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Conserved domains on  [gi|636855738|ref|WP_024375010|]
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MULTISPECIES: LuxR C-terminal-related transcriptional regulator [Vibrio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10100 super family cl32463
transcriptional regulator CsgD;
83-217 6.20e-35

transcriptional regulator CsgD;


The actual alignment was detected with superfamily member PRK10100:

Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 123.44  E-value: 6.20e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855738  83 AKEVVINCPPEAESKSLFKWQKLSGVFFADDDIEALVKGMNKILEDEMWLTRKLAQEYIMHyrAGAPAVTSQVYTRLTRR 162
Cdd:PRK10100  82 IKILLLNTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITH--SGNYRYNSTESALLTHR 159

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 636855738 163 EQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKSNI 217
Cdd:PRK10100 160 EKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDNL 214
 
Name Accession Description Interval E-value
PRK10100 PRK10100
transcriptional regulator CsgD;
83-217 6.20e-35

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 123.44  E-value: 6.20e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855738  83 AKEVVINCPPEAESKSLFKWQKLSGVFFADDDIEALVKGMNKILEDEMWLTRKLAQEYIMHyrAGAPAVTSQVYTRLTRR 162
Cdd:PRK10100  82 IKILLLNTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITH--SGNYRYNSTESALLTHR 159

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 636855738 163 EQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKSNI 217
Cdd:PRK10100 160 EKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDNL 214
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 158-213 1.07e-22

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 86.81  E-value: 1.07e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 636855738   158 RLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 149-213 1.28e-22

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


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 87.32  E-value: 1.28e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 636855738 149 PAVTSQVYTRLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:COG5905    3 PSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWA 67
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 159-215 6.13e-19

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: 77.19  E-value: 6.13e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 636855738 159 LTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKS 215
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
159-213 9.91e-17

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 71.46  E-value: 9.91e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 636855738  159 LTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 157-201 8.47e-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: 8.47e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 636855738  157 TRLTRREQQIIKL-LGSGASNIEIADKLYVSENTVKTHLHNVFKKI 201
Cdd:TIGR02937 109 EKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK10100 PRK10100
transcriptional regulator CsgD;
83-217 6.20e-35

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 123.44  E-value: 6.20e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855738  83 AKEVVINCPPEAESKSLFKWQKLSGVFFADDDIEALVKGMNKILEDEMWLTRKLAQEYIMHyrAGAPAVTSQVYTRLTRR 162
Cdd:PRK10100  82 IKILLLNTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITH--SGNYRYNSTESALLTHR 159

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 636855738 163 EQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKSNI 217
Cdd:PRK10100 160 EKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDNL 214
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 158-213 1.07e-22

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 86.81  E-value: 1.07e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 636855738   158 RLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 149-213 1.28e-22

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


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 87.32  E-value: 1.28e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 636855738 149 PAVTSQVYTRLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:COG5905    3 PSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWA 67
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 159-216 3.96e-22

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: 87.64  E-value: 3.96e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 636855738 159 LTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKSN 216
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 159-215 6.13e-19

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: 77.19  E-value: 6.13e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 636855738 159 LTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKS 215
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
158-213 2.35e-17

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 76.72  E-value: 2.35e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 636855738 158 RLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:COG2771  127 GLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALA 182
GerE pfam00196
Bacterial regulatory proteins, luxR family;
159-213 9.91e-17

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 71.46  E-value: 9.91e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 636855738  159 LTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
145-215 1.20e-15

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 72.04  E-value: 1.20e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 636855738 145 RAGAPAVTSQVYTRLTRREQ--QIIK--LLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKS 215
Cdd:COG2909  105 AAGRLLLRALALRALGDREEalAALRrrLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARE 179
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 107-213 2.46e-13

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 66.21  E-value: 2.46e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855738 107 GVFFADDDIEALVKGMNKILEDEMWLTRKLAQEYIMHYRAGAPAVTSQVyTRLTRREQQIIKLLGSGASNIEIADKLYVS 186
Cdd:PRK10651 105 GYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLAASLRANRATTERDV-NQLTPRERDILKLIAQGLPNKMIARRLDIT 183

                         90       100
                 ....*....|....*....|....*..
gi 636855738 187 ENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:PRK10651 184 ESTVKVHVKHMLKKMKLKSRVEAAVWV 210
PRK15369 PRK15369
two component system response regulator;
157-214 2.43e-12

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 63.56  E-value: 2.43e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 636855738 157 TRLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAK 214
Cdd:PRK15369 148 PLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWAR 205
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
159-215 1.11e-11

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 63.42  E-value: 1.11e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 636855738 159 LTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKS 215
Cdd:PRK04841 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQD 895
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 156-205 1.31e-11

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: 61.27  E-value: 1.31e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 636855738 156 YTRLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKN 205
Cdd:COG4566  135 LASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
156-211 2.42e-09

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 55.24  E-value: 2.42e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 636855738 156 YTRLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALI 211
Cdd:PRK10403 151 FSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATI 206
PRK10188 PRK10188
transcriptional regulator SdiA;
158-213 9.62e-08

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 50.94  E-value: 9.62e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 636855738 158 RLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWA 213
Cdd:PRK10188 179 NFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYA 234
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
140-215 3.41e-07

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 49.10  E-value: 3.41e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 636855738 140 YIMHYRAGAPAVTSQVytrLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQALIWAKS 215
Cdd:PRK09935 134 YIKSNKCSTNSSTDTV---LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKL 206
PRK15201 PRK15201
fimbriae biosynthesis transcriptional regulator FimW;
132-218 1.18e-04

fimbriae biosynthesis transcriptional regulator FimW;


Pssm-ID: 185123  Cd Length: 198  Bit Score: 41.57  E-value: 1.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855738 132 LTRKLAqeYIMHYRAGAPAVTSQVYTRLTRR-----EQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNR 206
Cdd:PRK15201 104 ITRKMI--LILHKRALRHSVPSGICHYCTTRhfsvtERHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTE 181

                         90
                 ....*....|..
gi 636855738 207 LQALIWAKSNIG 218
Cdd:PRK15201 182 QQFLKYIRVNLH 193
rcsA PRK15411
transcriptional regulator RcsA;
158-206 3.61e-04

transcriptional regulator RcsA;


Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 40.11  E-value: 3.61e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 636855738 158 RLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNR 206
Cdd:PRK15411 137 SLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNK 185
PRK10360 PRK10360
transcriptional regulator UhpA;
159-208 6.01e-04

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 39.58  E-value: 6.01e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 636855738 159 LTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHNVFKKINAKNRLQ 208
Cdd:PRK10360 138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVE 187
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 154-201 2.21e-03

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 37.62  E-value: 2.21e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 636855738 154 QVYTRLTRREQQIIKLLGSGASNIEIADKLYVSENTVKTHLHN---VFKKI 201
Cdd:PRK09639 108 EVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARakkKFRKI 158
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 157-201 8.47e-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: 8.47e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 636855738  157 TRLTRREQQIIKL-LGSGASNIEIADKLYVSENTVKTHLHNVFKKI 201
Cdd:TIGR02937 109 EKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 158-201 8.69e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 33.58  E-value: 8.69e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 636855738  158 RLTRREQQIIKLL-GSGASNIEIADKLYVSENTVKTHLHNVFKKI 201
Cdd:pfam08281  10 ELPPRQREVFLLRyLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
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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