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Conserved domains on  [gi|2315513203|dbj|GIU70101|]
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MAG: hypothetical protein KatS3mg002_1337 [Candidatus Woesearchaeota archaeon]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoD super family cl33954
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 29-134 1.34e-16

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


The actual alignment was detected with superfamily member COG0568:

Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 78.17  E-value: 1.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  29 YMKFVKKYKALSAKEQIELIEKYHKNStsesekKKILDAIIYSNQRMVISIVKReisinHTNgkAGLYLMDYIQEANIGL 108
Cdd:COG0568     2 YLREIGRVPLLTAEEEVELARRIQAGD------EEAKRKLVEANLRLVVSIAKK-----YQG--RGLPLLDLIQEGNLGL 68

                          90       100
                  ....*....|....*....|....*.
gi 2315513203 109 LKAFEKYKTEYNVLFYTYATYWIRHY 134
Cdd:COG0568    69 MKAVEKFDPERGFRFSTYATWWIRQA 94
FliA_WhiG super family cl37120
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 99-190 1.60e-05

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


The actual alignment was detected with superfamily member TIGR02479:

Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 45.34  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  99 DYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR----HYLnvfmntvvEENKIIPMTFKKKINTL---VAYIEEKLSKN 171
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRgamlDEL--------RRLDWVPRSLRQKARKLeraIRELEARLGRE 99

                          90
                  ....*....|....*....
gi 2315513203 172 iiPSSEEIIKKSKINKQEY 190
Cdd:TIGR02479 100 --PTEEEIAEELGMDLKEY 116
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 29-134 1.34e-16

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 78.17  E-value: 1.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  29 YMKFVKKYKALSAKEQIELIEKYHKNStsesekKKILDAIIYSNQRMVISIVKReisinHTNgkAGLYLMDYIQEANIGL 108
Cdd:COG0568     2 YLREIGRVPLLTAEEEVELARRIQAGD------EEAKRKLVEANLRLVVSIAKK-----YQG--RGLPLLDLIQEGNLGL 68

                          90       100
                  ....*....|....*....|....*.
gi 2315513203 109 LKAFEKYKTEYNVLFYTYATYWIRHY 134
Cdd:COG0568    69 MKAVEKFDPERGFRFSTYATWWIRQA 94
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 16-132 1.57e-13

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 70.40  E-value: 1.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  16 ITSDIGIEQSLYEYMKFVKKYKALSAKEQIELIEKYHKNStsESEKKKILDAiiysNQRMVISIVKREIsinhtnGKAGL 95
Cdd:PRK09210   88 VPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGD--EEAKQRLAEA----NLRLVVSIAKRYV------GRGML 155

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2315513203  96 YLmDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK09210  156 FL-DLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIR 191
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 71-133 9.03e-07

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: 45.66  E-value: 9.03e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2315513203  71 SNQRMVISIVKREisinhtnGKAGLYLMDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIRH 133
Cdd:pfam04542   4 RYLPLVYSLARRY-------LGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRN 59
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 99-190 1.60e-05

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 45.34  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  99 DYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR----HYLnvfmntvvEENKIIPMTFKKKINTL---VAYIEEKLSKN 171
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRgamlDEL--------RRLDWVPRSLRQKARKLeraIRELEARLGRE 99

                          90
                  ....*....|....*....
gi 2315513203 172 iiPSSEEIIKKSKINKQEY 190
Cdd:TIGR02479 100 --PTEEEIAEELGMDLKEY 116
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 65-135 3.09e-03

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: 37.71  E-value: 3.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2315513203  65 LDAIIYSNQRMVISIVKREISINHTngkaglyLMDYIQEANIGLLKAFEKYKTEYNvlFYTYATYWIRHYL 135
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDAD-------AEDLVQEAFLKLLEALDRFDPEGS--FKAWLFRIARNLI 64
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 29-134 1.34e-16

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 78.17  E-value: 1.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  29 YMKFVKKYKALSAKEQIELIEKYHKNStsesekKKILDAIIYSNQRMVISIVKReisinHTNgkAGLYLMDYIQEANIGL 108
Cdd:COG0568     2 YLREIGRVPLLTAEEEVELARRIQAGD------EEAKRKLVEANLRLVVSIAKK-----YQG--RGLPLLDLIQEGNLGL 68

                          90       100
                  ....*....|....*....|....*.
gi 2315513203 109 LKAFEKYKTEYNVLFYTYATYWIRHY 134
Cdd:COG0568    69 MKAVEKFDPERGFRFSTYATWWIRQA 94
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 16-132 1.57e-13

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 70.40  E-value: 1.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  16 ITSDIGIEQSLYEYMKFVKKYKALSAKEQIELIEKYHKNStsESEKKKILDAiiysNQRMVISIVKREIsinhtnGKAGL 95
Cdd:PRK09210   88 VPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGD--EEAKQRLAEA----NLRLVVSIAKRYV------GRGML 155

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2315513203  96 YLmDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK09210  156 FL-DLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIR 191
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 29-132 1.08e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 68.48  E-value: 1.08e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  29 YMKFVKKYKALSAKEQIEL---IEK--YHKNSTSESEK----------------KKILDAIIYSNQRMVISIVKReisin 87
Cdd:PRK05901  216 YLKQIGKVKLLNAEEEVELakrIEAglYAEELLAEGEKldpelrrdlqwigrdgKRAKNHLLEANLRLVVSLAKR----- 290

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2315513203  88 HTNgkAGLYLMDYIQEANIGLLKAFEK------YKteynvlFYTYATYWIR 132
Cdd:PRK05901  291 YTN--RGLSFLDLIQEGNLGLIKAVEKfdytkgYK------FSTYATWWIR 333
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 29-132 8.65e-12

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 64.75  E-value: 8.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  29 YMKFVKKYKALSAKEQIEL---IE----KYHKNSTSE---SEKKKILDAIIY-----------SNQRMVISIVKReisin 87
Cdd:PRK07921   31 YLNGIGKTALLTAADEVELakrIEaglyAEHLLETRKrlsEARKRDLAAVVRdgeaarrhlleANLRLVVSLAKR----- 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2315513203  88 HTnGKaGLYLMDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK07921  106 YT-GR-GMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIR 148
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 69-132 3.26e-11

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 63.05  E-value: 3.26e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2315513203  69 IYSNQRMVISIVKReiSINHtngkaGLYLMDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK05657   92 IESNLRLVVKIAKR--YLNR-----GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 148
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 23-132 1.63e-10

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 60.57  E-value: 1.63e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  23 EQSLYEYMKFVKKYKALSAKEQIELIEKYHKNSTSESEKKKILdaiiySNQRMVISIVKreisinhtnGKA--GLYLMDY 100
Cdd:PRK06596   13 EGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVL-----SHLRFVVHIAR---------GYRgyGLPQADL 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2315513203 101 IQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK06596   79 IQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIK 110
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 71-132 1.06e-09

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 59.42  E-value: 1.06e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2315513203  71 SNQRMVISIVKReisinHTNgkAGLYLMDYIQEANIGLLKAFEK--YKTEYNvlFYTYATYWIR 132
Cdd:PRK05658  388 ANLRLVISIAKK-----YTN--RGLQFLDLIQEGNIGLMKAVDKfeYRRGYK--FSTYATWWIR 442
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 66-132 2.95e-09

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 57.49  E-value: 2.95e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2315513203  66 DAIIYSNQRMVISIVKREISinhtngkAGLYLMDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK07406  139 EKMVQSNLRLVVSIAKKYMN-------RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIR 198
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 65-132 4.39e-09

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 56.58  E-value: 4.39e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2315513203  65 LDAIIYSNQRMVISIVKReisinhtNGKAGLYLMDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK07500   42 LHRIISAHMRLVISMAGK-------FRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIR 102
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 71-133 9.03e-07

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: 45.66  E-value: 9.03e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2315513203  71 SNQRMVISIVKREisinhtnGKAGLYLMDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIRH 133
Cdd:pfam04542   4 RYLPLVYSLARRY-------LGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRN 59
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 58-132 1.30e-06

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 49.48  E-value: 1.30e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2315513203  58 ESEKKKILDAIIYSNQRMVISIVKReisinHTNgkAGLYLMDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK07598  170 QKQGLRAKEHMIKANLRLVVSVAKK-----YQN--RGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIR 237
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
31-127 1.42e-06

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 48.81  E-value: 1.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  31 KFVKKYKALSAKEQIELIEKyhknstSESEKKKILDAIIYSNQRMVISIVKREISinhtngkAGLYLMDYIQEANIGLLK 110
Cdd:PRK05572    6 KNKKKKPQLKDEENKELIKK------SQDGDQEARDTLVEKNLRLVWSVVQRFLN-------RGYEPDDLFQIGCIGLLK 72

                          90
                  ....*....|....*..
gi 2315513203 111 AFEKYKTEYNVLFYTYA 127
Cdd:PRK05572   73 AVDKFDLSYDVKFSTYA 89
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 58-132 6.02e-06

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 47.06  E-value: 6.02e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2315513203  58 ESEKKKILDAiiysNQRMVISIVKREIsinhtngKAGLYLMDYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR 132
Cdd:PRK07405   80 EAAKRKMVEA----NLRLVVSVAKKYL-------KRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIR 143
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 43-132 1.29e-05

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 46.37  E-value: 1.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  43 EQIELIEKYHKNSTSESEKKKilDAIIYSNQRMVISIVKREisinhtnGKAGLYLMDYIQEANIGLLKAFEKYKTEYNVL 122
Cdd:PRK05949   73 EAVNLSETELKQTLKQGKRAK--QKMIEANLRLVVAIAKKY-------QKRNMEFLDLIQEGTLGLERGVEKFDPTRGYK 143

                          90
                  ....*....|
gi 2315513203 123 FYTYATYWIR 132
Cdd:PRK05949  144 FSTYAYWWIR 153
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 99-190 1.60e-05

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 45.34  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  99 DYIQEANIGLLKAFEKYKTEYNVLFYTYATYWIR----HYLnvfmntvvEENKIIPMTFKKKINTL---VAYIEEKLSKN 171
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRgamlDEL--------RRLDWVPRSLRQKARKLeraIRELEARLGRE 99

                          90
                  ....*....|....*....
gi 2315513203 172 iiPSSEEIIKKSKINKQEY 190
Cdd:TIGR02479 100 --PTEEEIAEELGMDLKEY 116
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 43-190 2.88e-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: 44.43  E-value: 2.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  43 EQIELIEKYHKNStsesekKKILDAIIYSNQRMVISIVKREIsinhtnGKAGLYLMDYIQEANIGLLKAFEKYKTEYNVL 122
Cdd:COG1191     1 DLEELLRRYQEGD------EEAREELIEEYLPLVKKIASRLA------GRLPAELDDLIQVGLIGLIEAIDRFDPSKGVS 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2315513203 123 FYTYATYWIR----HYLnvfmntvvEENKIIPMTFK---KKINTLVAYIEEKLSKNiiPSSEEIIKKSKINKQEY 190
Cdd:COG1191    69 FETYAVPRIRgailDYL--------RDEDWVPRSVRelaRKIEEAIEELEQELGRE--PTDEEIAEELGISLEEV 133
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
39-135 1.33e-04

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 42.63  E-value: 1.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2315513203  39 LSAKEQIELIEKYHKNSTSESEKkkildaIIYSNQRMVISIVKReisinHTNgkAGLYLMDYIQEANIGLLKAFEKYKTE 118
Cdd:PRK08215   19 LKNEEMRELFERMQNGDKEAREK------LINGNLRLVLSVIQR-----FNN--RGENVDDLFQVGCIGLMKAIDNFDLS 85

                          90       100
                  ....*....|....*....|.
gi 2315513203 119 YNVLFYTYATYWI----RHYL 135
Cdd:PRK08215   86 QNVKFSTYAVPMIigeiRRYL 106
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 65-135 3.09e-03

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: 37.71  E-value: 3.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2315513203  65 LDAIIYSNQRMVISIVKREISINHTngkaglyLMDYIQEANIGLLKAFEKYKTEYNvlFYTYATYWIRHYL 135
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDAD-------AEDLVQEAFLKLLEALDRFDPEGS--FKAWLFRIARNLI 64
 
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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