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Conserved domains on  [gi|1114584157|gb|APM38705|]
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sporulation sigma factor SigK [Clostridium kluyveri]

Protein Classification

RNA polymerase sporulation sigma factor SigK( domain architecture ID 11481669)

RNA polymerase sporulation sigma factor SigK is responsible for the expression of sporulation specific genes in the mother cell

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
1-233 9.59e-148

RNA polymerase sporulation sigma factor SigK;


:

Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 410.88  E-value: 9.59e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157   1 MFLTNCLLDILGNVVFMTAYVTNNSsFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLI 80
Cdd:PRK05803    2 MFLFAALLYIVKEILFLVSYVKNNS-FPQPLSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  81 SIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIV 160
Cdd:PRK05803   81 SIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVIEQV 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1114584157 161 EQKIQVKKLYSKINtCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELNYGAK 233
Cdd:PRK05803  161 ELKMEVEKLYKKID-ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRAEK 232
 
Name Accession Description Interval E-value
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
1-233 9.59e-148

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 410.88  E-value: 9.59e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157   1 MFLTNCLLDILGNVVFMTAYVTNNSsFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLI 80
Cdd:PRK05803    2 MFLFAALLYIVKEILFLVSYVKNNS-FPQPLSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  81 SIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIV 160
Cdd:PRK05803   81 SIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVIEQV 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1114584157 161 EQKIQVKKLYSKINtCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELNYGAK 233
Cdd:PRK05803  161 ELKMEVEKLYKKID-ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRAEK 232
SigK COG5814
Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, ...
 1-229 1.09e-136

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: 383.04  E-value: 1.09e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157   1 MFLTNCLLDILGNVVFMTAYVTNNSsFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLI 80
Cdd:COG5814     3 GFLLALLLSLIKGILLLVSYINNNA-FPQPLSEEEEAKYLERMAEGDEEARNILIEHNLRLVAHIVKKFENTGEDTEDLI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  81 SIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIV 160
Cdd:COG5814    82 SIGTIGLIKAINTFDPDKGTKLATYAARCIENEILMHLRSTKKTRKEVSLQDPIGTDKEGNEITLIDILGTDEDDVVDQV 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1114584157 161 EQKIQVKKLYSKINTcLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:COG5814   162 ELKLEKEKLYEKLKK-LSEREREVIELRYGLLNGEEKTQREIAKKLGISRSYVSRIEKRALMKLFKEFY 229
spore_sigmaK TIGR02846
RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also ...
 10-229 1.78e-136

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: 382.14  E-value: 1.78e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  10 ILGNVVFMTAYVTNNSSFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIK 89
Cdd:TIGR02846   9 IVKSLLFLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  90 AIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIVEQKIQVKKL 169
Cdd:TIGR02846  89 AIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKL 168

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 170 YSKInTCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:TIGR02846 169 YKKL-SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKELY 227
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 54-124 8.87e-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: 72.24  E-value: 8.87e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1114584157  54 LVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKI 124
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 176-224 6.60e-11

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 55.96  E-value: 6.60e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1114584157 176 CLSQREKSVVEMRYGllegKPKTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:cd06171    10 KLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKL 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 177-224 1.58e-04

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 38.66  E-value: 1.58e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1114584157  177 LSQREKSVVEMrygLLEGKpkTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:smart00421   4 LTPREREVLRL---LAEGL--TNKEIAERLGISEKTVKTHLSNIMRKL 46
 
Name Accession Description Interval E-value
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
1-233 9.59e-148

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 410.88  E-value: 9.59e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157   1 MFLTNCLLDILGNVVFMTAYVTNNSsFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLI 80
Cdd:PRK05803    2 MFLFAALLYIVKEILFLVSYVKNNS-FPQPLSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  81 SIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIV 160
Cdd:PRK05803   81 SIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVIEQV 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1114584157 161 EQKIQVKKLYSKINtCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELNYGAK 233
Cdd:PRK05803  161 ELKMEVEKLYKKID-ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRAEK 232
SigK COG5814
Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, ...
 1-229 1.09e-136

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: 383.04  E-value: 1.09e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157   1 MFLTNCLLDILGNVVFMTAYVTNNSsFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLI 80
Cdd:COG5814     3 GFLLALLLSLIKGILLLVSYINNNA-FPQPLSEEEEAKYLERMAEGDEEARNILIEHNLRLVAHIVKKFENTGEDTEDLI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  81 SIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIV 160
Cdd:COG5814    82 SIGTIGLIKAINTFDPDKGTKLATYAARCIENEILMHLRSTKKTRKEVSLQDPIGTDKEGNEITLIDILGTDEDDVVDQV 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1114584157 161 EQKIQVKKLYSKINTcLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:COG5814   162 ELKLEKEKLYEKLKK-LSEREREVIELRYGLLNGEEKTQREIAKKLGISRSYVSRIEKRALMKLFKEFY 229
spore_sigmaK TIGR02846
RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also ...
 10-229 1.78e-136

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: 382.14  E-value: 1.78e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  10 ILGNVVFMTAYVTNNSSFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIK 89
Cdd:TIGR02846   9 IVKSLLFLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  90 AIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIVEQKIQVKKL 169
Cdd:TIGR02846  89 AIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKL 168

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 170 YSKInTCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:TIGR02846 169 YKKL-SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKELY 227
SigE COG5811
Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell ...
 20-229 7.02e-81

Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444513 [Multi-domain]  Cd Length: 232  Bit Score: 241.62  E-value: 7.02e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  20 YVTNNSSFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKG 99
Cdd:COG5811    21 YIGGSEALPPPLTREEEAELLEKLEEGDESVRSTLIERNLRLVVYIARKFENTGIGIEDLISIGTIGLIKAVNTFNPDKK 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 100 TRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIVEQKIQVKKLYSKINTcLSQ 179
Cdd:COG5811   101 IKLATYASRCIENEILMYLRRNNKTKSEVSFDEPLNVDWDGNELLLSDILGTENDIIYKNIEEEVDRELLKKALKK-LSE 179

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1114584157 180 REKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:COG5811   180 RERKIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 229
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
1-229 3.88e-75

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 227.05  E-value: 3.88e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157   1 MFLTNCLLDILGNVVFMTAYVTNNSSFPQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLI 80
Cdd:PRK08301    4 RLLWYKLLLKLGLKTDEIYYIGGSEALPPPLSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  81 SIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKIKNEVYLQDPIGVDKEGNEISLMDVLSSDEDSIIEIV 160
Cdd:PRK08301   84 SIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDI 163

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1114584157 161 EQKIQVKKLYSKINTcLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:PRK08301  164 EDEVDRKLLKKALKK-LSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 31-224 2.67e-40

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: 139.03  E-value: 2.67e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  31 LNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCI 110
Cdd:COG0568    12 LTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWI 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 111 ENEILMLIRNN-----------------KKIKNE-----------------------------------VYLQDPIGvdk 138
Cdd:COG0568    92 RQAITRAIADQwrtirlpvhmaetlnklRRAKRQllqelgreptpeeiaeelgvpeekvremlrlarepVSLDAPVG--- 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 139 EGNEISLMDVLSSDE-DSIIEIVEQKIQVKKLYSKINTcLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIE 217
Cdd:COG0568   169 DDEDSELGDLLEDEEaPSPEEALEEELLREELREALDT-LTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIE 247


                  ....*..
gi 1114584157 218 KKALKKL 224
Cdd:COG0568   248 AKALRKL 254
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 54-229 4.28e-35

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 124.26  E-value: 4.28e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  54 LVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNN----------KK 123
Cdd:TIGR02980   8 LVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDtwavrvprrlKE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 124 IKNEVY------------------LQDPIGVDKE-------------------------GNEISLMDVLSsDEDSIIEIV 160
Cdd:TIGR02980  88 LGVKINkateeltqrlgrsptiaeIAERLGVSEEevvealeagnayqalsldasiedddGDPIALLDTLG-DEDDALETV 166

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1114584157 161 EQKIQVKKLYSKintcLSQREKSVVEMRYGllegKPKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:TIGR02980 167 EDRLALKPLLAA----LPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQLL 227
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 35-229 4.74e-35

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: 124.55  E-value: 4.74e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  35 EERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYS--YPgKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIEN 112
Cdd:COG1191     1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAgrLP-AELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 113 EILMLIR-----------NNKKIKNE----------------------------------------VYLQDPIgvdkeGN 141
Cdd:COG1191    80 AILDYLRdedwvprsvreLARKIEEAieeleqelgreptdeeiaeelgisleevqealeaanayqlLSLDEPL-----ED 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 142 EISLMDVLSS-DEDSIIEIVEQKIQVKKLyskINTcLSQREKSVVEMRYglleGKPKTQREIAKILGISRSYVSRIEKKA 220
Cdd:COG1191   155 GDDLLDLLESgDPEEELEHEELREALAEA---IEQ-LPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKA 226


                  ....*....
gi 1114584157 221 LKKLYKELN 229
Cdd:COG1191   227 LARLREYLK 235
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
17-229 1.22e-31

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 116.22  E-value: 1.22e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  17 MTAYVTNNSSFPQpLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDS 96
Cdd:PRK05572    1 MDIEVKNKKKKPQ-LKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  97 CKGTRLATYAAKCIENEILMLIRNNKKIK---------NEVY------------------LQDPIGVDKE---------- 139
Cdd:PRK05572   80 SYDVKFSTYAVPMIIGEIQRFLRDDGTVKvsrslketaNKIRkdkdelskelgreptieeLAEYLGVTPEevvlaqeasr 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 140 -------------GNEISLMDVLS-SDEDSIIEiveqKIQVKKLYSKintcLSQREKSVVEMRYglleGKPKTQREIAKI 205
Cdd:PRK05572  160 spqsihetvhendGDPITLLDQIAdQSEEDWFD----KIALKEAIRE----LDERERLIVYLRY----FKDKTQSEVAKR 227

                         250       260
                  ....*....|....*....|....
gi 1114584157 206 LGISRSYVSRIEKKALKKLYKELN 229
Cdd:PRK05572  228 LGISQVQVSRLEKKILKQMKEKLD 251
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
23-226 2.29e-31

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 115.43  E-value: 2.29e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  23 NNSSFPQpLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRL 102
Cdd:PRK08215   12 NTSKLPV-LKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKF 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 103 ATYAAKCIENEIL---------------------------MLIRNNKK------------------------IKNEVYLQ 131
Cdd:PRK08215   91 STYAVPMIIGEIRrylrdnnpirvsrslrdiaykalqvreKLINENSKeptveeiakelevpreevvfaldaIQDPVSLF 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 132 DPIGVDKeGNEISLMDVLsSDEDSIIEIVEQKIQVKKLYSKintcLSQREKSVVEMRYglLEGkpKTQREIAKILGISRS 211
Cdd:PRK08215  171 EPIYHDG-GDPIYVMDQI-SDEKNKDENWLEEIALKEAMKK----LNDREKLILNLRF--FQG--KTQMEVAEEIGISQA 240

                         250
                  ....*....|....*
gi 1114584157 212 YVSRIEKKALKKLYK 226
Cdd:PRK08215  241 QVSRLEKAALKHMRK 255
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 40-228 2.60e-29

RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131931 [Multi-domain]  Cd Length: 231  Bit Score: 109.42  E-value: 2.60e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  40 LRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIR 119
Cdd:TIGR02885   2 IKLAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 120 NNKKIK---------NEVY------------------LQDPIGVDKEgnEI-----------SLMDVLSSDEDSIIEIVE 161
Cdd:TIGR02885  82 DDGIIKvsrslkelaRKIRymkeelskelgreptineLAEALGVSPE--EIvmalesarspqSLYDTVHQDDGDPIYLLD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 162 Q-------------KIQVKKLYSKintcLSQREKSVVEMRYGllegKPKTQREIAKILGISRSYVSRIEKKALKKLYKEL 228
Cdd:TIGR02885 160 QiadkgsedsdwleKIALKEAISK----LDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 50-224 1.03e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 101.22  E-value: 1.03e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  50 AKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYA----------------------- 106
Cdd:PRK05901  272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYAtwwirqaitramadqartiripv 351

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 107 ---------AKcIENEILM-LIRN-------------NKKIKnEV--YLQDPIGVDK---EGNEISLMDvLSSDEDSI-- 156
Cdd:PRK05901  352 hmvetinklGR-IERELLQeLGREptpeelakemgftPEKVR-EIqkYNREPISLDKtigKEGDSQFGD-FIEDSEAVsp 428

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1114584157 157 IEIVEQKIQVKKLYSKINTcLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:PRK05901  429 VDAVSFTLLQDQLQEVLET-LSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKL 495
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 54-228 1.04e-24

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: 95.49  E-value: 1.04e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  54 LVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSckGTRLATYAAKCIENEILMLIRNNKKIKNEvylqdp 133
Cdd:TIGR02937   6 LYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLILDYLRRKRRLRRE------ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 134 igvdkegneISLMDVLSSDEDSIIEIVEQKIQVKKLYSKINTcLSQREKSVVEMRYglLEGKpkTQREIAKILGISRSYV 213
Cdd:TIGR02937  78 ---------LDLLEELLDSDPSPEEELEQEEEREALREALEK-LPEREREVLVLRY--LEGL--SYKEIAEILGISVGTV 143

                         170
                  ....*....|....*
gi 1114584157 214 SRIEKKALKKLYKEL 228
Cdd:TIGR02937 144 KRRLKRARKKLRELL 158
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 50-224 5.18e-24

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 97.49  E-value: 5.18e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  50 AKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEIL-------------- 115
Cdd:PRK07921   87 ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITrgmadqsrtirlpv 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 116 -MLIRNNK--KIKNEVYLQ-----------------------------DPIGVDK---EGNEISLMDVLssdEDSIIEIV 160
Cdd:PRK07921  167 hLVEQVNKlaRIKRELHQQlgreatdeelaeesgipeekiadllehsrDPVSLDMpvgSDEEAPLGDFI---EDSEATSA 243

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1114584157 161 EQKIQVKKLYSKINTC---LSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:PRK07921  244 ENAVIAGLLHTDIRSVlatLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKL 310
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 31-224 2.01e-22

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 93.90  E-value: 2.01e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  31 LNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYA---- 106
Cdd:PRK09210  111 LTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYAtwwi 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 107 -----------AKCIENEILM------LIRNNK------------------------------KIKNE-VYLQDPIGVDK 138
Cdd:PRK09210  191 rqaitraiadqARTIRIPVHMvetinkLIRVQRqllqelgreptpeeiaeemdmppekvreilKIAQEpVSLETPIGEED 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 139 E---GNEISLMDVLS-SDEDSIIEIVEQKIQVkklyskINTcLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVS 214
Cdd:PRK09210  271 DshlGDFIEDQDATSpADHAAYELLKEQLEDV------LDT-LTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIR 343

                         250
                  ....*....|
gi 1114584157 215 RIEKKALKKL 224
Cdd:PRK09210  344 QIEAKALRKL 353
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 31-224 1.43e-21

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 90.78  E-value: 1.43e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  31 LNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAA--- 107
Cdd:PRK05657   68 LTAEEEVYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATwwi 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 108 -KCIE--------------------NEILMLIRN-NKKIKNEVYLQD---------------------------PIGVDK 138
Cdd:PRK05657  148 rQTIEraimnqtrtirlpvhvvkelNVYLRAARElEHKLDHEPSAEEiaelldkpvddvsrmlalneritsldtPLGGDP 227

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 139 egnEISLMDVLSSDEDSIIEIVEQKIQVKKLYSKINTCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEK 218
Cdd:PRK05657  228 ---EKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQV 304


                  ....*.
gi 1114584157 219 KALKKL 224
Cdd:PRK05657  305 EALRRL 310
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 41-224 1.80e-20

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 88.30  E-value: 1.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  41 RKLKEGDLlAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRN 120
Cdd:PRK07406  129 RRLMLGRR-AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIAD 207

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 121 NKK-IKNEVYLQDPIGVDKEGNE------------------------------------ISLMDVLSSDEDSII-EIVEQ 162
Cdd:PRK07406  208 QSRtIRLPVHLYETISRIKKTTKvlsqefgrkpteeeiaesmemtieklrfiaksaqlpISLETPIGKEEDSRLgDFIEA 287

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1114584157 163 KI-----QVKK------LYSKINTcLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:PRK07406  288 DGetpedDVAKnllredLEGVLAT-LSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKL 359
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 40-224 2.25e-20

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 88.77  E-value: 2.25e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  40 LRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLI- 118
Cdd:PRK07598  166 LEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIa 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 119 --------------------RNNKKIKNE-------------------------------VYLQDPIGVDKEgneISLMD 147
Cdd:PRK07598  246 tqsrtirlpvhiteklnkikKAQRKISQEkgrtptiediaqelemtptqvrevllrvprsVSLETKVGKDKD---TELGD 322

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 148 VLSSDEDSIIE-IVEQKIQ--VKKLYSKintcLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:PRK07598  323 LLETDDISPEEmLMRESLQrdLQHLLAD----LTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKL 398
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 19-224 1.60e-18

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 81.76  E-value: 1.60e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  19 AYVTNNSSFPQpLNDEEERYYLRKLKE-GDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSC 97
Cdd:PRK06596   18 AYIQAVNKIPM-LTAEEEYMLAKRLREhGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  98 KGTRLATYAAKCIENEILMLIRNN-------------------KKIKNEVYLQDP---------IGVDKE---------- 139
Cdd:PRK06596   97 VGVRLVSFAVHWIKAEIHEYILRNwrivkvattkaqrklffnlRKAKKRLGWLNPeevemvaeeLGVSEEevremesrls 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 140 GNEISL--------------MDVLSSDEDSIIEIVEQK----IQVKKLYSKINTcLSQREKSVVEMRYglLEGKPKTQRE 201
Cdd:PRK06596  177 GQDASLdapiddddeesgapQDYLEDKSSDPADVLEEDnwedQRRALLADALEG-LDERSRDIIEARW--LDDDKSTLQE 253

                         250       260
                  ....*....|....*....|...
gi 1114584157 202 IAKILGISRSYVSRIEKKALKKL 224
Cdd:PRK06596  254 LAAEYGVSAERVRQIEKNAMKKL 276
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 25-224 6.88e-18

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 79.74  E-value: 6.88e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  25 SSFPQPLNDEEERYYLRKLKE-GDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLA 103
Cdd:PRK08583    4 SSQPTKLTKEEVNKWIAEYQEnQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 104 TYAAKCIENEILMLIRNNK--------------KIKNEV------------------YLQ-------------------- 131
Cdd:PRK08583   84 AFAVPTIIGEIKRYLRDKTwsvhvprrikelgpKIKKAVdelttelqrspkiseiadRLGvseeevleamemgksyqals 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 132 --DPIGVDKEGNEISLMDVLSSDEDSIiEIVEQKIQVKKLYSkintCLSQREKSVVEMRYglLEGKpkTQREIAKILGIS 209
Cdd:PRK08583  164 vdHSIEADSDGSTVTLLDIVGQQEDGY-ELTEQRMILEKILP----VLSDREKSIIQCTF--IENL--SQKETGERLGIS 234

                         250
                  ....*....|....*
gi 1114584157 210 RSYVSRIEKKALKKL 224
Cdd:PRK08583  235 QMHVSRLQRQAIKKL 249
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
44-209 1.10e-17

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 78.03  E-value: 1.10e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  44 KEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKK 123
Cdd:PRK08295   19 RSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANR 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 124 IKNEVyLQDPIGVDK----EGNEISLMDVLSSDEDSIIE-IVEQKIQVKKLYSKINTCLSQREKSVVEMrygLLEGkpKT 198
Cdd:PRK08295   99 QKHIP-LNSYVSLDKpiydEESDRTLLDVISEAKVTDPEeLIISKEELEDIEEKIEELLSELEKEVLEL---YLDG--KS 172

                         170
                  ....*....|.
gi 1114584157 199 QREIAKILGIS 209
Cdd:PRK08295  173 YQEIAEELNRH 183
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 54-124 8.87e-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: 72.24  E-value: 8.87e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1114584157  54 LVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNNKKI 124
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 54-228 3.15e-16

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: 74.62  E-value: 3.15e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  54 LVERNLRLVAHIVKKYSY---PGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEIL-----------MLIR 119
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSVglpSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLdelrrldwvprSLRQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 120 NNKKIKNEVY-LQDPIGVDKEGNEI------------------------SLMDVLSSDEDSII--------------EIV 160
Cdd:TIGR02479  81 KARKLERAIReLEARLGREPTEEEIaeelgmdlkeyrqalneinalslvSLDELLESGDDGGSlidrieddksedpeEEL 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 161 EQKIQVKKLYSKINTcLSQREKSVVEMRY--GLlegkpkTQREIAKILGISRSYVSRIEKKALKKLYKEL 228
Cdd:TIGR02479 161 EREELREALAEAIES-LSEREQLVLSLYYyeEL------NLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 34-228 1.38e-14

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: 69.25  E-value: 1.38e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  34 EEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSckGTRLATYAAKCIENE 113
Cdd:COG1595     2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG--RGSFRAWLYRIARNL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 114 ILMLIRnnKKIKNEVYLQDPIgvdkegneislmDVLSSDEDSIIEIVEQKIQVKKLYSKINTcLSQREKSVVEMRYglLE 193
Cdd:COG1595    80 AIDHLR--KRRRRRELLDELA------------EELPDEAADPEEALEAEELLEALLAALER-LPPRQREVLVLRY--LE 142

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1114584157 194 GKpkTQREIAKILGISRSYV-SRIeKKALKKLYKEL 228
Cdd:COG1595   143 GL--SYAEIAEILGISEGTVkSRL-SRARKKLREAL 175
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 35-226 1.78e-14

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 70.94  E-value: 1.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  35 EERYYLRKLKEGDLlAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEI 114
Cdd:PRK07405   68 SEEELRSAIAEGEA-AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAI 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 115 LMLI---------------RNNKKIKNEVYLQDPIGVDKEGNEIS----------------------------------L 145
Cdd:PRK07405  147 TRAIaeksrtirlpihiteKLNKIKKAQRQLSQQLGRAATIGELAeeleltpkqvreylerarqplsldlrvgdnqdteL 226

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 146 MDVLSSDEDSIIEIVEQKIQVKKLySKINTCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLY 225
Cdd:PRK07405  227 GELLEDTGASPEDFATQSSLQLDL-ERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305


                  .
gi 1114584157 226 K 226
Cdd:PRK07405  306 K 306
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 28-228 8.74e-14

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 68.56  E-value: 8.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  28 PQPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYSY---PGKDVDDLISIGTVGLIKAIDSFDSCKGTRLAT 104
Cdd:PRK06288   10 PKYAQQDETELWREYKKTGDPKIREYLILKYSPLVKYVAGRIAVgmpQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKT 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 105 YA-------------------------AKCIENEILML-IRNNKKIKNE-------------------------VYLQDP 133
Cdd:PRK06288   90 YAvtrirgaifdelrsidwiprsvrqkARQIERAIAMLeARLGRTPSDEeiadelgisleeynsllsklsgtsvVSLNDL 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 134 IGVDKEGNEISLMDVL-SSDEDSIIEIVEQKIQVKKLYSKINTcLSQREKSVVEMRY--GLlegkpkTQREIAKILGISR 210
Cdd:PRK06288  170 WFGGDEGDEVSLMDTLeSPAALNPDEIAEREEIKRVIVEAIKT-LPEREKKVLILYYyeDL------TLKEIGKVLGVTE 242

                         250
                  ....*....|....*...
gi 1114584157 211 SYVSRIEKKALKKLYKEL 228
Cdd:PRK06288  243 SRISQLHTKAVLQLRAKL 260
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 54-228 2.06e-13

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 67.49  E-value: 2.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  54 LVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNN-------KKIKn 126
Cdd:PRK07122   45 IVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNswsvkvpRRLK- 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 127 EVYLQ----------------------DPIGVDKE--------GN-----------------EISLMDVLsSDEDSIIEI 159
Cdd:PRK07122  124 ELHLRlgrataelsqrlgraptaselaAELGMDREevveglvaGSayntlsidsgggsgdddARAIADTL-GDVDAGLDQ 202

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1114584157 160 VEQKIQVKKLYSKintcLSQREKSVVEMRYglleGKPKTQREIAKILGISRSYVSRIEKKALKKLYKEL 228
Cdd:PRK07122  203 IENREALRPLLAA----LPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 177-226 5.74e-13

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: 61.29  E-value: 5.74e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1114584157 177 LSQREKSVVEMRYGllegKPKTQREIAKILGISRSYVSRIEKKALKKLYK 226
Cdd:pfam04545   5 LPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 41-224 1.59e-12

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 65.63  E-value: 1.59e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  41 RKLKEGDLlAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRN 120
Cdd:PRK05949   84 QTLKQGKR-AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQ 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 121 N-----------------KKIKNEV--------------------------YL---QDPIGVD---KEGNEISLMDVLSS 151
Cdd:PRK05949  163 QartirlpihiteklnkiKKTQRELsqklgrsatpaeiakelelepsqireYLsmaRQPISLDvrvGDNQDTELSELLED 242

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1114584157 152 DEDSiieiVEQKIQVKKLYSKINTCLSQ---REKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:PRK05949  243 EGPS----PDQYITQELLRQDLNNLLAEltpQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHL 314
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 75-229 2.80e-11

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 61.02  E-value: 2.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  75 DVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIR-----------NNKKIKNEV--------------Y 129
Cdd:PRK06986   37 DLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRsldwvprsvrrNAREVAQAIrqleqelgreptdtE 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 130 LQDPIGVDKE-----------GNEISLMDVLSSDEDSIIEI-----------VEQKIQVKKLYSKINTcLSQREKSVVEM 187
Cdd:PRK06986  117 VAEKLGLSLEeyremlldtniSQLFSIDELRGEHGDSILVTedhqdedplqqLEDEELREALVEAIES-LPEREQLVLSL 195

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1114584157 188 RY----GLlegkpktqREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:PRK06986  196 YYqeelNL--------KEIGAVLGVSESRVSQIHSQAIKRLRARLG 233
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 176-224 6.60e-11

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 55.96  E-value: 6.60e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1114584157 176 CLSQREKSVVEMRYGllegKPKTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:cd06171    10 KLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 54-229 1.06e-10

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 59.93  E-value: 1.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  54 LVERNLRLV---AH-IVKKYSYPgkdVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIR---------- 119
Cdd:PRK07408   30 LVELNLGLVrkeAHrWSNQCSEP---YEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRdksptvripr 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 120 -----NNKKIK-------------NEVYLQDPIGVD-KEGNEISL---------MDV-LSSDEDSII---EIV------- 160
Cdd:PRK07408  107 rwqelQRQAKKvrqelrqelgrqpTDQEIAQALDISlEEWQEIKLalqnrtplsLDApVNQDEDGSTslgDLLpdpryrs 186

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1114584157 161 -----EQKIQVKKLYSKintcLSQREKSVVEMRYglLEGkpKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:PRK07408  187 fqlaqEDRIRLQQALAQ----LEERTREVLEFVF--LHD--LTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 31-228 1.42e-09

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 56.97  E-value: 1.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  31 LNDEEERYYLRKLKEG-DLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKC 109
Cdd:PRK07500   21 LEREEEHALAYRWKDHrDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWW 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 110 IENEILMLIRNNKKI-------------------------------KNEVY--LQDPIGV---DKE-------GNEISL- 145
Cdd:PRK07500  101 IRASIQDYILRNWSIvrggtssaqkalffnlrrlrarlaqadeeltKQEIHreIATALGVslsDVEmmdarlsGPDASLn 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 146 -------------MDVLSSDEDSIIEIVEQKIQVKK----LYSKINTcLSQREKSVVEMRYglLEGKPKTQREIAKILGI 208
Cdd:PRK07500  181 apqseedegrserMDFLVDDSPLPDEQVESSIDGERrrrwLTQALQT-LNERELRIIRERR--LREDGATLEALGEELGI 257

                         250       260
                  ....*....|....*....|
gi 1114584157 209 SRSYVSRIEKKALKKLYKEL 228
Cdd:PRK07500  258 SKERVRQIEARALEKLRRAL 277
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
29-229 1.43e-09

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 56.59  E-value: 1.43e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  29 QPLNDEEERYYLRKLKEGDLLAKSILVERNLRLVAHIVKKYS--YPgKDV--DDLISIGTVGLIKAIDSFDSCKGTRLAT 104
Cdd:PRK07670    2 QSLTYEEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISvgLP-KSVskDDLKSLGMLGLYDALEKFDPSRDLKFDT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 105 YAAKCIENEILMLIRNN-----------KKIK---------------------------NEVY-------------LQDP 133
Cdd:PRK07670   81 YASFRIRGAIIDGLRKEdwlprsmrektKKVEaaiekleqrymrnvtpkevaaelgmteEEVEatmnegffanllsIDEK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 134 IGVDKEGNEISLMdvlSSDEDSII---EIVEQKiQVKKLYSKINTcLSQREKSVVEMRYglleGKPKTQREIAKILGISR 210
Cdd:PRK07670  161 THDQDDGENVSVT---IRDDKTPTpeeKLLKEE-LIEELAEKIKQ-LSEKEQLVISLFY----KEELTLTEIGQVLNLST 231

                         250
                  ....*....|....*....
gi 1114584157 211 SYVSRIEKKALKKLYKELN 229
Cdd:PRK07670  232 SRISQIHSKALFKLKKLLE 250
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 50-224 7.01e-08

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 52.49  E-value: 7.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  50 AKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYA---------------AKCIE--- 111
Cdd:PRK05658  381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAtwwirqaitrsiadqARTIRipv 460

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 112 ------NEIL-----ML----------------------IRNNKKIKNE-VYLQDPIGvdkegneislmdvlsSDEDS-- 155
Cdd:PRK05658  461 hmietiNKLNrisrqMLqeigreptpeelaerlgmpedkVRKVLKIAKEpISLETPIG---------------DDEDShl 525

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 156 --------IIEIVEQKIQVkKLYSKINTCLSQ---REKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:PRK05658  526 gdfiedknAELPIDAAIQE-SLREATTDVLASltpREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 604
COG1356 COG1356
Transcriptional regulator [Transcription];
177-226 2.38e-06

Transcriptional regulator [Transcription];


Pssm-ID: 440967 [Multi-domain]  Cd Length: 139  Bit Score: 45.61  E-value: 2.38e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1114584157 177 LSQREKSVVEMR-YGLlegkpkTQREIAKILGISRSYVSRIEKKALKKLYK 226
Cdd:COG1356     9 LTRRQAEVLALReRGL------TQQEIADILGTSRANVSSIEKSARENIEK 53
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 147-228 7.40e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 44.96  E-value: 7.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157 147 DVLSSDEDSIIEIVEQKIQVKKLYSKINTC---LSQREKSVVEMRYglLEGKpkTQREIAKILGIS----RSYVSRiekk 219
Cdd:PRK11924   93 DALEPEFAETAETPEAALLAKDDLARIDRCldaLPVKQREVFLLRY--VEGL--SYREIAEILGVPvgtvKSRLRR---- 164


                  ....*....
gi 1114584157 220 ALKKLYKEL 228
Cdd:PRK11924  165 ARQLLRECL 173
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
177-224 3.51e-05

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 43.21  E-value: 3.51e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1114584157 177 LSQREKSVVEMrygLLEGKpkTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:COG2771   128 LTPREREVLRL---LAEGL--TLKEIARILGISERTVRTHLKRIYRKL 170
tfx TIGR00721
DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges ...
 175-229 7.32e-05

DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges with significant hits only to other members of the family, which is restricted to the Archaea. Homology is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter. [Regulatory functions, DNA interactions]


Pssm-ID: 129804 [Multi-domain]  Cd Length: 137  Bit Score: 41.40  E-value: 7.32e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1114584157 175 TCLSQREKSVVEMRyglleGKPKTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:TIGR00721   5 TFLTERQIKVLELR-----EKGLSQKEIAKELKTTRANVSAIEKRAMENIEKARN 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 177-224 1.58e-04

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 38.66  E-value: 1.58e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1114584157  177 LSQREKSVVEMrygLLEGKpkTQREIAKILGISRSYVSRIEKKALKKL 224
Cdd:smart00421   4 LTPREREVLRL---LAEGL--TNKEIAERLGISEKTVKTHLSNIMRKL 46
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
196-220 1.94e-04

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


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 41.65  E-value: 1.94e-04
                          10        20
                  ....*....|....*....|....*
gi 1114584157 196 PKTQREIAKILGISRSYVSRIEKKA 220
Cdd:COG2390    10 GLTQREIAERLGISRRTVSRLLAEA 34
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
198-229 2.51e-04

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 38.82  E-value: 2.51e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1114584157 198 TQREIAKILGISRSYVSRIEK-------KALKKLYKELN 229
Cdd:COG1396    22 TQEELAERLGVSRSTISRIERgrrnpslETLLKLAKALG 60
tfx PRK03975
putative transcriptional regulator; Provisional
 177-229 2.75e-04

putative transcriptional regulator; Provisional


Pssm-ID: 179690 [Multi-domain]  Cd Length: 141  Bit Score: 39.87  E-value: 2.75e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1114584157 177 LSQREKSVVEMR-YGLlegkpkTQREIAKILGISRSYVSRIEKKALKKLYKELN 229
Cdd:PRK03975    7 LTERQIEVLRLReRGL------TQQEIADILGTSRANVSSIEKRARENIEKARE 54
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 177-224 7.38e-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: 38.33  E-value: 7.38e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1114584157 177 LSQREKSVVEMrygLLEGKpkTQREIAKILGIS----RSYVSRIekkaLKKL 224
Cdd:COG2197    70 LTPREREVLRL---LAEGL--SNKEIAERLGISertvKTHVSNI----LRKL 112
PRK08311 PRK08311
RNA polymerase sigma factor SigI;
39-132 1.70e-03

RNA polymerase sigma factor SigI;


Pssm-ID: 236233 [Multi-domain]  Cd Length: 237  Bit Score: 38.31  E-value: 1.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1114584157  39 YLRKLKEGDLLAKSILVERN----LRLVAHIVKKYSYPGKDvdDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEI 114
Cdd:PRK08311    8 ILEKIKNGDEELREELIEEYkpfiAKVVSSVCGRYIDWEND--DELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRL 85

                          90
                  ....*....|....*...
gi 1114584157 115 LMLIRNNKKIKNEVYLQD 132
Cdd:PRK08311   86 IDYFRKESKHNLVLSNSD 103
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 177-224 1.80e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 35.51  E-value: 1.80e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1114584157 177 LSQREKSVVEMRYglLEGKpkTQREIAKILGIS----RSYVSRiekkALKKL 224
Cdd:pfam08281  11 LPPRQREVFLLRY--LEGL--SYAEIAELLGISegtvKSRLSR----ARKKL 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
198-218 1.88e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.57  E-value: 1.88e-03
                           10        20
                   ....*....|....*....|.
gi 1114584157  198 TQREIAKILGISRSYVSRIEK 218
Cdd:smart00530  12 TQEELAEKLGVSRSTLSRIEN 32
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
196-227 2.52e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 34.72  E-value: 2.52e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1114584157  196 PKTQREIAKILGISRSYVSRIekkaLKKLYKE 227
Cdd:smart00419   8 PLTRQEIAELLGLTRETVSRT----LKRLEKE 35
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 191-218 2.66e-03

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 35.22  E-value: 2.66e-03
                          10        20
                  ....*....|....*....|....*...
gi 1114584157 191 LLEGKPKTQREIAKILGISRSYVSRIEK 218
Cdd:cd00093     7 LRKEKGLTQEELAEKLGVSRSTISRIEN 34
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
198-229 3.04e-03

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 35.21  E-value: 3.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1114584157 198 TQREIAKILGISRSYVSRIEK-------KALKKLYKELN 229
Cdd:COG1476    19 TQEELAELLGVSRQTISAIENgkynpslELALKIARALG 57
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 158-228 3.76e-03

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 36.85  E-value: 3.76e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1114584157 158 EIVEQKIQVKKLYSKINTClSQREKSVVEMRYGLLEGKpktqrEIAKILGISRSYVSRIE---KKALKKLYKEL 228
Cdd:PRK09639   95 EIWIRKEEITKVQEVLAKM-TERDRTVLLLRFSGYSYK-----EIAEALGIKESSVGTTLaraKKKFRKIYEQM 162
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 198-229 4.09e-03

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 34.91  E-value: 4.09e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1114584157 198 TQREIAKILGISRSYVSRIEK-------KALKKLYKELN 229
Cdd:COG1813    27 SQEELAEKLGVSESTIRRIERgeatpslDTLRKLEKALG 65
GerE pfam00196
Bacterial regulatory proteins, luxR family;
177-219 4.70e-03

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 34.48  E-value: 4.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1114584157 177 LSQREKSVVEMrygLLEGKpkTQREIAKILGIS----RSYVSRIEKK 219
Cdd:pfam00196   3 LSPREREVLRW---LAAGK--SNKEIADELGISektvKVHRSNIMRK 44
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 191-227 6.54e-03

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 34.58  E-value: 6.54e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1114584157 191 LLEGKPKTQREIAKILGISRSYVSRIekkaLKKLYKE 227
Cdd:cd00090    15 LLLEGPLTVSELAERLGLSQSTVSRH----LKKLEEA 47
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 198-218 8.14e-03

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 33.67  E-value: 8.14e-03
                          10        20
                  ....*....|....*....|.
gi 1114584157 198 TQREIAKILGISRSYVSRIEK 218
Cdd:pfam01381  11 SQEELAEKLGVSRSTISKIEN 31
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 197-217 8.83e-03

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 33.66  E-value: 8.83e-03
                          10        20
                  ....*....|....*....|.
gi 1114584157 197 KTQREIAKILGISRSYVSRIE 217
Cdd:pfam13560  15 LSQEALARRLGVSRSTLSRLE 35
 
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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