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Conserved domains on  [gi|500212335|ref|WP_011882516|]
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MULTISPECIES: RNA polymerase sigma factor [Burkholderia]

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 2.17e-25

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: 96.60  E-value: 2.17e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  15 LRKLLAARYAYLVRRLERVTGSKDGATDALHETWLRL-ENANVSTQVTNADAYILGMANNVAIDQHRRERRHLHDDDvET 93
Cdd:COG1595   19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLwRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD-EL 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  94 LLETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRMQE 173
Cdd:COG1595   98 AEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177

                 ....
gi 500212335 174 DGDS 177
Cdd:COG1595  178 EGAL 181
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
15-177 2.17e-25

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: 96.60  E-value: 2.17e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  15 LRKLLAARYAYLVRRLERVTGSKDGATDALHETWLRL-ENANVSTQVTNADAYILGMANNVAIDQHRRERRHLHDDDvET 93
Cdd:COG1595   19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLwRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD-EL 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  94 LLETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRMQE 173
Cdd:COG1595   98 AEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177

                 ....
gi 500212335 174 DGDS 177
Cdd:COG1595  178 EGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
15-171 5.51e-18

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 76.62  E-value: 5.51e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335   15 LRKLLAARYAYLVRRLERVTGSKDGATDALHETWLRL-ENANVSTQVTNADAYILGMANNVAIDQHRRERRHlhDDDVET 93
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLlEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRL--RRELDL 80
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 500212335   94 LLETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRM 171
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
23-173 1.92e-16

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 72.50  E-value: 1.92e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  23 YAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRRER----RHLHDDDVETLLETP 98
Cdd:PRK12527   5 YRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRvrqaEPLEVLDEEERLHSP 84
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500212335  99 DeladPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRMQE 173
Cdd:PRK12527  85 S----PQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
117-167 4.46e-08

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: 47.45  E-value: 4.46e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 500212335  117 LKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYC 167
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
121-165 8.74e-04

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 35.97  E-value: 8.74e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 500212335   121 LLGLPPRRRAIL-LAARvdGLLNREIAEQFGISLRLVESELSAAMK 165
Cdd:smart00421   1 LASLTPREREVLrLLAE--GLTNKEIAERLGISEKTVKTHLSNIMR 44
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
117-165 2.89e-03

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: 34.77  E-value: 2.89e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 500212335 117 LKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMK 165
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
15-177 2.17e-25

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: 96.60  E-value: 2.17e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  15 LRKLLAARYAYLVRRLERVTGSKDGATDALHETWLRL-ENANVSTQVTNADAYILGMANNVAIDQHRRERRHLHDDDvET 93
Cdd:COG1595   19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLwRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD-EL 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  94 LLETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRMQE 173
Cdd:COG1595   98 AEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177

                 ....
gi 500212335 174 DGDS 177
Cdd:COG1595  178 EGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
15-171 5.51e-18

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 76.62  E-value: 5.51e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335   15 LRKLLAARYAYLVRRLERVTGSKDGATDALHETWLRL-ENANVSTQVTNADAYILGMANNVAIDQHRRERRHlhDDDVET 93
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLlEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRL--RRELDL 80
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 500212335   94 LLETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRM 171
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
23-173 1.92e-16

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 72.50  E-value: 1.92e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  23 YAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRRER----RHLHDDDVETLLETP 98
Cdd:PRK12527   5 YRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRvrqaEPLEVLDEEERLHSP 84
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500212335  99 DeladPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRMQE 173
Cdd:PRK12527  85 S----PQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
23-165 3.59e-14

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: 66.43  E-value: 3.59e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335   23 YAYLVRRLERVTGSKDGATDALHETWLRL-ENANVSTQVTNADAYILGMANNVAIDQ-HRRERRHLHDDDVETLLETPDE 100
Cdd:TIGR02985  11 YPKLCAFARRYVKDEEDAEDIVQDVFLKLwENRETLEISESIKAYLFTIVKNRCLNYlRHKQVEEKYQEELAEIEERELS 90
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500212335  101 LADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMK 165
Cdd:TIGR02985  91 EADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALK 155
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
19-167 1.09e-12

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 62.78  E-value: 1.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  19 LAARYAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRRERRHL-HDDDVETLLET 97
Cdd:PRK07037   4 FVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQALENkYHGDEEDGLDV 83
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  98 PDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYC 167
Cdd:PRK07037  84 PSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC 153
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
15-176 1.99e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 62.30  E-value: 1.99e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  15 LRKLLAARYAYLVRRLERVTGSKDGATDALHETWLR-LENANVSTQVTNADAYILGMANNVAIDQHRRERRHLHDDDVET 93
Cdd:PRK11924  15 FSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRaWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDA 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  94 LL-ETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRMQ 172
Cdd:PRK11924  95 LEpEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174

                 ....
gi 500212335 173 EDGD 176
Cdd:PRK11924 175 AQWE 178
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
18-167 2.97e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 59.09  E-value: 2.97e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  18 LLAARYAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRR---ERRHLhdddvETL 94
Cdd:PRK12528   9 LYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRqdlERAYL-----EAL 83
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500212335  95 LETPDELADPER----IVAARRKVDTLKDvllGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYC 167
Cdd:PRK12528  84 AQLPERVAPSEEeraiILETLVELDQLLD---GLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 157
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
26-173 3.89e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 59.32  E-value: 3.89e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  26 LVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNA-DAYILGMANNVAIDQHRRE--RRHLHDDDVETLLETPDELA 102
Cdd:PRK12513  39 LYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARfRTWLYQIARNLLIDHWRRHgaRQAPSLDADEQLHALADDGA 118
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 500212335 103 DPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESElsaaMKYCLQRMQE 173
Cdd:PRK12513 119 APEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSR----LRYALQKLRE 185
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
23-173 2.24e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 56.88  E-value: 2.24e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  23 YAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRR---ERRHLhdddvETLLETPD 99
Cdd:PRK12525  19 YDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRqdlERAYL-----QSLAEAPE 93
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 500212335 100 ELA----DPERIVAARRKVDTLkdvLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRMQE 173
Cdd:PRK12525  94 AVQpspeEQWMVIETLLAIDRL---LDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQE 168
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
23-152 1.56e-09

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 54.18  E-value: 1.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  23 YAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQvTNADAYILGMANNVAIDQHRRERRHLHDDDVETLLETPDELA 102
Cdd:PRK09639  13 YPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGI-ENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQWQEVDNEP 91
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 500212335 103 DPERIVAARRKVDTLKDVLLGLPPRRRAILLaARVDGLLNREIAEQFGIS 152
Cdd:PRK09639  92 SPEEIWIRKEEITKVQEVLAKMTERDRTVLL-LRFSGYSYKEIAEALGIK 140
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
117-167 4.46e-08

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: 47.45  E-value: 4.46e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 500212335  117 LKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYC 167
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
26-160 1.35e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 48.78  E-value: 1.35e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  26 LVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRRERRHlHDDDVETLLETPDELADPE 105
Cdd:PRK12541  18 LFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKY-KTTTIEEFHLPNVPSTEHE 96
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 500212335 106 RIVaaRRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESEL 160
Cdd:PRK12541  97 YFI--KHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIEL 149
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
17-158 2.29e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 48.73  E-value: 2.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  17 KLLAARYAYLVRRLE-RVTGSKDGATDALHETWLRLENANVSTQVTNA--DAYILGMANNVAIDQHRRERRHLHDDDVET 93
Cdd:PRK12524  29 RALTLRLAPRALAVAtRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEArvSTWLYRVVCNLCTDRLRRRRRASVDLDDAP 108
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500212335  94 llETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVES 158
Cdd:PRK12524 109 --EPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVES 171
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
18-160 2.68e-07

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 48.26  E-value: 2.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  18 LLAARYA-YLVRRLERVTGSKDGATDALHETWLRL-ENANVSTQVTNADAYILGMANNVAIDQHRRERRHLHDDDVET-- 93
Cdd:PRK09652  14 LLVRRYQpRVKRLLSRLTRDPADAEDLVQETFIKAyRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPASDVDAee 93
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500212335  94 -----LLETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESEL 160
Cdd:PRK09652  94 aedfdLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
40-174 4.33e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 47.62  E-value: 4.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  40 ATDALHETWLRLENANVSTQ---VTNADAYILGMANNVAIDQHRRERrhLHDDDVETLLETPDEL-ADPER---IVAARR 112
Cdd:PRK12529  42 ADDLAHDIFLRILASRDGGQreaIRQPRAYLARIANCVLVSWRRRQS--LELAWLEALATLPEPLhPSPEQqsvILETLH 119
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500212335 113 KVDTLKDVLlglPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCLQRMQED 174
Cdd:PRK12529 120 EIDALLDTL---RPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMPDD 178
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
15-168 1.00e-06

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 46.73  E-value: 1.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  15 LRKLLAARYAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRRERrhLHDDDVETL 94
Cdd:PRK09651  12 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNA--LEKAYLEML 89
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500212335  95 LETPDELADPERIVAARRKVDTLKDVLL-GLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYCL 168
Cdd:PRK09651  90 ALMPEGGAPSPEERESQLETLQLLDSMLdGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
32-170 7.11e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 44.43  E-value: 7.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  32 RVTGSKDGATDALHETWLRLENANVSTQVT--NADAYILGMANNVAIDQHRRERRHlhDDDVETLLETPDELADPERIVA 109
Cdd:PRK12514  38 RVLKDRSEAEEALQDVYVKIWTKADRFAVSglSPMTWLITIARNHAIDRLRARKAV--AVDIDEAHDLADPSPGPEAEVI 115
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500212335 110 ARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAA---MKYCLQR 170
Cdd:PRK12514 116 AGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSllkLRECLSR 179
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
15-165 1.33e-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: 43.53  E-value: 1.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335   15 LRKLLAARYAYLVRRLERVTGSKDGATDALHET-------WLRLENANvstqvtNADAYILGMANNVAIDQHRRERRHLH 87
Cdd:TIGR02983   8 FTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEAlvrtyvrWDRIRDPD------APDAYVRRVLVNLARSRWRRRRLLEL 81
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 500212335   88 DDDVETLLETPDELADPErivaarrKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMK 165
Cdd:TIGR02983  82 PTRELPDAAAPDPAPDVA-------LRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA 152
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
15-165 1.44e-05

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 43.53  E-value: 1.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  15 LRKLLAARYAYLVRRLERVTGSKDGATDALHETWLRL-ENANVSTQVT-NADAYILGMANNVAIDQHR--RERRHLHDDD 90
Cdd:PRK09645  11 MRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAwQHPEVLADTGrSARAWLFTVARNLVIDERRsaRARPVEGGDD 90
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500212335  91 VETLLEtPDELADPERIVAARrkvdTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMK 165
Cdd:PRK09645  91 VLGVPE-QSAPDEVDRALDRL----LVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR 160
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
16-163 1.52e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 43.49  E-value: 1.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  16 RKLLAARYAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNA--DAYILGMANNVAIDQHRRERRHlhddDVET 93
Cdd:PRK05602  23 RVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEArfDTWLHRVVLNLCYDRLRRRREV----PVED 98
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  94 LLETPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAA 163
Cdd:PRK05602  99 APDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARG 168
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
25-167 1.50e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 40.60  E-value: 1.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  25 YLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRR---ERRHLhdddVETLLETPDEL 101
Cdd:PRK12523  22 WLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRaalEQAYL----AELALVPEAEQ 97
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500212335 102 ADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMKYC 167
Cdd:PRK12523  98 PSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
90-157 2.02e-04

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 40.47  E-value: 2.02e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500212335  90 DVETLLETPDE-LADPERIVAARRKVDTLKDVLLGLPPRRRAILLAArVDGLLNREIAEQFGISLRLVE 157
Cdd:COG4566  103 DDQALLDAVRRaLARDRARRAERARRAELRARLASLTPREREVLDLV-VAGLSNKQIARELGISPRTVE 170
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
78-171 3.37e-04

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: 39.71  E-value: 3.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335   78 QHRRER-----RHLHDDDVETLLETPDELadperivaaRRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGIS 152
Cdd:pfam07638  94 RQRQKRggdvqRRELDEVVDNGDSPNPDL---------LLDLDEALEQLFSLSPRQARLVELRFFAGLSNDEIAERLGVS 164
                          90
                  ....*....|....*....
gi 500212335  153 LRLVESELSAAMKYCLQRM 171
Cdd:pfam07638 165 ERTVERNWALARAWLHREL 183
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
19-177 5.46e-04

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 39.00  E-value: 5.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  19 LAARYAYLVRRLE-RVTGSKDGATDALHETWLRLENANVSTQVTNADAYILGMANNVAIDQHRRERRHLHD---DDVETL 94
Cdd:PRK09647  33 LVRQHADRVYRLAyRLSGNQHDAEDLTQETFIRVFRSLQNYQPGTFEGWLHRITTNLFLDMVRRRARIRMEalpEDYDRV 112
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  95 letPDELADPERIVAARRKVDTLKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESEL----SAAMKYCLQR 170
Cdd:PRK09647 113 ---PGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIhrgrQQLRAALAAH 189

                 ....*..
gi 500212335 171 MQEDGDS 177
Cdd:PRK09647 190 APHAECA 196
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
121-165 8.74e-04

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 35.97  E-value: 8.74e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 500212335   121 LLGLPPRRRAIL-LAARvdGLLNREIAEQFGISLRLVESELSAAMK 165
Cdd:smart00421   1 LASLTPREREVLrLLAE--GLTNKEIAERLGISEKTVKTHLSNIMR 44
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
32-82 8.93e-04

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 38.75  E-value: 8.93e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 500212335  32 RVTGSKDGATDALHETWLRLENANvSTQVTNADAYILGMANNVAIDQ-----HRRE 82
Cdd:PRK09636  23 RMLGSVADAEDIVQEAWLRWNNAD-RAQIRDPRAWLTRVVTRLCLDRlrsarHRRE 77
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
12-168 2.34e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 37.06  E-value: 2.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  12 RGGLRKLLAARYAYLVRRLERVTGSKDGATDALHETWLRLENANVSTQVTNADA--YILGMANNVAIDQHRRERRHLH-D 88
Cdd:PRK12537  22 RRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSArgWIYSVTRHLALNVLRDTRREVVlD 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  89 DDVETLLETPDELADPERIVAARRKVDtlkDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELS---AAMK 165
Cdd:PRK12537 102 DDAEETAQTLHEIIDDFDLWANSGKIH---RCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKrslKALR 178

                 ...
gi 500212335 166 YCL 168
Cdd:PRK12537 179 ECM 181
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
117-165 2.89e-03

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: 34.77  E-value: 2.89e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 500212335 117 LKDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMK 165
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
22-158 4.39e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 36.58  E-value: 4.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  22 RYAYLVRRLE-RVTGSKDGATDALHETWLRLE-NANVSTQVTNADAYILGMANNVAIDQHRRERRHL-------HDDDVE 92
Cdd:PRK12519  37 RHAGLVYGLAlKILGNSQEAEDLTQEIFLSLWrKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRRSRQrllerwqQELLGE 116
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500212335  93 TLLETPDE-LADPERIVAARrkvdtlkDVLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVES 158
Cdd:PRK12519 117 ASEDTPLEqASLAERSQRVQ-------TALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKA 176
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
40-165 7.18e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 35.80  E-value: 7.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  40 ATDALHETWLRLENA-----NVSTQvtNADAYILGMANNVAIDQHRRERRH---LHDDDVETLLETPDELADPERIVAAR 111
Cdd:PRK12542  36 AEDAVQETFITLYKNleklhSLNTQ--ELKRYILRVAKNKAIDSYRKNKRHetfLEEYERESIEAVDENIEEWEKRKMSE 113
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 500212335 112 RKVDTLkdvLLGLPPRRRAILLAARVDGLLNREIAEQFGISLRLVESELSAAMK 165
Cdd:PRK12542 114 VQIDTL---LKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARK 164
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
64-158 8.97e-03

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 35.35  E-value: 8.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335  64 DAYILGMANNVAIDQHRRERRhlhdddvETLLEtPDELA-DPERIVAARRKV-DTLKDVLLGLPPRRRAILLAARVDGLL 141
Cdd:PRK09637  53 KSWLYQIANNTIIDFYRKKNR-------SEELP-DDLLFeDEEREENAKKELaPCLRPFIDALPEKYAEALRLTELEGLS 124
                         90
                 ....*....|....*..
gi 500212335 142 NREIAEQFGISLRLVES 158
Cdd:PRK09637 125 QKEIAEKLGLSLSGAKS 141
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
19-84 9.00e-03

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: 33.72  E-value: 9.00e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212335   19 LAARYAYLVRRL-ERVTGSKDGATDALHETWLRLENA---NVSTQVTNADAYILGMANNVAIDQHRRERR 84
Cdd:pfam04542   1 LVERYLPLVYSLaRRYLGDGADAEDLVQEGFLGLWRAierFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
 
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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