI--SSRYSSDNQ--LTNRESEIL 156
Cdd:PRK15369  80 ILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPA-LNREAIlaLLNADDTNPplLTPRERQIL 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446438425 157 QLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMGV 207
Cdd:PRK15369 159 KLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGL 209
 
Name Accession Description Interval E-value
PRK15369 PRK15369
two component system response regulator;
1-207 2.97e-38

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 131.35  E-value: 2.97e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   1 MGKIKIVVSDQQPFMIDGIIGFLGHYPDlYEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAH 80
Cdd:PRK15369   1 MKNYKILLVDDHELIINGIKNMLAPYPR-YKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  81 IITFVAKMPYIDSIKLLEAGAKGCVWKTSHPAKLNRAIDSISNGYTYFDSVhMDCEKI--SSRYSSDNQ--LTNRESEIL 156
Cdd:PRK15369  80 ILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPA-LNREAIlaLLNADDTNPplLTPRERQIL 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446438425 157 QLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMGV 207
Cdd:PRK15369 159 KLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGL 209
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 3-206 3.16e-25

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: 95.34  E-value: 3.16e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   3 KIKIVVSDQQPFMIDGIIGFLGHYPDlYEVVGGYKDlkkaiaecnksaaqifilgefaggmmGAELVKWVKSHKIDAHII 82
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEPD-IEVVGEAAD--------------------------GEEALELLEELRPDVVLL 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  83 TFvaKMPYIDSIKLLeagakgcvwktshpaklnRAIdsisngytyfdsvhmdcekissryssdnqLTNRESEILQLIADG 162
Cdd:COG2197   54 DI--RMPGMDGLEAL------------------RRL-----------------------------LTPREREVLRLLAEG 84

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 446438425 163 KTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMG 206
Cdd:COG2197   85 LSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLG 128
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 148-202 3.16e-22

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 85.27  E-value: 3.16e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 446438425   148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTA 202
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 148-204 9.57e-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: 81.43  E-value: 9.57e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446438425 148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALR 204
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
148-199 1.63e-18

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 75.70  E-value: 1.63e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446438425  148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELI 199
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 146-190 9.09e-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: 38.48  E-value: 9.09e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 446438425  146 NQLTNRESEILQLIA-DGKTNKEIANFLQLSRKTVETHRLNIMKKL 190
Cdd:TIGR02937 109 EKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK15369 PRK15369
two component system response regulator;
1-207 2.97e-38

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 131.35  E-value: 2.97e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   1 MGKIKIVVSDQQPFMIDGIIGFLGHYPDlYEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAH 80
Cdd:PRK15369   1 MKNYKILLVDDHELIINGIKNMLAPYPR-YKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  81 IITFVAKMPYIDSIKLLEAGAKGCVWKTSHPAKLNRAIDSISNGYTYFDSVhMDCEKI--SSRYSSDNQ--LTNRESEIL 156
Cdd:PRK15369  80 ILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPA-LNREAIlaLLNADDTNPplLTPRERQIL 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446438425 157 QLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMGV 207
Cdd:PRK15369 159 KLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGL 209
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 3-206 3.16e-25

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: 95.34  E-value: 3.16e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   3 KIKIVVSDQQPFMIDGIIGFLGHYPDlYEVVGGYKDlkkaiaecnksaaqifilgefaggmmGAELVKWVKSHKIDAHII 82
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEPD-IEVVGEAAD--------------------------GEEALELLEELRPDVVLL 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  83 TFvaKMPYIDSIKLLeagakgcvwktshpaklnRAIdsisngytyfdsvhmdcekissryssdnqLTNRESEILQLIADG 162
Cdd:COG2197   54 DI--RMPGMDGLEAL------------------RRL-----------------------------LTPREREVLRLLAEG 84

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 446438425 163 KTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMG 206
Cdd:COG2197   85 LSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLG 128
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 148-202 3.16e-22

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 85.27  E-value: 3.16e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 446438425   148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTA 202
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 139-207 1.40e-21

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: 84.24  E-value: 1.40e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446438425 139 SSRYSSDNQLTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMGV 207
Cdd:COG5905    4 SSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGL 72
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 136-206 2.22e-21

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: 87.08  E-value: 2.22e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446438425 136 EKISSRYSSdnqLTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMG 206
Cdd:COG4566  129 AELRARLAS---LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLALALG 196
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
147-207 9.37e-21

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 85.58  E-value: 9.37e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446438425 147 QLTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMGV 207
Cdd:COG2771  127 GLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALRLGL 187
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 148-204 9.57e-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: 81.43  E-value: 9.57e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446438425 148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALR 204
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
5-194 4.76e-19

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 81.44  E-value: 4.76e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   5 KIVVSDQQPFMIDGIIGFLGHYPdLYEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAHIITF 84
Cdd:PRK10403   8 QVLIVDDHPLMRRGVRQLLELDP-GFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIIL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  85 VAKMPYIDSIKLLEAGAKGCVWKTSHPAKLNRAIDSISNGYTYF-DSVH---MDCEKISSRYSSDNQLTNRESEILQLIA 160
Cdd:PRK10403  87 TVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFsERVNqylREREMFGAEEDPFSVLTERELDVLHELA 166

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446438425 161 DGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHS 194
Cdd:PRK10403 167 QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200
GerE pfam00196
Bacterial regulatory proteins, luxR family;
148-199 1.63e-18

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 75.70  E-value: 1.63e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446438425  148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELI 199
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54
PRK10360 PRK10360
transcriptional regulator UhpA;
4-205 1.43e-17

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 77.32  E-value: 1.43e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   4 IKIVVSDQQPFMIDGIIGFLGHYPDLyEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKidAHIIT 83
Cdd:PRK10360   2 ITVALIDDHLIVRSGFAQLLGLEPDL-QVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGM--ATIML 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  84 FVAKMPYIDSiKLLEAGAKGCVWKTSHPAKLNRAIDSISNGYTYFDSvhmdceKISSRYSSDNQ--LTNRESEILQLIAD 161
Cdd:PRK10360  79 SVHDSPALVE-QALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTP------DIAIKLASGRQdpLTKRERQVAEKLAQ 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 446438425 162 GKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELiktALRM 205
Cdd:PRK10360 152 GMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL---ARRM 192
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
1-202 1.39e-16

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 74.91  E-value: 1.39e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   1 MGKIKIVVSDQQPFMIDGIIGFLGHYPDLyEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAH 80
Cdd:PRK09935   1 MKPASVIIMDTHPIIRMSIEVLLQKNSEL-QIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  81 IITFVAKMPYIDSIKLLEAGAKGCVWKTSHPAKLNRAIDSISNGYTYFDSV---HMDCEKISSRYSSDNQLTNRESEILQ 157
Cdd:PRK09935  80 VLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSEtlnYIKSNKCSTNSSTDTVLSNREVTILR 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 446438425 158 LIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTA 202
Cdd:PRK09935 160 YLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYA 204
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-199 2.71e-15

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 71.40  E-value: 2.71e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   1 MGKIKIVVSDQQPFMIDGIIGFLGHYpDLYEVVGGYKDLKKAIAECNKSAAQIFIL-----GEFAGGmmGAELVKWVKSH 75
Cdd:PRK10840   1 MNNMNVIIADDHPIVLFGIRKSLEQI-EWVNVVGEFEDSTALINNLPKLDAHVLITdlsmpGDKYGD--GITLIKYIKRH 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  76 KIDAHIItfVAKM---PYIDSIkLLEAGAKGCVWKTSHPAKLNRAIDSISNGYTYF-DSVHMDCEKISSRYSSDNQLTNR 151
Cdd:PRK10840  78 FPSLSII--VLTMnnnPAILSA-VLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTpESVSRLLEKISAGGYGDKRLSPK 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 446438425 152 ESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELI 199
Cdd:PRK10840 155 ESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALL 202
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
7-204 2.10e-14

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 68.77  E-value: 2.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   7 VVSDQQPFMIDGIIGFLGHypDLYEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAHIITFVA 86
Cdd:PRK09958   4 IIIDDHPLAIAAIRNLLIK--NDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  87 KMPYIDSIKLLEAGAKGCVWKTSHPAKLNRAIDSISNGYTYFDsvhMDCEKISSRYSSDNQ----LTNRESEILQLIADG 162
Cdd:PRK09958  82 KNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFP---FSLNRFVGSLTSDQQkldsLSKQEISVMRYILDG 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 446438425 163 KTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALR 204
Cdd:PRK09958 159 KDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQR 200
PRK09483 PRK09483
response regulator; Provisional
 32-208 2.98e-14

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 68.59  E-value: 2.98e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  32 VVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAHII--TFVAKMPYidSIKLLEAGAKGCVWKTS 109
Cdd:PRK09483  29 VVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIImlTVHTENPL--PAKVMQAGAAGYLSKGA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425 110 HPAKLNRAIDSISNGYTYFDS---VHMDCEKISSRYSSD-NQLTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLN 185
Cdd:PRK09483 107 APQEVVSAIRSVHSGQRYIASdiaQQMALSQIEPATENPfASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYR 186

                        170       180
                 ....*....|....*....|...
gi 446438425 186 IMKKLDVHSGIELIKTALRMGVC 208
Cdd:PRK09483 187 MFSKLNISGDVELTHLAIRHGLL 209
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 6-197 6.00e-14

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 67.75  E-value: 6.00e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   6 IVVSDQQPFMIDGIIGFLGHYPDLyEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAHIITFV 85
Cdd:PRK10651   9 ILLIDDHPMLRTGVKQLISMAPDI-TVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFS 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425  86 AKMPYIDSIKLLEAGAKGCVWKTSHPAKLNRAIDS-------ISNGYTYFDSVHMDcEKISSRYSSDNQLTNRESEILQL 158
Cdd:PRK10651  88 VSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQaaagemvLSEALTPVLAASLR-ANRATTERDVNQLTPRERDILKL 166

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446438425 159 IADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIE 197
Cdd:PRK10651 167 IAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
157-207 1.15e-12

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 63.57  E-value: 1.15e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446438425 157 QLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMGV 207
Cdd:COG2909  132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGL 182
fixJ PRK09390
response regulator FixJ; Provisional
 138-207 1.71e-09

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 55.39  E-value: 1.71e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425 138 ISSRYSSdnqLTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRMGV 207
Cdd:PRK09390 135 IRARIAS---LSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMALRAGR 201
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 6-121 2.79e-07

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: 47.51  E-value: 2.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425   6 IVVSDQQPFMIDGIIGFLGHYPDLyEVVGGYKDLKKAIAECNKSAAQIFILGEFAGGMMGAELVKWVKSHKIDAHIITFV 85
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDI-EVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLT 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446438425  86 AKMPYIDSIKLLEAGAKGCVWKTSHPAKLNRAIDSI 121
Cdd:cd17535   80 AHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
PRK10188 PRK10188
transcriptional regulator SdiA;
147-191 2.83e-06

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 46.32  E-value: 2.83e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446438425 147 QLTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLD 191
Cdd:PRK10188 179 NFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223
PRK10100 PRK10100
transcriptional regulator CsgD;
148-192 2.92e-06

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 46.40  E-value: 2.92e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446438425 148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDV 192
Cdd:PRK10100 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAV 200
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 148-202 3.78e-05

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 42.81  E-value: 3.78e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446438425 148 LTNRESEILQLIADGKTNKEIAnfLQLSR--KTVETHRLNIMKKLDVHSGIELIKTA 202
Cdd:PRK11475 135 LSPTEREILRFMSRGYSMPQIA--EQLERniKTIRAHKFNVMSKLGVSSDAGLLDAA 189
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
148-205 2.93e-04

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 41.08  E-value: 2.93e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446438425 148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIKTALRM 205
Cdd:PRK04841 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQDL 896
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 146-190 5.96e-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: 36.67  E-value: 5.96e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 446438425  146 NQLTNRESEILQLIA-DGKTNKEIANFLQLSRKTVETHRLNIMKKL 190
Cdd:pfam08281   9 EELPPRQREVFLLRYlEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 146-190 9.09e-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: 38.48  E-value: 9.09e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 446438425  146 NQLTNRESEILQLIA-DGKTNKEIANFLQLSRKTVETHRLNIMKKL 190
Cdd:TIGR02937 109 EKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 162-190 3.87e-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: 36.39  E-value: 3.87e-03
                          10        20
                  ....*....|....*....|....*....
gi 446438425  162 GKTNKEIANFLQLSRKTVETHRLNIMKKL 190
Cdd:TIGR02985 129 GLSNKEIAEELGISVKTVEYHITKALKFL 157
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 141-179 4.18e-03

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


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 37.52  E-value: 4.18e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 446438425 141 RYSSDNQLTNREsEILQLIADGKTNKEIANFLQLSRKTV 179
Cdd:COG3415   18 RKTKDAREARRL-RAVLLLAEGLSVREIAERLGVSRSTV 55
PRK15201 PRK15201
fimbriae biosynthesis transcriptional regulator FimW;
142-200 5.97e-03

fimbriae biosynthesis transcriptional regulator FimW;


Pssm-ID: 185123  Cd Length: 198  Bit Score: 36.56  E-value: 5.97e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446438425 142 YSSDNQLTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVHSGIELIK 200
Cdd:PRK15201 128 YCTTRHFSVTERHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQFLK 186
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
122-196 7.29e-03

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 35.62  E-value: 7.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446438425 122 SNGYT-YFdsvhmdceKISSRYSSDNQLT----NRES--EILQLIAD--GKTNKEIANFLQLSRKTVETHrlniMKKLdV 192
Cdd:COG3398   70 DGGRTrYF--------PNSGTYSEEEKKIlaylRRETprRILLYLLEnpGATNKELAEELGISRSTVSWH----LKRL-E 136


                 ....
gi 446438425 193 HSGI 196
Cdd:COG3398  137 EDGL 140
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 146-190 8.54e-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: 35.74  E-value: 8.54e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446438425 146 NQLTNRESEILQLIA-DGKTNKEIANFLQLSRKTVETHRLNIMKKL 190
Cdd:COG1595  126 ERLPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
rcsA PRK15411
transcriptional regulator RcsA;
148-193 8.67e-03

transcriptional regulator RcsA;


Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 35.88  E-value: 8.67e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446438425 148 LTNRESEILQLIADGKTNKEIANFLQLSRKTVETHRLNIMKKLDVH 193
Cdd:PRK15411 138 LSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTH 183
 
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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