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Conserved domains on  [gi|1863311427|gb|QLA09401|]
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RNA polymerase sigma factor [Enterobacter ludwigii]

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 3.24e-27

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: 101.22  E-value: 3.24e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  15 LNACRARLKAFIRGRTSVRDDADDILQEVTYQLMKVE---QPVENVAAWLFRAARNEMTDRARKKREvslsgyftgddED 91
Cdd:COG1595    23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLdsfRGRGSFRAWLYRIARNLAIDHLRKRRR-----------RR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  92 FPEDELAETLFGVPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFL 171
Cdd:COG1595    92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                  ....*.
gi 1863311427 172 RTRLRD 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 3.24e-27

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: 101.22  E-value: 3.24e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  15 LNACRARLKAFIRGRTSVRDDADDILQEVTYQLMKVE---QPVENVAAWLFRAARNEMTDRARKKREvslsgyftgddED 91
Cdd:COG1595    23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLdsfRGRGSFRAWLYRIARNLAIDHLRKRRR-----------RR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  92 FPEDELAETLFGVPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFL 171
Cdd:COG1595    92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                  ....*.
gi 1863311427 172 RTRLRD 177
Cdd:COG1595   172 REALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-175 4.14e-21

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: 84.71  E-value: 4.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  15 LNACRARLKAFIRGRTSVRDDADDILQEVTYQLMKVEQ---PVENVAAWLFRAARNEMTDRARKKREVSLsgyftgdded 91
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDrfdPEGSFKAWLFRIARNLILDYLRRKRRLRR---------- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  92 fpEDELAETLFGVPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFL 171
Cdd:TIGR02937  77 --ELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154


                  ....
gi 1863311427 172 RTRL 175
Cdd:TIGR02937 155 RELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 21-178 4.38e-20

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 82.55  E-value: 4.38e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  21 RLKAFIRGRTSVRDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEMTDRARK-KREVSLSGYFTGDDEDFPEDE 96
Cdd:PRK09652   22 RVKRLLSRLTRDPADAEDLVQETfikAYRALHSFRGGAAFYTWLYRIARNTAINYLRKqGRRPPASDVDAEEAEDFDLAD 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  97 LAETlfgvPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRTRLR 176
Cdd:PRK09652  102 ALRD----ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177


                  ..
gi 1863311427 177 DV 178
Cdd:PRK09652  178 PL 179
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 2.85e-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: 42.83  E-value: 2.85e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1863311427 119 EELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFL 171
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 118-172 1.22e-05

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 40.94  E-value: 1.22e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1863311427 118 WEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLR 172
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 15-177 3.24e-27

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: 101.22  E-value: 3.24e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  15 LNACRARLKAFIRGRTSVRDDADDILQEVTYQLMKVE---QPVENVAAWLFRAARNEMTDRARKKREvslsgyftgddED 91
Cdd:COG1595    23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLdsfRGRGSFRAWLYRIARNLAIDHLRKRRR-----------RR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  92 FPEDELAETLFGVPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFL 171
Cdd:COG1595    92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                  ....*.
gi 1863311427 172 RTRLRD 177
Cdd:COG1595   172 REALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-175 4.14e-21

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: 84.71  E-value: 4.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  15 LNACRARLKAFIRGRTSVRDDADDILQEVTYQLMKVEQ---PVENVAAWLFRAARNEMTDRARKKREVSLsgyftgdded 91
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDrfdPEGSFKAWLFRIARNLILDYLRRKRRLRR---------- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  92 fpEDELAETLFGVPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFL 171
Cdd:TIGR02937  77 --ELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154


                  ....
gi 1863311427 172 RTRL 175
Cdd:TIGR02937 155 RELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 21-178 4.38e-20

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 82.55  E-value: 4.38e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  21 RLKAFIRGRTSVRDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEMTDRARK-KREVSLSGYFTGDDEDFPEDE 96
Cdd:PRK09652   22 RVKRLLSRLTRDPADAEDLVQETfikAYRALHSFRGGAAFYTWLYRIARNTAINYLRKqGRRPPASDVDAEEAEDFDLAD 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  97 LAETlfgvPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRTRLR 176
Cdd:PRK09652  102 ALRD----ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177


                  ..
gi 1863311427 177 DV 178
Cdd:PRK09652  178 PL 179
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 19-178 2.65e-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: 77.79  E-value: 2.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  19 RARLKAFIRGRTSVRDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEMTDRAR-KKREVSLsgyftgddedfPE 94
Cdd:TIGR02959   5 RSELKAFIKSRVSDASDVEDLLQEVfikIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRsKSRSVEL-----------PE 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  95 DELAetlfgvPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAvlflRTR 174
Cdd:TIGR02959  74 SLLA------ADSAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRG----RKK 143


                  ....
gi 1863311427 175 LRDV 178
Cdd:TIGR02959 144 LKEL 147
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 19-178 1.09e-17

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 76.18  E-value: 1.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  19 RARLKAFIRGRTSVRDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEMTDRARKK-REVSLsgyftgddedfPE 94
Cdd:PRK09637   11 KAQLKAFLHSRVSNEADVDDLLQEVlikTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKnRSEEL-----------PD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  95 DELAETLfgvphtPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAvlflRTR 174
Cdd:PRK09637   80 DLLFEDE------EREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRG----RVK 149


                  ....
gi 1863311427 175 LRDV 178
Cdd:PRK09637  150 LKEL 153
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 20-175 6.27e-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: 68.36  E-value: 6.27e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  20 ARLKAFIRGRTSVRDDADDILQEVTYQLMKVEQ---PVENVAAWLFRAARNEMTDRARKK--REVSLSgyftgDDEDFPE 94
Cdd:TIGR02985  12 PKLCAFARRYVKDEEDAEDIVQDVFLKLWENREtleISESIKAYLFTIVKNRCLNYLRHKqvEEKYQE-----ELAEIEE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  95 DELAETlfgvphTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRTR 174
Cdd:TIGR02985  87 RELSEA------DPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKE 160


                  .
gi 1863311427 175 L 175
Cdd:TIGR02985 161 L 161
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 19-177 2.12e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 67.69  E-value: 2.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  19 RARLKAFIRGRTSVRDDADDILQEVtyqLMKVEQ------PVENVAAWLFRAARNEMTD--RARKKREVSLSGyftgdde 90
Cdd:PRK11924   23 APDLLRYARRQLGDRALAEDAVQEA---FLRAWRkadlfnGKGSARTWLLTIARNVCYDllRRRRREKAVLSD------- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  91 DFPEDELAETLfgvpHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLF 170
Cdd:PRK11924   93 DALEPEFAETA----ETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQL 168


                  ....*..
gi 1863311427 171 LRTRLRD 177
Cdd:PRK11924  169 LRECLEA 175
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 19-175 6.97e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 66.64  E-value: 6.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  19 RARLKAFIRGRTSVRDDADDILQEVTYQLMKVE---QPVENVAAWLFRAARNEMTDRARKKREVSLsgyftgddedfPED 95
Cdd:PRK12513   36 RTGLYRFLLRLARDRALAEDIFQETWLRVIRARaqyQPRARFRTWLYQIARNLLIDHWRRHGARQA-----------PSL 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  96 ELAETLFGVP---HTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLR 172
Cdd:PRK12513  105 DADEQLHALAddgAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLR 184


                  ...
gi 1863311427 173 TRL 175
Cdd:PRK12513  185 ELL 187
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 1-178 8.07e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 63.56  E-value: 8.07e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427   1 MKTGLAGESLLMSA-LNACRARLKAFIRGRTS----VRDDADDILQEVtyqLMKVE------QPVENVAAWLFRAARNEM 69
Cdd:PRK12512   13 MRSANAGDAAAYRRlLKAVTPVLRAAARRGLAragqPADQAEDIVQEI---LLAVHlkrhtwDPGAPFAPWLFAIARNKL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  70 TDRARKK-REVslsgyftgddeDFPEDELAETLFGVPHTPeeeylkTLLWEELGQALSELPPPQREVFEKTELQGYSIKM 148
Cdd:PRK12512   90 IDALRRRgRRV-----------FVDIDDFAETLPAEPATE------TLPAGDVGRHLETLPPRQRDVVQSISVEGASIKE 152

                         170       180       190
                  ....*....|....*....|....*....|
gi 1863311427 149 LAEETGASEQALLSRKHKAVLFLRTRLRDV 178
Cdd:PRK12512  153 TAAKLSMSEGAVRVALHRGLAALAAKFRSE 182
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 15-177 1.06e-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: 60.03  E-value: 1.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  15 LNACRARLKAFIRGRTSVRDDADDILQE---VTYQLMKVEQPVENVAAWLFRAARNE----MTDRARKKREVSlsgyftg 87
Cdd:TIGR02989   7 LTRHERALRAFVRSLVADRDDVDDVLQEtfvVAWRKFDQFDPGTNFVAWARGIARNKvlnyRRKLGRDRLVFD------- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  88 ddedfpeDELAETLfGVPHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALlsrkHKA 167
Cdd:TIGR02989  80 -------DDLLEAL-AAEAEPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAV----YKA 147

                         170
                  ....*....|
gi 1863311427 168 VLFLRTRLRD 177
Cdd:TIGR02989 148 LQRIRVSLRE 157
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 22-178 6.24e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 55.74  E-value: 6.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  22 LKAFIRGRTSVRDDADDILQEVTYQLMKVEQPVE---NVAAWLFRAARNEMTDRARKK-REVSLS-GYFTgddedfpeDE 96
Cdd:PRK12516   23 LRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEvgtNMKAWLFTILRNEFYSQMRKRgREVQDTdGMFT--------EQ 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  97 LAetlfgvpHTPEEeyLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAvlflRTRLR 176
Cdd:PRK12516   95 LA-------VHPSQ--YGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRA----RQRLQ 161


                  ..
gi 1863311427 177 DV 178
Cdd:PRK12516  162 EI 163
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
11-175 1.64e-08

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 51.62  E-value: 1.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  11 LMSALNACRAR-LKAFIRGRTSVRDDADDILQEVTYQLMK----VEQPVENVAAWLFRAARNEMTD--RARKKREVslsg 83
Cdd:PRK09645   10 LMRALYDEHAApLWRYALRLTGDRARAEDVVQETLLRAWQhpevLADTGRSARAWLFTVARNLVIDerRSARARPV---- 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  84 yFTGDDEDfpedelaetlfGVPHTPEEEYLKTLLWE-ELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLS 162
Cdd:PRK09645   86 -EGGDDVL-----------GVPEQSAPDEVDRALDRlLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKS 153

                         170
                  ....*....|...
gi 1863311427 163 RKHKAVLFLRTRL 175
Cdd:PRK09645  154 RLHYALRALRLAL 166
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 4-177 1.77e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 51.59  E-value: 1.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427   4 GLAGESLLMSA-LNACRARLKAFIRGRTSVR-DDADDILQEV---------TYQlmkVEQPVenvAAWLFRAARNEMTD- 71
Cdd:PRK12536   15 GLAGDAAAYRQfLSELAAHLRGFLRRRLPQLpDEVEDLVQEIllavhnarhTYR---ADQPL---TAWVHAIARYKLMDf 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  72 -RARKKREvSLSGYFTGDDEDF--PEDELAETLfgvphtpeeeylktllwEELGQALSELPPPQREVFEKTELQGYSIKM 148
Cdd:PRK12536   89 lRSRARRE-ALHDPLDDESELFatSDDEAAEAR-----------------RDLGKLLEQLPDRQRLPIVHVKLEGLSVAE 150

                         170       180
                  ....*....|....*....|....*....
gi 1863311427 149 LAEETGASEQALLSRKHKAVLFLRTRLRD 177
Cdd:PRK12536  151 TAQLTGLSESAVKVGIHRGLKALAAKIRG 179
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 22-175 4.69e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 47.91  E-value: 4.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  22 LKAFIRGRTSVRDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEM-TDRARKKREVslsgyftgddEDfPEDEL 97
Cdd:PRK12546   20 LRAFAISLTRNVAVADDLVQDTivkAWTNFDKFQEGTNLRAWLFTILRNTFySDRRKHKREV----------PD-PEGVH 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1863311427  98 AETLFGVPhtpeeEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAvlflRTRL 175
Cdd:PRK12546   89 AASLAVKP-----AHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRA----RARL 157
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 33-178 5.33e-07

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 47.77  E-value: 5.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  33 RDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEMTDRARKKR-EVSLSGYFTGDDEDFPEDELAETlfgvPHTP 108
Cdd:PRK09641   42 RHEAEDAAQEAfirAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKpDYYLDAEVAGTEGLTMYSQLAAD----DALP 117

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427 109 EEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRTRLRDV 178
Cdd:PRK09641  118 EEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRHL 187
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 22-178 5.51e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 47.18  E-value: 5.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  22 LKAFIRGRTSVRDDADDILQEVtyqLMKVE------QPVENVAAWLFRAARNEMTDRARKK-REVSLS-GYFTGDDEDFP 93
Cdd:PRK12547   19 LRAFAVSLSSKHDKAEDLVQDT---LMKAWakqdsfEMGTNLKAWLFTILRNEFYSQMRKRgREVQDSdGVFTARVAVHP 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  94 EDElaetlfgvphtpeeeylKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAvlflRT 173
Cdd:PRK12547   96 AQY-----------------GSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRA----RN 154


                  ....*
gi 1863311427 174 RLRDV 178
Cdd:PRK12547  155 RLQEL 159
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 36-179 6.60e-07

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 47.18  E-value: 6.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  36 ADDILQEVTYQ--LMKVEQPVENVAAWLFRAARNEMTDRARKKREVSlsgyftgddedFPEDELAETLFGvpHTPEEEYL 113
Cdd:PRK09644   28 AEDLLQETFYRayIYLEDYDNQKVKPWLFKVAYHTFIDFVRKEKKVS-----------FVGTDEIEAIQA--ESTEEYVV 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1863311427 114 KTLLWEELGQALSELPPPQREVfekteLQGYSIKMLAEETGASEQALLSRKHKAVLFL-RTRLRDVY 179
Cdd:PRK09644   95 AKNSYEKLIQIIHTLPVIEAQA-----ILLCDVHELTYEEAASVLDLKLNTYKSHLFRgRKRLKALL 156
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 33-177 8.50e-07

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 46.50  E-value: 8.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  33 RDDADDILQEVTYQLMKV--EQPVENVAAWLFRAARNEMTD--RARKKRE--VSLSGYF--TGDDEDFPEDELAETLFGV 104
Cdd:PRK09047    4 DDAALDIVQDAMIKLAEKygDRPAAEWPPLFQRILQNRIHDwfRRQKVRNtwVSLFSSFsdDDDDDDFDPLETLDSADEG 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1863311427 105 PHTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRTRLRD 177
Cdd:PRK09047   84 AESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 12-156 8.81e-07

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 46.60  E-value: 8.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  12 MSALNACRARLKAFIRGRTSVRDDADDILQEVTYQLMKVEQ--PVENVAAWLFRAARNEMTDRARKKrevSLSGYFTGDD 89
Cdd:PRK07037    1 LDVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNqdAVKQPVAYLFRIVRNLAIDHYRRQ---ALENKYHGDE 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  90 EDFpedelaetlFGVPH---TPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGAS 156
Cdd:PRK07037   78 EDG---------LDVPSpeaSPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVS 138
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 22-167 1.56e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 46.11  E-value: 1.56e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  22 LKAFIRGRTSVRDDADDILQEVTYQ-LMKVE--QPVENVAAWLFRAARNEM-TDRARKKREVslsgyftgddEDfPEDEL 97
Cdd:PRK12540   18 LRAFAISLSGNGDRADDLVQETLLRaLANIDsfQPGSNLPAWLFTILRNLFrSDYRKRRREV----------ED-ADGSY 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  98 AETLFGVPHTPEEeylktLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKA 167
Cdd:PRK12540   87 AKTLKSQPGQNAH-----LEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRA 151
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 2.85e-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: 42.83  E-value: 2.85e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1863311427 119 EELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFL 171
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 36-156 6.42e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 44.16  E-value: 6.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  36 ADDILQEVTYQ-LMKVEQ-PVENVAAWLFRAARNEMTDRARKKREvslsgYFTGDDEDFpedelaeTLFGVPHTPEEEYL 113
Cdd:PRK12541   32 AEDLMQETFYRmLVHIDYyKGEEIRPWLFTIAYNAFIDWYRKEKK-----YKTTTIEEF-------HLPNVPSTEHEYFI 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1863311427 114 KTLLWEELgQALSELPPPQREVFEKTELQGYSIKMLAEETGAS 156
Cdd:PRK12541  100 KHEIASWL-DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLS 141
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 22-176 1.03e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 43.61  E-value: 1.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  22 LKAFIRGRTSVRDDADDILQEVTYQLMK--VEQPVENVAAWLFRAARNEMTDRARKKREVSLSgyftgddedfPEDELA- 98
Cdd:PRK12527    8 LVRFLSARLGNRQAAEDVAHDAYLRVLErsSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAE----------PLEVLDe 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  99 ETLFGVPHTPEEEYLKTLLwEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQalLSRKH--KAVLFLRTRLR 176
Cdd:PRK12527   78 EERLHSPSPQTRLDLGQRL-ALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRS--LVEKHivNAMKHCRVRMR 154
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 118-172 1.22e-05

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 40.94  E-value: 1.22e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1863311427 118 WEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLR 172
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 35-177 1.45e-05

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 43.62  E-value: 1.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  35 DADDILQEVtyqLMKVEQPVENVAA-----WLFRAARNEMTDRARKKREVSLsgyftgddEDFPEDelAETLFGVPHTPE 109
Cdd:PRK09647   54 DAEDLTQET---FIRVFRSLQNYQPgtfegWLHRITTNLFLDMVRRRARIRM--------EALPED--YDRVPGDEPNPE 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1863311427 110 EEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAvlflRTRLRD 177
Cdd:PRK09647  121 QIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRG----RQQLRA 184
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-77 1.72e-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: 41.03  E-value: 1.72e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1863311427  16 NACRARLKAFIRGRTSVRDDADDILQEVTYQLMK-VEQ----PVENVAAWLFRAARNEMTDRARKKR 77
Cdd:pfam04542   3 ERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRaIERfdpeRGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 33-173 2.43e-05

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 42.63  E-value: 2.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  33 RDDADDILQEVTYQLMKVE-QPVENVAAWLFRAARNEMTD--RARKKREVSLSGYFTGDDEDFPEDelaetlfgvphtPE 109
Cdd:PRK09639   27 RTQAEDLAQEVFLRLYRSDfKGIENEKGWLIKSARNVAYNylRSEKRRRARILGEFQWQEVDNEPS------------PE 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1863311427 110 EEYLKTLLWEELGQALSELPPPQREVFeKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRT 173
Cdd:PRK09639   95 EIWIRKEEITKVQEVLAKMTERDRTVL-LLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 33-175 4.28e-05

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 42.04  E-value: 4.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  33 RDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEMTDRARK--KREVslsgyftgddedFPEDELAETLFGVPHT 107
Cdd:PRK09415   40 KEVAEDLTQEIfvkCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSwhNKKV------------IVTEDIFTYMESQKES 107

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1863311427 108 PEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRTRL 175
Cdd:PRK09415  108 VEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175
PRK12544 PRK12544
RNA polymerase factor sigma-70;
36-176 1.06e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 41.33  E-value: 1.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  36 ADDILQEVTYQLMKVEQPVENVAA---WLFRAARNEMTDRAR-KKREVSLSGYFTGDDEDFPEDELAETLFGVP------ 105
Cdd:PRK12544   45 AEDAVQEALIGALKNADSFAGRAAfktWVFAILKNKIIDLLRqKKRHVSASSLLRDEEEEEDFEELFDESGHWQkderpq 124

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1863311427 106 --HTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELqgysIKMLAEETGASEQalLSRKHKAVLFLRTRLR 176
Cdd:PRK12544  125 awGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVD--LSVSNLNVLLYRARLR 191
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 33-175 1.38e-04

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: 40.45  E-value: 1.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  33 RDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEMTDRARKKREvslsgyftgddEDFPEDELAETlfgvphTPE 109
Cdd:TIGR02983  30 PHEAEDLVQEAlvrTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRL-----------LELPTRELPDA------AAP 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1863311427 110 EEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRTRL 175
Cdd:TIGR02983  93 DPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 10-172 4.25e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 39.53  E-value: 4.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  10 LLMSALNACRARLKAFirGRTSVRD---DADDILQEVTYQLMKVEQPVENVAA---WLFRAARNEMTDRARKK-REVSLS 82
Cdd:PRK12532    6 LTDAELIESRKLLLHF--ARLQLPDhpdLAEDLVQETLLSAYSAGDSFQGRALvnsWLFAILKNKIIDALRQIgRQRKVF 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  83 GyfTGDDEDFpeDELAETLF---------GVPH---TPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLA 150
Cdd:PRK12532   84 T--LLDDELL--DEAFESHFsqnghwtpeGQPQhwnTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQ 159

                         170       180
                  ....*....|....*....|..
gi 1863311427 151 EETGASEQALLSRKHKAVLFLR 172
Cdd:PRK12532  160 QMCGISTSNYHTIMHRARESLR 181
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 33-134 5.88e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 38.86  E-value: 5.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  33 RDDADDILQEVTYQLMKVEQPVENVAA----WLFRAARNEMTDRARKKREVslsgyftgddedfPEDELAETLFGVPhTP 108
Cdd:PRK05602   44 PAEAEDVAQETFLRIWKQAPSWRPGEArfdtWLHRVVLNLCYDRLRRRREV-------------PVEDAPDVPDPAP-GP 109

                          90       100
                  ....*....|....*....|....*.
gi 1863311427 109 EEEYLKTLLWEELGQALSELPPPQRE 134
Cdd:PRK05602  110 DAGLEARQRARRVEQALAALPERQRE 135
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
18-175 8.07e-04

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 38.41  E-value: 8.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  18 CRARLKAFIRGRTSvrddADDILQEVTYQLMKVEQPVEN----VAAWLFRAARNEMTDRARkkrevslsgyFTGDDEDFP 93
Cdd:PRK09648   41 CRARLGGVERPGLS----ADDVAQEVCLAVITALPRYRDqgrpFLAFVYGIAAHKVADAHR----------AAGRDKAVP 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  94 EDELAETLFGVPhTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSikmlAEET----GASEQALLSRKHKAVL 169
Cdd:PRK09648  107 TEEVPERPSDDA-GPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLS----AEETaeavGSTPGAVRVAQHRALA 181


                  ....*.
gi 1863311427 170 FLRTRL 175
Cdd:PRK09648  182 RLRAEI 187
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 35-176 1.27e-03

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 38.36  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  35 DADDILQEVTYQLMKVEQP-VENVAAWLFRAARNEMTDR---ARKKREVslsgyFTGddEDFPE---DELAETLFGVpHT 107
Cdd:PRK09636   30 DAEDIVQEAWLRWNNADRAqIRDPRAWLTRVVTRLCLDRlrsARHRRET-----YVG--PWLPEpvvEELDDPLEAV-VA 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1863311427 108 PEEEYLKTLLweelgqALSELPPPQREVFEKTELQGYSIKMLAEETGASEQA---LLSRKHKAVLFLRTRLR 176
Cdd:PRK09636  102 AEDLSLALML------ALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAAcrqLASRARKHVRAARPRFP 167
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 1-172 2.53e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 37.11  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427   1 MKTGLAGESLLMSALNACRARLKAFIRGRTSVRDDADDILQEVtyqLMKVEQPVENVA-------AWLFRAARNEMTDRA 73
Cdd:PRK12514   11 VRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDV---YVKIWTKADRFAvsglspmTWLITIARNHAIDRL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  74 RKKREVSlsgyftgddEDFpeDELAETLFGVPhTPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEET 153
Cdd:PRK12514   88 RARKAVA---------VDI--DEAHDLADPSP-GPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERH 155

                         170
                  ....*....|....*....
gi 1863311427 154 GASEQALLSRKHKAVLFLR 172
Cdd:PRK12514  156 DVPLNTMRTWLRRSLLKLR 174
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 29-172 3.76e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 36.87  E-value: 3.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  29 RTSVRDDAD--DILQEVTYQLMKVEQPVENVAA---WLFRAARNEMTDRARKKR-----EVSLSGYFTGDDEDFPEDELA 98
Cdd:PRK11922   48 RAILRNDAEaeDVVQEAYLRAFRALGTFRGDASlstWLSRIVLNEALGRLRRRRrlvnlAEMVMASTIAGGERTPLADPA 127

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1863311427  99 ETlfgvphtPEEEYLKTLLWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLR 172
Cdd:PRK11922  128 ED-------PERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLR 194
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 33-177 5.67e-03

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 35.77  E-value: 5.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1863311427  33 RDDADDILQEV---TYQLMKVEQPVENVAAWLFRAARNEMTDRARKKREVSLSgyftgdDEDFPEDELAETLFGVPHTPE 109
Cdd:PRK09638   42 PDLAEDLVQETmlkAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLR------LQRAKEETLRKEKWEAAIKGA 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1863311427 110 EeylktllWEELGQALSELPPPQREVFEKTELQGYSIKMLAEETGASEQALLSRKHKAVLFLRTRLRD 177
Cdd:PRK09638  116 E-------WSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWGQ 176
 
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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