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Conserved domains on  [gi|446727572|ref|WP_000804885|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Bacteria]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11495650)

sigma-70 family RNA polymerase sigma factor is a general transcription factor that reversibly binds RNA polymerase and mediates transcription.

Gene Ontology:  GO:0003677|GO:0016987|GO:0006352
PubMed:  28117604

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 79-140 3.84e-12

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: 60.39  E-value: 3.84e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446727572  79 DLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEEFEE 140
Cdd:COG1595  119 EALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
Sig70_bacteroi1 super family cl37203
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 19-135 5.30e-06

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.


The actual alignment was detected with superfamily member TIGR02985:

Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 43.32  E-value: 5.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446727572   19 KRAMEDERKNYMLYLSRIAK--------REVSFSDVGDYLVSQFATTDNYSTDFQIFTLNGLsvgveNDLLSEALRELPD 90
Cdd:TIGR02985  42 NRETLEISESIKAYLFTIVKnrclnylrHKQVEEKYQEELAEIEERELSEADPEEELEAKEL-----EEIIEEAIEKLPE 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 446727572   91 KKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFM 135
Cdd:TIGR02985 117 QCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 79-140 3.84e-12

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: 60.39  E-value: 3.84e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446727572  79 DLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEEFEE 140
Cdd:COG1595  119 EALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 77-135 5.44e-11

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: 56.97  E-value: 5.44e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446727572   77 ENDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFM 135
Cdd:TIGR02937 100 EREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 79-123 2.34e-07

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: 44.75  E-value: 2.34e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 446727572   79 DLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRH 123
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSR 46
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 78-120 2.89e-07

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: 44.40  E-value: 2.89e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 446727572  78 NDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTV 120
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTV 43
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 81-137 1.74e-06

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 45.12  E-value: 1.74e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446727572  81 LSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEE 137
Cdd:PRK09415 121 LASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 19-135 5.30e-06

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: 43.32  E-value: 5.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446727572   19 KRAMEDERKNYMLYLSRIAK--------REVSFSDVGDYLVSQFATTDNYSTDFQIFTLNGLsvgveNDLLSEALRELPD 90
Cdd:TIGR02985  42 NRETLEISESIKAYLFTIVKnrclnylrHKQVEEKYQEELAEIEERELSEADPEEELEAKEL-----EEIIEEAIEKLPE 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 446727572   91 KKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFM 135
Cdd:TIGR02985 117 QCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 35-120 1.49e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 42.37  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446727572  35 RIAKREVSFSDVGDYLVsqfATTDNYSTDFQIftlnglsvgvENDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLK 114
Cdd:PRK12517  89 RFERKQFDLVDIEDDSI---EDDASHSSEEEM----------EQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILD 155


                 ....*.
gi 446727572 115 LNRSTV 120
Cdd:PRK12517 156 LNKNTV 161
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 85-126 6.93e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 32.88  E-value: 6.93e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 446727572    85 LRELPDKKREILLLFyFMDMSDSEIADLLKLNRSTVYRHRTS 126
Cdd:smart00421   1 LASLTPREREVLRLL-AEGLTNKEIAERLGISEKTVKTHLSN 41
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 79-140 3.84e-12

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: 60.39  E-value: 3.84e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446727572  79 DLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEEFEE 140
Cdd:COG1595  119 EALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 77-135 5.44e-11

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: 56.97  E-value: 5.44e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446727572   77 ENDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFM 135
Cdd:TIGR02937 100 EREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 79-137 7.38e-11

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 57.53  E-value: 7.38e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446727572  79 DLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEE 137
Cdd:COG1191  178 EALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 77-137 9.54e-09

RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 50.85  E-value: 9.54e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446727572   77 ENDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEE 137
Cdd:TIGR02983 100 LRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 79-123 2.34e-07

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: 44.75  E-value: 2.34e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 446727572   79 DLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRH 123
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSR 46
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 78-120 2.89e-07

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: 44.40  E-value: 2.89e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 446727572  78 NDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTV 120
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTV 43
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 81-137 1.74e-06

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 45.12  E-value: 1.74e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446727572  81 LSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEE 137
Cdd:PRK09415 121 LASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 19-135 5.30e-06

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: 43.32  E-value: 5.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446727572   19 KRAMEDERKNYMLYLSRIAK--------REVSFSDVGDYLVSQFATTDNYSTDFQIFTLNGLsvgveNDLLSEALRELPD 90
Cdd:TIGR02985  42 NRETLEISESIKAYLFTIVKnrclnylrHKQVEEKYQEELAEIEERELSEADPEEELEAKEL-----EEIIEEAIEKLPE 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 446727572   91 KKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFM 135
Cdd:TIGR02985 117 QCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 84-133 7.98e-06

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: 40.49  E-value: 7.98e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 446727572   84 ALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKK 133
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 69-116 1.31e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 42.72  E-value: 1.31e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 446727572  69 LNGLSVGVENDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLN 116
Cdd:PRK05602 110 DAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDIS 157
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 35-120 1.49e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 42.37  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446727572  35 RIAKREVSFSDVGDYLVsqfATTDNYSTDFQIftlnglsvgvENDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLK 114
Cdd:PRK12517  89 RFERKQFDLVDIEDDSI---EDDASHSSEEEM----------EQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILD 155


                 ....*.
gi 446727572 115 LNRSTV 120
Cdd:PRK12517 156 LNKNTV 161
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 78-140 1.54e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 42.41  E-value: 1.54e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446727572  78 NDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEEFEE 140
Cdd:PRK12543 108 NQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEI 170
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 76-120 5.99e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 40.72  E-value: 5.99e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446727572  76 VENDLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTV 120
Cdd:PRK11924 114 DDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTV 158
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 80-120 1.82e-04

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 39.67  E-value: 1.82e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 446727572  80 LLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTV 120
Cdd:PRK06288 205 VIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRI 245
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 83-128 3.24e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 38.89  E-value: 3.24e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446727572  83 EALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGL 128
Cdd:PRK12519 137 TALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGL 182
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 78-113 7.66e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 37.91  E-value: 7.66e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446727572  78 NDLLSEALRELPDKKREILLLFYFMDMSDSEIADLL 113
Cdd:PRK12538 162 SDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVM 197
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 76-137 8.69e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 37.61  E-value: 8.69e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446727572  76 VENDLLS--------EALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEE 137
Cdd:PRK06811 112 IENEIILkenkeeilKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLN 181
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 79-120 1.43e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 36.98  E-value: 1.43e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 446727572  79 DLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTV 120
Cdd:PRK12513 131 RRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETV 172
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 79-139 1.43e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 36.68  E-value: 1.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446727572  79 DLLSEALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTVYRHRTSGLALIKKFMEEFE 139
Cdd:PRK12527  97 ALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQWE 157
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
92-134 1.72e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 36.66  E-value: 1.72e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 446727572  92 KREILLLFYFMD-MSDSEIADLLKLNRSTVYRHRTSglaLIKKF 134
Cdd:COG2771  130 PREREVLRLLAEgLTLKEIARILGISERTVRTHLKR---IYRKL 170
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 77-129 2.86e-03

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


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 36.37  E-value: 2.86e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446727572  77 ENDLLSEALRELPDK---KREILLLFYFMDMSDSEIADLLKLNRSTVYRH----RTSGLA 129
Cdd:COG3415    9 ERRDLEKLLRKTKDAreaRRLRAVLLLAEGLSVREIAERLGVSRSTVYRWlkryREGGLA 68
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 92-126 3.45e-03

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: 33.66  E-value: 3.45e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446727572  92 KREILLLFYFMD-MSDSEIADLLKLNRSTVYRHRTS 126
Cdd:cd06170    3 PREREVLRLLAEgKTNKEIADILGISEKTVKTHLRN 38
Sig-70_X6 TIGR02999
RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the ...
 78-123 6.76e-03

RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.


Pssm-ID: 132044 [Multi-domain]  Cd Length: 183  Bit Score: 34.99  E-value: 6.76e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 446727572   78 NDLLSEALRELPDKkREILLLFYFMDMSDSEIADLLKLNRSTVYRH 123
Cdd:TIGR02999 126 DDALDKLAQVDPRQ-AEVVELRFFAGLTVEEIAELLGVSVRTVERD 170
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 85-126 6.93e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 32.88  E-value: 6.93e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 446727572    85 LRELPDKKREILLLFyFMDMSDSEIADLLKLNRSTVYRHRTS 126
Cdd:smart00421   1 LASLTPREREVLRLL-AEGLTNKEIAERLGISEKTVKTHLSN 41
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 83-120 7.36e-03

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 35.06  E-value: 7.36e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446727572  83 EALRELPDKKREILLLFYFMDMSDSEIADLLKLNRSTV 120
Cdd:PRK09641 132 EAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTV 169
 
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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