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Conserved domains on  [gi|895953810|ref|WP_049038674|]
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response regulator transcription factor [Elizabethkingia anophelis]

Protein Classification

response regulator transcription factor( domain architecture ID 11450879)

response regulator transcription factor with a signal receiver (REC) domain and a LuxR family helix-turn-helix (HTH) domain that may be part of a two-component regulatory system; similar to Staphylococcus aureus response regulator VraR

CATH:  1.10.10.10
Gene Ontology:  GO:0000160|GO:0006355|GO:0003677
PubMed:  10966457
SCOP:  3001179

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 ...
 191-251 3.71e-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: 3.71e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKLL 251
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 191-251 3.71e-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: 3.71e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKLL 251
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 191-245 2.03e-16

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 71.02  E-value: 2.03e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 895953810   191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYV 245
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 ...
 191-246 7.05e-16

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: 69.49  E-value: 7.05e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVI 246
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAI 56
GerE pfam00196
Bacterial regulatory proteins, luxR family;
190-245 7.14e-12

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 58.75  E-value: 7.14e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 895953810  190 NLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYV 245
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
PRK10100 PRK10100
transcriptional regulator CsgD;
191-248 1.04e-07

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 51.02  E-value: 1.04e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHH 248
Cdd:PRK10100 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 191-233 8.68e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 35.79  E-value: 8.68e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 895953810  191 LTERETEILR-FYNQGLSINEIAEKIFISVDTVKFHRRKLFDKL 233
Cdd:TIGR02937 111 LPEREREVLVlRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 191-251 3.71e-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: 3.71e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKLL 251
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
186-251 2.45e-17

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 77.49  E-value: 2.45e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 895953810 186 RKKTNLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKLL 251
Cdd:COG2771  123 ARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALRLGLI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 191-245 2.03e-16

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 71.02  E-value: 2.03e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 895953810   191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYV 245
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 ...
 191-246 7.05e-16

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: 69.49  E-value: 7.05e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVI 246
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAI 56
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 190-251 3.99e-13

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: 62.67  E-value: 3.99e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 895953810 190 NLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKLL 251
Cdd:COG5905   12 LLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLL 73
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
200-251 6.17e-12

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 62.41  E-value: 6.17e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 895953810 200 RFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKLL 251
Cdd:COG2909  132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLL 183
GerE pfam00196
Bacterial regulatory proteins, luxR family;
190-245 7.14e-12

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 58.75  E-value: 7.14e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 895953810  190 NLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYV 245
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 191-242 1.44e-10

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: 58.96  E-value: 1.44e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEAL 242
Cdd:COG4566  138 LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELV 189
PRK10100 PRK10100
transcriptional regulator CsgD;
191-248 1.04e-07

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 51.02  E-value: 1.04e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHH 248
Cdd:PRK10100 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 184-249 1.08e-07

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 50.80  E-value: 1.08e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 895953810 184 SERKKTNLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHK 249
Cdd:PRK10651 149 TERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQER 214
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
189-251 2.49e-07

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 49.87  E-value: 2.49e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 895953810 189 TNLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKLL 251
Cdd:PRK09935 148 TVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLHELL 210
PRK15369 PRK15369
two component system response regulator;
163-246 6.53e-07

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 48.54  E-value: 6.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 895953810 163 VTIGK--LNSDLLWEMDLMTNKWSERKKTNLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINE 240
Cdd:PRK15369 120 VAVGKryIDPALNREAILALLNADDTNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAE 199


                 ....*.
gi 895953810 241 ALAYVI 246
Cdd:PRK15369 200 LLNWAR 205
PRK10360 PRK10360
transcriptional regulator UhpA;
191-237 6.79e-06

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 45.35  E-value: 6.79e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNN 237
Cdd:PRK10360 138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSN 184
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
191-235 9.73e-06

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 45.23  E-value: 9.73e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEV 235
Cdd:PRK10403 154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198
PRK09483 PRK09483
response regulator; Provisional
 191-251 1.00e-05

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 45.10  E-value: 1.00e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKLL 251
Cdd:PRK09483 149 LSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLL 209
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
191-244 3.12e-04

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 41.85  E-value: 3.12e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAY 244
Cdd:PRK04841 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQH 892
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
190-250 5.49e-04

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 39.88  E-value: 5.49e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 895953810 190 NLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNNINEALAYVIHHKL 250
Cdd:PRK09958 143 SLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKI 203
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 191-233 1.36e-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: 35.87  E-value: 1.36e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 895953810  191 LTERETEILRF-YNQGLSINEIAEKIFISVDTVKFHRRKLFDKL 233
Cdd:pfam04545   5 LPPRERQVLVLrYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 191-234 2.21e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 38.05  E-value: 2.21e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 895953810 191 LTERETEILR-FYNQGLSINEIAEKIFISVDTVKFH----RRKLFDKLE 234
Cdd:COG1595  128 LPPRQREVLVlRYLEGLSYAEIAEILGISEGTVKSRlsraRKKLREALE 176
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 191-237 2.52e-03

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 37.89  E-value: 2.52e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 895953810 191 LTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVNN 237
Cdd:PRK10840 151 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVEN 197
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 177-236 2.85e-03

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 37.80  E-value: 2.85e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 895953810 177 DLMTNKWSERKKTNLTERETEILRFYNQGLSINEIAEKIFISVDTVKFHRRKLFDKLEVN 236
Cdd:PRK11475 121 DRLNNQWYINQSRMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVS 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 191-233 8.68e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 35.79  E-value: 8.68e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 895953810  191 LTERETEILR-FYNQGLSINEIAEKIFISVDTVKFHRRKLFDKL 233
Cdd:TIGR02937 111 LPEREREVLVlRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
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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