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Conserved domains on  [gi|400178498|gb|AFP72781|]
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sporulation sigma factor SigK, partial [Clostridium perfringens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
spore_sigmaK super family cl31255
RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also ...
 1-196 1.17e-118

RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


The actual alignment was detected with superfamily member TIGR02846:

Pssm-ID: 131893 [Multi-domain]  Cd Length: 227  Bit Score: 335.54  E-value: 1.17e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498    1 KIFLTGYVTGNSTFPKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNyqnSKEMDDLISIGTIGLIKA 80
Cdd:TIGR02846  13 LLFLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNT---GEDVDDLISIGTIGLIKA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   81 IDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEICLIDILSSDSDSVLEAVENSLQVKELY 160
Cdd:TIGR02846  90 IDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLY 169

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 400178498  161 KKMSdILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:TIGR02846 170 KKLS-VLDGREREVIEMRYGLGDGRRKTQREIAKIL 204
 
Name Accession Description Interval E-value
spore_sigmaK TIGR02846
RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also ...
 1-196 1.17e-118

RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131893 [Multi-domain]  Cd Length: 227  Bit Score: 335.54  E-value: 1.17e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498    1 KIFLTGYVTGNSTFPKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNyqnSKEMDDLISIGTIGLIKA 80
Cdd:TIGR02846  13 LLFLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNT---GEDVDDLISIGTIGLIKA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   81 IDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEICLIDILSSDSDSVLEAVENSLQVKELY 160
Cdd:TIGR02846  90 IDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLY 169

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 400178498  161 KKMSdILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:TIGR02846 170 KKLS-VLDGREREVIEMRYGLGDGRRKTQREIAKIL 204
SigK COG5814
Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, ...
 2-196 3.16e-115

Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444516 [Multi-domain]  Cd Length: 234  Bit Score: 327.18  E-value: 3.16e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   2 IFLTGYVTGNStFPKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNyqnSKEMDDLISIGTIGLIKAI 81
Cdd:COG5814   17 LLLVSYINNNA-FPQPLSEEEEAKYLERMAEGDEEARNILIEHNLRLVAHIVKKFENT---GEDTEDLISIGTIGLIKAI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  82 DSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEICLIDILSSDSDSVLEAVENSLQVKELYK 161
Cdd:COG5814   93 NTFDPDKGTKLATYAARCIENEILMHLRSTKKTRKEVSLQDPIGTDKEGNEITLIDILGTDEDDVVDQVELKLEKEKLYE 172

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 400178498 162 KMsDILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:COG5814  173 KL-KKLSEREREVIELRYGLLNGEEKTQREIAKKL 206
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
2-196 3.47e-111

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 316.89  E-value: 3.47e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   2 IFLTGYVTGNStFPKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNyqnSKEMDDLISIGTIGLIKAI 81
Cdd:PRK05803  16 LFLVSYVKNNS-FPQPLSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENT---GEDVDDLISIGTIGLIKAI 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  82 DSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEICLIDILSSDSDSVLEAVENSLQVKELYK 161
Cdd:PRK05803  92 ESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYK 171

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 400178498 162 KMsDILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:PRK05803 172 KI-DILDEREKEVIEMRYGLGNGKEKTQREIAKAL 205
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 41-114 1.49e-17

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: 73.39  E-value: 1.49e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 400178498   41 LVERNLRLVAHIVKKYSSNYQnskEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKT 114
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGA---DAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
 
Name Accession Description Interval E-value
spore_sigmaK TIGR02846
RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also ...
 1-196 1.17e-118

RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131893 [Multi-domain]  Cd Length: 227  Bit Score: 335.54  E-value: 1.17e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498    1 KIFLTGYVTGNSTFPKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNyqnSKEMDDLISIGTIGLIKA 80
Cdd:TIGR02846  13 LLFLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNT---GEDVDDLISIGTIGLIKA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   81 IDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEICLIDILSSDSDSVLEAVENSLQVKELY 160
Cdd:TIGR02846  90 IDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLY 169

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 400178498  161 KKMSdILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:TIGR02846 170 KKLS-VLDGREREVIEMRYGLGDGRRKTQREIAKIL 204
SigK COG5814
Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, ...
 2-196 3.16e-115

Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444516 [Multi-domain]  Cd Length: 234  Bit Score: 327.18  E-value: 3.16e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   2 IFLTGYVTGNStFPKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNyqnSKEMDDLISIGTIGLIKAI 81
Cdd:COG5814   17 LLLVSYINNNA-FPQPLSEEEEAKYLERMAEGDEEARNILIEHNLRLVAHIVKKFENT---GEDTEDLISIGTIGLIKAI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  82 DSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEICLIDILSSDSDSVLEAVENSLQVKELYK 161
Cdd:COG5814   93 NTFDPDKGTKLATYAARCIENEILMHLRSTKKTRKEVSLQDPIGTDKEGNEITLIDILGTDEDDVVDQVELKLEKEKLYE 172

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 400178498 162 KMsDILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:COG5814  173 KL-KKLSEREREVIELRYGLLNGEEKTQREIAKKL 206
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
2-196 3.47e-111

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 316.89  E-value: 3.47e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   2 IFLTGYVTGNStFPKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNyqnSKEMDDLISIGTIGLIKAI 81
Cdd:PRK05803  16 LFLVSYVKNNS-FPQPLSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENT---GEDVDDLISIGTIGLIKAI 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  82 DSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEICLIDILSSDSDSVLEAVENSLQVKELYK 161
Cdd:PRK05803  92 ESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYK 171

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 400178498 162 KMsDILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:PRK05803 172 KI-DILDEREKEVIEMRYGLGNGKEKTQREIAKAL 205
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
7-196 6.49e-61

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 189.30  E-value: 6.49e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   7 YVTGNSTFPKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNYQNskeMDDLISIGTIGLIKAIDSFDT 86
Cdd:PRK08301  23 YIGGSEALPPPLSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGIN---IEDLISIGTIGLIKAVNTFNP 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  87 NKGIRLATYAAKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEICLIDILSSDSDSVLEAVENSLQvKELYKKMSDI 166
Cdd:PRK08301 100 EKKIKLATYASRCIENEILMYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVD-RKLLKKALKK 178

                        170       180       190
                 ....*....|....*....|....*....|
gi 400178498 167 LSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:PRK08301 179 LSDREKQIMELRFGLNGGEEKTQKEVADML 208
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-196 1.43e-31

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: 115.15  E-value: 1.43e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  18 LNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYsSNYQNSkeMDDLISIGTIGLIKAIDSFDTNKGIRLATYAA 97
Cdd:COG0568   12 LTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKY-QGRGLP--LLDLIQEGNLGLMKAVEKFDPERGFRFSTYAT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  98 KCIDNEILMF-FRNT----------------KKTKGE-----------------------------------VFLQDPIG 125
Cdd:COG0568   89 WWIRQAITRAiADQWrtirlpvhmaetlnklRRAKRQllqelgreptpeeiaeelgvpeekvremlrlarepVSLDAPVG 168

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 400178498 126 vdkEGNEICLIDILSSDS-DSVLEAVENSLQVKELYKKMSDiLSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:COG0568  169 ---DDEDSELGDLLEDEEaPSPEEALEEELLREELREALDT-LTEREREILRLRFGLDDGEPHTLEEIGKEF 236
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 27-196 3.52e-25

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: 97.59  E-value: 3.52e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  27 LDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNYqnSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILM 106
Cdd:COG1191    6 LRRYQEGDEEAREELIEEYLPLVKKIASRLAGRL--PAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498 107 FFR-----------NTKK----------------TKGEV-------------FLQDPIGV------DKEGNEICLIDILS 140
Cdd:COG1191   84 YLRdedwvprsvreLARKieeaieeleqelgrepTDEEIaeelgisleevqeALEAANAYqllsldEPLEDGDDLLDLLE 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 400178498 141 SDS-DSVLEAVENslqvKELYKKMSDILSPREKEIIKMRY--GLldgdikTQREIAAIL 196
Cdd:COG1191  164 SGDpEEELEHEEL----REALAEAIEQLPERERLVLSLYYfeEL------TLKEIAEVL 212
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
18-193 3.22e-20

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 85.00  E-value: 3.22e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  18 LNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNYQNskeMDDLISIGTIGLIKAIDSFDTNKGIRLATYAA 97
Cdd:PRK08215  19 LKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGEN---VDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  98 KCIDNEILMFFRN------------------------TKKTKGE-----------------VF----LQDPIGV-----D 127
Cdd:PRK08215  96 PMIIGEIRRYLRDnnpirvsrslrdiaykalqvreklINENSKEptveeiakelevpreevVFaldaIQDPVSLfepiyH 175

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 400178498 128 KEGNEICLIDILSSDSDSVLEAVENsLQVKELYKKmsdiLSPREKEIIKMRYglLDGdiKTQREIA 193
Cdd:PRK08215 176 DGGDPIYVMDQISDEKNKDENWLEE-IALKEAMKK----LNDREKLILNLRF--FQG--KTQMEVA 232
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 41-114 1.49e-17

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: 73.39  E-value: 1.49e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 400178498   41 LVERNLRLVAHIVKKYSSNYQnskEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKT 114
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGA---DAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
17-196 2.51e-17

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 77.32  E-value: 2.51e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  17 PLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYS-SNYqnskEMDDLISIGTIGLIKAIDSFDTNKGIRLATY 95
Cdd:PRK05572  13 QLKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLnRGY----EPDDLFQIGCIGLLKAVDKFDLSYDVKFSTY 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  96 AAKCIDNEILMFFRN------------------------TKK-----TKGEvfLQDPIGVDKE----------------- 129
Cdd:PRK05572  89 AVPMIIGEIQRFLRDdgtvkvsrslketankirkdkdelSKElgrepTIEE--LAEYLGVTPEevvlaqeasrspqsihe 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 400178498 130 ------GNEICLIDILSSDSDsvlEAVENSLQVKELYKKmsdiLSPREKEIIKMRYgLLDgdiKTQREIAAIL 196
Cdd:PRK05572 167 tvhendGDPITLLDQIADQSE---EDWFDKIALKEAIRE----LDERERLIVYLRY-FKD---KTQSEVAKRL 228
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 36-196 1.63e-16

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: 73.15  E-value: 1.63e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   36 EAKRVLVERNLRLVAHIVKKYssnYQNSKEMDDLISIGTIGLIKAIDSFDTNKgiRLATYAAKCIDNEILMFFRNTKKTK 115
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRY---LGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRRLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  116 GEVFlqdpigvdkegneicLIDILSSDSDSVLEAVENSLQVKELYKKMsDILSPREKEIIKMRYglLDGdiKTQREIAAI 195
Cdd:TIGR02937  76 RELD---------------LLEELLDSDPSPEEELEQEEEREALREAL-EKLPEREREVLVLRY--LEG--LSYKEIAEI 135


                  .
gi 400178498  196 L 196
Cdd:TIGR02937 136 L 136
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
16-196 3.27e-16

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 73.40  E-value: 3.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  16 KPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYssnYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATY 95
Cdd:PRK08295   4 KDYDELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSY---FLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  96 AAKCIDNEILMFFR--NTKKTKgevFLQDPIGVDK----EGNEICLIDILSSDSDSVLE-AVENSLQVKELYKKMSDILS 168
Cdd:PRK08295  81 AELCITRQIITAIKtaNRQKHI---PLNSYVSLDKpiydEESDRTLLDVISEAKVTDPEeLIISKEELEDIEEKIEELLS 157

                        170       180
                 ....*....|....*....|....*...
gi 400178498 169 PREKEIIkMRYglLDGdiKTQREIAAIL 196
Cdd:PRK08295 158 ELEKEVL-ELY--LDG--KSYQEIAEEL 180
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 27-196 9.60e-16

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 74.14  E-value: 9.60e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  27 LDRLKDGDVEAKRVLVERNLRLVAHIVKKYssnyQNSK-EMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCID---- 101
Cdd:PRK07598 166 LEQIQKQGLRAKEHMIKANLRLVVSVAKKY----QNRGlELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRqgit 241

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498 102 --------------------NEILMFFRNTKKTKG--------------------EVFLQDP--------IGVDKEGNei 133
Cdd:PRK07598 242 raiatqsrtirlpvhiteklNKIKKAQRKISQEKGrtptiediaqelemtptqvrEVLLRVPrsvsletkVGKDKDTE-- 319

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 400178498 134 cLIDILSSDSDSVLE-AVENSLQvKELYKKMSDiLSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:PRK07598 320 -LGDLLETDDISPEEmLMRESLQ-RDLQHLLAD-LTSRERDVIRMRFGLADGHTYSLAEIGRAL 380
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 4-194 7.04e-15

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 70.97  E-value: 7.04e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   4 LTGYVTGNSTFPKpLNEKEEKIYLDRLKD-GDVEAKRVLVERNLRLVAHIVKKYSSnY---QNskemdDLISIGTIGLIK 79
Cdd:PRK06596  16 LDAYIQAVNKIPM-LTAEEEYMLAKRLREhGDLEAAKQLVLSHLRFVVHIARGYRG-YglpQA-----DLIQEGNIGLMK 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  80 AIDSFDTNKGIRLATYAAKCIDNEI----L----------------MFFrNTKKTKG--------EVFL----------- 120
Cdd:PRK06596  89 AVKRFDPEVGVRLVSFAVHWIKAEIheyiLrnwrivkvattkaqrkLFF-NLRKAKKrlgwlnpeEVEMvaeelgvseee 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498 121 ----------QD-----PIGvDKEGNEICLIDIL---SSDSDSVLEAVENSLQVKELYKKMSDILSPREKEIIKMRYglL 182
Cdd:PRK06596 168 vremesrlsgQDasldaPID-DDDEESGAPQDYLedkSSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEARW--L 244

                        250
                 ....*....|..
gi 400178498 183 DGDIKTQREIAA 194
Cdd:PRK06596 245 DDDKSTLQELAA 256
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 16-194 9.14e-15

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 71.14  E-value: 9.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  16 KPLNEKEEKIYLDRL-KDGDVEAKRVLVERNLRLVAHIVKKYSSnyqNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLAT 94
Cdd:PRK05657  65 SPLLTAEEEVYFARRaLRGDFAARQRMIESNLRLVVKIAKRYLN---RGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  95 YAA--------KCIDN-------------EILMFFRN----TKKTKGEVFLQD--------------------------- 122
Cdd:PRK05657 142 YATwwirqtieRAIMNqtrtirlpvhvvkELNVYLRAarelEHKLDHEPSAEEiaelldkpvddvsrmlalneritsldt 221

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 400178498 123 PIGVDKEGNeicLIDILSSDSDSVLEAVENSLQVKELYKKMSDILSPREKEIIKMRYGLLDGDIKTQREIAA 194
Cdd:PRK05657 222 PLGGDPEKS---LLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAR 290
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 18-96 4.32e-14

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 69.24  E-value: 4.32e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  18 LNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSsnyqnSKEMD--DLISIGTIGLIKAIDSFDTNKGIRLATY 95
Cdd:PRK09210 111 LTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYV-----GRGMLflDLIQEGNMGLMKAVEKFDYRKGFKFSTY 185


                 .
gi 400178498  96 A 96
Cdd:PRK09210 186 A 186
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 17-195 9.37e-14

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 68.27  E-value: 9.37e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  17 PLNEKEEKIYLDRlkdgdvEAKRVLVERNLRLVAHIVKKYssnyQNSK-EMDDLISIGTIGLIKAIDSFDTNKGIRLATY 95
Cdd:PRK07406 123 PLPKFRRRLMLGR------RAKEKMVQSNLRLVVSIAKKY----MNRGlSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTY 192

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  96 AA--------------------------------------------KCIDNEI----------LMFFRntKKTKGEVFLQ 121
Cdd:PRK07406 193 ATwwirqaitraiadqsrtirlpvhlyetisrikkttkvlsqefgrKPTEEEIaesmemtiekLRFIA--KSAQLPISLE 270

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 400178498 122 DPIGVDKEGNeicLIDILSSDSDSVLEAVENSLqVKELYKKMSDILSPREKEIIKMRYGLLDGDIKTQREIAAI 195
Cdd:PRK07406 271 TPIGKEEDSR---LGDFIEADGETPEDDVAKNL-LREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQI 340
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 5-194 2.81e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 67.33  E-value: 2.81e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   5 TGYVTGNSTFPKPLNEKEEKIYLDRLKDGDvEAKRVLVERNLRLVAHIVKKYSSnyqnsKEMD--DLISIGTIGLIKAID 82
Cdd:PRK05901 241 GLYAEELLAEGEKLDPELRRDLQWIGRDGK-RAKNHLLEANLRLVVSLAKRYTN-----RGLSflDLIQEGNLGLIKAVE 314

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  83 SFDTNKGIRLATYA---------------AKCI-----------------------------DNEIL--MFF-----RNT 111
Cdd:PRK05901 315 KFDYTKGYKFSTYAtwwirqaitramadqARTIripvhmvetinklgrierellqelgreptPEELAkeMGFtpekvREI 394

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498 112 KKtkgevFLQDPIGVDK---EGNEICLIDILsSDSDSV--LEAVENSLqvkeLYKKMSDI---LSPREKEIIKMRYGLLD 183
Cdd:PRK05901 395 QK-----YNREPISLDKtigKEGDSQFGDFI-EDSEAVspVDAVSFTL----LQDQLQEVletLSEREAGVIRMRFGLTD 464

                        250
                 ....*....|.
gi 400178498 184 GDIKTQREIAA 194
Cdd:PRK05901 465 GQPKTLDEIGQ 475
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 31-192 1.46e-12

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 64.75  E-value: 1.46e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  31 KDGdVEAKRVLVERNLRLVAHIVKKYSSnyqnsKEMD--DLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFF 108
Cdd:PRK07921  82 RDG-EAARRHLLEANLRLVVSLAKRYTG-----RGMPllDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGM 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498 109 RNTKKT-----------------KGEVFLQ-----------------------------DPIGVDK---EGNEICLID-I 138
Cdd:PRK07921 156 ADQSRTirlpvhlveqvnklariKRELHQQlgreatdeelaeesgipeekiadllehsrDPVSLDMpvgSDEEAPLGDfI 235

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 400178498 139 LSSDSDSVLEAVENSLQVKELyKKMSDILSPREKEIIKMRYGLLDGDIKTQREI 192
Cdd:PRK07921 236 EDSEATSAENAVIAGLLHTDI-RSVLATLDEREQQVIRLRFGLDDGQPRTLDQI 288
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 30-196 1.81e-10

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 58.62  E-value: 1.81e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  30 LKDGDVeAKRVLVERNLRLVAHIVKKYssnYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA------------- 96
Cdd:PRK07405  76 IAEGEA-AKRKMVEANLRLVVSVAKKY---LKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAywwirqaitraia 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  97 --AKCIDNEILMFFRNTKKTKGEVFLQDPIGVDKEGNEIC----------------------------------LIDILS 140
Cdd:PRK07405 152 ekSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAeeleltpkqvreylerarqplsldlrvgdnqdteLGELLE 231

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 400178498 141 SDSDSVLE-AVENSLQVkELYKKMSDiLSPREKEIIKMRYGLLDGDIKTQREIAAIL 196
Cdd:PRK07405 232 DTGASPEDfATQSSLQL-DLERLMED-LTPQQKEVIALRFGLEDGQPLTLAKIGERL 286
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 41-109 9.76e-10

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 56.08  E-value: 9.76e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 400178498  41 LVERNLRLV---AH-IVKKYSSNYqnskemDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFR 109
Cdd:PRK07408  30 LVELNLGLVrkeAHrWSNQCSEPY------EDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLR 96
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 18-96 1.13e-09

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 56.39  E-value: 1.13e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 400178498  18 LNEKEEKIYLDRLKdgdvEAKRVLVERNLRLVAHIVKKYSsnyQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96
Cdd:PRK05949  77 LSETELKQTLKQGK----RAKQKMIEANLRLVVAIAKKYQ---KRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYA 148
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 41-105 1.41e-09

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: 55.36  E-value: 1.41e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 400178498   41 LVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEIL 105
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAML 65
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 27-196 2.54e-09

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: 54.23  E-value: 2.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  27 LDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSkemDDLISIGTIGLIKAIDSFDTNKgiRLATYAAKCIDNEILM 106
Cdd:COG1595    8 LERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADA---EDLVQETFLRLWRKLDSFRGRG--SFRAWLYRIARNLAID 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498 107 FFRntKKTKGEVFLQDpigvdkegneicLIDILSSDSDSVLEAVENSLQVKELYKKMSDiLSPREKEIIKMRYglLDGdi 186
Cdd:COG1595   83 HLR--KRRRRRELLDE------------LAEELPDEAADPEEALEAEELLEALLAALER-LPPRQREVLVLRY--LEG-- 143

                        170
                 ....*....|
gi 400178498 187 KTQREIAAIL 196
Cdd:COG1595  144 LSYAEIAEIL 153
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 15-96 4.00e-09

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 54.69  E-value: 4.00e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  15 PKPLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLAT 94
Cdd:PRK06288  10 PKYAQQDETELWREYKKTGDPKIREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKT 89


                 ..
gi 400178498  95 YA 96
Cdd:PRK06288  90 YA 91
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 16-179 1.53e-07

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 50.08  E-value: 1.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  16 KPLNEKEEKIYL---DRLKDGDVEAKRVLVERNLRLVAHIVKKYSsnyQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRL 92
Cdd:PRK08583   6 QPTKLTKEEVNKwiaEYQENQDEEAQEKLVKHYKNLVESLAYKYS---KGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  93 ATYAAKCIDNEILMFFRNT-----------------KK------------------------TKGEVF------------ 119
Cdd:PRK08583  83 EAFAVPTIIGEIKRYLRDKtwsvhvprrikelgpkiKKavdelttelqrspkiseiadrlgvSEEEVLeamemgksyqal 162

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 400178498 120 -LQDPIGVDKEGNEICLIDILSSdSDSVLEAVENSLqvkeLYKKMSDILSPREKEIIKMRY 179
Cdd:PRK08583 163 sVDHSIEADSDGSTVTLLDIVGQ-QEDGYELTEQRM----ILEKILPVLSDREKSIIQCTF 218
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
17-105 2.21e-07

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 49.66  E-value: 2.21e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  17 PLNEKEEKIYLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96
Cdd:PRK07670   3 SLTYEEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYA 82


                 ....*....
gi 400178498  97 AKCIDNEIL 105
Cdd:PRK07670  83 SFRIRGAII 91
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 36-96 8.84e-07

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 48.25  E-value: 8.84e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 400178498  36 EAKRVLVERNLRLVAHIVKKYSSnyqnskemdDLISIGTIGLIKAIDSFDTNKGIRLATYA 96
Cdd:PRK05658 380 RAKKEMVEANLRLVISIAKKYTNrgl---qflDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 437
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 41-100 1.06e-06

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 47.53  E-value: 1.06e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  41 LVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCI 100
Cdd:PRK06986  13 LVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRI 72
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 17-96 3.34e-06

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 46.18  E-value: 3.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  17 PLNEKEEKIYLD-RLKDG-DVEAKRVLVERNLRLVAHIVKKYSsNYQNSkeMDDLISIGTIGLIKAIDSFDTNKGIRLAT 94
Cdd:PRK07500  19 PYLEREEEHALAyRWKDHrDEDALHRIISAHMRLVISMAGKFR-RFGLP--MNDLIQEGYVGLLEAAARFEPDREVRFST 95


                 ..
gi 400178498  95 YA 96
Cdd:PRK07500  96 YA 97
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 27-111 5.55e-06

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 45.54  E-value: 5.55e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  27 LDRLKDGDVEAKRV---LVERNLRLVAHIVKKYSSNYQNskeMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNE 103
Cdd:PRK07122  28 LAGLPAGSPEFQRQrdrIVTRCLPLADHIARRFDGRGEP---RDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGE 104


                 ....*...
gi 400178498 104 ILMFFRNT 111
Cdd:PRK07122 105 VRRHFRDN 112
PRK08311 PRK08311
RNA polymerase sigma factor SigI;
26-165 1.00e-05

RNA polymerase sigma factor SigI;


Pssm-ID: 236233 [Multi-domain]  Cd Length: 237  Bit Score: 44.48  E-value: 1.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498  26 YLDRLKDGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLiSIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEIL 105
Cdd:PRK08311   8 ILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDEL-SIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLI 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 400178498 106 MFFRNTKKTKGEVFLQDPigvdkEGNEICLIDI--LSSDSDSVLEAVENSLQVKELYKKMSD 165
Cdd:PRK08311  87 DYFRKESKHNLVLSNSDE-----EDEEENDIEIelSLEEYQEEEENEERREEIEEFKKELKE 143
spore_sigI TIGR02895
RNA polymerase sigma-I factor; Members of this sigma factor protein family are strictly ...
 36-122 3.07e-05

RNA polymerase sigma-I factor; Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock () in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (). [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131941 [Multi-domain]  Cd Length: 218  Bit Score: 43.21  E-value: 3.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400178498   36 EAKRVLVERNLRLVAHIVKKYSSNYQNSKEmDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTK 115
Cdd:TIGR02895   9 EEREELIRQYKPFIAKIVSSVCGRYIDTKS-DDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQKYQ 87


                  ....*..
gi 400178498  116 GEVFLQD 122
Cdd:TIGR02895  88 NLLYLDE 94
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 34-105 1.01e-04

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 41.91  E-value: 1.01e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 400178498  34 DVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEIL 105
Cdd:PRK05911  21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAII 92
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 165-196 7.21e-03

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: 33.56  E-value: 7.21e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 400178498  165 DILSPREKEIIKMRYglldGDIKTQREIAAIL 196
Cdd:pfam04545   3 ASLPPRERQVLVLRY----GEGLTLEEIGERL 30
PRK09277 PRK09277
aconitate hydratase AcnA;
119-162 9.06e-03

aconitate hydratase AcnA;


Pssm-ID: 236445 [Multi-domain]  Cd Length: 888  Bit Score: 36.25  E-value: 9.06e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 400178498 119 FLQDPIGVDKEGNEICLIDILSSDsDSVLEAVENSLQvKELYKK 162
Cdd:PRK09277 563 LEKDPLGTDKDGNPVYLKDIWPSD-EEIDAVVAKAVK-PEMFRK 604
 
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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