3IYD


Conserved Protein Domain Family
RpoD_Cterm

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TIGR02393: RpoD_Cterm (this model, PSSM-Id:162836 is obsolete and has been replaced by 274108)
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RNA polymerase sigma factor RpoD, C-terminal domain
This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Statistics
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PSSM-Id: 162836
View PSSM: TIGR02393
Aligned: 18 rows
Threshold Bit Score: -1
Threshold Setting Gi: 0
Created: 2-Mar-2011
Updated: 7-Mar-2011
Structure
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Program:
Drawing:
Aligned Rows:
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3IYD_F       375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 454
gi 26399555  347 AKKELVKANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATWWIRQAITRAISDQARTIRVPV 426
gi 39722223  217 AKDILVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPV 296
gi 32262093  384 AKAKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGFKFSTYATWWIRQAISRAIADQARTIRIPI 463
gi 1350862   246 AINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWWIKQAITRAIADQARTVRIPV 325
gi 284812078 394 AINQLVTSNLRLVTSIAKKYLNRGLDFVDLIQEGSIGLMKAISKFNYKLGNKFSTYATWWIRQAITRAIADQARTVRIPV 473
gi 3915854   391 AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPV 470
gi 15606649  338 AKQVMIQSNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 417
gi 22298160  182 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 261
gi 163849112 159 ARQQMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATWWIKQALSRALADQSRLVRLPV 238
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3IYD_F       455 HMIETINKLNRISRQMLQEMGREPTPEELAERML-----MPEDKIRKVLKIAKEPISMETPIGD--DEDSHLGDFIEDTT 527
gi 26399555  427 HMIEQVNKVIRETRLFIQEFGRDPNNEEIAERLG-----WPVQKVKMVKNVAREPISLEIPVGS--EEDSELGDFIPDTE 499
gi 39722223  297 HIVETINKMALCTRKLTQKLKKKPTVEELADKMN-----ISAEKIRSIQYIEKKPISLEAPAREneEDETSLGDFISDPN 371
gi 32262093  464 HMIETINRIHKIMRKHVQETGKEPDIDFIAKEVG-----LPIDKVKNVIKITKEPVSLDAPIGS--DDDGKFGDFVEDKS 536
gi 1350862   326 HMVETINRLAKAERALYQELGREPTDEELAEKMGgqaegFNVKKIAEIKRLSLDPVSLDKTVGH--DEESQFGDFVKDTD 403
gi 284812078 474 HMVETINKLIKTERMLTQQLGRDPTLEELTEAMGgqvngFTPKKVADIKKLNQEPVSLDKPIGH--DEESQFVDFVKDRD 551
gi 3915854   471 HMIEQINRLNRETRYLIQVLGKDPTDEELSDRLG-----WELKKVKTVKSVSREPVSLETPIGE--EEDSVLSDFIEDKA 543
gi 15606649  418 HMIETINKIIKASKKLFQENGREPTPEEIAEYLD-----IPVEKVKKVMKFSQEPISLETPIGD--DDDTFLKDFIEDKS 490
gi 22298160  262 HLYETISRIKKTTKLLSQEMGRKPTEEEIADRME-----MTIEKLRFIAKSAQLPISLETPIGK--EEDSRLGDFIE-SD 333
gi 163849112 239 HLGETLNRIQSARRQLTQSLGREPTDTELANHLG-----MSEEKLRELRRTAQDPVSLATPVGE--EADSTLADFIPDPH 311
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3IYD_F       528 LELPLDSATTESLRAATHDVLA-GLTAREAKVLRMRFGIDMN-TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 605
gi 26399555  500 VETPVNAAASSILAEQIRQVLH-TLPAREQKVIRMRFGLDDG-YPQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSRSK 577
gi 39722223  372 ILSPHEYMMKEVTQKLLDEVLEnTLTDREEKVLKMRYGLLDG-KTHTLEEVGTLFGVTRERIRQIESKALRRLRTPAKQS 450
gi 32262093  537 SVGPMDYILKEDLKVQIDEVLE-QLNDREKAVIRMRFGLLDDeSDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGR 615
gi 1350862   404 AQTPDEFTESRSNSEKIDELLNnNLSEQEELIVRMRIGMPPYnEPKTLDEVGQKILIPREKIRQIENKAIRKLRHAVRNN 483
gi 284812078 552 ILKPDEYTEKLIVTEHINELFInTLTKKEEQIIRMRYGLHPWhQQMTLEEVGQKFNVTRERIRQIESKALRKLKHPSKNA 631
gi 3915854   544 IKNPANHTSFVVLQDQIRAILG-TLPEREQEVVKMRFGLEDG-YSLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQ 621
gi 15606649  491 IPNPEEQVTRKLLREQLQKVLS-TLSEKEREILMYRYGLVDG-TEYTLEQVGKMFNVTRERIRQIENKALRKLRHPARAK 568
gi 22298160  334 GETPEDQVSKHLLREDLETVLC-TLSPRERDVLKLRYGLDDG-RMKTLEEIGQLFNVTRERIRQIEAKALRKLRHPNRNS 411
gi 163849112 312 ALDADDAAASGMLRQQITAALD-QLSERERRVLELRYGLVDG-QPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPRLGK 389

                 ....*...
3IYD_F       606 VLR-SFLD 612
gi 26399555  578 KLK-DYID 584
gi 39722223  451 KLK-SLYH 457
gi 32262093  616 KLK-NYIE 622
gi 1350862   484 PISmSFLR 491
gi 284812078 632 RLR-SFLK 638
gi 3915854   622 KLK-DYLE 628
gi 15606649  569 YLK-DFef 575
gi 22298160  412 VLK-EYIR 418
gi 163849112 390 LLK-DYLD 396
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