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Conserved domains on  [gi|940202334|gb|KPY14248|]
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RNA polymerase sigma-70 factor, ECF subfamily [Pseudomonas savastanoi pv. nerii]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11485971)

sigma-70 family RNA polymerase sigma factor; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 11-168 7.08e-111

RNA polymerase sigma factor; Provisional


:

Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 312.16  E-value: 7.08e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  11 HTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQAL 90
Cdd:PRK12528   4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEAL 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 940202334  91 AELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRCYFAL 168
Cdd:PRK12528  84 AQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCYFAL 161
 
Name Accession Description Interval E-value
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 11-168 7.08e-111

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 312.16  E-value: 7.08e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  11 HTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQAL 90
Cdd:PRK12528   4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEAL 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 940202334  91 AELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRCYFAL 168
Cdd:PRK12528  84 AQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCYFAL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-163 2.02e-34

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: 118.94  E-value: 2.02e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  14 ESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDT-PQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQALAE 92
Cdd:COG1595   20 EELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAE 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 940202334  93 LPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA--ALR 163
Cdd:COG1595  100 ELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRArkKLR 172
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-160 2.57e-29

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: 105.12  E-value: 2.57e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   14 ESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIE-PRAFLTTIAKRVLCNHYRRQDLEHAYYQALAE 92
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGsFKAWLFRIARNLILDYLRRKRRLRRELDLLEE 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 940202334   93 LPEcVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:TIGR02937  84 LLD-SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRA 150
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-81 5.18e-13

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 60.68  E-value: 5.18e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 940202334   16 LYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGAR---DTPQIIEPRAFLTTIAKRVLCNHYRRQD 81
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIerfDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-160 2.06e-05

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: 40.17  E-value: 2.06e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 940202334 111 LVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRA 50
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 134-160 3.92e-04

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 36.74  E-value: 3.92e-04
                           10        20
                   ....*....|....*....|....*..
gi 940202334   134 VDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:smart00421  16 AEGLTNKEIAERLGISEKTVKTHLSNI 42
transpos_IS21 NF033546
IS21 family transposase;
135-162 5.46e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 36.03  E-value: 5.46e-03
                         10        20
                 ....*....|....*....|....*...
gi 940202334 135 DGLSHGQIAAELGISIATVKRHLNKAAL 162
Cdd:NF033546   7 QGLSIREIARELGISRNTVRKYLRRAGL 34
 
Name Accession Description Interval E-value
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 11-168 7.08e-111

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 312.16  E-value: 7.08e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  11 HTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQAL 90
Cdd:PRK12528   4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEAL 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 940202334  91 AELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRCYFAL 168
Cdd:PRK12528  84 AQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCYFAL 161
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 6-168 2.51e-54

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 169.36  E-value: 2.51e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   6 HSALNHTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEHA 85
Cdd:PRK12525   4 GSIKNTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLERA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  86 YYQALAELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRCY 165
Cdd:PRK12525  84 YLQSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163


                 ...
gi 940202334 166 FAL 168
Cdd:PRK12525 164 QGF 166
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 2-168 1.18e-52

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 165.41  E-value: 1.18e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   2 MPIAHSALNHTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQD 81
Cdd:PRK12523   1 MSSAQSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  82 LEHAYYQALAELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAA 161
Cdd:PRK12523  81 LEQAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGL 160


                 ....*..
gi 940202334 162 LRCYFAL 168
Cdd:PRK12523 161 RQCYIAL 167
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 11-164 3.31e-52

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 164.21  E-value: 3.31e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  11 HTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQAL 90
Cdd:PRK09651  10 LTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEML 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 940202334  91 AELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRC 164
Cdd:PRK09651  90 ALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 13-164 2.40e-42

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 139.30  E-value: 2.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  13 VESLYRAHNTWLTTWLRRRLgcpHS-----AADLAQDTFIKVLGARDTPQ---IIEPRAFLTTIAKRVLCNHYRRQDLEH 84
Cdd:PRK12529  15 VATLYRENHAWLRNWLAYRL---RSwgrgvADDLAHDIFLRILASRDGGQreaIRQPRAYLARIANCVLVSWRRRQSLEL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  85 AYYQALAELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRC 164
Cdd:PRK12529  92 AWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTC 171
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-163 2.02e-34

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: 118.94  E-value: 2.02e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  14 ESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDT-PQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQALAE 92
Cdd:COG1595   20 EELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAE 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 940202334  93 LPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA--ALR 163
Cdd:COG1595  100 ELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRArkKLR 172
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-168 1.81e-31

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 111.22  E-value: 1.81e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   1 MMPIAHSALNHTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQII-EPRAFLTTIAKRVLCNHYRR 79
Cdd:PRK11924   3 LMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKgSARTWLLTIARNVCYDLLRR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  80 QDLEHAYYQALAELPECV--APSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHL 157
Cdd:PRK11924  83 RRREKAVLSDDALEPEFAetAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRL 162

                        170
                 ....*....|.
gi 940202334 158 NKAALRCYFAL 168
Cdd:PRK11924 163 RRARQLLRECL 173
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-160 2.57e-29

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: 105.12  E-value: 2.57e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   14 ESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIE-PRAFLTTIAKRVLCNHYRRQDLEHAYYQALAE 92
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGsFKAWLFRIARNLILDYLRRKRRLRRELDLLEE 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 940202334   93 LPEcVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:TIGR02937  84 LLD-SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRA 150
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 24-164 8.88e-24

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 90.99  E-value: 8.88e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  24 LTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEHAY-YQALAELPECVAPSEE 102
Cdd:PRK12527   8 LVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEpLEVLDEEERLHSPSPQ 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 940202334 103 ERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRC 164
Cdd:PRK12527  88 TRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 14-160 3.93e-23

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: 89.54  E-value: 3.93e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   14 ESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDT-PQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQALAE 92
Cdd:TIGR02985   4 EQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETlEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   93 LP--ECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:TIGR02985  84 IEerELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKA 153
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 19-164 1.41e-17

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 75.11  E-value: 1.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  19 AHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQALAELPECVA 98
Cdd:PRK07037   6 DNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDGLDVPS 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 940202334  99 P--SEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRC 164
Cdd:PRK07037  86 PeaSPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC 153
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 28-163 1.17e-14

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 67.91  E-value: 1.17e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  28 LRRRLGCPHSAADLAQDTFIKVLgaRDTPQIIEPRAF---LTTIAKRVLCNHYRRQ---------DLEHA-YYQALAELP 94
Cdd:PRK09652  27 LSRLTRDPADAEDLVQETFIKAY--RALHSFRGGAAFytwLYRIARNTAINYLRKQgrrppasdvDAEEAeDFDLADALR 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 940202334  95 ECVAPSEEERAIILETlvELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA--ALR 163
Cdd:PRK09652 105 DISTPENELLSAELEQ--RVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAreALR 173
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 14-160 9.05e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 65.87  E-value: 9.05e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  14 ESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQiiePRAFLTT----IAKRVLCNHYRRQDL---EHAY 86
Cdd:PRK12513  29 EALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQ---PRARFRTwlyqIARNLLIDHWRRHGArqaPSLD 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 940202334  87 YQALAELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK12513 106 ADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYA 179
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-81 5.18e-13

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 60.68  E-value: 5.18e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 940202334   16 LYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGAR---DTPQIIEPRAFLTTIAKRVLCNHYRRQD 81
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIerfDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 111-164 1.96e-11

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: 55.93  E-value: 1.96e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 940202334  111 LVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALRC 164
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 13-163 2.54e-10

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: 55.86  E-value: 2.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   13 VESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARD-TPQIIEPRAFLTTIAKRVLCNHYRRQDLEHAyyqALA 91
Cdd:TIGR02983   8 FTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDrIRDPDAPDAYVRRVLVNLARSRWRRRRLLEL---PTR 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 940202334   92 ELPECVAPSEEERAIILETLVeldQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNK--AALR 163
Cdd:TIGR02983  85 ELPDAAAPDPAPDVALRAALA---RALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRalARLR 155
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 12-154 2.82e-10

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 56.15  E-value: 2.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  12 TVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKV---LGARDTPQIIepRAFLTTIAKRVLCNHYRRQdlehayyQ 88
Cdd:PRK09637   2 KLESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKThsnLHSLKDGSSI--KSWLYQIANNTIIDFYRKK-------N 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 940202334  89 ALAELP--ECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVK 154
Cdd:PRK09637  73 RSEELPddLLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAK 140
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 11-159 1.07e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 54.17  E-value: 1.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  11 HTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEHAYYQAL 90
Cdd:PRK12541   5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTTTIEE 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 940202334  91 AELPEcvAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNK 159
Cdd:PRK12541  85 FHLPN--VPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 37-160 2.59e-09

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 53.51  E-value: 2.59e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  37 SAADLAQDTFIKVLGA-RDTPQIIEPRAFLTTIAKRVLCNHYRRqdLEHAYYQALAELPECVApSEEERAIILETLVELD 115
Cdd:PRK09649  49 SADDLTQETFLRAIGAiPRFSARSSARTWLLAIARHVVADHIRH--VRSRPRTTRGARPEHLI-DGDRHARGFEDLVEVT 125

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 940202334 116 QLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK09649 126 TMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARA 170
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
11-163 3.42e-08

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 50.46  E-value: 3.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  11 HTVESLYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIK------VLGARDTPqiiePRAFLTTIAKRVLCNHYR-RQDLE 83
Cdd:PRK09645   9 ALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRawqhpeVLADTGRS----ARAWLFTVARNLVIDERRsARARP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  84 HAYYQALAELPECVAPSEEERAIILETLVE-LDQLLDGLPVLVKRAFLMsqvdGLSHGQIAAELGISIATVKRHLNKA-- 160
Cdd:PRK09645  85 VEGGDDVLGVPEQSAPDEVDRALDRLLVADaLAQLSPEHRAVLVRSYYR----GWSTAQIAADLGIPEGTVKSRLHYAlr 160


                 ...
gi 940202334 161 ALR 163
Cdd:PRK09645 161 ALR 163
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 27-167 6.97e-08

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 49.78  E-value: 6.97e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  27 WLRRRL-GCPHSAADLAQDTFIKVLGARDTPQiiePRAF---LTTIAKRVLCNHYRRQdlEHAYYQALAELPECVaPSEE 102
Cdd:PRK09647  43 RLAYRLsGNQHDAEDLTQETFIRVFRSLQNYQ---PGTFegwLHRITTNLFLDMVRRR--ARIRMEALPEDYDRV-PGDE 116

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 940202334 103 ---ERAIILETL-VELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKR--HLNKAALRCYFA 167
Cdd:PRK09647 117 pnpEQIYHDARLdPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSriHRGRQQLRAALA 187
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 38-160 1.36e-07

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 48.41  E-value: 1.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  38 AADLAQDTFIKVLgaRDTPQIIE-PRAFLTTIAKRVLCNHYRRQDLEHAYYQALAELPEC-VAPSEEERAIILETLVELD 115
Cdd:PRK09639  30 AEDLAQEVFLRLY--RSDFKGIEnEKGWLIKSARNVAYNYLRSEKRRRARILGEFQWQEVdNEPSPEEIWIRKEEITKVQ 107

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 940202334 116 QLLDGLPVLvKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK09639 108 EVLAKMTER-DRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARA 151
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 32-163 1.59e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 48.90  E-value: 1.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  32 LGCPHSAADLAQDTFIKvLGARDT--PQIIEPRAFLTTIAKRVLCNHYRRQD-----LEHAYYQALAELPEcvaPSEEER 104
Cdd:PRK12519  50 LGNSQEAEDLTQEIFLS-LWRKSSydPKRGSLSSYLLTLTRSRAIDRLRSRRsrqrlLERWQQELLGEASE---DTPLEQ 125

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 940202334 105 AIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALR 163
Cdd:PRK12519 126 ASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLK 184
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 17-154 2.24e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 45.43  E-value: 2.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  17 YRAHNTWLTT----WLRRRL-GCPHSAADLAQDTFIKVLGARDTPQIIEP-RAFLTTIAKRVLCNHYRRQDLEHAYYQAL 90
Cdd:PRK12536  23 YRQFLSELAAhlrgFLRRRLpQLPDEVEDLVQEILLAVHNARHTYRADQPlTAWVHAIARYKLMDFLRSRARREALHDPL 102

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 940202334  91 AELPECVAPSEEERAiilETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVK 154
Cdd:PRK12536 103 DDESELFATSDDEAA---EARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVK 163
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-160 2.06e-05

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: 40.17  E-value: 2.06e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 940202334 111 LVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRA 50
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 41-157 3.22e-05

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 42.02  E-value: 3.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334   41 LAQDTFIKVLGARDTPQIIEPRAFLTTIAK---RVLCNHYRR-QDLEHAYYQALAELPECVAPSEEERAIILETLVELDQ 116
Cdd:pfam07638  52 LVHEAFVRLVDTEDFPDWSGRGHFFAAAAEamrRILIDHARRrQRQKRGGDVQRRELDEVVDNGDSPNPDLLLDLDEALE 131

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 940202334  117 LLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHL 157
Cdd:pfam07638 132 QLFSLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNW 172
PRK06930 PRK06930
positive control sigma-like factor; Validated
 116-163 4.42e-05

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 41.64  E-value: 4.42e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 940202334 116 QLLDGLPVLVKR---AFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALR 163
Cdd:PRK06930 107 RIEDALSVLTERekeVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKK 157
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
38-154 4.71e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 41.64  E-value: 4.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  38 AADLAQDTFIKVLGARDTPQIIEP-RAFLTTIAKRVLCNHYRRQdlehayYQALAELP----ECVAPSEEERAIilETLV 112
Cdd:PRK12539  52 AEDLVQEALMAIHTRRHTYDPEQPlTPWVYAIARYKLIDHLRRT------RASLADVPiddaDELVAHDDHAAV--ESTL 123

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 940202334 113 ELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVK 154
Cdd:PRK12539 124 DLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK 165
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 36-163 5.21e-05

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 41.40  E-value: 5.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  36 HSAADLAQDTFIKVLGARDTPQIIEPRAFLTTIAKRVLCNHYRRQDLEhaYYQALAELPECVAPSEEERAIILETLVELD 115
Cdd:PRK09644  26 HAAEDLLQETFYRAYIYLEDYDNQKVKPWLFKVAYHTFIDFVRKEKKV--SFVGTDEIEAIQAESTEEYVVAKNSYEKLI 103

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 940202334 116 QLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALR 163
Cdd:PRK09644 104 QIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKR 151
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 30-160 5.82e-05

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 41.83  E-value: 5.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  30 RRLGCPHSAADLAQDTFIKVLGArDTPQIIEPRAFLTTIAKRvLC------NHYRRQdlehayyQALAE-LPEcvaPSEE 102
Cdd:PRK09636  23 RMLGSVADAEDIVQEAWLRWNNA-DRAQIRDPRAWLTRVVTR-LCldrlrsARHRRE-------TYVGPwLPE---PVVE 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 940202334 103 ERAIILETLVELDQL-------LDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK09636  91 ELDDPLEAVVAAEDLslalmlaLERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRA 155
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 35-163 6.53e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 41.31  E-value: 6.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  35 PHSAADLAQDTFIKVLGARDTpqiIEP----RAFLTTIAKRVLCNHYRRQDLEHAYYQALAELPECVAPSEEERAIileT 110
Cdd:PRK12511  28 SAEAEDLVHDALVRALERRAS---FRSggnlRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQEHAV---R 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 940202334 111 LVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLN--KAALR 163
Cdd:PRK12511 102 LAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGraRAALR 156
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 30-154 1.25e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 40.64  E-value: 1.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  30 RRLGCPHSAADLAQDTFIKVLgaRDTPQIIEPRAFLTTIAKRVLCN----HYRRQDLEHAYYQALAELPEcVAPSEEERA 105
Cdd:PRK12524  45 RVLGDRAEAEDVTQEAMLRLW--RIAPDWRQGEARVSTWLYRVVCNlctdRLRRRRRASVDLDDAPEPAD-AAPGAEEAL 121

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 940202334 106 IILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVK 154
Cdd:PRK12524 122 IEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVE 170
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 38-160 2.32e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 39.95  E-value: 2.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  38 AADLAQDTFIKVLGARDT--PQIIEPrAFLTTIAKRVLCNHYRR-----QDLEHAYYQALAELPECVAPSEEEraiilet 110
Cdd:PRK12540  32 ADDLVQETLLRALANIDSfqPGSNLP-AWLFTILRNLFRSDYRKrrrevEDADGSYAKTLKSQPGQNAHLEFE------- 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 940202334 111 lvELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK12540 104 --EFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRA 151
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 28-163 2.70e-04

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 39.51  E-value: 2.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  28 LRRRLGC-PHSAADLAQDTFIKVL-GARD-TPQIIEPRAFLTTIAKRVLCNHYRRqdlehayyqaLAELPECVAPSEEER 104
Cdd:PRK13919  39 LARRMGLdGAAAEDVVQEVFIRVWkKAKEfDPRRGSARAWLLALAHHAAVDHVRR----------RAARPQPLEPDEREP 108

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334 105 AII------LETLVELDQL-----LDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALR 163
Cdd:PRK13919 109 EAFdlpgpgLDEEGHLDRTrlgraLKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSR 178
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 134-160 3.92e-04

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 36.74  E-value: 3.92e-04
                           10        20
                   ....*....|....*....|....*..
gi 940202334   134 VDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:smart00421  16 AEGLTNKEIAERLGISEKTVKTHLSNI 42
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 32-163 4.68e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 38.79  E-value: 4.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  32 LGCPHSAADLAQDTFIKVLGARDTPQI-IEPRAFLTTIAKRVLCNHYRR-----QDLEHAYYQALAELPECVAPSEeera 105
Cdd:PRK12516  31 IGRHDRADDLVQDTIMKAWAKQDHFEVgTNMKAWLFTILRNEFYSQMRKrgrevQDTDGMFTEQLAVHPSQYGTLD---- 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 940202334 106 iiletLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALR 163
Cdd:PRK12516 107 -----LQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQR 159
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
82-160 6.80e-04

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 38.53  E-value: 6.80e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 940202334  82 LEHAYYQALAELPECVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQvdGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:COG2909   85 LALDPEEALALLERLLALAEAAGRLLLRALALRALGDREEALAALRRRLLAE--GLSNKEIAERLFISVNTVKTHLRNI 161
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 30-163 1.25e-03

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 37.75  E-value: 1.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  30 RRLGCPHSAADLAQDTFIKVLGARDTPQiiEPRAFLT---TIAKRVLCNHYRRQ------DLEHA------YYQALAElp 94
Cdd:PRK09641  37 RMLGNRHEAEDAAQEAFIRAYVNIDSYD--INRKFSTwlyRIATNLTIDRLRKRkpdyylDAEVAgtegltMYSQLAA-- 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 940202334  95 ecVAPSEEERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKR--HLNKAALR 163
Cdd:PRK09641 113 --DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTriHRGREALR 181
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 35-160 2.02e-03

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 37.09  E-value: 2.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  35 PHSAADLAQDTFIKVLgaRDTPQIIEPRAFLTTI-------AKRVLCNHYRRQ-----DLEHA-YYQALAELPECVAPse 101
Cdd:PRK11923  44 TAEAQDVAQEAFIKAY--RALGNFRGDSAFYTWLyriaintAKNHLVSRGRRPpdsdvSSEDAeFYDGDHALKDIESP-- 119

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 940202334 102 eERAII---LETLVEldQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK11923 120 -ERALLrdeIEGTVH--RTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRA 178
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 32-160 2.46e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 36.80  E-value: 2.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  32 LGCPHSAADLAQDTFIKVLGA------RDTPqiiepRAFLTTIAKRVLCNHYR----RQDLEHAYYQALAelpecVAPSE 101
Cdd:PRK12535  45 LGGHDIADDLTQETYLRVMSAlprfaaRSSA-----RTWLLSLARRVWVDNIRhdmaRPRKSATEYEDAA-----ATTAS 114

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 940202334 102 EERAIILETLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK12535 115 NETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARA 173
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 134-158 2.61e-03

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: 36.02  E-value: 2.61e-03
                         10        20
                 ....*....|....*....|....*
gi 940202334 134 VDGLSHGQIAAELGISIATVKRHLN 158
Cdd:COG2197   82 AEGLSNKEIAERLGISERTVKTHVS 106
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 16-160 2.85e-03

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 36.54  E-value: 2.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  16 LYRAHNTWLTTWLRRRLGCPHSAADLAQDTFIKVLGARDTPQiiePRA----FLTTIAKRVLCNHYRRQDLEHAYYQALA 91
Cdd:PRK09638  23 LFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQ---GRSkfstWLISIASRLYKDHLRKQKREKLRLQRAK 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 940202334  92 ELPE-----CVAPSEEERAIILETLVELDQLLDgLPVLVKRAFlmsqvdGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK09638 100 EETLrkekwEAAIKGAEWSEMLDALSKLDPEFR-APVILKHYY------GYTYEEIAKMLNIPEGTVKSRVHHG 166
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 117-160 2.97e-03

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 34.33  E-value: 2.97e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 940202334  117 LLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRA 44
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 135-160 3.24e-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: 34.43  E-value: 3.24e-03
                         10        20
                 ....*....|....*....|....*.
gi 940202334 135 DGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:cd06170   14 EGKTNKEIADILGISEKTVKTHLRNI 39
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 134-158 4.76e-03

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: 34.17  E-value: 4.76e-03
                         10        20
                 ....*....|....*....|....*
gi 940202334 134 VDGLSHGQIAAELGISIATVKRHLN 158
Cdd:COG5905   25 AEGLTNKEIARQLFISEKTVKNHVS 49
near_KaiC_dom TIGR03879
probable regulatory domain; This model describes a common domain shared by two different ...
 109-157 5.18e-03

probable regulatory domain; This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.


Pssm-ID: 163591  Cd Length: 73  Bit Score: 34.32  E-value: 5.18e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 940202334  109 ETLVELDQLLDGLPVLVKRAFLMSQvdglshGQIAAELGISIATVKRHL 157
Cdd:TIGR03879  11 ERLTWVDSLAEAAAALAREEAGKTA------SEIAEELGRTEQTVRNHL 53
transpos_IS21 NF033546
IS21 family transposase;
135-162 5.46e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 36.03  E-value: 5.46e-03
                         10        20
                 ....*....|....*....|....*...
gi 940202334 135 DGLSHGQIAAELGISIATVKRHLNKAAL 162
Cdd:NF033546   7 QGLSIREIARELGISRNTVRKYLRRAGL 34
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 35-163 7.24e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 35.59  E-value: 7.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  35 PHSAADLAQDTFIKVLGARDTPQI-IEPRAFLTTIAKRVLCNHYRRQ-----DLEHAYYQALAELPEcvapsEEERAiil 108
Cdd:PRK12546  31 VAVADDLVQDTIVKAWTNFDKFQEgTNLRAWLFTILRNTFYSDRRKHkrevpDPEGVHAASLAVKPA-----HDGRL--- 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 940202334 109 eTLVELDQLLDGLPVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKAALR 163
Cdd:PRK12546 103 -AMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARAR 156
TnsD pfam15978
Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins ...
 122-159 9.14e-03

Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins type D.


Pssm-ID: 379756  Cd Length: 360  Bit Score: 35.47  E-value: 9.14e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 940202334  122 PVLVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNK 159
Cdd:pfam15978 185 PVWEERLKILVEDEGLSLREIAKELGVDIKTVKRYARK 222
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 38-160 9.93e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 34.84  E-value: 9.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940202334  38 AADLAQDTFIKVLGARDTPQIIEP-RAFLTTIAKRVLCNHYRRQ--------DLEHAYYQALAELPECVAPSEEE-RAII 107
Cdd:PRK12522  30 AEDIFQETWIKVFSSRHQLSYVENyKKWITTICVRTFYDFYRKKkrwkdrilDLFHKEDGGEIEFADDVNISEEFiQKVE 109

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 940202334 108 LETLVELDQLLDGLpvlVKRAFLMSQVDGLSHGQIAAELGISIATVKRHLNKA 160
Cdd:PRK12522 110 AEMIREVIQLLNEK---YKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYA 159
 
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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