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Conserved domains on  [gi|15597622|ref|NP_251116|]
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extracytoplasmic-function sigma-70 factor [Pseudomonas aeruginosa PAO1]

Protein Classification

RNA polymerase factor sigma-70( domain architecture ID 11482538)

RNA polymerase factor sigma-70 similar to Pseudomonas aeruginosa PvdS, a probable alternative sigma factor that may be required for synthesis of pyoverdine and many other extracellular products in response to iron starvation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 15-176 4.50e-107

extracytoplasmic-function sigma-70 factor; Validated


:

Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 303.53  E-value: 4.50e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   15 LQAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQiTSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGPEEE 94
Cdd:PRK07037   1 LDVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPN-QDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEED 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   95 GLNVVIQGASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRKVTAE 174
Cdd:PRK07037  80 GLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159


                 ..
gi 15597622  175 RQ 176
Cdd:PRK07037 160 CH 161
 
Name Accession Description Interval E-value
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 15-176 4.50e-107

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 303.53  E-value: 4.50e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   15 LQAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQiTSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGPEEE 94
Cdd:PRK07037   1 LDVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPN-QDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEED 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   95 GLNVVIQGASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRKVTAE 174
Cdd:PRK07037  80 GLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159


                 ..
gi 15597622  175 RQ 176
Cdd:PRK07037 160 CH 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 25-170 2.65e-29

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: 106.62  E-value: 2.65e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622  25 LVKIAARITGCRSRAEDVVQDAFFRL-QSAPQI--TSSFKAqlsYLFQIVRNLAIDHYRKQALEQKYSgpEEEGLNVVIQ 101
Cdd:COG1595  30 LYRYARRLLGDRADAEDLVQETFLRLwRKLDSFrgRGSFRA---WLYRIARNLAIDHLRKRRRRRELL--DELAEELPDE 104

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597622 102 GASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRK 170
Cdd:COG1595 105 AADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-170 1.18e-26

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: 98.96  E-value: 1.18e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622    16 QAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQ---ITSSFKAqlsYLFQIVRNLAIDHYRKQALEQKYSGPE 92
Cdd:TIGR02937   5 ELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDrfdPEGSFKA---WLFRIARNLILDYLRRKRRLRRELDLL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15597622    93 EEGLNVViqgASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRK 170
Cdd:TIGR02937  82 EELLDSD---PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 18-83 1.77e-10

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: 54.52  E-value: 1.77e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597622    18 FVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSA-----PQITSSFKAqlsYLFQIVRNLAIDHYRKQA 83
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAierfdPERGVSFST---WLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 115-169 5.51e-04

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: 36.70  E-value: 5.51e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15597622 115 LEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCR 169
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 15-176 4.50e-107

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 303.53  E-value: 4.50e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   15 LQAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQiTSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGPEEE 94
Cdd:PRK07037   1 LDVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPN-QDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEED 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   95 GLNVVIQGASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRKVTAE 174
Cdd:PRK07037  80 GLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159


                 ..
gi 15597622  175 RQ 176
Cdd:PRK07037 160 CH 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 25-170 2.65e-29

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: 106.62  E-value: 2.65e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622  25 LVKIAARITGCRSRAEDVVQDAFFRL-QSAPQI--TSSFKAqlsYLFQIVRNLAIDHYRKQALEQKYSgpEEEGLNVVIQ 101
Cdd:COG1595  30 LYRYARRLLGDRADAEDLVQETFLRLwRKLDSFrgRGSFRA---WLYRIARNLAIDHLRKRRRRRELL--DELAEELPDE 104

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597622 102 GASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRK 170
Cdd:COG1595 105 AADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-170 1.18e-26

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: 98.96  E-value: 1.18e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622    16 QAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQ---ITSSFKAqlsYLFQIVRNLAIDHYRKQALEQKYSGPE 92
Cdd:TIGR02937   5 ELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDrfdPEGSFKA---WLFRIARNLILDYLRRKRRLRRELDLL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15597622    93 EEGLNVViqgASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRK 170
Cdd:TIGR02937  82 EELLDSD---PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 25-170 1.77e-25

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: 96.09  E-value: 1.77e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622    25 LVKIAARITGCRSRAEDVVQDAFFRLQSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGPEEEGLNVVIQGAS 104
Cdd:TIGR02985  14 LCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEERELSEAD 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597622   105 PEtSHINYATLE-HIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRK 170
Cdd:TIGR02985  94 PE-EELEAKELEeIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 20-168 9.60e-20

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 81.44  E-value: 9.60e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   20 DNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQITSSFKAQlSYLFQIVRNLAIDHYRKQALEQKYSG-----PEEE 94
Cdd:PRK12523  18 DHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPR-AFLAAVAKGLMFDHFRRAALEQAYLAelalvPEAE 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15597622   95 GlnvviqgASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHC 168
Cdd:PRK12523  97 Q-------PSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 7-173 1.45e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 81.17  E-value: 1.45e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622    7 TRRCDTPLLQAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPqitSSFKAQLS---YLFQIVRNLAIDHYRKQA 83
Cdd:PRK11924   8 ATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKA---DLFNGKGSartWLLTIARNVCYDLLRRRR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   84 LEQKYSGPEEEGLNVVIQGASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRD 163
Cdd:PRK11924  85 REKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRR 164

                        170
                 ....*....|
gi 15597622  164 ALVHCRKVTA 173
Cdd:PRK11924 165 ARQLLRECLE 174
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 37-153 1.13e-16

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: 73.55  E-value: 1.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622    37 SRAEDVVQDAFFRLQSA-PQITSSFKAQlSYLFQIVRNLAIDHYRKQaleqkysGPEEEGLNVVIQGASPETSHINYATL 115
Cdd:TIGR02959  20 SDVEDLLQEVFIKIHRNlPSLKDGQKIQ-SWLYQIARNTIIDFYRSK-------SRSVELPESLLAADSAREETFVKELS 91

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 15597622   116 EHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVS 153
Cdd:TIGR02959  92 QCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLS 129
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 22-174 4.99e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 72.41  E-value: 4.99e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   22 RTILVKIAARITGCRSRAEDVVQDAFFRL---QSAPQITSSFKaqlSYLFQIVRNLAIDHYRKQALEQKYSGPEEEGLNV 98
Cdd:PRK12513  36 RTGLYRFLLRLARDRALAEDIFQETWLRViraRAQYQPRARFR---TWLYQIARNLLIDHWRRHGARQAPSLDADEQLHA 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597622   99 VI-QGASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRKVTAE 174
Cdd:PRK12513 113 LAdDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAE 189
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 25-169 2.67e-14

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 67.11  E-value: 2.67e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   25 LVKIAARITGCRSRAEDVVQDAFFRL---QSAPQITSSfkaqLSYLFQIVRNLAIDHYRKQALEQkySGP-----EEEGL 96
Cdd:PRK12527   8 LVRFLSARLGNRQAAEDVAHDAYLRVlerSSSAQIEHP----RAFLYRTALNLVVDRHRRHRVRQ--AEPlevldEEERL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15597622   97 NVviqgASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCR 169
Cdd:PRK12527  82 HS----PSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCR 150
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 39-153 6.83e-13

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 63.47  E-value: 6.83e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   39 AEDVVQDAFFRLQSA-PQITSSFKAQlSYLFQIVRNLAIDHYRKQAleqkysgPEEEGLNVVIQGASPETSHINYATLEH 117
Cdd:PRK09637  28 VDDLLQEVLIKTHSNlHSLKDGSSIK-SWLYQIANNTIIDFYRKKN-------RSEELPDDLLFEDEEREENAKKELAPC 99

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 15597622  118 IADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVS 153
Cdd:PRK09637 100 LRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLS 135
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 39-168 2.06e-12

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 62.13  E-value: 2.06e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   39 AEDVVQDAFFRLQSAPQITSsFKAQLSYLFQIVRNLAIDHYRKQALEQKYsgpeeegLNVVIQ-----GASPETSHINYA 113
Cdd:PRK09651  37 ADDIAQDTFLRVMVSETLST-IRDPRSFLCTIAKRVMVDLFRRNALEKAY-------LEMLALmpeggAPSPEERESQLE 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15597622  114 TLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHC 168
Cdd:PRK09651 109 TLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 16-174 2.38e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 61.89  E-value: 2.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   16 QAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQiTSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGPEEEG 95
Cdd:PRK12525  13 QMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPD-PASIREPRALLTTIARRLMYEGWRRQDLERAYLQSLAEA 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597622   96 LNVViqGASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRKVTAE 174
Cdd:PRK12525  92 PEAV--QPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQE 168
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 31-168 2.47e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 59.09  E-value: 2.47e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   31 RITGCRSRAEDVVQDAFFRLQSAPQiTSSFKAQLSYLFQIVRNLAIDHYRKQALEQKY-----SGPEEEGlnvviqgASP 105
Cdd:PRK12528  23 RRLGCPQSAADLAQDTFVKVLVARE-TAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYlealaQLPERVA-------PSE 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15597622  106 ETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHC 168
Cdd:PRK12528  95 EERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 157
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 25-153 3.83e-11

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 59.05  E-value: 3.83e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   25 LVKIAARITGCRSRAEDVVQDAFFRL-QSAPQI--TSSFKAqlsYLFQIVRNLAIDHYRKQ---ALEQKYSGPEEEGLNV 98
Cdd:PRK09652  23 VKRLLSRLTRDPADAEDLVQETFIKAyRALHSFrgGAAFYT---WLYRIARNTAINYLRKQgrrPPASDVDAEEAEDFDL 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597622   99 VIQGASPETSHINYATLE---HIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVS 153
Cdd:PRK09652 100 ADALRDISTPENELLSAEleqRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCP 157
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 36-168 1.10e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 57.64  E-value: 1.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   36 RSRAEDVVQDAFFRLQSAPQIT--SSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSgpeeEGLNVVIQG--ASPETSHIN 111
Cdd:PRK12529  39 RGVADDLAHDIFLRILASRDGGqrEAIRQPRAYLARIANCVLVSWRRRQSLELAWL----EALATLPEPlhPSPEQQSVI 114

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15597622  112 YATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHC 168
Cdd:PRK12529 115 LETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTC 171
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 18-83 1.77e-10

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: 54.52  E-value: 1.77e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597622    18 FVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSA-----PQITSSFKAqlsYLFQIVRNLAIDHYRKQA 83
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAierfdPERGVSFST---WLYTIIRNAIIDYLRKQR 69
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 17-175 3.27e-10

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


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 56.24  E-value: 3.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622    17 AFVDNR-TILVKIAARITGCRSRAEDVVQDAFFRLQSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQALEqkysgpeeeg 95
Cdd:TIGR02983  10 AFVAARyPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLL---------- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622    96 lnVVIQGASPETS--HINYATLEH--IADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRKV 171
Cdd:TIGR02983  80 --ELPTRELPDAAapDPAPDVALRaaLARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLREL 157


                  ....
gi 15597622   172 TAER 175
Cdd:TIGR02983 158 LEEP 161
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 118-168 1.26e-09

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: 51.69  E-value: 1.26e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15597622   118 IADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHC 168
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 26-153 2.02e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 54.51  E-value: 2.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   26 VKIAARITGCRSRAEDVVQDAFFRLQSAPQITSSFKAQLS-YLFQIVRNLAIDHYRKqaleQKYSGPEEEGLNVVIQGAS 104
Cdd:PRK12524  40 LAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVStWLYRVVCNLCTDRLRR----RRRASVDLDDAPEPADAAP 115

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 15597622  105 P-ETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVS 153
Cdd:PRK12524 116 GaEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIG 165
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
25-157 2.08e-09

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 53.93  E-value: 2.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   25 LVKIAARITGCRSRAEDVVQDAFFRL-QSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGPEEEGlnvVIQGA 103
Cdd:PRK09645  22 LWRYALRLTGDRARAEDVVQETLLRAwQHPEVLADTGRSARAWLFTVARNLVIDERRSARARPVEGGDDVLG---VPEQS 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15597622  104 SPETSHINYATLEhIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLV 157
Cdd:PRK09645  99 APDEVDRALDRLL-VADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTV 151
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 28-169 2.77e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 53.91  E-value: 2.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   28 IAARITGCRSRAEDVVQDAFFRLQSapqiTSSFKAQ----LSYLFQIVRNLAIDHYRKQALEQKysgPEEEGLNVVIQGA 103
Cdd:PRK12519  45 LALKILGNSQEAEDLTQEIFLSLWR----KSSYDPKrgslSSYLLTLTRSRAIDRLRSRRSRQR---LLERWQQELLGEA 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597622  104 SPETSHINYATLE---HIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCR 169
Cdd:PRK12519 118 SEDTPLEQASLAErsqRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 25-154 8.80e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 49.65  E-value: 8.80e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   25 LVKIAARITGCRSRAEDVVQDAFFRL-QSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQALEqkysgPEEEGLNVVIQGA 103
Cdd:PRK05602  33 LLALATRMLGDPAEAEDVAQETFLRIwKQAPSWRPGEARFDTWLHRVVLNLCYDRLRRRREV-----PVEDAPDVPDPAP 107

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 15597622  104 SPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSP 154
Cdd:PRK05602 108 GPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISV 158
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 11-154 9.32e-08

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 50.69  E-value: 9.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   11 DTPLLQAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSA--PQITSSfKAqlsYLFQIVRNLAIDHYRKQALE-QK 87
Cdd:PRK09636   3 MADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNAdrAQIRDP-RA---WLTRVVTRLCLDRLRSARHRrET 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597622   88 YSGP---------EEEGLNVVIQGASpetshINYATLEhiadALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSP 154
Cdd:PRK09636  79 YVGPwlpepvveeLDDPLEAVVAAED-----LSLALML----ALERLSPLERAAFLLHDVFGVPFDEIASTLGRSP 145
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 25-170 1.00e-07

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 49.18  E-value: 1.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   25 LVKIAARITGCRSRAEDVVQDAFFRL-QSAPQITSSFKAqlsYLFQIVRNLAIDHYRKQALEQKysgpEEEGL---NVVI 100
Cdd:PRK09639  16 VVQQIFYIVKDRTQAEDLAQEVFLRLyRSDFKGIENEKG---WLIKSARNVAYNYLRSEKRRRA----RILGEfqwQEVD 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622  101 QGASPETSHINYATLEHIADALTELPKRTRYAFEMyRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRK 170
Cdd:PRK09639  89 NEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLL-RFSGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 25-169 1.55e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 49.05  E-value: 1.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   25 LVKIAARITGCRSRAEDVVQDAFFRL-QSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQaleQKYSGPEEEGLNVVIQGA 103
Cdd:PRK12514  32 LFGICLRVLKDRSEAEEALQDVYVKIwTKADRFAVSGLSPMTWLITIARNHAIDRLRAR---KAVAVDIDEAHDLADPSP 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597622  104 SPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCR 169
Cdd:PRK12514 109 GPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 74-154 3.65e-07

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 48.67  E-value: 3.65e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622  74 LAIDHYRKQALEQKYSgpEEEGLNVVIQGASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVS 153
Cdd:COG1191 138 EAANAYQLLSLDEPLE--DGDDLLDLLESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVS 215


                .
gi 15597622 154 P 154
Cdd:COG1191 216 E 216
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 11-151 7.83e-07

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 48.04  E-value: 7.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   11 DTPLLQAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQitSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYsg 90
Cdd:PRK09635   4 HDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPV--GDIDDERGWLIVVTSRLCLDHIKSASTRRER-- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597622   91 PEEEGLNVVIQGASPETSHINYATL-EHIADALTELPKR----TRYAFEMYRLHGVPQKDIAKELG 151
Cdd:PRK09635  80 PQDIAAWHDGDASVSSVDPADRVTLdDEVRLALLIMLERlgpaERVVFVLHEIFGLPYQQIATTIG 145
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 28-130 2.00e-06

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 45.84  E-value: 2.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   28 IAARITGCRSRAEDVVQDAFFRlqsAPQITSSFKAQL---SYLFQIVRNLAIDHYRKQ----ALEQKYSGpeEEGLNVVI 100
Cdd:PRK09641  34 LCYRMLGNRHEAEDAAQEAFIR---AYVNIDSYDINRkfsTWLYRIATNLTIDRLRKRkpdyYLDAEVAG--TEGLTMYS 108

                         90       100       110
                 ....*....|....*....|....*....|....
gi 15597622  101 Q----GASPETSHINYATLEHIADALTELPKRTR 130
Cdd:PRK09641 109 QlaadDALPEEQVVSLELQETIQEAILQLPEKYR 142
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 25-165 3.28e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 45.43  E-value: 3.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   25 LVKIAARITGCRSRAEDVVQDAFFRL-QSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGPEEEGlNVVIQGA 103
Cdd:PRK12534  38 LFGVCLRMIPQRAEAEEVLQDVFTLIwHKAGQFDPSRARGLTWLAMIARNKAIDHLRANAPQRRNVALDDAG-ELRAADA 116

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597622  104 SPETSHINYATLEHIADALTEL-PKRT---RYAFemyrLHGVPQKDIAKELGVSPTLVNFMIRDAL 165
Cdd:PRK12534 117 SPLERTERASTRRRIDHCLAELePPRSeliRTAF----FEGITYEELAARTDTPIGTVKSWIRRGL 178
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 31-153 3.40e-06

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: 44.75  E-value: 3.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622    31 RITGCRSRAEDVVQDAFFRlqsAPQITSSFKAQ--LSYLFQIVRNLAIDHYRKQALEQKYSG---PEEEGLNVviqgASP 105
Cdd:TIGR02950  14 RLTKDKHLAEDLLQETFLK---AYIHLHSFKDSsiKPWLFRIARNAFIDWYRKDKKIQTIDDdaiGDLEQHPV----ESP 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 15597622   106 ETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVS 153
Cdd:TIGR02950  87 EHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLS 134
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 40-157 1.25e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 43.55  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   40 EDVVQDAFFRL-QSAPQITSsfKAQLS-YLFQIVRNLAIDhYRKQALEQKysgPEEEGLNVVIQGASPETS----HINYA 113
Cdd:PRK12518  38 DDLVQEVFLRVwKGLPKLRN--PAYFStWLYRITWNVATD-ARRQFAQRP---SRIQDDSLNDQPSRPSDTpdlmQLHYQ 111

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 15597622  114 TLehIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLV 157
Cdd:PRK12518 112 DL--VQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTV 153
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 32-153 5.25e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 41.85  E-value: 5.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   32 ITGCRSRAEDVVQDAFFRLQSApqiTSSFKAQ--LSYLFQIVRNLAIDHYRKqalEQKYSGPEEEGLNVVIQgasPETSH 109
Cdd:PRK12541  25 LTGDSHFAEDLMQETFYRMLVH---IDYYKGEeiRPWLFTIAYNAFIDWYRK---EKKYKTTTIEEFHLPNV---PSTEH 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 15597622  110 iNYATLEHIA---DALTELPKRTRYAFEMYRLHGVPQKDIAKELGVS 153
Cdd:PRK12541  96 -EYFIKHEIAswlDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLS 141
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 39-155 5.61e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 41.84  E-value: 5.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   39 AEDVVQDAFFRLQSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGPE-----EEGLNVVI-QGA--------- 103
Cdd:PRK12532  33 AEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLddellDEAFESHFsQNGhwtpegqpq 112

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15597622  104 ---SPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPT 155
Cdd:PRK12532 113 hwnTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTS 167
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 39-135 6.03e-05

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 41.49  E-value: 6.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   39 AEDVVQDAFFRL------QSApqitssfkAQLSYLFQ-IVRNLAIDHYRKQ-------ALEQKYSGPEEEGLNVVIQ--- 101
Cdd:PRK09047   7 ALDIVQDAMIKLaekygdRPA--------AEWPPLFQrILQNRIHDWFRRQkvrntwvSLFSSFSDDDDDDDFDPLEtld 78

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 15597622  102 -----GASPETSHINYATLEHIADALTELPKRTRYAFEM 135
Cdd:PRK09047  79 sadegAESPADKLERAQVLQLIEEAIQKLPARQREAFLL 117
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 18-152 1.96e-04

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 40.39  E-value: 1.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   18 FVDNRTILVKIAARITGCRSRAEDVVQDAFFRlqsAPQITSSFK--AQLS-YLFQIVRNLAIDHYRKQALEQKYSGPEEE 94
Cdd:PRK09638  24 FQQHYSFLYKYLLKLTLDPDLAEDLVQETMLK---AIENLSSFQgrSKFStWLISIASRLYKDHLRKQKREKLRLQRAKE 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597622   95 GLNVVIQGASPETSHinyaTLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGV 152
Cdd:PRK09638 101 ETLRKEKWEAAIKGA----EWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNI 154
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 115-169 5.51e-04

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: 36.70  E-value: 5.51e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15597622 115 LEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCR 169
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 117-157 9.21e-04

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 38.75  E-value: 9.21e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 15597622  117 HIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLV 157
Cdd:PRK07408 196 RLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTV 236
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 39-164 1.08e-03

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 38.19  E-value: 1.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   39 AEDVVQDAFFR-LQSAPQIT--SSFKAqlsYLFQIVRNLAIDhYRKQALEQKYSGPEEEGLNVVIQGASPETSHINYATL 115
Cdd:PRK09415  43 AEDLTQEIFVKcYKSLHTYKgkSSLKT---WLYRIAINHCKD-YLKSWHNKKVIVTEDIFTYMESQKESVEEEVIQNAED 118

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 15597622  116 EHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDA 164
Cdd:PRK09415 119 ERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKA 167
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 13-151 1.23e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 38.02  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   13 PLLQAFvdnrtilvkiAARITGCRSRAEDVVQDAFFRlqsAPQITSSFKAQL---SYLFQIVRNLAIDHYRKQALEQkys 89
Cdd:PRK12540  16 PSLRAF----------AISLSGNGDRADDLVQETLLR---ALANIDSFQPGSnlpAWLFTILRNLFRSDYRKRRREV--- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15597622   90 gPEEEGLNVVIQGASP-ETSHINYatlEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELG 151
Cdd:PRK12540  80 -EDADGSYAKTLKSQPgQNAHLEF---EEFRAALDKLPQDQREALILVGASGFSYEDAAAICG 138
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 37-174 1.42e-03

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 37.97  E-value: 1.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   37 SRAEDVVQDAFFRL-QSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQALEQKYSGP---EEEGLNVVIQGASpETSHINY 112
Cdd:PRK13919  48 AAAEDVVQEVFIRVwKKAKEFDPRRGSARAWLLALAHHAAVDHVRRRAARPQPLEPderEPEAFDLPGPGLD-EEGHLDR 126

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15597622  113 ATLEHiadALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRDALVHCRKVTAE 174
Cdd:PRK13919 127 TRLGR---ALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 28-132 1.65e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 37.91  E-value: 1.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   28 IAARITGCRSRAEDVVQDAFFRLQSAPQITSSFKAQLS-YLFQIVRNLAIDHYRKQALEQKYSGPEeeglnvVIQGASPE 106
Cdd:PRK12538  79 IALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFStWLYRVVSNRCIDLRRKPRTENVDAVPE------VADGKPDA 152

                         90       100
                 ....*....|....*....|....*..
gi 15597622  107 TSHINYATLEHIAD-ALTELPKRTRYA 132
Cdd:PRK12538 153 VSVIERNELSDLLEaAMQRLPEQQRIA 179
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 16-157 2.61e-03

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 37.00  E-value: 2.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   16 QAFVDNRTILVKIAARITGCRSRAEDVVQDAFFrlqSAPQITSSFKAQL---SYLFQIVRNLAIDHYRKQALEQKYSGPE 92
Cdd:PRK09643  31 ELFRRHHRRLWAVARRTSGTREDAADALQDAML---SAHRAAGSFRGDAavsSWLHRIVVNACLDRLRRAKARPTVPLDD 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15597622   93 EEGLNvviQGASPETSHINyaTLEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLV 157
Cdd:PRK09643 108 VYPVA---QLERDPTARVE--TALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTV 167
PRK12544 PRK12544
RNA polymerase factor sigma-70;
11-94 2.89e-03

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 37.09  E-value: 2.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   11 DTPLLQafvDNRTILVKIAARITGCRSRAEDVVQDAffrLQSAPQITSSFKAQL---SYLFQIVRNLAIDHYRKQ----A 83
Cdd:PRK12544  20 DPVFLE---DLRKQMIKFATLQLSDLHLAEDAVQEA---LIGALKNADSFAGRAafkTWVFAILKNKIIDLLRQKkrhvS 93

                         90
                 ....*....|.
gi 15597622   84 LEQKYSGPEEE 94
Cdd:PRK12544  94 ASSLLRDEEEE 104
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 38-152 4.79e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 36.30  E-value: 4.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   38 RAEDVVQDAFFRlqsAPQITSSFKAQL---SYLFQIVRNLAIDHYRKQALEQKYSGPEEEGLNVVIqgASPETSHINyat 114
Cdd:PRK12511  30 EAEDLVHDALVR---ALERRASFRSGGnlrTWLMSILHNAFIDELRRRRVEARRADELAVLADASL--PAAQEHAVR--- 101

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 15597622  115 LEHIADALTELPKRTRYAFEMYRLHGVPQKDIAKELGV 152
Cdd:PRK12511 102 LAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGI 139
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 25-151 8.68e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 35.52  E-value: 8.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597622   25 LVKIAARITGCRSRAEDVVQDAFFRLQSApqiTSSFKAQ----LSYLFQIVRNLAIDHYRKQALEQKYSGPEEEGLNVVI 100
Cdd:PRK12537  36 LLGVARRIVRDRALAEDIVHDAFIKIWTG---AASFDPArgsaRGWIYSVTRHLALNVLRDTRREVVLDDDAEETAQTLH 112

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 15597622  101 QGASPETSHINYAtleHIADALTEL-PKRTRYAFEMYrLHGVPQKDIAKELG 151
Cdd:PRK12537 113 EIIDDFDLWANSG---KIHRCLEQLePARRNCILHAY-VDGCSHAEIAQRLG 160
 
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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