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Conserved domains on  [gi|1195211048|gb|OUG52683|]
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fecI [Klebsiella pneumoniae]

Protein Classification

PRK09651 family protein( domain architecture ID 11484450)

PRK09651 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 2-173 1.15e-119

RNA polymerase sigma factor FecI; Provisional


:

Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 334.86  E-value: 1.15e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048   2 SDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNA 81
Cdd:PRK09651    1 SDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  82 LEKAYLEMLALMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAV 161
Cdd:PRK09651   81 LEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT 160

                         170
                  ....*....|..
gi 1195211048 162 EHCLLFRLEHGL 173
Cdd:PRK09651  161 EHCLLFRLEYGL 172
 
Name Accession Description Interval E-value
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 2-173 1.15e-119

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 334.86  E-value: 1.15e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048   2 SDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNA 81
Cdd:PRK09651    1 SDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  82 LEKAYLEMLALMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAV 161
Cdd:PRK09651   81 LEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT 160

                         170
                  ....*....|..
gi 1195211048 162 EHCLLFRLEHGL 173
Cdd:PRK09651  161 EHCLLFRLEYGL 172
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-164 2.04e-40

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: 134.35  E-value: 2.04e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSS-ETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLA 91
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKlDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELA 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1195211048  92 LMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:COG1595    99 EELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 13-164 3.46e-32

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: 112.83  E-value: 3.46e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSS-ETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLA 91
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEAlDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1195211048  92 LMPEGgAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:TIGR02937  83 ELLDS-DPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-81 8.34e-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: 60.29  E-value: 8.34e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1195211048  16 LYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNA 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 ...
 111-164 1.68e-10

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: 53.65  E-value: 1.68e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1195211048 111 LQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 126-162 3.26e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 34.43  E-value: 3.26e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1195211048  126 REAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKAVE 162
Cdd:smart00421   7 REREVLRLLaEGLTNKEIAERLGISEKTVKTHLSNIMR 44
 
Name Accession Description Interval E-value
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 2-173 1.15e-119

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 334.86  E-value: 1.15e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048   2 SDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNA 81
Cdd:PRK09651    1 SDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  82 LEKAYLEMLALMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAV 161
Cdd:PRK09651   81 LEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT 160

                         170
                  ....*....|..
gi 1195211048 162 EHCLLFRLEHGL 173
Cdd:PRK09651  161 EHCLLFRLEYGL 172
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 10-164 1.62e-56

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 175.03  E-value: 1.62e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  10 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEM 89
Cdd:PRK12528    3 SATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1195211048  90 LALMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:PRK12528   83 LAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 157
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 15-164 8.96e-55

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 170.80  E-value: 8.96e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  15 SLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMP 94
Cdd:PRK12523   14 ALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRAALEQAYLAELALVP 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  95 EGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:PRK12523   94 EAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 16-164 6.94e-51

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 160.88  E-value: 6.94e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  16 LYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPE 95
Cdd:PRK12525   14 MFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLERAYLQSLAEAPE 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1195211048  96 GGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:PRK12525   94 AVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCC 162
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 15-165 8.91e-44

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 143.15  E-value: 8.91e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  15 SLYGTHHGWLKSWLTRKLQSAFD--ADDIAQDTFLRVMSSETLS---TIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEM 89
Cdd:PRK12529   17 TLYRENHAWLRNWLAYRLRSWGRgvADDLAHDIFLRILASRDGGqreAIRQPRAYLARIANCVLVSWRRRQSLELAWLEA 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1195211048  90 LALMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHCL 165
Cdd:PRK12529   97 LATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTCL 172
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-164 2.04e-40

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: 134.35  E-value: 2.04e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSS-ETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLA 91
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKlDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELA 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1195211048  92 LMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:COG1595    99 EELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 5-164 4.72e-33

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 115.45  E-value: 4.72e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048   5 ATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMS-SETLSTIRDPRSFLCTIAKRVMVDLFRRNALE 83
Cdd:PRK11924    7 DATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRkADLFNGKGSARTWLLTIARNVCYDLLRRRRRE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  84 KAYLEMLALMPEGG--APSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAV 161
Cdd:PRK11924   87 KAVLSDDALEPEFAetAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166


                  ...
gi 1195211048 162 EHC 164
Cdd:PRK11924  167 QLL 169
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 13-164 3.46e-32

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: 112.83  E-value: 3.46e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSS-ETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLA 91
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEAlDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1195211048  92 LMPEGgAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:TIGR02937  83 ELLDS-DPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 24-164 8.59e-29

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 104.09  E-value: 8.59e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  24 LKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAY-LEMLALMPEGGAPSPE 102
Cdd:PRK12527    8 LVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEpLEVLDEEERLHSPSPQ 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1195211048 103 ERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:PRK12527   88 TRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 14-160 1.15e-18

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 78.49  E-value: 1.15e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  14 ESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSetLSTIRDP---RSFLCTIAKRVMVDLFRRNALEKAYLEML 90
Cdd:PRK09637    4 ESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSN--LHSLKDGssiKSWLYQIANNTIIDFYRKKNRSEELPDDL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  91 AlmpegGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK09637   82 L-----FEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRG 146
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 38-164 1.55e-17

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 75.11  E-value: 1.55e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  38 ADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYL----EMLALMPEGgaPSPEERESQLETLQL 113
Cdd:PRK07037   25 AEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHgdeeDGLDVPSPE--ASPEAALINRDTLRH 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1195211048 114 VDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:PRK07037  103 VADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC 153
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 13-154 5.52e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 68.95  E-value: 5.52e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRDP-RSFLCTIAKRVMVDLFR----RNALEKAYL 87
Cdd:PRK12513   28 FEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARfRTWLYQIARNLLIDHWRrhgaRQAPSLDAD 107

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1195211048  88 EMLALMPEGGaPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 154
Cdd:PRK12513  108 EQLHALADDG-AAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVK 173
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 12-163 6.86e-15

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 68.05  E-value: 6.86e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  12 TFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSeTLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLA 91
Cdd:PRK09639    4 TFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS-DFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGEF 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1195211048  92 LMPEG-GAPSPEERESQLETLQLVDSMLDGLNGKTReAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEH 163
Cdd:PRK09639   83 QWQEVdNEPSPEEIWIRKEEITKVQEVLAKMTERDR-TVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKK 154
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 32-171 8.06e-14

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 65.83  E-value: 8.06e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  32 LQSAFDADDIAQDTFLRVMSS-ETLSTIRDPRSFLCTIAKRVMVDLFRRnalekayLEMLALMPEGGAP----SPEERES 106
Cdd:PRK09649   44 LSDVGSADDLTQETFLRAIGAiPRFSARSSARTWLLAIARHVVADHIRH-------VRSRPRTTRGARPehliDGDRHAR 116

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1195211048 107 QLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEhCLLFRLEH 171
Cdd:PRK09649  117 GFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD-ALLADAEP 180
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-81 8.34e-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: 60.29  E-value: 8.34e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1195211048  16 LYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNA 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 4.48e-12

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: 57.85  E-value: 4.48e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1195211048 111 LQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 38-160 2.34e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 59.53  E-value: 2.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  38 ADDIAQDTFLRVMSS-ETLSTIRDPRSFLCTIAKRVMVDLFR----RNALEKAYLEMLAlmpeGGAPSPEERESQLETLQ 112
Cdd:PRK12535   51 ADDLTQETYLRVMSAlPRFAARSSARTWLLSLARRVWVDNIRhdmaRPRKSATEYEDAA----ATTASNETTGSWSEWID 126

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1195211048 113 lVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK12535  127 -VRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARA 173
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 30-163 4.76e-11

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 59.55  E-value: 4.76e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  30 RKLQSAFDADDIAQDTFLRVMSSETlSTIRDPRSFLCTIAKRVMVDLFRRNALEK-AYLEMlaLMPEggaPSPEERESQL 108
Cdd:PRK09636   23 RMLGSVADAEDIVQEAWLRWNNADR-AQIRDPRAWLTRVVTRLCLDRLRSARHRReTYVGP--WLPE---PVVEELDDPL 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1195211048 109 ETLQLVDS-------MLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEH 163
Cdd:PRK09636   97 EAVVAAEDlslalmlALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH 158
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-164 1.68e-10

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: 53.65  E-value: 1.68e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1195211048 111 LQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 15-160 2.33e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 56.61  E-value: 2.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  15 SLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIR-DPRSFLCTIAKRVMVDLFR--RNA---LEKAYLE 88
Cdd:PRK12519   33 VLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRgSLSSYLLTLTRSRAIDRLRsrRSRqrlLERWQQE 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1195211048  89 MLAlmpEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK12519  113 LLG---EASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQG 181
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 12-163 4.47e-10

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 55.58  E-value: 4.47e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  12 TFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSetLSTIRDPRSF---LCTIAKRVMVDLFRRNALEKAYLE 88
Cdd:PRK09652   11 AFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRA--LHSFRGGAAFytwLYRIARNTAINYLRKQGRRPPASD 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  89 MLALMPEGGAPSPEER-----ESQLETLQL---VDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK09652   89 VDAEEAEDFDLADALRdistpENELLSAELeqrVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRA 168


                  ...
gi 1195211048 161 VEH 163
Cdd:PRK09652  169 REA 171
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 13-161 9.15e-10

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 54.64  E-value: 9.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMssETLSTIRDPRSF---LCTIAKRVMVDLFRRNALEKAYLEM 89
Cdd:PRK09638   20 LTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAI--ENLSSFQGRSKFstwLISIASRLYKDHLRKQKREKLRLQR 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1195211048  90 LAlmpeGGAPSPEERESQLETLQLVDsMLDGLNG---KTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAV 161
Cdd:PRK09638   98 AK----EETLRKEKWEAAIKGAEWSE-MLDALSKldpEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGI 167
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 37-154 2.26e-09

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 54.02  E-value: 2.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  37 DADDIAQDTFLRVMSSetLSTIRdPRSF---LCTIAKRVMVDLFRRnaleKAYLEMLALmPE------GGAPSPEE--RE 105
Cdd:PRK09647   54 DAEDLTQETFIRVFRS--LQNYQ-PGTFegwLHRITTNLFLDMVRR----RARIRMEAL-PEdydrvpGDEPNPEQiyHD 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1195211048 106 SQLETLqlVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 154
Cdd:PRK09647  126 ARLDPD--LQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVR 172
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 30-171 1.32e-08

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 51.62  E-value: 1.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  30 RKLQSAFDADDIAQDTFLRV-MSSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEkAYLE----------MLALMPEGGa 98
Cdd:PRK09641   37 RMLGNRHEAEDAAQEAFIRAyVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPD-YYLDaevagtegltMYSQLAADD- 114

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1195211048  99 PSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEhCLLFRLEH 171
Cdd:PRK09641  115 ALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGRE-ALRKQLRH 186
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 12-155 2.02e-08

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 50.78  E-value: 2.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  12 TFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMssETLSTIRDPRSF---LCTIAkRVMVDLFRRN------AL 82
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAW--RKFDQFDPGTNFvawARGIA-RNKVLNYRRKlgrdrlVF 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1195211048  83 EKAYLEMLALMPEggapsPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKK 155
Cdd:TIGR02989  79 DDDLLEALAAEAE-----PTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYK 146
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
5-154 8.69e-08

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 49.31  E-value: 8.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048   5 ATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVM--SSETLSTIRDPRSFLCTIAKRVMVDLFR--RN 80
Cdd:PRK09645    3 MATAEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWqhPEVLADTGRSARAWLFTVARNLVIDERRsaRA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1195211048  81 ALEKAYLEMLALmPEggAPSPEERESQLETLQLVDSmLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 154
Cdd:PRK09645   83 RPVEGGDDVLGV-PE--QSAPDEVDRALDRLLVADA-LAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVK 152
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 28-160 1.11e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 49.01  E-value: 1.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  28 LTRklqSAFDADDIAQDTFLRVMSSE-TLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPEGGAPSPEEreS 106
Cdd:PRK12511   24 LTR---DSAEAEDLVHDALVRALERRaSFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQE--H 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1195211048 107 QLETLQLVDSMLDgLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK12511   99 AVRLAQIRDAFFD-LPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRA 151
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 67-171 1.39e-07

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 48.43  E-value: 1.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  67 TIAKRVMVDLFRRNALEKAYLEML-----------------ALMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAF 129
Cdd:PRK09047   36 RILQNRIHDWFRRQKVRNTWVSLFssfsdddddddfdpletLDSADEGAESPADKLERAQVLQLIEEAIQKLPARQREAF 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1195211048 130 LLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVeHCLLFRLEH 171
Cdd:PRK09047  116 LLRYWEDMDVAETAAAMGCSEGSVKTHCSRAT-HALAKALEA 156
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 20-160 1.84e-07

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 49.58  E-value: 1.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  20 HHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETlSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMpEGGAP 99
Cdd:PRK09635   14 HRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPV-GDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAW-HDGDA 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1195211048 100 SP-------------EERESQLEtlqlvdsMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK09635   92 SVssvdpadrvtlddEVRLALLI-------MLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRA 158
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 24-160 2.47e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 48.57  E-value: 2.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  24 LKSWLTrklQSAFDADDIAQDTFLRVMssETLSTIR--DPRSFLCTIAKRVMVDLFRR--NALEKAYLE--MLALMPEGG 97
Cdd:PRK12533   34 LARWLC---GNASDADDVVQEACMRAL--RFFDSFRgdNARPWLLAIVRHTWYSEWRRraNAHEVAAPDtlDDADSLDDW 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1195211048  98 APSPEERESQL---ETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK12533  109 QPAGEDPLALLlraEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARA 174
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 38-160 3.57e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 47.74  E-value: 3.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  38 ADDIAQDTFLRVMSS----ETLSTiRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMP-EGGAPSPEERESQLETLQ 112
Cdd:PRK12542   36 AEDAVQETFITLYKNleklHSLNT-QELKRYILRVAKNKAIDSYRKNKRHETFLEEYERESiEAVDENIEEWEKRKMSEV 114

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1195211048 113 LVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK12542  115 QIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERA 162
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 10-161 1.21e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 46.59  E-value: 1.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  10 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSetlSTIRDPR-----SFLCTIAKRVMVDLFRRNALEK 84
Cdd:PRK12534   24 RHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHK---AGQFDPSrarglTWLAMIARNKAIDHLRANAPQR 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1195211048  85 --AYLEMLALMPEGGApSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAV 161
Cdd:PRK12534  101 rnVALDDAGELRAADA-SPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGL 178
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
33-154 2.53e-06

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 45.35  E-value: 2.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  33 QSAFDADDIAQDTFLRVMSSetLSTIRDP-RSFLC---TIAKRVMVDLFRRNALEKAYleMLALMPEG--GAPSPEERES 106
Cdd:PRK09648   50 RPGLSADDVAQEVCLAVITA--LPRYRDQgRPFLAfvyGIAAHKVADAHRAAGRDKAV--PTEEVPERpsDDAGPEERAL 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1195211048 107 QLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 154
Cdd:PRK09648  126 RSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVR 173
PRK06930 PRK06930
positive control sigma-like factor; Validated
 102-160 5.03e-06

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 44.33  E-value: 5.03e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1195211048 102 EERESQL---ETLQLVDSMLdGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK06930   94 EEPESVIsewDKIRIEDALS-VLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERA 154
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
4-153 5.34e-06

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 45.31  E-value: 5.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048   4 RATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSS----ETLSTIrdpRSFLCTIAKRVMVDLFR- 78
Cdd:PRK08241   12 RAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGydrfEGRSSL---RTWLYRIATNVCLDALEg 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  79 --RNAL-------------------EKAYLE-MLALMPEGGAPSPEERESQLETLQL--VDSMLDgLNGKTREAFLLSQL 134
Cdd:PRK08241   89 raRRPLptdlgapaadpvdelverpEVPWLEpYPDALLDPAAADPAARVVARESVRLafVAALQH-LPPRQRAVLILRDV 167

                         170
                  ....*....|....*....
gi 1195211048 135 DGLTYSEIAHKLGVSVSSV 153
Cdd:PRK08241  168 LGWSAAEVAELLDTSVAAV 186
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 29-159 5.68e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 44.50  E-value: 5.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  29 TRKLQSAFDADDIAQDTFLRVMssETLSTIRDPRSFLCTIAKRVMVDLF---RRNALEKAYLEMLALMPEGGAPSPEERE 105
Cdd:PRK12524   44 TRVLGDRAEAEDVTQEAMLRLW--RIAPDWRQGEARVSTWLYRVVCNLCtdrLRRRRRASVDLDDAPEPADAAPGAEEAL 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1195211048 106 SQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAK 159
Cdd:PRK12524  122 IEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTAR 175
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 29-173 8.19e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 43.87  E-value: 8.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  29 TRKLQSAFDADDIAQDTFLRVMSSEtlSTIRDPRSFLCTIAKRVMVDL-FRRNALEKAYLEMLALMPEGGAPSPEERESQ 107
Cdd:PRK05602   38 TRMLGDPAEAEDVAQETFLRIWKQA--PSWRPGEARFDTWLHRVVLNLcYDRLRRRREVPVEDAPDVPDPAPGPDAGLEA 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1195211048 108 LETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVssvkkyvaKAVEhCLLFRLEHGL 173
Cdd:PRK05602  116 RQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISV--------DALE-SLLARGRRAL 172
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 1-157 9.36e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 43.66  E-value: 9.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048   1 MSDRATttasltFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSETLSTIRD--PRSFLCTIAKRVMVDLFR 78
Cdd:PRK12514   15 LGDRDA------FSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGlsPMTWLITIARNHAIDRLR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  79 -RNALEKAYLEMLALMPEggAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYV 157
Cdd:PRK12514   89 aRKAVAVDIDEAHDLADP--SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWL 166
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
13-154 1.44e-05

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 43.51  E-value: 1.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSetlSTIRDPR-----SFLCTIAKRVMVDLFR--RNALEKA 85
Cdd:PRK09646   32 FAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRT---ASRFDPArgsalAWLLTLAHRRAVDRVRseQAASQRE 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1195211048  86 YLEMLALMPEGGAPSPEERESQLETLQLVDSmLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 154
Cdd:PRK09646  109 VRYGARNVDPAFDQVAEEVEARLERERVRDC-LDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVK 176
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 118-164 1.68e-05

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 1.68e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1195211048 118 LDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHC 164
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 38-160 3.98e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 42.26  E-value: 3.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  38 ADDIAQDTFLRVMS-SETLSTIRDPRSFLCTIAKRVMVDLFRRNALE-----KAYLEMLALMPeggapspeereSQLETL 111
Cdd:PRK12516   37 ADDLVQDTIMKAWAkQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREvqdtdGMFTEQLAVHP-----------SQYGTL 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1195211048 112 QLVD--SMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK12516  106 DLQDfrAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRA 156
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 72-158 1.19e-04

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: 39.88  E-value: 1.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  72 VMVD---LFRRnalekAYLEMLALMPE----GGAPSPEERESQLETLQ----LVDSMLDGLNGKTREAFLLSQ------- 133
Cdd:COG2197     5 LIVDdhpLVRE-----GLRALLEAEPDievvGEAADGEEALELLEELRpdvvLLDIRMPGMDGLEALRRLLTPrerevlr 79

                          90       100
                  ....*....|....*....|....*..
gi 1195211048 134 --LDGLTYSEIAHKLGVSVSSVKKYVA 158
Cdd:COG2197    80 llAEGLSNKEIAERLGISERTVKTHVS 106
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
25-154 4.18e-04

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 38.94  E-value: 4.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  25 KSWLTRKLQSAFDADDIAQDTflrVMSSETLSTIRDPRSFLC----TIAKRVMVDLFRRNALEKAYL------EMLALMP 94
Cdd:PRK12539   39 KGKLARIGRGAEEAEDLVQEA---LMAIHTRRHTYDPEQPLTpwvyAIARYKLIDHLRRTRASLADVpiddadELVAHDD 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  95 EGGApspeerESQLETLQLvdsmLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 154
Cdd:PRK12539  116 HAAV------ESTLDLGRL----LARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK 165
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 38-160 4.98e-04

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 38.71  E-value: 4.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  38 ADDIAQDTFLRVMSSETLSTIRDPRSFLCTIAKRVMVDLFRRNalEKAYLEMLALMPEGGAPSPEERESQLETLQLVDSM 117
Cdd:PRK09644   28 AEDLLQETFYRAYIYLEDYDNQKVKPWLFKVAYHTFIDFVRKE--KKVSFVGTDEIEAIQAESTEEYVVAKNSYEKLIQI 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1195211048 118 LDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 160
Cdd:PRK09644  106 IHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRG 148
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 13-154 6.16e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 38.55  E-value: 6.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTrKLQSAFDADDIAQDTFLRVMSSetLSTIRDPRSF---LCTIAKRVMVDLFRRNALEKAYLEM 89
Cdd:PRK12518   13 FRQLYRRYQQKVRSTLY-QLCGRELLDDLVQEVFLRVWKG--LPKLRNPAYFstwLYRITWNVATDARRQFAQRPSRIQD 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1195211048  90 LALMPEGGAPSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 154
Cdd:PRK12518   90 DSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVK 154
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 98-162 1.25e-03

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: 37.88  E-value: 1.25e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1195211048  98 APSPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVE 162
Cdd:COG1191   164 SGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALA 228
PRK09191 PRK09191
two-component response regulator; Provisional
 75-162 1.59e-03

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 37.91  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  75 DLFRRNALEkAYLEMLALMPEGGAP---------------SPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTY 139
Cdd:PRK09191   29 DAYVAATLE-ALLADPSIFPEASSPrvglyrlfhrlwssaGANDPEPGSPFEARAERRLAGLTPLPRQAFLLTALEGFSV 107

                          90       100
                  ....*....|....*....|...
gi 1195211048 140 SEIAHKLGVSVSSVKKYVAKAVE 162
Cdd:PRK09191  108 EEAAEILGVDPAEAEALLDDARA 130
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 38-162 1.74e-03

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 37.20  E-value: 1.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  38 ADDIAQDTFLRVMSSETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPEG-GAPSPE-ERESQLETLQL 113
Cdd:PRK13919   50 AEDVVQEVFIRVWKKAKEFDPRrgSARAWLLALAHHAAVDHVRRRAARPQPLEPDEREPEAfDLPGPGlDEEGHLDRTRL 129

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1195211048 114 vDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVE 162
Cdd:PRK13919  130 -GRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALS 177
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 13-171 2.68e-03

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 37.00  E-value: 2.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  13 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMSSEtlSTIRDP---RSFLCTIAKRVMVDLFRRNALEKAYL-- 87
Cdd:PRK09643   29 FGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAA--GSFRGDaavSSWLHRIVVNACLDRLRRAKARPTVPld 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  88 EMLALMPEGGAPSpeereSQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAVEHcLLF 167
Cdd:PRK09643  107 DVYPVAQLERDPT-----ARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRAR-LAE 180


                  ....
gi 1195211048 168 RLEH 171
Cdd:PRK09643  181 LLGY 184
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 126-162 3.26e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 34.43  E-value: 3.26e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1195211048  126 REAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKAVE 162
Cdd:smart00421   7 REREVLRLLaEGLTNKEIAERLGISEKTVKTHLSNIMR 44
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
99-153 4.45e-03

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 36.42  E-value: 4.45e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1195211048  99 PSPEER-ESQLETLQLVDSMLDGLNGKTREAFLLsQLDGLTYSEIAHKLGVSVSSV 153
Cdd:PRK08295  133 TDPEELiISKEELEDIEEKIEELLSELEKEVLEL-YLDGKSYQEIAEELNRHVKSI 187
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
135-162 4.99e-03

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 36.74  E-value: 4.99e-03
                          10        20
                  ....*....|....*....|....*...
gi 1195211048 135 DGLTYSEIAHKLGVSVSSVKKYVAKAVE 162
Cdd:COG4584    16 EGLSIREIARELGISRNTVRKYLRRAEE 43
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 38-153 5.34e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 35.82  E-value: 5.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  38 ADDIAQDTFLRVMSSetLSTIRDP---RSFLCTIAKRVMVDLFRRNALEKAYLEMlALMPEGGAPSPEERESQletlQLV 114
Cdd:PRK12517   50 AEDLVQETFLRAWRS--LDSLKDEkaaKAWLITILRRENARRFERKQFDLVDIED-DSIEDDASHSSEEEMEQ----EWL 122

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1195211048 115 DSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSV 153
Cdd:PRK12517  123 RRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTV 161
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 22-154 5.43e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 35.83  E-value: 5.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195211048  22 GWLKSWLTRKLQSAFDADDIAQDTFLRV-MSSETLSTIRDPRSFLCTIAKRVMVDLFRRNALE-----KAYLEMLALMPE 95
Cdd:PRK12512   37 AAARRGLARAGQPADQAEDIVQEILLAVhLKRHTWDPGAPFAPWLFAIARNKLIDALRRRGRRvfvdiDDFAETLPAEPA 116

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1195211048  96 ggAPSPEEREsqletlqlVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 154
Cdd:PRK12512  117 --TETLPAGD--------VGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVR 165
PRK12544 PRK12544
RNA polymerase factor sigma-70;
100-152 8.05e-03

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 35.55  E-value: 8.05e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1195211048 100 SPEERESQLETLQLVDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSS 152
Cdd:PRK12544  128 NPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSVSN 180
 
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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