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Conserved domains on  [gi|1472313288|gb|RHQ74561|]
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RNA polymerase subunit sigma [Butyricicoccus sp. AF24-19AC]

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]; ...
 1-156 2.97e-34

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: 118.17  E-value: 2.97e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   1 MDREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPY 80
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRREL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  81 ---------DAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRK 151
Cdd:COG1595    94 ldelaeelpDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173


                  ....*
gi 1472313288 152 DLKGA 156
Cdd:COG1595   174 ALEEE 178
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-156 2.97e-34

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: 118.17  E-value: 2.97e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   1 MDREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPY 80
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRREL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  81 ---------DAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRK 151
Cdd:COG1595    94 ldelaeelpDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173


                  ....*
gi 1472313288 152 DLKGA 156
Cdd:COG1595   174 ALEEE 178
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 2-155 3.50e-32

RNA polymerase sigma-70 factor, TIGR02954 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. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 112.50  E-value: 3.50e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPYD 81
Cdd:TIGR02954  14 NKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKVIPFD 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  82 AAAAEAIPA--PAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKG 155
Cdd:TIGR02954  94 PNTSIEKGEceTHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLEE 169
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-155 3.53e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 92.34  E-value: 3.53e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR----- 76
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRRekavl 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  77 --LAPYDAAAAEA----IPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLR 150
Cdd:PRK11924   91 sdDALEPEFAETAetpeAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170


                  ....*
gi 1472313288 151 KDLKG 155
Cdd:PRK11924  171 ECLEA 175
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 15-76 4.63e-10

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 52.59  E-value: 4.63e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1472313288  15 PTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTR--YFKTWLVRILINECSTILRRQQR 76
Cdd:pfam04542   7 PLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERgvSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-150 6.51e-07

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: 44.02  E-value: 6.51e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1472313288 102 AITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLR 150
Cdd:cd06171     7 ALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 120-147 1.47e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 35.20  E-value: 1.47e-03
                           10        20
                   ....*....|....*....|....*...
gi 1472313288  120 EGFKTREIAGMLGISENTVKTRLRAARE 147
Cdd:smart00421  17 EGLTNKEIAERLGISEKTVKTHLSNIMR 44
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-156 2.97e-34

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: 118.17  E-value: 2.97e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   1 MDREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPY 80
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRREL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  81 ---------DAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRK 151
Cdd:COG1595    94 ldelaeelpDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173


                  ....*
gi 1472313288 152 DLKGA 156
Cdd:COG1595   174 ALEEE 178
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 2-155 3.50e-32

RNA polymerase sigma-70 factor, TIGR02954 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. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 112.50  E-value: 3.50e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPYD 81
Cdd:TIGR02954  14 NKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKVIPFD 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  82 AAAAEAIPA--PAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKG 155
Cdd:TIGR02954  94 PNTSIEKGEceTHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLEE 169
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-151 7.71e-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: 98.57  E-value: 7.71e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   4 EQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPY--- 80
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRREldl 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  81 -----DAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRK 151
Cdd:TIGR02937  81 leellDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-155 3.53e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 92.34  E-value: 3.53e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR----- 76
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRRekavl 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  77 --LAPYDAAAAEA----IPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLR 150
Cdd:PRK11924   91 sdDALEPEFAETAetpeAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170


                  ....*
gi 1472313288 151 KDLKG 155
Cdd:PRK11924  171 ECLEA 175
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 15-153 3.72e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 85.79  E-value: 3.72e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  15 PTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR---LAPYDAAAAEAIPAP 91
Cdd:PRK11922   41 RRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRlvnLAEMVMASTIAGGER 120

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1472313288  92 AADDYSD---------------LYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDL 153
Cdd:PRK11922  121 TPLADPAedperaaarreiralLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 2-156 3.01e-20

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 82.16  E-value: 3.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPYD 81
Cdd:PRK09652    8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPAS 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  82 AAAAEAIPAPAADD-----------------YSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRA 144
Cdd:PRK09652   88 DVDAEEAEDFDLADalrdistpenellsaelEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFR 167

                         170
                  ....*....|..
gi 1472313288 145 AREYLRKDLKGA 156
Cdd:PRK09652  168 AREALRAKLQPL 179
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 2-154 1.13e-19

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 80.45  E-value: 1.13e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQ------- 74
Cdd:PRK09638   16 DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQkreklrl 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  75 QRLAPYDAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:PRK09638   96 QRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG 175
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 2-153 2.98e-19

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 79.74  E-value: 2.98e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQrlaPYD 81
Cdd:PRK09641   16 DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRK---PDY 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  82 AAAAEAIPAPAADDYSDLYA--------------------AITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTR 141
Cdd:PRK09641   93 YLDAEVAGTEGLTMYSQLAAddalpeeqvvslelqetiqeAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTR 172

                         170
                  ....*....|..
gi 1472313288 142 LRAAREYLRKDL 153
Cdd:PRK09641  173 IHRGREALRKQL 184
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 15-153 5.83e-18

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: 5.83e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  15 PTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPY--DAAAAEAIPAPA 92
Cdd:TIGR02985  12 PKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYqeELAEIEERELSE 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  93 ADDYSDLYA---------AITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDL 153
Cdd:TIGR02985  92 ADPEEELEAkeleeiieeAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 19-156 1.62e-17

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 75.17  E-value: 1.62e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  19 RVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRR--QQRLAPYDAAAAEAIPAP----- 91
Cdd:PRK09415   31 QLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSwhNKKVIVTEDIFTYMESQKesvee 110

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1472313288  92 ---AADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKGA 156
Cdd:PRK09415  111 eviQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEE 178
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 1-153 3.73e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 71.64  E-value: 3.73e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   1 MDREQ-FTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQ-RLA 78
Cdd:PRK12517   19 LSKQRrYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRRENARRFERKQfDLV 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1472313288  79 PYDAAAAEAIPAPAADDYSD---LYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDL 153
Cdd:PRK12517   99 DIEDDSIEDDASHSSEEEMEqewLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 3-153 5.83e-14

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: 65.49  E-value: 5.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   3 REQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRL-APYD 81
Cdd:TIGR02983   5 EEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLeLPTR 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1472313288  82 AA--AAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDL 153
Cdd:TIGR02983  85 ELpdAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 2-153 3.57e-12

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 61.21  E-value: 3.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTR-YFKTWLVRILINECSTILRRQQRLA-- 78
Cdd:PRK05602   18 DPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEaRFDTWLHRVVLNLCYDRLRRRREVPve 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1472313288  79 ----PYDAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDL 153
Cdd:PRK05602   98 dapdVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQL 176
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 2-149 1.50e-11

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 59.34  E-value: 1.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQ--QRLAP 79
Cdd:PRK09643   25 DRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAkaRPTVP 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  80 YDAAAAEAIPAPAADDYSDLyaAITALEEKLRLPVE------LYYLEGFKTREIAGMLGISENTVKTRLRAAREYL 149
Cdd:PRK09643  105 LDDVYPVAQLERDPTARVET--ALAVQRALMRLPVEqraalvAVDMQGYSVADAARMLGVAEGTVKSRCARGRARL 178
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 33-154 2.10e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 58.96  E-value: 2.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  33 DAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECS----TILRRQQRLAPYDAAAAEAIPAPAAD----DYSDLYA-AI 103
Cdd:PRK12518   39 DLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATdarrQFAQRPSRIQDDSLNDQPSRPSDTPDlmqlHYQDLVQqGL 118

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1472313288 104 TALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:PRK12518  119 QTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 2-154 2.70e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 58.82  E-value: 2.70e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAP-- 79
Cdd:PRK12516    8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQdt 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1472313288  80 ---YDAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:PRK12516   88 dgmFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 4-150 2.88e-10

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 55.40  E-value: 2.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   4 EQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR------- 76
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRdrlvfdd 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  77 --LAPYDAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLR 150
Cdd:TIGR02989  81 dlLEALAAEAEPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLR 156
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 1-150 3.80e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 55.56  E-value: 3.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   1 MDREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPY 80
Cdd:PRK12511    1 MERKSKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  81 DAAAAEAIPAPAADD------YSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLR 150
Cdd:PRK12511   81 ADELAVLADASLPAAqehavrLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALR 156
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 15-76 4.63e-10

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 52.59  E-value: 4.63e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1472313288  15 PTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTR--YFKTWLVRILINECSTILRRQQR 76
Cdd:pfam04542   7 PLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERgvSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 99-149 8.48e-10

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 51.69  E-value: 8.48e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1472313288  99 LYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYL 149
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 15-140 1.17e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 54.51  E-value: 1.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  15 PTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTR-YFKTWLVRILINECSTILRRQQRLA--------PYDAAAA 85
Cdd:PRK12524   37 PRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEaRVSTWLYRVVCNLCTDRLRRRRRASvdlddapePADAAPG 116

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1472313288  86 EAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKT 140
Cdd:PRK12524  117 AEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVES 171
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 22-157 1.60e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 53.84  E-value: 1.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  22 KTMLRS----EHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINecsTIL---RRQQR---LAPYDAAAAEAIPAP 91
Cdd:PRK09637   15 KAFLHSrvsnEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANN---TIIdfyRKKNRseeLPDDLLFEDEEREEN 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1472313288  92 AADDYSD-LYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKGAC 157
Cdd:PRK09637   92 AKKELAPcLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCC 158
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 6-154 4.77e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 52.19  E-value: 4.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   6 FTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAP-----Y 80
Cdd:PRK12547    8 FKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQdsdgvF 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1472313288  81 DAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:PRK12547   88 TARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 2-154 1.06e-08

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 51.73  E-value: 1.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAP-Y 80
Cdd:PRK11923   18 DKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRPPdS 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  81 DAAAAEAIPAPAADDYSDL----------------YAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRA 144
Cdd:PRK11923   98 DVSSEDAEFYDGDHALKDIesperallrdeiegtvHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFR 177

                         170
                  ....*....|
gi 1472313288 145 AREYLRKDLK 154
Cdd:PRK11923  178 AREAIDKALQ 187
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 18-156 1.79e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 51.27  E-value: 1.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  18 YRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR--------LAPYDAAAAEAIP 89
Cdd:PRK12515   36 YRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRRKHeeiddeaaAAIEDGADTPEVA 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1472313288  90 APAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKGA 156
Cdd:PRK12515  116 LQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAA 182
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 18-154 2.35e-08

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 50.94  E-value: 2.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  18 YRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRyFKTWLVRILINECSTILRRQQRLA----PYDAAAAEAIPAPAA 93
Cdd:PRK09647   42 YRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPGT-FEGWLHRITTNLFLDMVRRRARIRmealPEDYDRVPGDEPNPE 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1472313288  94 DDYS------DLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:PRK09647  121 QIYHdarldpDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 17-155 2.27e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 47.94  E-value: 2.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  17 LYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR-----LAPYDAAAAEAIPAP 91
Cdd:PRK12522   16 IYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRwkdriLDLFHKEDGGEIEFA 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1472313288  92 AADDYSD----------LYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKG 155
Cdd:PRK12522   96 DDVNISEefiqkveaemIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 14-156 6.39e-07

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 46.86  E-value: 6.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  14 EPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPYDAAAAEAIPAPAA 93
Cdd:PRK09640   36 QRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLMDALSLDPLEEAS 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  94 DDYSDLYAAITALEEKL-------RLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKGA 156
Cdd:PRK09640  116 EEKAPKPEERGGLDRWLvhvnpidREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFAGL 185
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-150 6.51e-07

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: 44.02  E-value: 6.51e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1472313288 102 AITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLR 150
Cdd:cd06171     7 ALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
18-150 7.11e-07

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 47.24  E-value: 7.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  18 YRvaktMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILR-RQQRLAPYDAAAAEAIPAPAADD- 95
Cdd:PRK08241   37 YR----MLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEgRARRPLPTDLGAPAADPVDELVEr 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  96 --------YSDLY--------AAITALEEKLRLP--VELYYLE-------------GFKTREIAGMLGISENTVKTRLRA 144
Cdd:PRK08241  113 pevpwlepYPDALldpaaadpAARVVARESVRLAfvAALQHLPprqravlilrdvlGWSAAEVAELLDTSVAAVNSALQR 192


                  ....*.
gi 1472313288 145 AREYLR 150
Cdd:PRK08241  193 ARATLA 198
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 10-149 1.18e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 46.11  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  10 VLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAP-----YDAAA 84
Cdd:PRK12540   11 ILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREVEdadgsYAKTL 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1472313288  85 AEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYL 149
Cdd:PRK12540   91 KSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155
SigX5 TIGR02960
RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of ...
 24-81 2.31e-06

RNA polymerase sigma-70 factor, TIGR02960 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: 132005 [Multi-domain]  Cd Length: 324  Bit Score: 46.01  E-value: 2.31e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1472313288  24 MLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINEC-STILRRQQRLAPYD 81
Cdd:TIGR02960  25 MLGSLHEAEDLVQETLLRAWRARDRFEGRSSVRTWLYRIATNAClDALEARQRRPRPVG 83
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 2-151 4.22e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 44.34  E-value: 4.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECST----------IL 71
Cdd:PRK12543    5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSwrrkrwrrfrIF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  72 RRQQRLApYDAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRK 151
Cdd:PRK12543   85 EKAEEQR-KPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163
PRK12544 PRK12544
RNA polymerase factor sigma-70;
19-77 1.28e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 43.25  E-value: 1.28e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1472313288  19 RVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRL 77
Cdd:PRK12544   33 KFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRH 91
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 15-149 1.31e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 43.29  E-value: 1.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  15 PTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR-LAPYDAAAAEAIPAPAA 93
Cdd:PRK12546   18 PALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKReVPDPEGVHAASLAVKPA 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  94 DD----YSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYL 149
Cdd:PRK12546   98 HDgrlaMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL 157
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 102-151 1.83e-05

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: 40.10  E-value: 1.83e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1472313288 102 AITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRK 151
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 18-155 2.02e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 42.92  E-value: 2.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  18 YRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRY-FKTWLVRILINECSTiLRRQQRLAPYDA------AAAEAIPA 90
Cdd:PRK12538   77 YAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAkFSTWLYRVVSNRCID-LRRKPRTENVDAvpevadGKPDAVSV 155

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  91 PAADDYSDLY-AAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKG 155
Cdd:PRK12538  156 IERNELSDLLeAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRR 221
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 2-150 3.57e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 41.84  E-value: 3.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQ---LDSLRSTryFKTWLVRILINECSTILRRQQRLA 78
Cdd:PRK12531   25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKahlFDGQKSA--LSTWIYTIIRNLCFDLLRKQKGKD 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  79 PYDAAAAEAIPAPAADDYSDLYAA------------ITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAR 146
Cdd:PRK12531  103 LHIHADDIWPSDYYPPDLVDHYSPeqdmlkeqvmkfLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAV 182


                  ....
gi 1472313288 147 EYLR 150
Cdd:PRK12531  183 EKLR 186
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 94-155 3.97e-05

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: 41.64  E-value: 3.97e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  94 DDYSDLYAAITALE----EKLRLpVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKG 155
Cdd:pfam07638 121 DLLLDLDEALEQLFslspRQARL-VELRFFAGLSNDEIAERLGVSERTVERNWALARAWLHRELRD 185
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 55-153 4.22e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 41.60  E-value: 4.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  55 FKTWLVRILINECSTILRRQ-QRLAPYDAAAAEAIPAPAADDYSD-----------LYAAITALEEKLRLPVELYYLEGF 122
Cdd:PRK12513   77 FRTWLYQIARNLLIDHWRRHgARQAPSLDADEQLHALADDGAAPEqqlslfrdrrrLQAALETLPDEQREVFLLREHGDL 156

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1472313288 123 KTREIAGMLGISENTVKTRLRAAREYLRKDL 153
Cdd:PRK12513  157 ELEEIAELTGVPEETVKSRLRYALQKLRELL 187
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 94-155 5.96e-05

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 41.73  E-value: 5.96e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1472313288  94 DDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKG 155
Cdd:COG1191   175 ELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
PRK12545 PRK12545
RNA polymerase factor sigma-70;
17-76 6.78e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 41.09  E-value: 6.78e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  17 LYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR 76
Cdd:PRK12545   21 LLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQR 80
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 101-155 6.82e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 41.20  E-value: 6.82e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1472313288 101 AAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKG 155
Cdd:PRK12519  137 TALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQD 191
Sig-70_X6 TIGR02999
RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the ...
 94-154 3.15e-04

RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.


Pssm-ID: 132044 [Multi-domain]  Cd Length: 183  Bit Score: 39.22  E-value: 3.15e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1472313288  94 DDYSDLYAAITALE---EKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:TIGR02999 120 EELLDLDDALDKLAqvdPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWLADELS 183
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 8-158 4.96e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 38.76  E-value: 4.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   8 SAVLAAEPTLYRVAKTMLRSEHDCA-DAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQRLAPYDAAAAE 86
Cdd:PRK12532    9 AELIESRKLLLHFARLQLPDHPDLAeDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLDD 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  87 AIPAPAAD----------------DYSDLYAAITALEEKLRLPVELYYLE-------------GFKTREIAGMLGISENT 137
Cdd:PRK12532   89 ELLDEAFEshfsqnghwtpegqpqHWNTPEKSLNNNEFQKILQSCLYNLPentarvftlkeilGFSSDEIQQMCGISTSN 168

                         170       180
                  ....*....|....*....|.
gi 1472313288 138 VKTRLRAAREYLRKDLKGACF 158
Cdd:PRK12532  169 YHTIMHRARESLRQCLQIKWF 189
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 120-147 7.31e-04

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 37.56  E-value: 7.31e-04
                          10        20
                  ....*....|....*....|....*...
gi 1472313288 120 EGFKTREIAGMLGISENTVKTRLRAARE 147
Cdd:COG2197    83 EGLSNKEIAERLGISERTVKTHVSNILR 110
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
15-155 1.06e-03

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 37.75  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  15 PTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSL-RSTRYFKTWLV----RILINEcstilRRQQRLAP-YDAAAAEAI 88
Cdd:PRK09645   20 APLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFtvarNLVIDE-----RRSARARPvEGGDDVLGV 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1472313288  89 PAPAADDYSD-------LYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKG 155
Cdd:PRK09645   95 PEQSAPDEVDraldrllVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQE 168
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 120-147 1.47e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 35.20  E-value: 1.47e-03
                           10        20
                   ....*....|....*....|....*...
gi 1472313288  120 EGFKTREIAGMLGISENTVKTRLRAARE 147
Cdd:smart00421  17 EGLTNKEIAERLGISEKTVKTHLSNIMR 44
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 97-145 1.65e-03

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 37.68  E-value: 1.65e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1472313288  97 SDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKT-------RLRAA 145
Cdd:PRK05911  197 SILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQihskallKLRAT 252
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 2-143 1.81e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 37.11  E-value: 1.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFK-TWLVRILINECSTILRRQQRLAP- 79
Cdd:PRK12514   17 DRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPmTWLITIARNHAIDRLRARKAVAVd 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1472313288  80 -------YDAAAAEAIPAPAADDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLR 143
Cdd:PRK12514   97 ideahdlADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLR 167
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 119-143 1.81e-03

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 35.32  E-value: 1.81e-03
                          10        20
                  ....*....|....*....|....*
gi 1472313288 119 LEGFKTREIAGMLGISENTVKTRLR 143
Cdd:COG5905    25 AEGLTNKEIARQLFISEKTVKNHVS 49
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
94-156 2.57e-03

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 36.57  E-value: 2.57e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1472313288  94 DDYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKGA 156
Cdd:PRK09646  131 LERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCLGVS 193
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 99-158 2.65e-03

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 36.82  E-value: 2.65e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  99 LYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLKGACF 158
Cdd:PRK07408  197 LQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPEDD 256
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 17-154 3.90e-03

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 36.01  E-value: 3.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  17 LYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRyFKTWLVRILINECSTILRRQQRLAPYDAAAAEAIPAPAADDY 96
Cdd:PRK09644   14 VYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQK-VKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAIQAESTEEY 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1472313288  97 S---DLYAAITALEEKL----RLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:PRK09644   93 VvakNSYEKLIQIIHTLpvieAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 95-154 4.72e-03

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 36.05  E-value: 4.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  95 DYSDLYAAITALEEKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:PRK13919  125 DRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 102-154 5.27e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 35.33  E-value: 5.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288 102 AITALEEKLR-LPVE------LYYLEGFKTREIAGMLGISENTVKTRLRAAREYLRKDLK 154
Cdd:PRK09047   96 VLQLIEEAIQkLPARqreaflLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 2-149 5.56e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 35.86  E-value: 5.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288   2 DREQFTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYfKTWLVRILINECSTILRRQQ--RLAP 79
Cdd:PRK12533   16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGDNA-RPWLLAIVRHTWYSEWRRRAnaHEVA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1472313288  80 YDAAAAEAIPAPAADDYSDLYAAITALEEKLR--------LPVE------LYYLEGFKTREIAGMLGISENTVKTRLRAA 145
Cdd:PRK12533   95 APDTLDDADSLDDWQPAGEDPLALLLRAEDVRlvnaalakLPVEyrevlvLRELEDMSYREIAAIADVPVGTVMSRLARA 174


                  ....
gi 1472313288 146 REYL 149
Cdd:PRK12533  175 RRRL 178
Phage_antitermQ pfam06530
Phage antitermination protein Q; This family consists of several phage antitermination protein ...
 108-149 6.03e-03

Phage antitermination protein Q; This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream.


Pssm-ID: 428991  Cd Length: 118  Bit Score: 34.91  E-value: 6.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1472313288 108 EKLRLPVELYYLEGFKTREIAGMLGISENTVKTRLRAAREYL 149
Cdd:pfam06530  65 PEEHDLLVDYYVFGMSKRAIARKLKCSEGEIRKKLQTAEGFI 106
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 6-76 8.95e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 35.09  E-value: 8.95e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1472313288   6 FTSAVLAAEPTLYRVAKTMLRSEHDCADAAQQAILRAWEQLDSLRSTRYFKTWLVRILINECSTILRRQQR 76
Cdd:PRK12520    4 APAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSGRR 74
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
116-147 9.86e-03

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 35.10  E-value: 9.86e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1472313288 116 LYYLEGFKTREIAGMLGISENTVKTRLRAARE 147
Cdd:COG2390     5 LYYVEGLTQREIAERLGISRRTVSRLLAEARE 36
 
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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