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Conserved domains on  [gi|1418711638|gb|RAY78054|]
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DNA-binding response regulator [Enterobacter roggenkampii]

Protein Classification

response regulator transcription factor( domain architecture ID 13308614)

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:0003677|GO:0003700|GO:0000160
PubMed:  15808743|19076237|10473770|8831795|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 ...
 141-198 6.73e-21

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: 83.79  E-value: 6.73e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1418711638 141 LSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMYYTRA 198
Cdd:COG2197    70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
PRK15369 super family cl33127
two component system response regulator;
2-190 1.63e-09

two component system response regulator;


The actual alignment was detected with superfamily member PRK15369:

Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 55.08  E-value: 1.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638   2 RVIMFDRQSLFIHGaIHSLQRLIPEINITGtcQAED---LWTQISASPSAIVMIDGNLIQDEGSTLLEAILHRFPAIRVI 78
Cdd:PRK15369    5 KILLVDDHELIING-IKNMLAPYPRYKIVG--QVDNgleVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNIL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  79 LILAKKEAKCAEQLRQRNVMAIVPRNANPERFSAVLDSVSRG-----------MVCfpgEWVREPTSPQALLSLseRQRE 147
Cdd:PRK15369   82 VLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGkryidpalnreAIL---ALLNADDTNPPLLTP--RERQ 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1418711638 148 VLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQ 190
Cdd:PRK15369  157 ILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAE 199
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 141-198 6.73e-21

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: 83.79  E-value: 6.73e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1418711638 141 LSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMYYTRA 198
Cdd:COG2197    70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 138-194 1.35e-19

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 78.34  E-value: 1.35e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1418711638  138 LLSLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMY 194
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
140-194 2.77e-19

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 77.24  E-value: 2.77e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1418711638 140 SLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMY 194
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 141-194 1.43e-17

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: 72.95  E-value: 1.43e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1418711638 141 LSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMY 194
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 130-194 6.67e-14

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 67.36  E-value: 6.67e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1418711638 130 REPTSPQ--ALLSLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMY 194
Cdd:PRK10651  143 RANRATTerDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVW 209
PRK15369 PRK15369
two component system response regulator;
2-190 1.63e-09

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 55.08  E-value: 1.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638   2 RVIMFDRQSLFIHGaIHSLQRLIPEINITGtcQAED---LWTQISASPSAIVMIDGNLIQDEGSTLLEAILHRFPAIRVI 78
Cdd:PRK15369    5 KILLVDDHELIING-IKNMLAPYPRYKIVG--QVDNgleVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNIL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  79 LILAKKEAKCAEQLRQRNVMAIVPRNANPERFSAVLDSVSRG-----------MVCfpgEWVREPTSPQALLSLseRQRE 147
Cdd:PRK15369   82 VLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGkryidpalnreAIL---ALLNADDTNPPLLTP--RERQ 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1418711638 148 VLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQ 190
Cdd:PRK15369  157 ILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAE 199
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 136-183 1.01e-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: 41.18  E-value: 1.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1418711638 136 QALLSLSERQREVLKLLA-AGESNKEIGRNLNISAATVKAHLEALFRRL 183
Cdd:TIGR02937 106 EALEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 141-198 6.73e-21

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: 83.79  E-value: 6.73e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1418711638 141 LSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMYYTRA 198
Cdd:COG2197    70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 138-194 1.35e-19

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 78.34  E-value: 1.35e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1418711638  138 LLSLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMY 194
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
140-194 2.77e-19

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 77.24  E-value: 2.77e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1418711638 140 SLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMY 194
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 141-194 1.43e-17

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: 72.95  E-value: 1.43e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1418711638 141 LSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMY 194
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 140-198 1.19e-15

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: 68.45  E-value: 1.19e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1418711638 140 SLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMYYTRA 198
Cdd:COG5905    12 LLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRL 70
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 130-194 6.67e-14

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 67.36  E-value: 6.67e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1418711638 130 REPTSPQ--ALLSLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMY 194
Cdd:PRK10651  143 RANRATTerDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVW 209
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 140-187 2.41e-12

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: 62.81  E-value: 2.41e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1418711638 140 SLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKN 187
Cdd:COG4566   137 SLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
136-197 3.33e-12

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 62.47  E-value: 3.33e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1418711638 136 QALLSLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMYYTR 197
Cdd:COG2771   123 ARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALR 184
PRK10100 PRK10100
transcriptional regulator CsgD;
141-191 3.99e-12

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 62.58  E-value: 3.99e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1418711638 141 LSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQA 191
Cdd:PRK10100  156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQA 206
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
151-192 6.37e-10

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 55.87  E-value: 6.37e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1418711638 151 LLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAA 192
Cdd:COG2909   133 LLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAV 174
PRK15369 PRK15369
two component system response regulator;
2-190 1.63e-09

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 55.08  E-value: 1.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638   2 RVIMFDRQSLFIHGaIHSLQRLIPEINITGtcQAED---LWTQISASPSAIVMIDGNLIQDEGSTLLEAILHRFPAIRVI 78
Cdd:PRK15369    5 KILLVDDHELIING-IKNMLAPYPRYKIVG--QVDNgleVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNIL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  79 LILAKKEAKCAEQLRQRNVMAIVPRNANPERFSAVLDSVSRG-----------MVCfpgEWVREPTSPQALLSLseRQRE 147
Cdd:PRK15369   82 VLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGkryidpalnreAIL---ALLNADDTNPPLLTP--RERQ 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1418711638 148 VLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQ 190
Cdd:PRK15369  157 ILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAE 199
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
141-195 6.52e-09

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 53.70  E-value: 6.52e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1418711638 141 LSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAAMYY 195
Cdd:PRK10403  154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILF 208
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
46-187 8.41e-08

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 50.26  E-value: 8.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  46 PSAIVMIDGNLIQDEGSTLLEAILHRFPAIRVILILAKKEAKCAEQLRQRNVMAIVP-RNANPERFSAVlDSVSRGMVCF 124
Cdd:PRK09935   49 PVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSkCNDQNDIFHAV-QMILSGYTFF 127

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1418711638 125 PGEWV------REPTSPQALLSLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKN 187
Cdd:PRK09935  128 PSETLnyiksnKCSTNSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196
fixJ PRK09390
response regulator FixJ; Provisional
 140-175 1.04e-06

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 47.30  E-value: 1.04e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1418711638 140 SLSERQREVLKLLAAGESNKEIGRNLNISAATVKAH 175
Cdd:PRK09390  141 SLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVY 176
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 136-183 1.66e-05

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: 43.44  E-value: 1.66e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1418711638 136 QALLSLSERQREVLKLLA-AGESNKEIGRNLNISAATVKAHLEALFRRL 183
Cdd:COG1595   123 AALERLPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
133-197 2.59e-05

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 44.16  E-value: 2.59e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1418711638 133 TSPqallsLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRtQAAMYYTR 197
Cdd:PRK04841  836 TSP-----LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHR-QEAVQHAQ 894
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-187 4.32e-05

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 42.51  E-value: 4.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638   1 MRVIMFDRQSLFIHGAIHSLQRlIPEINITGtcQAEDLWTQISASP---SAIVMIDGNLIQD---EGSTLLEAILHRFPA 74
Cdd:PRK10840    4 MNVIIADDHPIVLFGIRKSLEQ-IEWVNVVG--EFEDSTALINNLPkldAHVLITDLSMPGDkygDGITLIKYIKRHFPS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  75 IRVILILAKKEAKCAEQLRQRNVMAIVPRNANPERFSAVLDSVSRGMVCFPgEWVRE-----PTSPQALLSLSERQREVL 149
Cdd:PRK10840   81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTP-ESVSRllekiSAGGYGDKRLSPKESEVL 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1418711638 150 KLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKN 187
Cdd:PRK10840  160 RLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVEN 197
PRK10360 PRK10360
transcriptional regulator UhpA;
68-192 5.97e-05

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 42.27  E-value: 5.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  68 ILHRFP-AIRVILILAKKEAKCAEQLRQRNVMAIVPRNANPERFSAVLDSVSRGMvCFPGEWVREPTSPQALLSLSERQR 146
Cdd:PRK10360   65 LLSQLPkGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGG-CYLTPDIAIKLASGRQDPLTKRER 143

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1418711638 147 EVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDVKNRTQAA 192
Cdd:PRK10360  144 QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELA 189
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
1-187 6.87e-05

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 42.19  E-value: 6.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638   1 MRVIMFDRQSLfihgAIHSLQRLIPEINITGTCQAEDLWTQISASPSA---IVMIDGNLIQDEGSTLLEAILHRFPAIRV 77
Cdd:PRK09958    1 MNAIIIDDHPL----AIAAIRNLLIKNDIEILAELTEGGSAVQRVETLkpdIVIIDVDIPGVNGIQVLETLRKRQYSGII 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  78 ILILAKKEAKCAEQLRQRNVMAIVPRNANPERFSAVLDSVSRGMVCFPGEWVREPTS----PQALLSLSERQREVLKLLA 153
Cdd:PRK09958   77 IIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFSLNRFVGSltsdQQKLDSLSKQEISVMRYIL 156

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1418711638 154 AGESNKEIGRNLNISAATVKAHLEALFRRLDVKN 187
Cdd:PRK09958  157 DGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKS 190
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 136-183 1.01e-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: 41.18  E-value: 1.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1418711638 136 QALLSLSERQREVLKLLA-AGESNKEIGRNLNISAATVKAHLEALFRRL 183
Cdd:TIGR02937 106 EALEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 136-176 1.05e-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: 38.59  E-value: 1.05e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1418711638 136 QALLSLSERQREVLKLLAA-GESNKEIGRNLNISAATVKAHL 176
Cdd:pfam08281   6 RALEELPPRQREVFLLRYLeGLSYAEIAELLGISEGTVKSRL 47
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 136-176 1.75e-04

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: 40.24  E-value: 1.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1418711638 136 QALLSLSERQREVLKL-LAAGESNKEIGRNLNISAATVKAHL 176
Cdd:TIGR02985 109 EAIEKLPEQCREIFILsRFEGLSNKEIAEELGISVKTVEYHI 150
rcsA PRK15411
transcriptional regulator RcsA;
28-199 5.02e-04

transcriptional regulator RcsA;


Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 39.34  E-value: 5.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  28 NITGTCQAEDLWTQISASPSAIVMI--DGNLIQDEGSTLLEAILHRFPAIRVILILAKKEAKCAEQLRQRNVMAIVPRNA 105
Cdd:PRK15411   29 EINDIETVDDLAIACDSLRPSVVFIneDCFIHDASNSQRIKQIINQHPNTLFIVFMAIANIHFDEYLLVRKNLLISSKSI 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638 106 NPERFSAVLDSvsrgmvCFPGEWVREPTSPQALLSLSERQREVLKLLAAGESNKEIGRNLNISAATVKAHLEALFRRLDV 185
Cdd:PRK15411  109 KPESLDDLLGD------ILKKETTITSFLNLPTLSLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182

                         170
                  ....*....|....
gi 1418711638 186 KNRtQAAMYYTRAT 199
Cdd:PRK15411  183 HNK-QVIYHVVRLT 195
PRK09483 PRK09483
response regulator; Provisional
 27-185 5.48e-04

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 39.32  E-value: 5.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638  27 INITGTCQ-AEDLWTQISASPSAIVMIDGNLiqdEGSTLLEA---ILHRFPAIRVILILAKKEAKCAEQLRQRNVMAIVP 102
Cdd:PRK09483   27 IKVVGEACcGEDAVKWCRTNAVDVVLMDMNM---PGIGGLEAtrkILRYTPDVKIIMLTVHTENPLPAKVMQAGAAGYLS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1418711638 103 RNANPERFSAVLDSVSRGMVCFPGEWVR-------EPTSPQALLSLSERQREVLKLLAAGESNKEIGRNLNISAATVKAH 175
Cdd:PRK09483  104 KGAAPQEVVSAIRSVHSGQRYIASDIAQqmalsqiEPATENPFASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSY 183

                         170
                  ....*....|
gi 1418711638 176 LEALFRRLDV 185
Cdd:PRK09483  184 RYRMFSKLNI 193
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 139-172 1.75e-03

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


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 35.18  E-value: 1.75e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1418711638 139 LSLSERqREVLKLLAAGESNKEIGRNLNISAATV 172
Cdd:pfam13936   5 LSLEER-EEIARLLAEGLSLREIARRLGRSPSTI 37
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 137-183 2.62e-03

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 34.71  E-value: 2.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1418711638 137 ALLSLSERQREVLKL-LAAGESNKEIGRNLNISAATVKAHLEALFRRL 183
Cdd:pfam04545   1 ALASLPPRERQVLVLrYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 137-174 2.97e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 36.96  E-value: 2.97e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1418711638 137 ALLSLSERQREVLKLLA-AGESNKEIGRNLNISAATVKA 174
Cdd:PRK12519  138 ALAQLPESQRQVLELAYyEGLSQSEIAKRLGIPLGTVKA 176
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 143-176 5.08e-03

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 33.84  E-value: 5.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1418711638 143 ERQREVLKLLAAGESNKEIGRNLNISAATVKAHL 176
Cdd:cd00569     9 EQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 136-173 6.95e-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: 33.62  E-value: 6.95e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1418711638 136 QALLSLSERQREVLkLLAAGE--SNKEIGRNLNISAATVK 173
Cdd:cd06171     6 EALDKLPEREREVI-LLRFGEglSYEEIAEILGISRSTVR 44
 
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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