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Conserved domains on  [gi|15597583|ref|NP_251077|]
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RNA polymerase sigma factor [Pseudomonas aeruginosa PAO1]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11485970)

sigma-70 family RNA polymerase sigma factor is an initiation factor that promotes the attachment of RNA polymerase to specific initiation sites and is then released

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 1-159 1.61e-84

RNA polymerase sigma factor; Reviewed


:

Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 245.07  E-value: 1.61e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    1 MENHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEG 80
Cdd:PRK12527   1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEEER 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597583   81 LASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMREWEAD 159
Cdd:PRK12527  81 LHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQWESG 159
 
Name Accession Description Interval E-value
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 1-159 1.61e-84

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 245.07  E-value: 1.61e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    1 MENHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEG 80
Cdd:PRK12527   1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEEER 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597583   81 LASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMREWEAD 159
Cdd:PRK12527  81 LHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQWESG 159
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-159 1.65e-26

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: 98.53  E-value: 1.65e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   1 MENHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQ-AQIEHPKAFLYRTALNLAVDeHRRSRVRRAEPLEVLDDEE 79
Cdd:COG1595  23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAID-HLRKRRRRRELLDELAEEL 101

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583  80 GLASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMREWEAD 159
Cdd:COG1595 102 PDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-153 1.65e-18

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: 77.00  E-value: 1.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583     4 HYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIE-HPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEglA 82
Cdd:TIGR02937  10 YLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEgSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD--S 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597583    83 SPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRM 153
Cdd:TIGR02937  88 DPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 96-149 3.33e-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: 52.46  E-value: 3.33e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15597583    96 LDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHC 149
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 99-150 3.90e-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: 39.40  E-value: 3.90e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15597583  99 LQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCR 150
Cdd:cd06171   4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 1-159 1.61e-84

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 245.07  E-value: 1.61e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    1 MENHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEG 80
Cdd:PRK12527   1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEEER 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597583   81 LASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMREWEAD 159
Cdd:PRK12527  81 LHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQWESG 159
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-159 1.65e-26

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: 98.53  E-value: 1.65e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   1 MENHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQ-AQIEHPKAFLYRTALNLAVDeHRRSRVRRAEPLEVLDDEE 79
Cdd:COG1595  23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAID-HLRKRRRRRELLDELAEEL 101

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583  80 GLASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMREWEAD 159
Cdd:COG1595 102 PDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-153 1.65e-18

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: 77.00  E-value: 1.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583     4 HYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIE-HPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEglA 82
Cdd:TIGR02937  10 YLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEgSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD--S 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597583    83 SPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRM 153
Cdd:TIGR02937  88 DPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 4-149 9.24e-17

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 72.92  E-value: 9.24e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    4 HYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEpLEVLDDEEGLAS 83
Cdd:PRK09651  19 HHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAY-LEMLALMPEGGA 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597583   84 PSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHC 149
Cdd:PRK09651  98 PSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-158 9.76e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 70.38  E-value: 9.76e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    1 MENHYRELLRFLSARLGDRHAAADVAHDAYLRVLE-RSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRA-EPLEVLDDE 78
Cdd:PRK11924  19 FRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRkADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAvLSDDALEPE 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   79 EGLASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRM-REWE 157
Cdd:PRK11924  99 FAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLeAQWE 178


                 .
gi 15597583  158 A 158
Cdd:PRK11924 179 A 179
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 6-150 6.69e-15

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 67.79  E-value: 6.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    6 RELLRFLSAR-LGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVrraEPLEVLDDEEGLASP 84
Cdd:PRK07037   8 RSMLVKIAARiVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQAL---ENKYHGDEEDGLDVP 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   85 ----SPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCR 150
Cdd:PRK07037  85 speaSPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCR 154
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 2-155 8.55e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 67.66  E-value: 8.55e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    2 ENHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEpLEVLDDEEGL 81
Cdd:PRK12525  16 QQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLERAY-LQSLAEAPEA 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597583   82 ASPSPQ---TVVDQGQRLDnlqRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMRE 155
Cdd:PRK12525  95 VQPSPEeqwMVIETLLAID---RLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQE 168
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 4-149 4.50e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 65.64  E-value: 4.50e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    4 HYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEpLEVLDDEEGLAS 83
Cdd:PRK12528  13 HHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAY-LEALAQLPERVA 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597583   84 PSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHC 149
Cdd:PRK12528  92 PSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 157
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 2-150 8.89e-14

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 64.97  E-value: 8.89e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    2 ENHYRELLRFLSARLGDRHAAADVAHDAYLRVLeRSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEGL 81
Cdd:PRK09639  10 EQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLY-RSDFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQWQEVD 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597583   82 ASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRkLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCR 150
Cdd:PRK09639  89 NEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKFR 156
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 3-151 3.43e-13

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 63.72  E-value: 3.43e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    3 NHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEGLa 82
Cdd:PRK12523  18 DHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRAALEQAYLAELALVPEAE- 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597583   83 SPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRV 151
Cdd:PRK12523  97 QPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 36-150 2.12e-12

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: 61.04  E-value: 2.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    36 RSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRA---EPLEVLDDEEGLASPSPQTVVDQGQRLdnLQRALAELPAICRS 112
Cdd:TIGR02985  43 RETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKyqeELAEIEERELSEADPEEELEAKELEEI--IEEAIEKLPEQCRE 120

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 15597583   113 SFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCR 150
Cdd:TIGR02985 121 IFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLR 158
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 4-159 1.10e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 59.70  E-value: 1.10e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    4 HYRELLRFLSARLGDRHAAADVAHDAYLRVLerSSQAQIEHPKAF---LYRTALNLAVDEHRRSRVRRAEPLEVLDDEEG 80
Cdd:PRK12513  35 HRTGLYRFLLRLARDRALAEDIFQETWLRVI--RARAQYQPRARFrtwLYQIARNLLIDHWRRHGARQAPSLDADEQLHA 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   81 LA--SPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMREWEA 158
Cdd:PRK12513 113 LAddGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEEVA 192


                 .
gi 15597583  159 D 159
Cdd:PRK12513 193 V 193
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 45-139 1.21e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 57.21  E-value: 1.21e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   45 PKAFLYRTALNLAVDEHRRSRVRRAepleVLDDEEGLASPSP--QTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGL 122
Cdd:PRK12524  78 VSTWLYRVVCNLCTDRLRRRRRASV----DLDDAPEPADAAPgaEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGL 153

                         90
                 ....*....|....*..
gi 15597583  123 SHSQIAEHLNISRSLVE 139
Cdd:PRK12524 154 SNPEIAEVMEIGVEAVE 170
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 96-149 3.33e-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: 52.46  E-value: 3.33e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15597583    96 LDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHC 149
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 1-155 6.70e-08

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: 49.31  E-value: 6.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583     1 MENHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQ-AQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEE 79
Cdd:TIGR02983  12 VAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRiRDPDAPDAYVRRVLVNLARSRWRRRRLLELPTRELPDAAA 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597583    80 GLASPSPQTVVDqgqrldnLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMRE 155
Cdd:TIGR02983  92 PDPAPDVALRAA-------LARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 46-134 2.86e-07

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 47.49  E-value: 2.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   46 KAFLYRTALNLAVDEHRRSRVRRAE---PLEVLDDEEGLA----SPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRK 118
Cdd:PRK09652  62 YTWLYRIARNTAINYLRKQGRRPPAsdvDAEEAEDFDLADalrdISTPENELLSAELEQRVRAAIESLPEELRTAITLRE 141

                         90
                 ....*....|....*.
gi 15597583  119 LDGLSHSQIAEHLNIS 134
Cdd:PRK09652 142 IEGLSYEEIAEIMGCP 157
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 30-150 1.71e-06

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 46.07  E-value: 1.71e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   30 YLRvLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRR--------AEPLevlddEEGLASPSPQTVVDQGQRLdNLQR 101
Cdd:PRK09636  39 WLR-WNNADRAQIRDPRAWLTRVVTRLCLDRLRSARHRRetyvgpwlPEPV-----VEELDDPLEAVVAAEDLSL-ALML 111

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 15597583  102 ALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCR 150
Cdd:PRK09636 112 ALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVR 160
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 50-141 1.84e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 45.34  E-value: 1.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   50 YRTALNLAVDEHRRSRVRRA-----------------EPLEVLDDEEGLAsPSPQTVVDQGQRLDNLQRALAELPAICRS 112
Cdd:PRK09047  35 QRILQNRIHDWFRRQKVRNTwvslfssfsdddddddfDPLETLDSADEGA-ESPADKLERAQVLQLIEEAIQKLPARQRE 113

                         90       100
                 ....*....|....*....|....*....
gi 15597583  113 SFLLRKLDGLSHSQIAEHLNISRSLVEKH 141
Cdd:PRK09047 114 AFLLRYWEDMDVAETAAAMGCSEGSVKTH 142
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 30-153 2.19e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 45.31  E-value: 2.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   30 YLRVLERSSQAQ---IEHPKAFLYRTALNLAVDEHRRSRVRRAEpLEVLDDEEGLASPSPQTVVDQGQRLDNLQRALAEL 106
Cdd:PRK12529  50 FLRILASRDGGQreaIRQPRAYLARIANCVLVSWRRRQSLELAW-LEALATLPEPLHPSPEQQSVILETLHEIDALLDTL 128

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 15597583  107 PAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRM 153
Cdd:PRK12529 129 RPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 16-154 1.72e-05

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 42.76  E-value: 1.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   16 LGDRHAAADVAHDAYLRVLERSSQAQIEHP-KAFLYRTALNLAVDehrrsRVRRAEPLEVLDDE----EGLA-------- 82
Cdd:PRK09641  39 LGNRHEAEDAAQEAFIRAYVNIDSYDINRKfSTWLYRIATNLTID-----RLRKRKPDYYLDAEvagtEGLTmysqlaad 113

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15597583   83 SPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCRVRMR 154
Cdd:PRK09641 114 DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLR 185
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 1-139 3.05e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 41.95  E-value: 3.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    1 MENHYRELLRFLSARLGDRHAAADVAHDAYLRV--LERSSQAQIEHPKAFLYRTALNLAVDEHRRSR-VRRAEPLEVLDD 77
Cdd:PRK05602  26 VARKLPRLLALATRMLGDPAEAEDVAQETFLRIwkQAPSWRPGEARFDTWLHRVVLNLCYDRLRRRReVPVEDAPDVPDP 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15597583   78 eeglaSPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVE 139
Cdd:PRK05602 106 -----APGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALE 162
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 99-150 3.90e-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: 39.40  E-value: 3.90e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15597583  99 LQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCR 150
Cdd:cd06171   4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 42-156 5.20e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 41.24  E-value: 5.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   42 IEHPKAF---LYRTALNLAVDeHRRSRVRRaePLEVLDDEEGLASPSPQTVVDQGQ--RLDNLQRALAELPAICRSSFLL 116
Cdd:PRK12518  55 LRNPAYFstwLYRITWNVATD-ARRQFAQR--PSRIQDDSLNDQPSRPSDTPDLMQlhYQDLVQQGLQTLSLEHRAVLVL 131

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 15597583  117 RKLDGLSHSQIAEHLNISRSLVEKHIVnamkHCRVRMREW 156
Cdd:PRK12518 132 HDLEDLPQKEIAEILNIPVGTVKSRLF----YARRQLRKF 167
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 49-142 9.27e-05

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 40.92  E-value: 9.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   49 LYRTALNLAVDE-HRRSRVRraepLEVL-DDEEGLAS--PSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSH 124
Cdd:PRK09647  82 LHRITTNLFLDMvRRRARIR----MEALpEDYDRVPGdePNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSY 157

                         90
                 ....*....|....*...
gi 15597583  125 SQIAEHLNISRSLVEKHI 142
Cdd:PRK09647 158 EEIAATLGVKLGTVRSRI 175
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 102-150 9.48e-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: 38.18  E-value: 9.48e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15597583   102 ALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMKHCR 150
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 49-134 1.03e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 40.72  E-value: 1.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   49 LYRTALNLAVDEHRRSRvRRAEPLEVLDD---------EEGLASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKL 119
Cdd:PRK11922  85 LSRIVLNEALGRLRRRR-RLVNLAEMVMAstiaggertPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVV 163

                         90
                 ....*....|....*
gi 15597583  120 DGLSHSQIAEHLNIS 134
Cdd:PRK11922 164 EELSVEETAQALGLP 178
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
2-133 1.13e-04

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 40.45  E-value: 1.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    2 ENHYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQ-AQIEHP-KAFLYRTALNLAVDEHrrsRVRRAEPLEVLDDEE 79
Cdd:PRK09645  16 DEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVlADTGRSaRAWLFTVARNLVIDER---RSARARPVEGGDDVL 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15597583   80 GLASPSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNI 133
Cdd:PRK09645  93 GVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGI 146
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 4-129 3.02e-04

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 39.56  E-value: 3.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    4 HYRELLRFLSARLGDRHAAADVAHDAYLRvLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEGLAS 83
Cdd:PRK09635  14 HRAYLVDLAFRMVGDIGVAEDMVQEAFSR-LLRAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAWHDGDAS 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15597583   84 PSpqtVVDQGQRL---DNLQRALAEL-----PAIcRSSFLLRKLDGLSHSQIAE 129
Cdd:PRK09635  93 VS---SVDPADRVtldDEVRLALLIMlerlgPAE-RVVFVLHEIFGLPYQQIAT 142
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 16-133 7.72e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 37.88  E-value: 7.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   16 LGDRHAAADVAHDAYLRVLERSSQAQIE--HPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEEGLASPSPQTV-VDQ 92
Cdd:PRK12514  40 LKDRSEAEEALQDVYVKIWTKADRFAVSglSPMTWLITIARNHAIDRLRARKAVAVDIDEAHDLADPSPGPEAEVIaGDE 119

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 15597583   93 GQRLDNlqrALAELPAICRSSFLLRKLDGLSHSQIAEHLNI 133
Cdd:PRK12514 120 GQRIDA---CLEELEKDRAAAVRRAYLEGLSYKELAERHDV 157
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 48-129 1.79e-03

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 37.09  E-value: 1.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   48 FLYRTALNLAVDeHRRSRVRR-------AEPLEVLDDEEGLAS-PSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKL 119
Cdd:PRK11923  74 WLYRIAINTAKN-HLVSRGRRppdsdvsSEDAEFYDGDHALKDiESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF 152

                         90
                 ....*....|
gi 15597583  120 DGLSHSQIAE 129
Cdd:PRK11923 153 DGLSYEDIAS 162
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 49-133 1.82e-03

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 37.00  E-value: 1.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   49 LYRTALNLAVDEHRRSRVRRAEPlevLDDEEGLASPSPQTVVDQGQRLDnLQRALAELPAICRSSFLLRKLDGLSHSQIA 128
Cdd:PRK09643  82 LHRIVVNACLDRLRRAKARPTVP---LDDVYPVAQLERDPTARVETALA-VQRALMRLPVEQRAALVAVDMQGYSVADAA 157


                 ....*
gi 15597583  129 EHLNI 133
Cdd:PRK09643 158 RMLGV 162
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 55-133 3.01e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 36.30  E-value: 3.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   55 NLAVDEHRRSRV--RRAEPLEVLDDEeglASPSPQtvvDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLN 132
Cdd:PRK12511  65 NAFIDELRRRRVeaRRADELAVLADA---SLPAAQ---EHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLG 138


                 .
gi 15597583  133 I 133
Cdd:PRK12511 139 I 139
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 4-139 3.05e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 36.07  E-value: 3.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583    4 HYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEvlddEEGLAS 83
Cdd:PRK12541  14 HMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTTTIE----EFHLPN 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15597583   84 -PSPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVE 139
Cdd:PRK12541  90 vPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVK 146
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 46-136 3.82e-03

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 36.12  E-value: 3.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583   46 KAFLYRTALNLAVDeHRRSRVRRAEPLevlDDEEGLASPSPQTVVDQGQRLdnLQRALAELPAICRSSFLLRKLDGLSHS 125
Cdd:PRK09637  53 KSWLYQIANNTIID-FYRKKNRSEELP---DDLLFEDEEREENAKKELAPC--LRPFIDALPEKYAEALRLTELEGLSQK 126

                         90
                 ....*....|.
gi 15597583  126 QIAEHLNISRS 136
Cdd:PRK09637 127 EIAEKLGLSLS 137
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 4-131 5.18e-03

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: 35.37  E-value: 5.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597583     4 HYRELLRFLSARLGDRHAAADVAHDAYLRVLERSSQAQIEHP-KAFLYRTALNLAVDEHRRSRVRRaeplEVLDDE--EG 80
Cdd:TIGR02989  10 HERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNfVAWARGIARNKVLNYRRKLGRDR----LVFDDDllEA 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15597583    81 LASPSPQTVVDQGQ-RLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHL 131
Cdd:TIGR02989  86 LAAEAEPTEAERLSdDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQT 137
PRK06930 PRK06930
positive control sigma-like factor; Validated
 99-147 9.51e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 34.70  E-value: 9.51e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 15597583   99 LQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVNAMK 147
Cdd:PRK06930 108 IEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEK 156
 
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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