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Conserved domains on  [gi|1729712800|ref|WP_148205203|]
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RNA polymerase sigma factor [Candidatus Methylacidiphilum infernorum]

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]; ...
 1-158 1.68e-37

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: 127.03  E-value: 1.68e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   1 MNRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLF---LRSKKREERY 77
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAidhLRKRRRRREL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  78 qymgIEEMENFLVEENKG-----EITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKK 152
Cdd:COG1595    94 ----LDELAEELPDEAADpeealEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169


                  ....*.
gi 1729712800 153 SLRNLI 158
Cdd:COG1595   170 KLREAL 175
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-158 1.68e-37

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: 127.03  E-value: 1.68e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   1 MNRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLF---LRSKKREERY 77
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAidhLRKRRRRREL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  78 qymgIEEMENFLVEENKG-----EITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKK 152
Cdd:COG1595    94 ----LDELAEELPDEAADpeealEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169


                  ....*.
gi 1729712800 153 SLRNLI 158
Cdd:COG1595   170 KLREAL 175
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-163 7.25e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 105.05  E-value: 7.25e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRL---FLRSKKREERYQ 78
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVcydLLRRRRREKAVL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  79 ---YMGIEEMENFLVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:PRK11924   91 sddALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170


                  ....*...
gi 1729712800 156 NLILAKGS 163
Cdd:PRK11924  171 ECLEAQWE 178
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-158 5.78e-27

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: 99.34  E-value: 5.78e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   4 QEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRL---FLRSKKREERYQYM 80
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLildYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1729712800  81 GIEEMENFLVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLI 158
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 102-154 3.66e-12

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: 58.24  E-value: 3.66e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1729712800 102 QYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSL 154
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-155 2.63e-11

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: 55.96  E-value: 2.63e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1729712800 102 QYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-158 1.68e-37

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: 127.03  E-value: 1.68e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   1 MNRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLF---LRSKKREERY 77
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAidhLRKRRRRREL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  78 qymgIEEMENFLVEENKG-----EITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKK 152
Cdd:COG1595    94 ----LDELAEELPDEAADpeealEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169


                  ....*.
gi 1729712800 153 SLRNLI 158
Cdd:COG1595   170 KLREAL 175
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-163 7.25e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 105.05  E-value: 7.25e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRL---FLRSKKREERYQ 78
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVcydLLRRRRREKAVL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  79 ---YMGIEEMENFLVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:PRK11924   91 sddALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170


                  ....*...
gi 1729712800 156 NLILAKGS 163
Cdd:PRK11924  171 ECLEAQWE 178
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-158 5.78e-27

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: 99.34  E-value: 5.78e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   4 QEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRL---FLRSKKREERYQYM 80
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLildYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1729712800  81 GIEEMENFLVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLI 158
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 3-158 2.19e-25

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 96.03  E-value: 2.19e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   3 RQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLF---LRSKKREERYQY 79
Cdd:PRK09652    9 RAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAinyLRKQGRRPPASD 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  80 MGIEEMENFLVEENKGEITVDCQYVLDCLF---------QLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRA 150
Cdd:PRK09652   89 VDAEEAEDFDLADALRDISTPENELLSAELeqrvraaieSLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRA 168


                  ....*...
gi 1729712800 151 KKSLRNLI 158
Cdd:PRK09652  169 REALRAKL 176
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 19-156 2.03e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 88.30  E-value: 2.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  19 RFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLF---LRSKKREERYQYMgIEEMENFLVEENKg 95
Cdd:PRK12511   19 RYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFideLRRRRVEARRADE-LAVLADASLPAAQ- 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1729712800  96 EITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRN 156
Cdd:PRK12511   97 EHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
SigH_actino TIGR02947
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 3-170 2.61e-21

RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.


Pssm-ID: 131992 [Multi-domain]  Cd Length: 193  Bit Score: 85.79  E-value: 2.61e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   3 RQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLFLRS-KKREERYQYMG 81
Cdd:TIGR02947  10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSyRKAQRRPQQSD 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  82 IEEMENFLVEENKGEITVDC-------------QYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIF 148
Cdd:TIGR02947  90 DDDIEDWQLAKAASHTSNGLrsaelealdglpdQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLH 169

                         170       180
                  ....*....|....*....|..
gi 1729712800 149 RAKKSLRNLILAKGSNKGKNKR 170
Cdd:TIGR02947 170 RGRKQLRKQLVDVAGERGFGPR 191
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 4-155 9.11e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 78.76  E-value: 9.11e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   4 QEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLFLRSKKREERYqymgIE 83
Cdd:PRK12522    3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRW----KD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  84 EMENFLVEENKGEI--------------TVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFR 149
Cdd:PRK12522   79 RILDLFHKEDGGEIefaddvniseefiqKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNY 158


                  ....*.
gi 1729712800 150 AKKSLR 155
Cdd:PRK12522  159 AKKQMR 164
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 5-168 1.37e-18

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 78.00  E-value: 1.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   5 EFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNAlKVKNWLFTTLYRLFLRSKKREERYQYMGIEE 84
Cdd:PRK09644    2 EIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ-KVKPWLFKVAYHTFIDFVRKEKKVSFVGTDE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  85 MENFLVEENKGEITVDCQY--VLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLIlakG 162
Cdd:PRK09644   81 IEAIQAESTEEYVVAKNSYekLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL---K 157


                  ....*.
gi 1729712800 163 SNKGKN 168
Cdd:PRK09644  158 EEKSQN 163
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 10-158 3.93e-18

RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot:


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 76.72  E-value: 3.93e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  10 FEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNAlKVKNWLFTTLYRLFLRSKKREERYQY-----MGIEE 84
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDS-SIKPWLFRIARNAFIDWYRKDKKIQTidddaIGDLE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1729712800  85 MENFLVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLI 158
Cdd:TIGR02950  80 QHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 6-156 1.05e-17

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: 75.68  E-value: 1.05e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   6 FEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRL---FLRSKKREERYQYMGI 82
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRclnYLRHKQVEEKYQEELA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729712800  83 EEMENFLVEENKGEITVD---CQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRN 156
Cdd:TIGR02985  83 EIEERELSEADPEEELEAkelEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 2-155 3.34e-17

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 74.67  E-value: 3.34e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLF---TTLYRLFLRSKKREERYQ 78
Cdd:PRK09638   16 DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLIsiaSRLYKDHLRKQKREKLRL 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729712800  79 YMGIEEMENFLVEENKGEiTVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:PRK09638   96 QRAKEETLRKEKWEAAIK-GAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR 171
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 1-166 1.02e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 73.57  E-value: 1.02e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   1 MNRQE-FEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRlflRSKKREERYQY 79
Cdd:PRK12517   19 LSKQRrYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRR---ENARRFERKQF 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  80 MGIEEMENFLVEENKGEITVDC-QYVL-DCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNL 157
Cdd:PRK12517   96 DLVDIEDDSIEDDASHSSEEEMeQEWLrRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEA 175


                  ....*....
gi 1729712800 158 ILAKGSNKG 166
Cdd:PRK12517  176 LEKPDVQRG 184
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 2-156 1.78e-16

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 72.81  E-value: 1.78e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLFL-RSKKREERY--- 77
Cdd:PRK09641   16 DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIdRLRKRKPDYyld 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  78 -QYMGIEEM--------ENFLVEEN--KGEITVDCQYVLDclfQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSR 146
Cdd:PRK09641   96 aEVAGTEGLtmysqlaaDDALPEEQvvSLELQETIQEAIL---QLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTR 172

                         170
                  ....*....|
gi 1729712800 147 IFRAKKSLRN 156
Cdd:PRK09641  173 IHRGREALRK 182
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 14-161 5.76e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 67.06  E-value: 5.76e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  14 HKDA-YRFALSLCRQPDQACDLVQQAFVLLYT-----HKENLKNALK--VKNWLFTTLYRlflRSKKREERYQ------- 78
Cdd:PRK12533   27 HLDAaYNLARWLCGNASDADDVVQEACMRALRffdsfRGDNARPWLLaiVRHTWYSEWRR---RANAHEVAAPdtlddad 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  79 -----YMGIEEMENFLVEENkgeitvDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKS 153
Cdd:PRK12533  104 slddwQPAGEDPLALLLRAE------DVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRR 177


                  ....*...
gi 1729712800 154 LRNLILAK 161
Cdd:PRK12533  178 LAALLGGA 185
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
10-155 1.96e-13

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 64.71  E-value: 1.96e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  10 FEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALK-VKNWLFTTLYRLFL---RSkkREERYQYMGIEEM 85
Cdd:PRK09645   15 YDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRsARAWLFTVARNLVIderRS--ARARPVEGGDDVL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1729712800  86 ENFL-VEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:PRK09645   93 GVPEqSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 3-157 3.86e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 63.80  E-value: 3.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   3 RQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNAlKVKNWLFTTLYRLFLRSKKREERYQYMGI 82
Cdd:PRK12541    4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKKYKTTTI 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729712800  83 EE--MENFLVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNL 157
Cdd:PRK12541   83 EEfhLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 2-166 6.89e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 63.60  E-value: 6.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWL-----FTTLYRLflRSKKREER 76
Cdd:PRK12515   20 DRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLlsiarFKALSAL--RRRKHEEI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  77 YQYM------GIEEMENFLVEENKGEItvdcqyVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRA 150
Cdd:PRK12515   98 DDEAaaaiedGADTPEVALQKSDTSAA------LRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYA 171

                         170
                  ....*....|....*.
gi 1729712800 151 KKSLRNLILAKGSNKG 166
Cdd:PRK12515  172 RKKLAELLKAAGVERG 187
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 102-154 3.66e-12

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: 58.24  E-value: 3.66e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1729712800 102 QYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSL 154
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 11-158 8.40e-12

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 60.53  E-value: 8.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  11 EEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLfttlYRL-------FLRS---KK---REERY 77
Cdd:PRK09415   23 NEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWL----YRIainhckdYLKSwhnKKvivTEDIF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  78 QYMGIEEMenfLVEENKGEITVDcQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNL 157
Cdd:PRK09415   99 TYMESQKE---SVEEEVIQNAED-ERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174


                  .
gi 1729712800 158 I 158
Cdd:PRK09415  175 L 175
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 3-157 1.47e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 59.58  E-value: 1.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   3 RQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLY----THKENLknalkvKNWLFTTLYRL---FLRSKKR-- 73
Cdd:PRK09639    2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYrsdfKGIENE------KGWLIKSARNVaynYLRSEKRrr 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  74 ---EERYQYmgiEEMENFLVEEN----KGEItvdcQYVLDCLFQLDEPYRIVLLLYYMDeLSYLDISEILNVPIGTVMSR 146
Cdd:PRK09639   76 ariLGEFQW---QEVDNEPSPEEiwirKEEI----TKVQEVLAKMTERDRTVLLLRFSG-YSYKEIAEALGIKESSVGTT 147

                         170
                  ....*....|.
gi 1729712800 147 IFRAKKSLRNL 157
Cdd:PRK09639  148 LARAKKKFRKI 158
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 20-158 1.80e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 59.12  E-value: 1.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  20 FALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLF---LRSKKREeryqymgieemenflVEENKGE 96
Cdd:PRK12547   22 FAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFysqMRKRGRE---------------VQDSDGV 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1729712800  97 IT------------VDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLI 158
Cdd:PRK12547   87 FTarvavhpaqygsLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 18-160 2.58e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 59.30  E-value: 2.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  18 YRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFT-TLYRLF--LRSKKREERY-----QYMGIEEMENFL 89
Cdd:PRK12519   43 YGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTlTRSRAIdrLRSRRSRQRLlerwqQELLGEASEDTP 122

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1729712800  90 VEENKGEITVdcQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLILA 160
Cdd:PRK12519  123 LEQASLAERS--QRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQD 191
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-155 2.63e-11

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: 55.96  E-value: 2.63e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1729712800 102 QYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 13-155 3.64e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 58.64  E-value: 3.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  13 YHKDAYRF---ALSLCRQPDQACDLVQQAFVLLYTHKENLKNAL-KVKNWLFTTLYRL---FLRSKKREERYQYMGIEEM 85
Cdd:PRK12537   29 YQQESARLlgvARRIVRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLalnVLRDTRREVVLDDDAEETA 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  86 ENFLVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:PRK12537  109 QTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 14-158 4.19e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 58.70  E-value: 4.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  14 HKDAYR-FALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLFLRSKKREERYqymgieemenflVEE 92
Cdd:PRK12546   16 HLPALRaFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKRE------------VPD 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1729712800  93 NKGEITV--------DCQYVLD----CLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLI 158
Cdd:PRK12546   84 PEGVHAAslavkpahDGRLAMSdfraAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 7-160 8.41e-11

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 57.69  E-value: 8.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   7 EKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRL---FLRSKKREEryqymGIE 83
Cdd:PRK09637    4 ESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTiidFYRKKNRSE-----ELP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  84 EMENFLVEENKGEITvdcQYVLDCLF----QLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLIL 159
Cdd:PRK09637   79 DDLLFEDEEREENAK---KELAPCLRpfidALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155


                  .
gi 1729712800 160 A 160
Cdd:PRK09637  156 G 156
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 20-164 1.50e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 57.28  E-value: 1.50e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  20 FALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLF---LRSKKREeryqymgIEEMENFLVE----- 91
Cdd:PRK12516   26 FAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFysqMRKRGRE-------VQDTDGMFTEqlavh 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1729712800  92 -ENKGeiTVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLILAKGSN 164
Cdd:PRK12516   99 pSQYG--TLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEGEA 170
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 2-162 2.55e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 56.26  E-value: 2.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCrQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLF-------TTLYRLFLRSKKRE 74
Cdd:PRK12518    9 DRQSFRQLYRRYQQKVRSTLYQLC-GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYritwnvaTDARRQFAQRPSRI 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  75 EryQYMGIEEMENFLVEENKGEITVDcQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSL 154
Cdd:PRK12518   88 Q--DDSLNDQPSRPSDTPDLMQLHYQ-DLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQL 164


                  ....*...
gi 1729712800 155 RNLILAKG 162
Cdd:PRK12518  165 RKFLQQQG 172
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 20-163 7.93e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 54.97  E-value: 7.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  20 FALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLFlRSKKREERYQYMGIEEMENFLVEENKGEIT- 98
Cdd:PRK12540   21 FAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLF-RSDYRKRRREVEDADGSYAKTLKSQPGQNAh 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1729712800  99 VDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLILAKGS 163
Cdd:PRK12540  100 LEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 18-158 3.84e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 51.12  E-value: 3.84e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  18 YRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFT-TLYRLFLRSKKREERyqyMGIEEMENFLVEENKGE 96
Cdd:PRK11922   44 YRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRiVLNEALGRLRRRRRL---VNLAEMVMASTIAGGER 120

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729712800  97 ITVDC-----------QYVLDCLFQ----LDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLI 158
Cdd:PRK11922  121 TPLADpaedperaaarREIRALLERaidaLPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 26-154 7.74e-08

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 49.80  E-value: 7.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  26 RQPDQACDLVQQAFVLLYTHKENLKNalkvKNWLFTTLYRL-------FLRSKKREERYQYMGIEEMENFLVEENKGEIT 98
Cdd:PRK11923   42 HDTAEAQDVAQEAFIKAYRALGNFRG----DSAFYTWLYRIaintaknHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIE 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1729712800  99 VDCQYVL---------DCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSL 154
Cdd:PRK11923  118 SPERALLrdeiegtvhRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAI 182
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 2-158 1.20e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 48.96  E-value: 1.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLY--------------RLF 67
Cdd:PRK12543    5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIkqihswrrkrwrrfRIF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  68 LRSKKREERYQYMGIEEMenfLVEENKGEITVDCQyvldclfQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRI 147
Cdd:PRK12543   85 EKAEEQRKPVSIDFSEDV---LSKESNQELIELIH-------KLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRI 154

                         170
                  ....*....|.
gi 1729712800 148 FRAKKSLRNLI 158
Cdd:PRK12543  155 HAALKKLRQKE 165
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 2-154 2.63e-07

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 48.11  E-value: 2.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLcRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLF---LRSKKREERYQ 78
Cdd:PRK09649   22 NGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVadhIRHVRSRPRTT 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1729712800  79 YMGIEEMenFLVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSL 154
Cdd:PRK09649  101 RGARPEH--LIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 14-155 3.35e-07

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 48.24  E-value: 3.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  14 HKD-AYRFALSLCRQPDQACDLVQQAFVLLYthkENLKN--ALKVKNWLFTTLYRLFLRSKKREERYQYMGI-EEMENFL 89
Cdd:PRK09647   37 HADrVYRLAYRLSGNQHDAEDLTQETFIRVF---RSLQNyqPGTFEGWLHRITTNLFLDMVRRRARIRMEALpEDYDRVP 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1729712800  90 VEE-------NKGEITVDCQYVLDclfQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:PRK09647  114 GDEpnpeqiyHDARLDPDLQAALD---SLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLR 183
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 9-76 1.06e-06

RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 46.68  E-value: 1.06e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1729712800   9 FFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTL-YRLF--LRSKKREER 76
Cdd:TIGR02943   7 ELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILkNKIIdaLRAKGREVK 77
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
3-156 1.15e-06

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 46.59  E-value: 1.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   3 RQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYthkenlKNALK-------VKNWLFTTLYRLF---LRS-- 70
Cdd:PRK09646   29 QDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVW------RTASRfdpargsALAWLLTLAHRRAvdrVRSeq 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  71 --KKREERYQYMGIEEMENFLVEEnkGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIF 148
Cdd:PRK09646  103 aaSQREVRYGARNVDPAFDQVAEE--VEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMR 180


                  ....*...
gi 1729712800 149 RAKKSLRN 156
Cdd:PRK09646  181 DGLIRLRD 188
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 107-156 1.39e-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. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 43.19  E-value: 1.39e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1729712800 107 CLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRN 156
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 2-170 1.60e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 46.04  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFaLSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRLFLRSKKREERYQYMG 81
Cdd:PRK12535   23 DRAALTEFIRETQDDVWRL-LAHLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHDMARPRKS 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  82 IEEMENFLVEENKGEIT------VDCQYVLDclfQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKslr 155
Cdd:PRK12535  102 ATEYEDAAATTASNETTgswsewIDVRTLID---ALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARA--- 175

                         170
                  ....*....|....*
gi 1729712800 156 NLILAKGSNKGKNKR 170
Cdd:PRK12535  176 DLIAATATGQASAER 190
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 2-155 1.87e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 46.08  E-value: 1.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYtHKENLKNALK--VKNWLFTTLYRL---FLRSKKREER 76
Cdd:PRK12531   25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVW-QKAHLFDGQKsaLSTWIYTIIRNLcfdLLRKQKGKDL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  77 YQYMGIEEMENF----LVEENKGEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKK 152
Cdd:PRK12531  104 HIHADDIWPSDYyppdLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVE 183


                  ...
gi 1729712800 153 SLR 155
Cdd:PRK12531  184 KLR 186
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 9-76 9.36e-06

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: 41.80  E-value: 9.36e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   9 FFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLK--NALKVKNWLFTTLYRLFLRSKKREER 76
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpeRGVSFSTWLYTIIRNAIIDYLRKQRR 70
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 17-158 1.19e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 43.49  E-value: 1.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  17 AYRFALSLCRQPDQACDLVQQAFVLLYTHKENLK-NALKVKNWLF-TTLYRLFLRSKKREERYQYMGIEEMENFLVEENK 94
Cdd:PRK05602   33 LLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRpGEARFDTWLHrVVLNLCYDRLRRRREVPVEDAPDVPDPAPGPDAG 112

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1729712800  95 GEITVDCQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLRNLI 158
Cdd:PRK05602  113 LEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQL 176
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 4-158 5.19e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 41.96  E-value: 5.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   4 QEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYthkenlKNALKVKNWLFTTLYRLFLRSKKREERYQYMGIE 83
Cdd:PRK12542    9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLY------KNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  84 EMENFLVEENKGEITVDCQYV------------LDCLF-QLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRA 150
Cdd:PRK12542   83 RHETFLEEYERESIEAVDENIeewekrkmsevqIDTLLkELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERA 162


                  ....*...
gi 1729712800 151 KKSLRNLI 158
Cdd:PRK12542  163 RKRVQNMI 170
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 2-156 4.28e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 39.40  E-value: 4.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800   2 NRQEFEKFFEEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYtHKENLKNALK--VKNWLFTTL----YRLFLRSKKREE 75
Cdd:PRK12526   36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVW-RKAHLYNGDKgaATTWVYTVMrnaaFDMLRKIKAKKE 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  76 RYQYMGIEEMENFLVEENKGEITVD----CQYVLDCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAK 151
Cdd:PRK12526  115 QNLGDDIWPIEQALAESQSESEEFSdhlmDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLAL 194


                  ....*
gi 1729712800 152 KSLRN 156
Cdd:PRK12526  195 AKLKV 199
PRK09642 PRK09642
RNA polymerase sigma factor;
11-155 1.40e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 37.39  E-value: 1.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  11 EEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLK-NALKVKNWLFTTLYRL-FLRSKKREERYQYMGIEEMENF 88
Cdd:PRK09642    2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQfRGLKTWMARIATNHAIdYKRKKARENEELSLCKETEENI 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  89 LVEENKGEITVDCQYVL---DCLFQLDEPYRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR 155
Cdd:PRK09642   82 KSSHNIEDLLLTKEQKLliaQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIK 151
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 11-73 3.46e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 36.67  E-value: 3.46e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1729712800  11 EEYHKDAYRFALSLCRQPDQACDLVQQAFVLLYTHKENLKNALKVKNWLFTTLYRL---FLRSKKR 73
Cdd:PRK12530   14 EEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKiidLIRYRKR 79
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 86-164 8.82e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 35.30  E-value: 8.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729712800  86 ENFLVEENKGEITVdcqyVLDCLFQLDepyRIVLLLYYMDELSYLDISEILNVPIGTVMSRIFRAKKSLR---NLILAKG 162
Cdd:PRK06811  114 NEIILKENKEEILK----LINDLEKLD---REIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQknkLNISLGG 186


                  ..
gi 1729712800 163 SN 164
Cdd:PRK06811  187 EV 188
 
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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