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Conserved domains on  [gi|15599094|ref|NP_252588|]
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RNA polymerase sigma factor [Pseudomonas aeruginosa PAO1]

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
 14-167 1.20e-99

RNA polymerase sigma factor; Provisional


:

Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 284.04  E-value: 1.20e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLP 93
Cdd:PRK12528   8 GLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEALAQLP 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599094   94 EREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRCYFAE 167
Cdd:PRK12528  88 ERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCYFAL 161
 
Name Accession Description Interval E-value
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 14-167 1.20e-99

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 284.04  E-value: 1.20e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLP 93
Cdd:PRK12528   8 GLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEALAQLP 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599094   94 EREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRCYFAE 167
Cdd:PRK12528  88 ERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCYFAL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-163 1.17e-33

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: 117.02  E-value: 1.17e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094  14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAAR-IDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASL 92
Cdd:COG1595  21 ELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRgRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEE 100

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15599094  93 PEREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:COG1595 101 LPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-163 9.76e-27

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: 98.57  E-value: 9.76e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094    14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDE-PRAFLTTIARRVLCNHYRRQDVERAYLEALASL 92
Cdd:TIGR02937   5 ELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGsFKAWLFRIARNLILDYLRRKRRLRRELDLLEEL 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15599094    93 PEREvPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:TIGR02937  85 LDSD-PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 15-80 1.30e-12

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: 59.52  E-value: 1.30e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15599094    15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSR---QAARIDEPRAFLTTIARRVLCNHYRRQD 80
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIerfDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 110-163 1.55e-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: 40.55  E-value: 1.55e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15599094 110 LVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 14-167 1.20e-99

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 284.04  E-value: 1.20e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLP 93
Cdd:PRK12528   8 GLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEALAQLP 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599094   94 EREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRCYFAE 167
Cdd:PRK12528  88 ERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCYFAL 161
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 14-163 2.31e-55

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 172.30  E-value: 2.31e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLP 93
Cdd:PRK09651  14 SLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMP 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   94 EREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:PRK09651  94 EGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 15-164 6.89e-54

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 168.20  E-value: 6.89e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLPE 94
Cdd:PRK12525  14 MFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLERAYLQSLAEAPE 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   95 REVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRCY 164
Cdd:PRK12525  94 AVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 15-166 1.85e-50

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 159.63  E-value: 1.85e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLPE 94
Cdd:PRK12523  15 LYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRAALEQAYLAELALVPE 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15599094   95 REVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRCYFA 166
Cdd:PRK12523  95 AEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 14-163 1.87e-42

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 139.69  E-value: 1.87e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQN--AADLAQDTFVKVLVSRQAAR---IDEPRAFLTTIARRVLCNHYRRQDVERAYLEA 88
Cdd:PRK12529  17 TLYRENHAWLRNWLAYRLRSWGRgvADDLAHDIFLRILASRDGGQreaIRQPRAYLARIANCVLVSWRRRQSLELAWLEA 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15599094   89 LASLPEREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:PRK12529  97 LATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTC 171
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-163 1.17e-33

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: 117.02  E-value: 1.17e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094  14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAAR-IDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASL 92
Cdd:COG1595  21 ELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRgRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEE 100

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15599094  93 PEREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:COG1595 101 LPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 15-164 1.66e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 106.21  E-value: 1.66e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVL-VSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLP 93
Cdd:PRK11924  18 LFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWrKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDALEP 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599094   94 ER--EVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRCY 164
Cdd:PRK11924  98 EFaeTAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-163 9.76e-27

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: 98.57  E-value: 9.76e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094    14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDE-PRAFLTTIARRVLCNHYRRQDVERAYLEALASL 92
Cdd:TIGR02937   5 ELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGsFKAWLFRIARNLILDYLRRKRRLRRELDLLEEL 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15599094    93 PEREvPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:TIGR02937  85 LDSD-PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 19-163 1.64e-24

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 92.92  E-value: 1.64e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   19 HHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAY-LEALASLPEREV 97
Cdd:PRK12527   4 YYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEpLEVLDEEERLHS 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599094   98 PSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:PRK12527  84 PSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 28-159 9.21e-19

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: 77.99  E-value: 9.21e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094    28 RRRLGCPQNAADLAQDTFVKVLVSRQA-ARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLPERE--VPSEETRA 104
Cdd:TIGR02985  19 RRYVKDEEDAEDIVQDVFLKLWENRETlEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEERElsEADPEEEL 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 15599094   105 IVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKA 159
Cdd:TIGR02985  99 EAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKA 153
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 18-163 7.50e-15

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 67.79  E-value: 7.50e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   18 DHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYL----EALaSLP 93
Cdd:PRK07037   6 DNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHgdeeDGL-DVP 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   94 EREvPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKrYMLKAAQRC 163
Cdd:PRK07037  85 SPE-ASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVN-FMIRDALVH 152
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 16-162 2.05e-13

RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot:


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 64.01  E-value: 2.05e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094    16 YSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVER-AYLEALASLPE 94
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDSSIKPWLFRIARNAFIDWYRKDKKIQtIDDDAIGDLEQ 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599094    95 REVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQR 162
Cdd:TIGR02950  81 HPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKE 148
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 16-158 5.22e-13

RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).


Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 63.15  E-value: 5.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094    16 YSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVS-RQAARIDEPRAFLTTIARRVLCNHYRRQdveRAYLEALASLPE 94
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNlPSLKDGQKIQSWLYQIARNTIIDFYRSK---SRSVELPESLLA 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094    95 REVPSEETraIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK------RYMLK 158
Cdd:TIGR02959  78 ADSAREET--FVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKsrvqrgRKKLK 145
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 15-80 1.30e-12

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: 59.52  E-value: 1.30e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15599094    15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSR---QAARIDEPRAFLTTIARRVLCNHYRRQD 80
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIerfDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 14-153 1.36e-12

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 62.52  E-value: 1.36e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLvsRQAARIDEPRAF---LTTIARRVLCNHYRRQDVERAYLEALA 90
Cdd:PRK09652  14 LLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAY--RALHSFRGGAAFytwLYRIARNTAINYLRKQGRRPPASDVDA 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15599094   91 SLPEREVPSEETRAIV-LETLV-------ELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK 153
Cdd:PRK09652  92 EEAEDFDLADALRDIStPENELlsaeleqRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 15-162 2.42e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 62.01  E-value: 2.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLvsrQAARIDEPRAFLTT----IARRVLCNHYRRQDVERA----YL 86
Cdd:PRK12513  31 LYARHRTGLYRFLLRLARDRALAEDIFQETWLRVI---RARAQYQPRARFRTwlyqIARNLLIDHWRRHGARQApsldAD 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599094   87 EALASLPEREvPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQR 162
Cdd:PRK12513 108 EQLHALADDG-AAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQK 182
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 15-153 6.23e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 60.34  E-value: 6.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASLPe 94
Cdd:PRK12541  10 IYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTTTIEEFHLP- 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15599094   95 rEVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK 153
Cdd:PRK12541  89 -NVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVK 146
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 15-158 1.72e-11

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 59.23  E-value: 1.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVS----RQAARIdepRAFLTTIARRVLCNHYRRQDVERAyLEALA 90
Cdd:PRK09637   6 IWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNlhslKDGSSI---KSWLYQIANNTIIDFYRKKNRSEE-LPDDL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599094   91 SLPEREVPSEetraIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK------RYMLK 158
Cdd:PRK09637  82 LFEDEEREEN----AKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKsrvqrgRVKLK 151
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 15-153 3.61e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 58.42  E-value: 3.61e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPrAFLTTIARRVLCNHYRRQDVERAYLEALASLPE 94
Cdd:PRK09639   8 LFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIENEK-GWLIKSARNVAYNYLRSEKRRRARILGEFQWQE 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   95 RE-VPSEETRAI----------VLETLVELDRLLdglpplaketfLLAQLDGLGYAEIATQLGISLSSVK 153
Cdd:PRK09639  87 VDnEPSPEEIWIrkeeitkvqeVLAKMTERDRTV-----------LLLRFSGYSYKEIAEALGIKESSVG 145
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 110-163 1.20e-10

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: 54.00  E-value: 1.20e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15599094   110 LVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 36-159 3.60e-10

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 55.82  E-value: 3.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   36 NAADLAQDTFVKVL--VSRQAARiDEPRAFLTTIARRVLCNHYRR-QDVERAyleALASLPEREVpSEETRAIVLETLVE 112
Cdd:PRK09649  49 SADDLTQETFLRAIgaIPRFSAR-SSARTWLLAIARHVVADHIRHvRSRPRT---TRGARPEHLI-DGDRHARGFEDLVE 123

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 15599094  113 LDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKA 159
Cdd:PRK09649 124 VTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARA 170
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 26-160 1.43e-07

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 49.01  E-value: 1.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   26 WLRRRL-GCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQdvERAYLEALASLPEReVPSEETRA 104
Cdd:PRK09647  43 RLAYRLsGNQHDAEDLTQETFIRVFRSLQNYQPGTFEGWLHRITTNLFLDMVRRR--ARIRMEALPEDYDR-VPGDEPNP 119

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599094  105 IVLETLVELD----RLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK------RYMLKAA 160
Cdd:PRK09647 120 EQIYHDARLDpdlqAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRsrihrgRQQLRAA 185
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
21-153 3.29e-07

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 47.80  E-value: 3.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   21 HWLTGWLR-------RRLG-CPQNAADLAQDTFVKVLVSRQAARIDEP-RAFLTTIARRVLCNHYRRQdveRAyleALAS 91
Cdd:PRK12539  28 ERLSGHLRayykgklARIGrGAEEAEDLVQEALMAIHTRRHTYDPEQPlTPWVYAIARYKLIDHLRRT---RA---SLAD 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599094   92 LPEREVPS--EETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK 153
Cdd:PRK12539 102 VPIDDADElvAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK 165
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 14-153 3.74e-07

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 47.71  E-value: 3.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVsrqaaRID--EPRA----FLTTIARRVLCNHYRRQDVERAYLE 87
Cdd:PRK09638  22 TLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIE-----NLSsfQGRSkfstWLISIASRLYKDHLRKQKREKLRLQ 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599094   88 ALASLPEREVPSEEtrAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK 153
Cdd:PRK09638  97 RAKEETLRKEKWEA--AIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVK 160
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 23-153 5.84e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 46.97  E-value: 5.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   23 LTGWLRRRL-GCPQNAADLAQDTFVKVLVSRQAARIDEP-RAFLTTIARRVLCNHYRRQDVERAYLEALA------SLPE 94
Cdd:PRK12536  34 LRGFLRRRLpQLPDEVEDLVQEILLAVHNARHTYRADQPlTAWVHAIARYKLMDFLRSRARREALHDPLDdeselfATSD 113

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15599094   95 REvPSEETRaivletlvELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK 153
Cdd:PRK12536 114 DE-AAEARR--------DLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVK 163
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 19-162 7.84e-07

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 47.65  E-value: 7.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   19 HHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSrQAARIDEPRAFLTTIARRVLCNHYRRQDVER------AYLEALASL 92
Cdd:PRK09635  14 HRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRA-PVGDIDDERGWLIVVTSRLCLDHIKSASTRRerpqdiAAWHDGDAS 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599094   93 PEREVPS------EETRAIVLEtlveldrLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQR 162
Cdd:PRK09635  93 VSSVDPAdrvtldDEVRLALLI-------MLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRK 161
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 14-159 1.25e-06

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: 45.84  E-value: 1.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094    14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQ-AARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASL 92
Cdd:TIGR02983  10 AFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDrIRDPDAPDAYVRRVLVNLARSRWRRRRLLELPTRELPDA 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599094    93 PERE-VPSEETRAIVLetlveldRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKA 159
Cdd:TIGR02983  90 AAPDpAPDVALRAALA-------RALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRA 150
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 14-154 1.38e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 46.21  E-value: 1.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKvLVSRQA--ARIDEPRAFLTTIARRVLCNHYRRQD-----VERAYL 86
Cdd:PRK12519  33 VLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLS-LWRKSSydPKRGSLSSYLLTLTRSRAIDRLRSRRsrqrlLERWQQ 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599094   87 EALASLPEReVPSEetRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKR 154
Cdd:PRK12519 112 ELLGEASED-TPLE--QASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKA 176
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 37-162 2.72e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 45.34  E-value: 2.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   37 AADLAQDTFVKVLVSRQAARI-DEPRAFLTTIARRVLCNHYRR-----QDVERAYLEALASLPEREVPSEetraivletL 110
Cdd:PRK12516  37 ADDLVQDTIMKAWAKQDHFEVgTNMKAWLFTILRNEFYSQMRKrgrevQDTDGMFTEQLAVHPSQYGTLD---------L 107

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 15599094  111 VELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQR 162
Cdd:PRK12516 108 QDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQR 159
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 23-155 3.40e-06

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 44.93  E-value: 3.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   23 LTGWLRRRLGCPQNAADLAQDTFVKVLVS-RQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALaSLPEREVPSEE 101
Cdd:PRK09640  39 LFNVCARYLGNDRDADDVCQEVMLKVLYGlKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLMDAL-SLDPLEEASEE 117

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15599094  102 tRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK-RY 155
Cdd:PRK09640 118 -KAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKmRY 171
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 31-159 5.49e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 44.50  E-value: 5.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   31 LGCPQNAADLAQDTFVKVL--VSRQAARiDEPRAFLTTIARRVLCNHYRrQDVER-----AYLEALASLpereVPSEETR 103
Cdd:PRK12535  45 LGGHDIADDLTQETYLRVMsaLPRFAAR-SSARTWLLSLARRVWVDNIR-HDMARprksaTEYEDAAAT----TASNETT 118

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 15599094  104 AIVLEtLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKA 159
Cdd:PRK12535 119 GSWSE-WIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARA 173
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 34-147 1.48e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 43.24  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   34 PQNAADLAQDTFVKVLVSRQAARIDEP-RAFLTTIARRVLCNHYRRQDVERAYLEALASLPEREVPSEETRAIvleTLVE 112
Cdd:PRK12511  28 SAEAEDLVHDALVRALERRASFRSGGNlRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQEHAV---RLAQ 104

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 15599094  113 LDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGI 147
Cdd:PRK12511 105 IRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGI 139
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 110-163 1.55e-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: 40.55  E-value: 1.55e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15599094 110 LVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
15-153 1.73e-05

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 42.76  E-value: 1.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLvsRQAARIDEP----RAFLTTIARRVLCN-----HYRRQDVERAY 85
Cdd:PRK09645  14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAW--QHPEVLADTgrsaRAWLFTVARNLVIDerrsaRARPVEGGDDV 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599094   86 LEAlaslPEREVPSEETRAivLETLvELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK 153
Cdd:PRK09645  92 LGV----PEQSAPDEVDRA--LDRL-LVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVK 152
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
25-156 3.12e-05

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 42.35  E-value: 3.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   25 GWLRRRLGCPQNAADLAQDTFVKVLvsRQAARIDEPR----AFLTTIARRVLCNHYRRQDVERAYlEALASLPEREVPSE 100
Cdd:PRK09646  45 GLVRRVLRDPGYSEETTQEVYLEVW--RTASRFDPARgsalAWLLTLAHRRAVDRVRSEQAASQR-EVRYGARNVDPAFD 121

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15599094  101 ETRAIVlETLVELDRL---LDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYM 156
Cdd:PRK09646 122 QVAEEV-EARLERERVrdcLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRM 179
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 37-162 4.98e-05

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 41.40  E-value: 4.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   37 AADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNhYRRQDVERAYL--EALASLperEVPSEETRAIVLETLVELD 114
Cdd:PRK09644  28 AEDLLQETFYRAYIYLEDYDNQKVKPWLFKVAYHTFID-FVRKEKKVSFVgtDEIEAI---QAESTEEYVVAKNSYEKLI 103

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15599094  115 RLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQR 162
Cdd:PRK09644 104 QIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKR 151
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 35-161 6.23e-05

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 41.11  E-value: 6.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   35 QNAADLAQDTFVKvLVSRQAARidePRAFLTTIARRVLCN----HYRRQDVERAY------------------LEALASl 92
Cdd:PRK09047   5 DAALDIVQDAMIK-LAEKYGDR---PAAEWPPLFQRILQNrihdWFRRQKVRNTWvslfssfsdddddddfdpLETLDS- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15599094   93 PEREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQ 161
Cdd:PRK09047  80 ADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATH 148
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 62-154 7.50e-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: 41.25  E-value: 7.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094    62 AFLTTIARRVLCNHYRR-QDVERAYLEALASLPEREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAE 140
Cdd:pfam07638  77 AAAAEAMRRILIDHARRrQRQKRGGDVQRRELDEVVDNGDSPNPDLLLDLDEALEQLFSLSPRQARLVELRFFAGLSNDE 156

                          90
                  ....*....|....
gi 15599094   141 IATQLGISLSSVKR 154
Cdd:pfam07638 157 IAERLGVSERTVER 170
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 29-148 7.58e-05

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 41.83  E-value: 7.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   29 RRLGCPQNAADLAQDTFVKvLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVER-AY---------LEALASLPEREVP 98
Cdd:PRK09636  23 RMLGSVADAEDIVQEAWLR-WNNADRAQIRDPRAWLTRVVTRLCLDRLRSARHRReTYvgpwlpepvVEELDDPLEAVVA 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 15599094   99 SEETRaivLETLVELDRLldglPPLAKETFLLAQLDGLGYAEIATQLGIS 148
Cdd:PRK09636 102 AEDLS---LALMLALERL----SPLERAAFLLHDVFGVPFDEIASTLGRS 144
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 28-152 9.76e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 40.79  E-value: 9.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   28 RRRLGCPQNAADLAQDTFVKVLvsRQAARIDEPRAFLTTIARRVLCNH-YRRQDVERAYLEALASLPEREVPSEETRAIV 106
Cdd:PRK05602  38 TRMLGDPAEAEDVAQETFLRIW--KQAPSWRPGEARFDTWLHRVVLNLcYDRLRRRREVPVEDAPDVPDPAPGPDAGLEA 115

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 15599094  107 LETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSV 152
Cdd:PRK05602 116 RQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDAL 161
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 14-168 1.04e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 40.87  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   14 TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLvsRQAARIdEPRAFLTT----IAR-RVLCNHYRRQDVE-----R 83
Cdd:PRK12515  26 TLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVW--RQAGQF-EGRSQVSTwllsIARfKALSALRRRKHEEiddeaA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   84 AYLEALASLPEREVPSEETRAIvletlveLDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAaqRC 163
Cdd:PRK12515 103 AAIEDGADTPEVALQKSDTSAA-------LRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYA--RK 173


                 ....*
gi 15599094  164 YFAEL 168
Cdd:PRK12515 174 KLAEL 178
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 35-162 1.27e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 40.42  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   35 QNAADLAQDTFV---KVLVSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALaslpERE--------VPSEETR 103
Cdd:PRK12542  34 QQAEDAVQETFItlyKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHETFLEEY----EREsieavdenIEEWEKR 109

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15599094  104 AIvleTLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQR 162
Cdd:PRK12542 110 KM---SEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKR 165
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 37-163 1.87e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 40.15  E-value: 1.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   37 AADLAQDTFVKVLvsRQAARID----EPRAFLTTIARR----VLCNHYRRQDVERAYLEALASLPEREVPSEetraiVLE 108
Cdd:PRK12537  50 AEDIVHDAFIKIW--TGAASFDpargSARGWIYSVTRHlalnVLRDTRREVVLDDDAEETAQTLHEIIDDFD-----LWA 122

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15599094  109 TLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYM---LKAAQRC 163
Cdd:PRK12537 123 NSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIkrsLKALREC 180
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 15-156 3.58e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 39.03  E-value: 3.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   15 LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVL--VSRQAARIDEPRAFLTTIARRVLCNHYRRQDVERAYLEALASL 92
Cdd:PRK12514  24 LYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWtkADRFAVSGLSPMTWLITIARNHAIDRLRARKAVAVDIDEAHDL 103

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599094   93 PErEVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYM 156
Cdd:PRK12514 104 AD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWL 166
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 29-153 6.30e-04

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 38.52  E-value: 6.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   29 RRLGCPQNAADLAQDTFVKVLVSRQaaRIDEPRAFLTTIARRV--LCNHYRRQDVERAYLEA-------------LAS-- 91
Cdd:PRK09641  37 RMLGNRHEAEDAAQEAFIRAYVNID--SYDINRKFSTWLYRIAtnLTIDRLRKRKPDYYLDAevagtegltmysqLAAdd 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599094   92 -LPEREVPSEETRAIVLETLveldrllDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVK 153
Cdd:PRK09641 115 aLPEEQVVSLELQETIQEAI-------LQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVK 170
PRK06930 PRK06930
positive control sigma-like factor; Validated
 69-159 1.04e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.79  E-value: 1.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   69 RRVLCNHYRRQDVERAY--LEALASLPEREVpSEETRaivletlVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLG 146
Cdd:PRK06930  70 REVICDPLLIQRYFRSMedLEWDIEEPESVI-SEWDK-------IRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLN 141

                         90
                 ....*....|...
gi 15599094  147 ISLSSVKRYMLKA 159
Cdd:PRK06930 142 IKKSTVQSMIERA 154
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 27-162 1.29e-03

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 37.59  E-value: 1.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   27 LRRRLGC-PQNAADLAQDTFVKVLvsrQAARIDEP-----RAFLTTIARRVLCNHYRRQDVERAYLEALASLPER-EVPS 99
Cdd:PRK13919  39 LARRMGLdGAAAEDVVQEVFIRVW---KKAKEFDPrrgsaRAWLLALAHHAAVDHVRRRAARPQPLEPDEREPEAfDLPG 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599094  100 EETRAIVLETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQR 162
Cdd:PRK13919 116 PGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSR 178
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 19-159 1.48e-03

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 37.47  E-value: 1.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   19 HHHWLTGWLRRRLGCPQNAADLAQDTFVKVLvsRQAARIDEPRAFLTTI-------ARRVLCNHYRRQ-----DVERA-Y 85
Cdd:PRK11923  29 YQHKILGLIVRFVHDTAEAQDVAQEAFIKAY--RALGNFRGDSAFYTWLyriaintAKNHLVSRGRRPpdsdvSSEDAeF 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15599094   86 LEALASL-----PEREVPSEETRAIVLETLveldrllDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKA 159
Cdd:PRK11923 107 YDGDHALkdiesPERALLRDEIEGTVHRTI-------QQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRA 178
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 116-163 1.62e-03

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 35.10  E-value: 1.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15599094   116 LLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRC 163
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 23-162 2.97e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 36.63  E-value: 2.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   23 LTGWLrrrLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCNHYRR--QDVERAY---LEALASLPEREV 97
Cdd:PRK12533  34 LARWL---CGNASDADDVVQEACMRALRFFDSFRGDNARPWLLAIVRHTWYSEWRRraNAHEVAApdtLDDADSLDDWQP 110

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15599094   98 PSEETRAIVL--ETLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQR 162
Cdd:PRK12533 111 AGEDPLALLLraEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRR 177
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 37-168 4.73e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 35.97  E-value: 4.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094   37 AADLAQDTFVKVLVSrqaarIDE------PRAFLTTIARRVLCNHYRRQ--DVERAYLEALASLPERevPSEETRAivle 108
Cdd:PRK12546  34 ADDLVQDTIVKAWTN-----FDKfqegtnLRAWLFTILRNTFYSDRRKHkrEVPDPEGVHAASLAVK--PAHDGRL---- 102

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599094  109 TLVELDRLLDGLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRcyFAEL 168
Cdd:PRK12546 103 AMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARAR--LAEL 160
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
80-152 8.17e-03

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 35.27  E-value: 8.17e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15599094   80 DVERAYLEALA----SLPEREVPSEETRAIVLETLVELdrlldgLPPLAKETFLLaQLDGLGYAEIATQLGISLSSV 152
Cdd:PRK08295 118 ESDRTLLDVISeakvTDPEELIISKEELEDIEEKIEEL------LSELEKEVLEL-YLDGKSYQEIAEELNRHVKSI 187
 
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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