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Conserved domains on  [gi|75216509|sp|Q9ZSL6|]
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RecName: Full=RNA polymerase sigma factor sigD, chloroplastic; Short=Sigma factor D; Short=Sigma-D; AltName: Full=RNA polymerase sigma factor sig4; Short=Atsig4; Short=Sigma factor 4; Flags: Precursor

Protein Classification

RNA polymerase sigma factor RpoD/SigA( domain architecture ID 11426268)

RNA polymerase sigma factor RpoD/SigA is the primary sigma factor during exponential growth

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 177-403 8.32e-90

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: 272.70  E-value: 8.32e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKL 256
Cdd:COG0568  29 EEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRL 108

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 257 PGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPE 336
Cdd:COG0568 109 PVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPE 188

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 75216509 337 EMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:COG0568 189 EALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLR 255
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 177-403 8.32e-90

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: 272.70  E-value: 8.32e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKL 256
Cdd:COG0568  29 EEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRL 108

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 257 PGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPE 336
Cdd:COG0568 109 PVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPE 188

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 75216509 337 EMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:COG0568 189 EALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLR 255
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 158-403 1.03e-83

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 258.33  E-value: 1.03e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   158 LASGRGKKKRSANEILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYW 237
Cdd:TIGR02997  54 WAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYW 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   238 WIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQ 317
Cdd:TIGR02997 134 WIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGD 213

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   318 NGRMTLQEIVRGPDETrPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGI 397
Cdd:TIGR02997 214 EEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAK 292


                  ....*.
gi 75216509   398 ALKKLR 403
Cdd:TIGR02997 293 ALRKLR 298
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 172-414 1.92e-60

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 200.78  E-value: 1.92e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  172 ILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKS 251
Cdd:PRK07406 130 RLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQS 209

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  252 RLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPD 331
Cdd:PRK07406 210 RTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG 289

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  332 ETrPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVNDL 411
Cdd:PRK07406 290 ET-PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVL 368


                 ...
gi 75216509  412 KIY 414
Cdd:PRK07406 369 KEY 371
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 185-252 2.00e-20

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: 84.56  E-value: 2.00e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 75216509   185 RCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSR 252
Cdd:pfam04542   3 ERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 347-403 2.79e-06

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 44.02  E-value: 2.79e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 75216509 347 EIEQLLGSLTARESRVLGLYFGLNgetpMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:cd06171   3 RLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 177-403 8.32e-90

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: 272.70  E-value: 8.32e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKL 256
Cdd:COG0568  29 EEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRL 108

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 257 PGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPE 336
Cdd:COG0568 109 PVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPE 188

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 75216509 337 EMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:COG0568 189 EALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLR 255
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 158-403 1.03e-83

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 258.33  E-value: 1.03e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   158 LASGRGKKKRSANEILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYW 237
Cdd:TIGR02997  54 WAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYW 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   238 WIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQ 317
Cdd:TIGR02997 134 WIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGD 213

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   318 NGRMTLQEIVRGPDETrPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGI 397
Cdd:TIGR02997 214 EEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAK 292


                  ....*.
gi 75216509   398 ALKKLR 403
Cdd:TIGR02997 293 ALRKLR 298
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 172-414 1.92e-60

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 200.78  E-value: 1.92e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  172 ILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKS 251
Cdd:PRK07406 130 RLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQS 209

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  252 RLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPD 331
Cdd:PRK07406 210 RTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG 289

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  332 ETrPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVNDL 411
Cdd:PRK07406 290 ET-PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVL 368


                 ...
gi 75216509  412 KIY 414
Cdd:PRK07406 369 KEY 371
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 170-403 1.57e-59

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 196.99  E-value: 1.57e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  170 NEILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAH 249
Cdd:PRK05949  83 KQTLKQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQ 162

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  250 KSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRG 329
Cdd:PRK05949 163 QARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLED 242

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 75216509  330 pDETRPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK05949 243 -EGPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 177-417 6.19e-59

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 197.78  E-value: 6.19e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKL 256
Cdd:PRK07598 174 LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRL 253

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  257 PGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRgPDETRPE 336
Cdd:PRK07598 254 PVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPE 332

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  337 EMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVNDLKIYYS 416
Cdd:PRK07598 333 EMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412


                 .
gi 75216509  417 S 417
Cdd:PRK07598 413 L 413
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 166-403 7.86e-58

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 191.90  E-value: 7.86e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  166 KRSANEILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILR 245
Cdd:PRK07405  69 EEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITR 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  246 AIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQE 325
Cdd:PRK07405 149 AIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGE 228

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 75216509  326 IVRGPDETrPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK07405 229 LLEDTGAS-PEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 177-405 1.13e-57

RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 131447 [Multi-domain]  Cd Length: 285  Bit Score: 190.71  E-value: 1.13e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKL 256
Cdd:TIGR02394  45 FEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRL 124

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   257 PGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPE 336
Cdd:TIGR02394 125 PVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPE 204

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 75216509   337 EMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNV 405
Cdd:TIGR02394 205 SLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI 273
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 107-416 6.13e-56

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 187.25  E-value: 6.13e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  107 AETISVPVVGASRSGFLSRLEEVQLCLYLKEGAKLENLgtsVEENEMVSVllasgrgKKKRSANEILCRRKEAREKITRC 186
Cdd:PRK07921  25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL---LETRKRLSE-------ARKRDLAAVVRDGEAARRHLLEA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  187 YRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAK 266
Cdd:PRK07921  95 NLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNK 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  267 VAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPEEMVKREHMKH 346
Cdd:PRK07921 175 LARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHT 254

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  347 EIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVNDLKIYYS 416
Cdd:PRK07921 255 DIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYAS 324
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 133-414 8.79e-55

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 185.57  E-value: 8.79e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  133 LYLKEGAKLeNLGTSVEENEmvsvlLAsgrgKKKRSANEilcrrkEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEG 212
Cdd:PRK09210 100 MYLKEIGRV-PLLTAEEEIE-----LA----KRIEEGDE------EAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEG 163

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  213 SIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLN 292
Cdd:PRK09210 164 NMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMD 243

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  293 LNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGE 372
Cdd:PRK09210 244 MPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDG 323

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 75216509  373 TPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVNDLKIY 414
Cdd:PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 178-403 1.05e-47

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 165.90  E-value: 1.05e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  178 EAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLP 257
Cdd:PRK05657  86 AARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLP 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  258 GSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVR--LAV-ERSRS---PVSLDRVASqngrmtLQEIVRGPD 331
Cdd:PRK05657 166 VHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSrmLALnERITSldtPLGGDPEKS------LLDILADEQ 239

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 75216509  332 ETRPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK05657 240 ENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 189-403 1.67e-46

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 167.09  E-value: 1.67e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  189 RLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVA 268
Cdd:PRK05901 282 RLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLG 361

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  269 EASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDrvasqngrmtlQEIvrGPDE-------------TRP 335
Cdd:PRK05901 362 RIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLD-----------KTI--GKEGdsqfgdfiedseaVSP 428

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 75216509  336 EEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK05901 429 VDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 176-403 3.20e-41

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: 145.74  E-value: 3.20e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 176 RKEAREKITRCYRRLVVSIATGYQGKGL-NLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIahkSRLV 254
Cdd:COG1191  13 DEEAREELIEEYLPLVKKIASRLAGRLPaELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYL---RDED 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 255 KLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVR--LAVERSRSPVSLDRVASQNGrmTLQEIVRGPDe 332
Cdd:COG1191  90 WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQeaLEAANAYQLLSLDEPLEDGD--DLLDLLESGD- 166

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 75216509 333 trPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNgetpMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:COG1191 167 --PEEELEHEELREALAEAIEQLPERERLVLSLYYFEE----LTLKEIAEVLGVSESRVSRLHKKALARLR 231
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 189-404 3.25e-37

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 143.01  E-value: 3.25e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  189 RLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVA 268
Cdd:PRK05658 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 470

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  269 EASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLdrvasqngrmtlqEIVRGPDE-------------TRP 335
Cdd:PRK05658 471 RISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISL-------------ETPIGDDEdshlgdfiedknaELP 537

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 75216509  336 EEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRN 404
Cdd:PRK05658 538 IDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 606
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 175-403 7.91e-31

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 119.76  E-value: 7.91e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  175 RRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLV 254
Cdd:PRK07500  37 RDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIV 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  255 K---------LPGSMWELTAKVAEASNVLTRKLRRQpsceEIAEHLNLNVSAVRLAVER-SRSPVSLDRVASQNG----- 319
Cdd:PRK07500 117 RggtssaqkaLFFNLRRLRARLAQADEELTKQEIHR----EIATALGVSLSDVEMMDARlSGPDASLNAPQSEEDegrse 192

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  320 RM-TLQEIVRGPDETrPEEMVKREHMKHEIEQLLGSLTARESRVlgLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIA 398
Cdd:PRK07500 193 RMdFLVDDSPLPDEQ-VESSIDGERRRRWLTQALQTLNERELRI--IRERRLREDGATLEALGEELGISKERVRQIEARA 269


                 ....*
gi 75216509  399 LKKLR 403
Cdd:PRK07500 270 LEKLR 274
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 189-404 1.64e-29

alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 115.46  E-value: 1.64e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   189 RLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLPgsmwelTAKva 268
Cdd:TIGR02392  46 RFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVA------TTK-- 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   269 eASNVLTRKLRR----------QPSCEEIAEHLNLNVSAVRLAVERSRSP-VSLDRVASQNGRMTLQEIVRGPDETR-PE 336
Cdd:TIGR02392 118 -AQRKLFFNLRKmkkrlqgwlnPEEVEAIAEELGVSEREVREMESRLSGQdMSLNASIDDDEDDGGAPIAYLVDKRSdPE 196

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 75216509   337 EMVKR----EHMKHEIEQLLGSLTAR-----ESRVLglyfglnGETPMSFEEIGKSLKLSRERVRQINGIALKKLRN 404
Cdd:TIGR02392 197 DTLEEeqweELQRQALANALGSLDARsrriiEARWL-------DDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 189-403 1.53e-26

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 107.57  E-value: 1.53e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  189 RLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKlpgsmweltakVA 268
Cdd:PRK06596  59 RFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVK-----------VA 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  269 EASNvlTRKL----RRQPS---------CEEIAEHLNlnvsavrlaversrspVSLDRVASQNGRMTLQEI-----VRGP 330
Cdd:PRK06596 128 TTKA--QRKLffnlRKAKKrlgwlnpeeVEMVAEELG----------------VSEEEVREMESRLSGQDAsldapIDDD 189

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  331 DETR-------------PEEMV-KREHMKHEIEQL---LGSLTARESRVLGLYFgLNgETPMSFEEIGKSLKLSRERVRQ 393
Cdd:PRK06596 190 DEESgapqdyledkssdPADVLeEDNWEDQRRALLadaLEGLDERSRDIIEARW-LD-DDKSTLQELAAEYGVSAERVRQ 267

                        250
                 ....*....|
gi 75216509  394 INGIALKKLR 403
Cdd:PRK06596 268 IEKNAMKKLK 277
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 178-403 1.76e-22

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 95.91  E-value: 1.76e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  178 EAREKITRCYRRLVVSIAtGYQGKGL----NLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAI---LRAIAhk 250
Cdd:PRK06288  31 KIREYLILKYSPLVKYVA-GRIAVGMpqnvEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdeLRSID-- 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  251 srlvKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSR--SPVSLDRV---ASQNGRMTLQE 325
Cdd:PRK06288 108 ----WIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSgtSVVSLNDLwfgGDEGDEVSLMD 183

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 75216509  326 IVRGPDETRPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFglngETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK06288 184 TLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 177-403 2.00e-21

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 92.84  E-value: 2.00e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKL 256
Cdd:PRK08583  28 EEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHV 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  257 PGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRS--PVSLDRV---ASQNGRMTLQEIVRGPD 331
Cdd:PRK08583 108 PRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSyqALSVDHSieaDSDGSTVTLLDIVGQQE 187

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 75216509  332 ETRpeEMVKREHMkheIEQLLGSLTARESRVLGLYFGLNgetpMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK08583 188 DGY--ELTEQRMI---LEKILPVLSDREKSIIQCTFIEN----LSQKETGERLGISQMHVSRLQRQAIKKLR 250
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
206-403 2.22e-21

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 92.42  E-value: 2.22e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  206 QDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRlvkLPGSMWELTAKVAEASNVLTRKLRRQPSCE 285
Cdd:PRK07670  53 DDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW---LPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  286 EIAEHLNLNVSAVRLAVERS--RSPVSLDRVASQNGR-MTLQEIVRGPDETRPEEMVKREHMKHEIEQLLGSLTARESRV 362
Cdd:PRK07670 130 EVAAELGMTEEEVEATMNEGffANLLSIDEKTHDQDDgENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 75216509  363 LGLYFglNGEtpMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK07670 210 ISLFY--KEE--LTLTEIGQVLNLSTSRISQIHSKALFKLK 246
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 185-252 2.00e-20

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: 84.56  E-value: 2.00e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 75216509   185 RCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSR 252
Cdd:pfam04542   3 ERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 204-367 7.65e-20

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 88.44  E-value: 7.65e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  204 NLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPS 283
Cdd:PRK07408  52 PYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPT 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  284 CEEIAEHLNLNVS---AVRLAVeRSRSPVSLDRVASQN--GRMTLQEIVrgPDeTRPEEMVKREHMKHEIEQLLGSLTAR 358
Cdd:PRK07408 132 DQEIAQALDISLEewqEIKLAL-QNRTPLSLDAPVNQDedGSTSLGDLL--PD-PRYRSFQLAQEDRIRLQQALAQLEER 207


                 ....*....
gi 75216509  359 ESRVLGLYF 367
Cdd:PRK07408 208 TREVLEFVF 216
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 262-339 7.23e-19

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 80.34  E-value: 7.23e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 75216509   262 ELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPEEMV 339
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 205-403 2.61e-18

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 83.36  E-value: 2.61e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  205 LQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIahkSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSC 284
Cdd:PRK06986  38 LDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDEL---RSLDWVPRSVRRNAREVAQAIRQLEQELGREPTD 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  285 EEIAEHLNLNVSAVR--LAVERSRSPVSLDRVASQNGRMTlqEIVRGPDETRPEEMVKREHMKHEIEQLLGSLTARESRV 362
Cdd:PRK06986 115 TEVAEKLGLSLEEYRemLLDTNISQLFSIDELRGEHGDSI--LVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQLV 192

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 75216509  363 LGLYFglngETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK06986 193 LSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
177-318 1.31e-17

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 81.94  E-value: 1.31e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSrLVKL 256
Cdd:PRK05572  31 QEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKV 109

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 75216509  257 PGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVASQN 318
Cdd:PRK05572 110 SRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHEN 171
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
177-404 9.55e-17

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 79.61  E-value: 9.55e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRlVKL 256
Cdd:PRK08215  36 KEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNP-IRV 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  257 PGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSL-DRVASQNGR----MTLQEIVRGPD 331
Cdd:PRK08215 115 SRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLfEPIYHDGGDpiyvMDQISDEKNKD 194

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 75216509  332 ETRPEEMVKREHMKheieqllgSLTARESRVLGLYFgLNGETPMSF-EEIGkslkLSRERVRQINGIALKKLRN 404
Cdd:PRK08215 195 ENWLEEIALKEAMK--------KLNDREKLILNLRF-FQGKTQMEVaEEIG----ISQAQVSRLEKAALKHMRK 255
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 178-403 1.14e-16

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 79.28  E-value: 1.14e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  178 EAREKITRCYRRLVVSIA----TGYQGKgLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRl 253
Cdd:PRK05911  23 EYRDVLIEFYLPLVKNVAhrliSGMPSH-VKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW- 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  254 vkLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVR--LAVERSRSPVSL--DRVASQNGR--MTLQEiv 327
Cdd:PRK05911 101 --VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSgwFSSARPALILSLneEFPCQSDDEagLALEE-- 176

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 75216509  328 RGPDEtRPE---EMVKREHMKHEIEQLLGSLTARESRVLGLYFglngETPMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:PRK05911 177 RIADE-RAEtgyDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 178-404 9.61e-15

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: 71.22  E-value: 9.61e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   178 EAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDrgYKLSTYVYWWIKQAILRAIahksrlvklp 257
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYL---------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509   258 gsmweltakvaeasnvltRKLRRQPSCEEIAEHLNlnvsavrlaversrspvsldrvasqngrmtlqeivrgPDETRPEE 337
Cdd:TIGR02937  69 ------------------RRKRRLRRELDLLEELL-------------------------------------DSDPSPEE 93

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 75216509   338 MVKREHMKHEIEQLLGSLTARESRVLGLYFGLNgetpMSFEEIGKSLKLSRERVRQINGIALKKLRN 404
Cdd:TIGR02937  94 ELEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLRE 156
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
177-402 6.72e-14

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 70.74  E-value: 6.72e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILraiahksrlvkl 256
Cdd:PRK05803  48 EEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEIL------------ 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  257 pgsMWELTAKvaeasnvltrKLRRQPSCEEiaehlnlnvsavrlaversrsPVSLDRVASQngrMTLQEIVrGPDETRPE 336
Cdd:PRK05803 116 ---MHLRNLK----------KTKKEVSLQD---------------------PIGVDKEGNE---ISLIDIL-GSEEDDVI 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 75216509  337 EMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKL 402
Cdd:PRK05803 158 EQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKL 223
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 180-404 2.56e-13

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 69.42  E-value: 2.56e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  180 REKI-TRCYRrLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLPG 258
Cdd:PRK07122  42 RDRIvTRCLP-LADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPR 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  259 SMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAV--RLAVERSRSPVSLDRVASqNGRMTLQEIVR--GPDETR 334
Cdd:PRK07122 121 RLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVveGLVAGSAYNTLSIDSGGG-SGDDDARAIADtlGDVDAG 199

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  335 PEEMVKREHMKheieQLLGSLTARESRVLGLYFGLNgetpMSFEEIGKSLKLSRERVRQINGIALKKLRN 404
Cdd:PRK07122 200 LDQIENREALR----PLLAALPERERTVLVLRFFES----MTQTQIAERVGISQMHVSRLLAKTLARLRD 261
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
177-385 1.31e-10

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 60.69  E-value: 1.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIahksrlvkl 256
Cdd:PRK08295  23 KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAI--------- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  257 pgsmweltakvaeasnvltRKLRRQpsceeiaEHLNLNvsavrlaversrSPVSLDRVA--SQNGRmTLQEIVRGPDETR 334
Cdd:PRK08295  94 -------------------KTANRQ-------KHIPLN------------SYVSLDKPIydEESDR-TLLDVISEAKVTD 134

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 75216509  335 PEEMV-KREHMKHEIEQLLGSLTARESRVLGLYfgLNGetpMSFEEIGKSLK 385
Cdd:PRK08295 135 PEELIiSKEELEDIEEKIEELLSELEKEVLELY--LDG---KSYQEIAEELN 181
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 351-404 1.26e-09

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: 53.59  E-value: 1.26e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 75216509   351 LLGSLTARESRVLGLYFGlngeTPMSFEEIGKSLKLSRERVRQINGIALKKLRN 404
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
206-404 2.22e-09

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 57.56  E-value: 2.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  206 QDLIQEGSIGLLRGAERFD-PDRGYklSTYVYWWIKQAIL---RAIAHKSRLVKlpgsmwELTAKVAEASNVLTRKLRRQ 281
Cdd:PRK12427  46 EDMEQIALMGLLEALRRYGhPDEQF--AAYAVHRIRGAILdelRELDWRPRRLR------QKTHKTNDAIREIAKRLGHE 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509  282 PSCEEIAEHLNLNVSAVR--LAVERSRSPVSLDRVASQNGRmtlqeivRGPDETRP--EEMVKREHMKHEieqlLGSLTA 357
Cdd:PRK12427 118 PNFEEISAELNLTAEEYQeyLLLENAGTLESLDELLALEAH-------NDILQSRDleENIIIEDNLKQA----LSQLDE 186

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 75216509  358 RESRVLGLYFglngETPMSFEEIGKSLKLSRERVRQINGIALKKLRN 404
Cdd:PRK12427 187 REQLILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIKS 229
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 347-403 2.79e-06

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 44.02  E-value: 2.79e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 75216509 347 EIEQLLGSLTARESRVLGLYFGLNgetpMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:cd06171   3 RLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
189-244 2.85e-06

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 48.31  E-value: 2.85e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 75216509  189 RLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAIL 244
Cdd:PRK08301  63 RLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEIL 118
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 177-403 4.24e-04

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: 41.13  E-value: 4.24e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 177 KEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRgyKLSTYvywwikqaiLRAIAHksrlvkl 256
Cdd:COG1595  16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRG--SFRAW---------LYRIAR------- 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75216509 257 pgsmweltakvaeasNVLTRKLRRqpsceeiaehlnlnvsavrlaveRSRSPVSLDRVASQNGrmtlqeivrgPDETRPE 336
Cdd:COG1595  78 ---------------NLAIDHLRK-----------------------RRRRRELLDELAEELP----------DEAADPE 109

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 75216509 337 EMVKREHMKHEIEQLLGSLTARESRVLGLYFgLNGetpMSFEEIGKSLKLSRERVRQINGIALKKLR 403
Cdd:COG1595 110 EALEAEELLEALLAALERLPPRQREVLVLRY-LEG---LSYAEIAEILGISEGTVKSRLSRARKKLR 172
 
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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