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Conserved domains on  [gi|556330948|ref|WP_023296645|]
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MULTISPECIES: RNA polymerase sigma factor [Enterobacter]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

CATH:  1.10.1740.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  28575802
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 15-177 1.41e-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: 99.30  E-value: 1.41e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  15 LNACRARLKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARKKHEvslpgyltaddED 91
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETflrLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRR-----------RR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  92 FPEQEIAETLFGVPQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFL 171
Cdd:COG1595   92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                 ....*.
gi 556330948 172 RSRLKD 177
Cdd:COG1595  172 REALEE 177
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 15-177 1.41e-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: 99.30  E-value: 1.41e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  15 LNACRARLKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARKKHEvslpgyltaddED 91
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETflrLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRR-----------RR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  92 FPEQEIAETLFGVPQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFL 171
Cdd:COG1595   92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                 ....*.
gi 556330948 172 RSRLKD 177
Cdd:COG1595  172 REALEE 177
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 21-177 1.55e-23

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 91.41  E-value: 1.55e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  21 RLKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARK-KHEVSLPGYLTADDEDFPEQE 96
Cdd:PRK09652  22 RVKRLLSRLTRDPADAEDLVQETfikAYRALHSFRGGAAFYTWLYRIARNTAINYLRKqGRRPPASDVDAEEAEDFDLAD 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  97 IAETlfgvPQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLK 176
Cdd:PRK09652 102 ALRD----ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177


                 .
gi 556330948 177 D 177
Cdd:PRK09652 178 P 178
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-175 2.01e-20

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: 82.78  E-value: 2.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   15 LNACRARLKAFIRGRTAVRDDVDDILQEVTWQLMKVEQ---PVENVAAWLFRAARNEMIDRARKKHEVSLPGYLTADDED 91
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDrfdPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   92 FPEqeiaetlfgvpqTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFL 171
Cdd:TIGR02937  87 SDP------------SPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154


                  ....
gi 556330948  172 RSRL 175
Cdd:TIGR02937 155 RELL 158
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 118-172 2.37e-06

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: 42.86  E-value: 2.37e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 556330948 118 WEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLR 172
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 119-171 7.96e-06

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: 41.67  E-value: 7.96e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 556330948  119 EELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFL 171
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 15-177 1.41e-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: 99.30  E-value: 1.41e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  15 LNACRARLKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARKKHEvslpgyltaddED 91
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETflrLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRR-----------RR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  92 FPEQEIAETLFGVPQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFL 171
Cdd:COG1595   92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                 ....*.
gi 556330948 172 RSRLKD 177
Cdd:COG1595  172 REALEE 177
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 21-177 1.55e-23

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 91.41  E-value: 1.55e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  21 RLKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARK-KHEVSLPGYLTADDEDFPEQE 96
Cdd:PRK09652  22 RVKRLLSRLTRDPADAEDLVQETfikAYRALHSFRGGAAFYTWLYRIARNTAINYLRKqGRRPPASDVDAEEAEDFDLAD 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  97 IAETlfgvPQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLK 176
Cdd:PRK09652 102 ALRD----ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177


                 .
gi 556330948 177 D 177
Cdd:PRK09652 178 P 178
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 19-181 1.73e-20

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 83.50  E-value: 1.73e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  19 RARLKAFIRGRTAVRDDVDDILQEVtwqLMKVEQPVEN------VAAWLFRAARNEMIDRARKKHEVSLPgyltADDEDF 92
Cdd:PRK09637  11 KAQLKAFLHSRVSNEADVDDLLQEV---LIKTHSNLHSlkdgssIKSWLYQIANNTIIDFYRKKNRSEEL----PDDLLF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  93 PEQEiaetlfgvpqtpEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAvrflR 172
Cdd:PRK09637  84 EDEE------------REENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRG----R 147


                 ....*....
gi 556330948 173 SRLKDIYEA 181
Cdd:PRK09637 148 VKLKELLEG 156
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-175 2.01e-20

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: 82.78  E-value: 2.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   15 LNACRARLKAFIRGRTAVRDDVDDILQEVTWQLMKVEQ---PVENVAAWLFRAARNEMIDRARKKHEVSLPGYLTADDED 91
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDrfdPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   92 FPEqeiaetlfgvpqTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFL 171
Cdd:TIGR02937  87 SDP------------SPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154


                  ....
gi 556330948  172 RSRL 175
Cdd:TIGR02937 155 RELL 158
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 19-180 2.98e-18

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: 77.41  E-value: 2.98e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   19 RARLKAFIRGRTAVRDDVDDILQEVtwqLMKVE------QPVENVAAWLFRAARNEMIDRAR-KKHEVSLPgyltaDDED 91
Cdd:TIGR02959   5 RSELKAFIKSRVSDASDVEDLLQEV---FIKIHrnlpslKDGQKIQSWLYQIARNTIIDFYRsKSRSVELP-----ESLL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   92 FPEqeiaetlfgvpqTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAvrfl 171
Cdd:TIGR02959  77 AAD------------SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRG---- 140


                  ....*....
gi 556330948  172 RSRLKDIYE 180
Cdd:TIGR02959 141 RKKLKELLE 149
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 20-175 2.52e-15

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: 69.51  E-value: 2.52e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   20 ARLKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARKK--HEVSlpgyltadDEDFPE 94
Cdd:TIGR02985  12 PKLCAFARRYVKDEEDAEDIVQDVflkLWENRETLEISESIKAYLFTIVKNRCLNYLRHKqvEEKY--------QEELAE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   95 QEIAETLFgvpQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSR 174
Cdd:TIGR02985  84 IEERELSE---ADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKE 160


                  .
gi 556330948  175 L 175
Cdd:TIGR02985 161 L 161
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 19-177 7.77e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 66.15  E-value: 7.77e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  19 RARLKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMID--RARKKHEVslpgyLTADDEDFP 93
Cdd:PRK11924  23 APDLLRYARRQLGDRALAEDAVQEAflrAWRKADLFNGKGSARTWLLTIARNVCYDllRRRRREKA-----VLSDDALEP 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  94 EQEIAEtlfgvpQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRS 173
Cdd:PRK11924  98 EFAETA------ETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171


                 ....
gi 556330948 174 RLKD 177
Cdd:PRK11924 172 CLEA 175
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 19-175 2.87e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 64.71  E-value: 2.87e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  19 RARLKAFIRGRTAVRDDVDDILQEVTWQLMKVE---QPVENVAAWLFRAARNEMIDRARKkHEVSLPGYLTADDEdfpeq 95
Cdd:PRK12513  36 RTGLYRFLLRLARDRALAEDIFQETWLRVIRARaqyQPRARFRTWLYQIARNLLIDHWRR-HGARQAPSLDADEQ----- 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  96 eiAETLFGVPQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRL 175
Cdd:PRK12513 110 --LHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 15-175 2.60e-11

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: 58.87  E-value: 2.60e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   15 LNACRARLKAFIRGRTAVRDDVDDILQE---VTWQLMKVEQPVENVAAWLFRAARNEMIDRARKKHEVSLpgyltADDED 91
Cdd:TIGR02989   7 LTRHERALRAFVRSLVADRDDVDDVLQEtfvVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRL-----VFDDD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   92 FPEQeIAETLfgvpqTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALlsrkHKAVRFL 171
Cdd:TIGR02989  82 LLEA-LAAEA-----EPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAV----YKALQRI 151


                  ....
gi 556330948  172 RSRL 175
Cdd:TIGR02989 152 RVSL 155
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 15-177 3.71e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 53.55  E-value: 3.71e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  15 LNACRARLKAFIRGRTA----VRDDVDDILQEV---------TWqlmKVEQPVenvAAWLFRAARNEMIDRARKKhevsl 81
Cdd:PRK12512  28 LKAVTPVLRAAARRGLAragqPADQAEDIVQEIllavhlkrhTW---DPGAPF---APWLFAIARNKLIDALRRR----- 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  82 pGYLTADDEDfpeqEIAETLfgvPQTPEEEYLNMLlweELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALL 161
Cdd:PRK12512  97 -GRRVFVDID----DFAETL---PAEPATETLPAG---DVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVR 165

                        170
                 ....*....|....*.
gi 556330948 162 SRKHKAVRFLRSRLKD 177
Cdd:PRK12512 166 VALHRGLAALAAKFRS 181
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 22-178 1.36e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 51.89  E-value: 1.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  22 LKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARKK-HEVSLP-GYLTADDEDFPEQe 96
Cdd:PRK12516  23 LRAFAVSLIGRHDRADDLVQDTimkAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRgREVQDTdGMFTEQLAVHPSQ- 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  97 iaetlFGVpqtpeeeylnmLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAvrflRSRLK 176
Cdd:PRK12516 102 -----YGT-----------LDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRA----RQRLQ 161


                 ..
gi 556330948 177 DI 178
Cdd:PRK12516 162 EI 163
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
2-172 2.41e-08

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 51.23  E-value: 2.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   2 KAGEAGESLLISALNACRAR-LKAFIRGRTAVRDDVDDILQEV---TWQLMKV-EQPVENVAAWLFRAARNEMID--RAR 74
Cdd:PRK09645   1 SGMATAEAALMRALYDEHAApLWRYALRLTGDRARAEDVVQETllrAWQHPEVlADTGRSARAWLFTVARNLVIDerRSA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  75 KkhevslpgyltaddedFPEQEIAETLFGVPQTPEEEYLNMLLWE-ELGQALSELPPPQREVFEKTEFEGYSMKMLAEET 153
Cdd:PRK09645  81 R----------------ARPVEGGDDVLGVPEQSAPDEVDRALDRlLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADL 144

                        170
                 ....*....|....*....
gi 556330948 154 GDSVQALLSRKHKAVRFLR 172
Cdd:PRK09645 145 GIPEGTVKSRLHYALRALR 163
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 22-176 2.77e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 47.85  E-value: 2.77e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  22 LKAFIRGRTAVRDDVDDILQEVTWQLMK--VEQPVENVAAWLFRAARNEMIDRARKkHEVSLPGYLTADDEDfpeqeiaE 99
Cdd:PRK12527   8 LVRFLSARLGNRQAAEDVAHDAYLRVLErsSSAQIEHPRAFLYRTALNLVVDRHRR-HRVRQAEPLEVLDEE-------E 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556330948 100 TLFgVPQTPEEEYLNMLLwEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQalLSRKH--KAVRFLRSRLK 176
Cdd:PRK12527  80 RLH-SPSPQTRLDLGQRL-ALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRS--LVEKHivNAMKHCRVRMR 154
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 60-177 3.28e-07

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 48.15  E-value: 3.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  60 WLFRAARNEMIDRARK-KHEVSLPGYLTADDEDFPEQEIAETlfgvPQTPEEEYLNMLLWEELGQALSELPPPQREVFEK 138
Cdd:PRK09641  72 WLYRIATNLTIDRLRKrKPDYYLDAEVAGTEGLTMYSQLAAD----DALPEEQVVSLELQETIQEAILQLPEKYRTVIVL 147

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 556330948 139 TEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLKD 177
Cdd:PRK09641 148 KYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 22-180 4.46e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 47.91  E-value: 4.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  22 LKAFIRGRTavRDDV--DDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARK-KHEVslpgyltaddEDfPEQ 95
Cdd:PRK12546  20 LRAFAISLT--RNVAvaDDLVQDTivkAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKhKREV----------PD-PEG 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  96 EIAETLFGVPqtpeeEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAvrflRSRL 175
Cdd:PRK12546  87 VHAASLAVKP-----AHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRA----RARL 157


                 ....*
gi 556330948 176 KDIYE 180
Cdd:PRK12546 158 AELLQ 162
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 15-178 6.73e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 47.35  E-value: 6.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  15 LNACRARLKAFIRGRTAVR-DDVDDILQEVtwqLMKVE------QPVENVAAWLFRAARNEMID--RARKKHEvSLPGYL 85
Cdd:PRK12536  27 LSELAAHLRGFLRRRLPQLpDEVEDLVQEI---LLAVHnarhtyRADQPLTAWVHAIARYKLMDflRSRARRE-ALHDPL 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  86 TADDEDF--PEQEIAETLfgvpqtpeeeylnmllwEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSR 163
Cdd:PRK12536 103 DDESELFatSDDEAAEAR-----------------RDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVG 165

                        170
                 ....*....|....*
gi 556330948 164 KHKAVRFLRSRLKDI 178
Cdd:PRK12536 166 IHRGLKALAAKIRGE 180
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 19-156 1.27e-06

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 46.22  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  19 RARLKAFIRGRTAVRDDVDDILQEVTWQLMKVEQ--PVENVAAWLFRAARNEMIDRARKKhevSLPGYLTADDEDFpeqe 96
Cdd:PRK07037   8 RSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNqdAVKQPVAYLFRIVRNLAIDHYRRQ---ALENKYHGDEEDG---- 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556330948  97 iaetlFGVPQ---TPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDS 156
Cdd:PRK07037  81 -----LDVPSpeaSPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVS 138
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 37-174 1.65e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 45.70  E-value: 1.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  37 DDILQEVTWQ-LMKVEQ-PVENVAAWLFRAARNEMIDRARKkhevslpgyltadDEDFPEQEIAEtlFGVPQTPEEEYLN 114
Cdd:PRK12541  33 EDLMQETFYRmLVHIDYyKGEEIRPWLFTIAYNAFIDWYRK-------------EKKYKTTTIEE--FHLPNVPSTEHEY 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556330948 115 MLLWEELG--QALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSR 174
Cdd:PRK12541  98 FIKHEIASwlDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 22-178 1.80e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 45.64  E-value: 1.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  22 LKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARKK-HEVS-LPGYLTADDEDFPEQE 96
Cdd:PRK12547  19 LRAFAVSLSSKHDKAEDLVQDTlmkAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRgREVQdSDGVFTARVAVHPAQY 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  97 IAETLfgvpqtpeeeylnmllwEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAvrflRSRLK 176
Cdd:PRK12547  99 GSLDL-----------------QDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRA----RNRLQ 157


                 ..
gi 556330948 177 DI 178
Cdd:PRK12547 158 EL 159
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 118-172 2.37e-06

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: 42.86  E-value: 2.37e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 556330948 118 WEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLR 172
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 22-175 4.83e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 44.96  E-value: 4.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  22 LKAFIRGRTAVRDDVDDILQEVTWQ-LMKVE--QPVENVAAWLFRAARNEMIDRARKKHEvslpgyltaddedfpEQEIA 98
Cdd:PRK12540  18 LRAFAISLSGNGDRADDLVQETLLRaLANIDsfQPGSNLPAWLFTILRNLFRSDYRKRRR---------------EVEDA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556330948  99 ETLFGVPQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAvrflRSRL 175
Cdd:PRK12540  83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRA----RSKL 155
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 119-171 7.96e-06

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: 41.67  E-value: 7.96e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 556330948  119 EELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFL 171
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 19-175 2.16e-05

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: 42.76  E-value: 2.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   19 RARLKAFIRGRTAVRDDVDDILQEV---TWQLMKVEQPVENVAAWLFRAARNEMIDRARKKHEVSLPgyltadDEDFPEQ 95
Cdd:TIGR02983  16 YPRLLRTAYLLTGDPHEAEDLVQEAlvrTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLELP------TRELPDA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   96 EIaetlfgvpqtpEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRL 175
Cdd:TIGR02983  90 AA-----------PDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-76 5.70e-05

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: 39.49  E-value: 5.70e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556330948   16 NACRARLKAFIRGRTAVRDDVDDILQEVT---WQLMKVEQP--VENVAAWLFRAARNEMIDRARKK 76
Cdd:pfam04542   3 ERYLPLVYSLARRYLGDGADAEDLVQEGFlglWRAIERFDPerGVSFSTWLYTIIRNAIIDYLRKQ 68
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 35-177 6.37e-05

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 41.70  E-value: 6.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  35 DVDDILQEVtwqLMKVEQPVENVAA-----WLFRAARNEMIDRARKKHEVSLpgyltaddEDFPEQeiAETLFGVPQTPE 109
Cdd:PRK09647  54 DAEDLTQET---FIRVFRSLQNYQPgtfegWLHRITTNLFLDMVRRRARIRM--------EALPED--YDRVPGDEPNPE 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556330948 110 EEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLKD 177
Cdd:PRK09647 121 QIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 33-185 6.79e-05

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 41.47  E-value: 6.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  33 RDDVDDILQEVTWQLMKVE-QPVENVAAWLFRAARNEMID--RARKKHEVSLpgyltadDEDFPEQEIAETLfgvpqTPE 109
Cdd:PRK09639  27 RTQAEDLAQEVFLRLYRSDfKGIENEKGWLIKSARNVAYNylRSEKRRRARI-------LGEFQWQEVDNEP-----SPE 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556330948 110 EEYLNMLLWEELGQALSELPPPQREVFeKTEFEGYSMKMLAEETG---DSVQALLSRKHKavrflrsRLKDIYEALTGQ 185
Cdd:PRK09639  95 EIWIRKEEITKVQEVLAKMTERDRTVL-LLRFSGYSYKEIAEALGikeSSVGTTLARAKK-------KFRKIYEQMEEE 165
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 37-185 7.75e-05

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 41.40  E-value: 7.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  37 DDILQEVTWQ--LMKVEQPVENVAAWLFRAARNEMIDRARKKHEVSlpgYLTADdedfpeqEIAETLFGVPQTPEEEyln 114
Cdd:PRK09644  29 EDLLQETFYRayIYLEDYDNQKVKPWLFKVAYHTFIDFVRKEKKVS---FVGTD-------EIEAIQAESTEEYVVA--- 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556330948 115 MLLWEELGQALSELPPPQREVFEKtefegYSMKMLAEETGDSVQALLSRKHKAVRFL-RSRLKDIYEALTGQ 185
Cdd:PRK09644  96 KNSYEKLIQIIHTLPVIEAQAILL-----CDVHELTYEEAASVLDLKLNTYKSHLFRgRKRLKALLKEEKSQ 162
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 33-177 8.93e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 41.18  E-value: 8.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  33 RDDVDDILQEV---TWQLMKVEQPVE-NVAAWLFRAARNEMIDRARKKHEVSLpgyltaddEDFPEQEIAETLfgvpqtP 108
Cdd:PRK05602  44 PAEAEDVAQETflrIWKQAPSWRPGEaRFDTWLHRVVLNLCYDRLRRRREVPV--------EDAPDVPDPAPG------P 109

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556330948 109 EEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLKD 177
Cdd:PRK05602 110 DAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 37-177 1.92e-04

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 40.28  E-value: 1.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  37 DDILQEV---TWQLMKVEQPVENVA-AWLFRAARNEMIDRARKKHEVSLPgylTADDEDFPEqeiAETLFGvPQTPEEEY 112
Cdd:PRK13919  51 EDVVQEVfirVWKKAKEFDPRRGSArAWLLALAHHAAVDHVRRRAARPQP---LEPDEREPE---AFDLPG-PGLDEEGH 123

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556330948 113 LNMLlweELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLKD 177
Cdd:PRK13919 124 LDRT---RLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 33-180 2.18e-04

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 40.12  E-value: 2.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  33 RDDVDDILQEVtwqLMKVEQPVE------NVAAWLFRAARNEMIDRARKKHEVSLpgyltaddedFPEQEIAETLFGVPQ 106
Cdd:PRK09415  40 KEVAEDLTQEI---FVKCYKSLHtykgksSLKTWLYRIAINHCKDYLKSWHNKKV----------IVTEDIFTYMESQKE 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556330948 107 TPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAvrflRSRLKDIYE 180
Cdd:PRK09415 107 SVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKA----KELLKKGLE 176
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 33-176 4.70e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 39.27  E-value: 4.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  33 RDDVDDILQEV---TWQLMKVEQPVENVA-AWLFRAARNEMID----RARKKHEVSL--PGYLTADDEDfpeqeiaetlf 102
Cdd:PRK12534  49 RAEAEEVLQDVftlIWHKAGQFDPSRARGlTWLAMIARNKAIDhlraNAPQRRNVALddAGELRAADAS----------- 117

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556330948 103 gvpqtPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLK 176
Cdd:PRK12534 118 -----PLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 60-177 1.65e-03

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 37.69  E-value: 1.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  60 WLFRAARNEMIDRARKKHEVSLPgyltadDEDFPEQEIAETLFGVPQTPEEeylnmllWEELGQALSELPPPQREVFEKT 139
Cdd:PRK09638  72 WLISIASRLYKDHLRKQKREKLR------LQRAKEETLRKEKWEAAIKGAE-------WSEMLDALSKLDPEFRAPVILK 138

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 556330948 140 EFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLKD 177
Cdd:PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWGQ 176
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 32-136 2.43e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 36.87  E-value: 2.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  32 VRDDVD--DILQEVTWQLMKV--EQPVENVAAWLFRAARNEMID----RARKKHEVSLPGYLTA--DDEDFPEQEIAETL 101
Cdd:PRK09047   1 VRDDDAalDIVQDAMIKLAEKygDRPAAEWPPLFQRILQNRIHDwfrrQKVRNTWVSLFSSFSDddDDDDFDPLETLDSA 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 556330948 102 FGVPQTPEEEYLNMLLWEELGQALSELPPPQREVF 136
Cdd:PRK09047  81 DEGAESPADKLERAQVLQLIEEAIQKLPARQREAF 115
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
18-175 3.03e-03

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 36.87  E-value: 3.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  18 CRARLKAFIRGRTavrdDVDDILQEVTWQLMKVEQPVEN----VAAWLFRAARNEMID--RARKKHEvslpgylTADDED 91
Cdd:PRK09648  41 CRARLGGVERPGL----SADDVAQEVCLAVITALPRYRDqgrpFLAFVYGIAAHKVADahRAAGRDK-------AVPTEE 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948  92 FPEQEIAEtlfgvpQTPEEEYLNMLLWEELGQALSELPPPQREVFEKTEFEGYSmkmlAEETGDSVQ----ALLSRKHKA 167
Cdd:PRK09648 110 VPERPSDD------AGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLS----AEETAEAVGstpgAVRVAQHRA 179


                 ....*...
gi 556330948 168 VRFLRSRL 175
Cdd:PRK09648 180 LARLRAEI 187
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 59-177 5.85e-03

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


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 35.86  E-value: 5.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556330948   59 AWLFRAARNEMIDRARKKHEVSLPGyltaddeDFPEQEIAETLFGVPQTPEEEYLNMllwEELGQALSELPPPQREVFEK 138
Cdd:pfam07638  77 AAAAEAMRRILIDHARRRQRQKRGG-------DVQRRELDEVVDNGDSPNPDLLLDL---DEALEQLFSLSPRQARLVEL 146

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 556330948  139 TEFEGYSMKMLAEETGDSVQALLSRKHKAVRFLRSRLKD 177
Cdd:pfam07638 147 RFFAGLSNDEIAERLGVSERTVERNWALARAWLHRELRD 185
 
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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