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Conserved domains on  [gi|985002316|gb|AMC96402|]
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helix-turn-helix transcriptional regulator [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 13296807)

helix-turn-helix (HTH) transcriptional regulator containing a LuxR family HTH DNA-binding domain; may act as a transcription activator/repressor, or have a dual role for different sites

Gene Ontology:  GO:0006355|GO:0003677|GO:0003700
PubMed:  15808743|19076237|10473770|8831795

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 ...
 142-196 1.36e-20

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: 83.02  E-value: 1.36e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 985002316 142 LSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMML 196
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLA 124
PRK09935 super family cl32434
fimbriae biosynthesis transcriptional regulator FimZ;
42-188 1.24e-06

fimbriae biosynthesis transcriptional regulator FimZ;


The actual alignment was detected with superfamily member PRK09935:

Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 47.18  E-value: 1.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316  42 LESYPEALVMLDGDQDGEFCYWLLQKTVVQFPEVKVLITATDCNKRWLQEVIHFNVLAIVPRDSTVETFALAVNSAAMGM 121
Cdd:PRK09935  45 LRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGY 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 985002316 122 MFLPGDW-----RTTPEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKN 188
Cdd:PRK09935 125 TFFPSETlnyikSNKCSTNSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 142-196 1.36e-20

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: 83.02  E-value: 1.36e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 985002316 142 LSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMML 196
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLA 124
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 139-196 2.48e-20

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 80.26  E-value: 2.48e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 985002316   139 LKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMML 196
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE pfam00196
Bacterial regulatory proteins, luxR family;
141-195 4.38e-20

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 79.55  E-value: 4.38e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 985002316  141 SLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMM 195
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 ...
 142-198 3.81e-18

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: 74.49  E-value: 3.81e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 985002316 142 LSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMMLNI 198
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 113-193 2.60e-14

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 68.52  E-value: 2.60e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316 113 AVNSAAMGMMFLP--------GDWRTTPEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRL 184
Cdd:PRK10651 119 ALQQAAAGEMVLSealtpvlaASLRANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198


                 ....*....
gi 985002316 185 EVKNRTQAA 193
Cdd:PRK10651 199 KLKSRVEAA 207
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
42-188 1.24e-06

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 47.18  E-value: 1.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316  42 LESYPEALVMLDGDQDGEFCYWLLQKTVVQFPEVKVLITATDCNKRWLQEVIHFNVLAIVPRDSTVETFALAVNSAAMGM 121
Cdd:PRK09935  45 LRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGY 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 985002316 122 MFLPGDW-----RTTPEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKN 188
Cdd:PRK09935 125 TFFPSETlnyikSNKCSTNSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 139-184 4.33e-06

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: 45.03  E-value: 4.33e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 985002316  139 LKSLSARQREILTMLA-AGESNKEIGRALNISTGTVKAHLESLYRRL 184
Cdd:TIGR02937 108 LEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 142-196 1.36e-20

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: 83.02  E-value: 1.36e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 985002316 142 LSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMML 196
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLA 124
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 139-196 2.48e-20

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 80.26  E-value: 2.48e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 985002316   139 LKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMML 196
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE pfam00196
Bacterial regulatory proteins, luxR family;
141-195 4.38e-20

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 79.55  E-value: 4.38e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 985002316  141 SLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMM 195
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 ...
 142-198 3.81e-18

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: 74.49  E-value: 3.81e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 985002316 142 LSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMMLNI 198
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
117-196 1.34e-17

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 76.72  E-value: 1.34e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316 117 AAMGMMFLPGDWRTTPEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMML 196
Cdd:COG2771  103 ALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALA 182
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 132-194 1.24e-16

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 71.14  E-value: 1.24e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 985002316 132 PEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAM 194
Cdd:COG5905    3 PSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVV 65
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 113-193 2.60e-14

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 68.52  E-value: 2.60e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316 113 AVNSAAMGMMFLP--------GDWRTTPEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRL 184
Cdd:PRK10651 119 ALQQAAAGEMVLSealtpvlaASLRANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198


                 ....*....
gi 985002316 185 EVKNRTQAA 193
Cdd:PRK10651 199 KLKSRVEAA 207
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
144-193 1.38e-13

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 65.88  E-value: 1.38e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 985002316 144 ARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAA 193
Cdd:COG2909  125 ALAALRRRLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAV 174
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 139-196 4.90e-13

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: 64.74  E-value: 4.90e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 985002316 139 LKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMML 196
Cdd:COG4566  135 LASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLA 192
PRK10100 PRK10100
transcriptional regulator CsgD;
142-197 9.18e-13

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 64.12  E-value: 9.18e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 985002316 142 LSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMMLN 197
Cdd:PRK10100 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWAN 211
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
142-195 2.71e-08

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 51.78  E-value: 2.71e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 985002316 142 LSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMM 195
Cdd:PRK10403 154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATIL 207
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 139-185 8.83e-07

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: 47.30  E-value: 8.83e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 985002316 139 LKSLSARQREILTMLA-AGESNKEIGRALNISTGTVKAHL----ESLYRRLE 185
Cdd:COG1595  125 LERLPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLsrarKKLREALE 176
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
42-188 1.24e-06

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 47.18  E-value: 1.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316  42 LESYPEALVMLDGDQDGEFCYWLLQKTVVQFPEVKVLITATDCNKRWLQEVIHFNVLAIVPRDSTVETFALAVNSAAMGM 121
Cdd:PRK09935  45 LRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGY 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 985002316 122 MFLPGDW-----RTTPEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKN 188
Cdd:PRK09935 125 TFFPSETlnyikSNKCSTNSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 139-184 4.33e-06

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: 45.03  E-value: 4.33e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 985002316  139 LKSLSARQREILTMLA-AGESNKEIGRALNISTGTVKAHLESLYRRL 184
Cdd:TIGR02937 108 LEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 139-177 2.19e-05

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 40.52  E-value: 2.19e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 985002316  139 LKSLSARQREILTMLAA-GESNKEIGRALNISTGTVKAHL 177
Cdd:pfam08281   8 LEELPPRQREVFLLRYLeGLSYAEIAELLGISEGTVKSRL 47
PRK15369 PRK15369
two component system response regulator;
73-191 2.51e-05

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 43.14  E-value: 2.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316  73 PEVKVL-ITATDCNKRwLQEVIHFNVLAIVPRDSTVETFALAVNSAAMGMMFL-PGDWRTTPEKDIK----DLKSLSARQ 146
Cdd:PRK15369  76 PAMNILvLTARQEEHM-ASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIdPALNREAILALLNaddtNPPLLTPRE 154

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 985002316 147 REILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQ 191
Cdd:PRK15369 155 RQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAE 199
fixJ PRK09390
response regulator FixJ; Provisional
 139-176 4.13e-05

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 42.68  E-value: 4.13e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 985002316 139 LKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAH 176
Cdd:PRK09390 139 IASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVY 176
PRK10360 PRK10360
transcriptional regulator UhpA;
113-193 2.33e-04

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 40.35  E-value: 2.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316 113 AVNSAAMGMMFLpgdwrtTPEKDIK----DLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKN 188
Cdd:PRK10360 111 AVHTVATGGCYL------TPDIAIKlasgRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSN 184


                 ....*
gi 985002316 189 RTQAA 193
Cdd:PRK10360 185 DVELA 189
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
146-192 3.17e-04

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 40.70  E-value: 3.17e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 985002316 146 QRE--ILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQA 192
Cdd:PRK04841 841 QREwqVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEA 889
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 140-184 5.20e-04

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: 36.53  E-value: 5.20e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 985002316 140 KSLSARQ-REILTMLAAGESNKEIGRALNISTGTvkahlesLYRRL 184
Cdd:cd00569    4 PKLTPEQiAEARRLLAAGESVAEIARELGVSRST-------LYRYL 42
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 130-177 7.19e-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: 38.70  E-value: 7.19e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 985002316  130 TTPEKDI--KDLK--------SLSARQREILTM-LAAGESNKEIGRALNISTGTVKAHL 177
Cdd:TIGR02985  92 ADPEEELeaKELEeiieeaieKLPEQCREIFILsRFEGLSNKEIAEELGISVKTVEYHI 150
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 139-177 7.29e-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. 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: 36.25  E-value: 7.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 985002316  139 LKSLSARQREILTM-LAAGESNKEIGRALNISTGTVKAHL 177
Cdd:pfam04545   2 LASLPPRERQVLVLrYGEGLTLEEIGERLGISRERVRQIE 41
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 141-173 7.33e-04

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: 35.95  E-value: 7.33e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 985002316  141 SLSARqREILTMLAAGESNKEIGRALNISTGTV 173
Cdd:pfam13936   6 SLEER-EEIARLLAEGLSLREIARRLGRSPSTI 37
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 139-182 1.12e-03

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 36.51  E-value: 1.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 985002316 139 LKSLSARQR-EILTMLAAGE-SNKEIGRALNISTGTVKAHLESLYR 182
Cdd:cd00090    1 LKALSDPTRlRILRLLLEGPlTVSELAERLGLSQSTVSRHLKKLEE 46
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 139-174 2.14e-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: 35.16  E-value: 2.14e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 985002316 139 LKSLSARQREILTMLAAGE-SNKEIGRALNISTGTVK 174
Cdd:cd06171    8 LDKLPEREREVILLRFGEGlSYEEIAEILGISRSTVR 44
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
146-180 2.98e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 34.33  E-value: 2.98e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 985002316  146 QREILTMLA--AGESNKEIGRALNISTGTVKAHLESL 180
Cdd:pfam13412   3 DRKILNLLQenPRISQRELAERLGLSPSTVNRRLKRL 39
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
99-188 3.88e-03

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 36.80  E-value: 3.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316  99 AIVPRDSTVETFALAVNSAAMGMMFLP---GDWRTTPEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKA 175
Cdd:PRK09958  98 GFVSKKEGMNNIIAAIEAAKNGYCYFPfslNRFVGSLTSDQQKLDSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVST 177

                         90
                 ....*....|...
gi 985002316 176 HLESLYRRLEVKN 188
Cdd:PRK09958 178 YKSRLMEKLECKS 190
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-188 4.61e-03

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 36.74  E-value: 4.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316   1 MQIVMFDRQSIFIHGMKISLQQrIPGVSIQGASQ-ADELWQKLESYPEALVMLD----GDQDGEFCYwLLQKTVVQFPEV 75
Cdd:PRK10840   4 MNVIIADDHPIVLFGIRKSLEQ-IEWVNVVGEFEdSTALINNLPKLDAHVLITDlsmpGDKYGDGIT-LIKYIKRHFPSL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985002316  76 KVLITATDCNKRWLQEVIHFNVLAIVPRDSTVETFALAVNSAAMGMMFLPGDWRTTPEKDIKDL---KSLSARQREILTM 152
Cdd:PRK10840  82 SIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGygdKRLSPKESEVLRL 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 985002316 153 LAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKN 188
Cdd:PRK10840 162 FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVEN 197
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
146-183 5.21e-03

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


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 36.01  E-value: 5.21e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 985002316 146 QREILTMLAAGE--SNKEIGRALNISTGTVKAHLESLYRR 183
Cdd:COG3398   99 PRRILLYLLENPgaTNKELAEELGISRSTVSWHLKRLEED 138
LexA_DNA_bind pfam01726
LexA DNA binding domain; This is the DNA binding domain of the LexA SOS regulon repressor ...
 142-183 5.93e-03

LexA DNA binding domain; This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.


Pssm-ID: 396335 [Multi-domain]  Cd Length: 63  Bit Score: 34.28  E-value: 5.93e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 985002316  142 LSARQREILTMLAA-------GESNKEIGRALNI-STGTVKAHLESLYRR 183
Cdd:pfam01726   2 LTERQREVLDFIKAsieetgyPPSRREIARALGLrSPNAAEEHLKALERK 51
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
148-182 6.65e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 34.11  E-value: 6.65e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 985002316   148 EILTMLAAGE-SNKEIGRALNISTGTVKAHLESLYR 182
Cdd:smart00418   1 KILKLLAEGElCVCELAEILGLSQSTVSHHLKKLRE 36
 
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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