Citrus Sinensis ID: 014241

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------43
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFSSLNA
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccHHHHHHHcccHHHHHHHcccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHccccHHHHHHHHHHHcccccccccccccccHHHHHHHHcccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHcccccccHHHHHHcccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHcc
ccccHHccccccccccccccccccccccccccccccccccccccccEcccccccHHccccccEEcccccccccccHcccccccHHHHHHHccccccEEEcccccccccHHHHHHHHHHHHHccccHHHccccccccccccccccccccccccccccccccccHHHHHHHHHcHcHHHHHHHHHHcccccccccccccccccccHHHccEEccccHHHHHHHHcccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHcHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccEEEccHHHHHHHHHHHHHHHHHHHccc
meagrnllssppsfpsrtrvkhslsssasssssssVLMHneqsapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQyqgrgislHDLLQGSMGLMKSVEkfkpqagcrfasYAYWWVRQTIRKAIFQHSrtirlpvmtfnlspiyiFKFYVFSSLNA
meagrnllssppsfpsrtrVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFSSLNA
MEAGRNLLSSPPSFPSRTRVKHslsssasssssssVLMHNEQsapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFSSLNA
**************************************************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDL************KLINANLRLVVHVAKQYQGRGISLHDLLQGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFS****
***********PS****************************Q************VARHFPTSVLLQEQ********************************************VQDLEHQFLH***************************************************************************************************************************************RLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS*********PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFSS***
******************************************************VARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFSSLNA
***************************************************TSS**RHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPP**************************EPFDAVALARKALSASKEAASLAENPKLN****************************************************************DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFSSL**
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFSSLNA
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query428 2.2.26 [Sep-21-2011]
Q9LD95 547 RNA polymerase sigma fact yes no 0.892 0.698 0.505 2e-98
O22056 572 RNA polymerase sigma fact no no 0.450 0.337 0.394 7e-38
P26683 390 RNA polymerase sigma fact yes no 0.448 0.492 0.393 8e-35
Q31ME3 320 RNA polymerase sigma fact yes no 0.357 0.478 0.454 8e-34
Q31QG5 320 RNA polymerase sigma fact no no 0.378 0.506 0.448 1e-32
P38023 399 RNA polymerase sigma fact no no 0.364 0.390 0.445 7e-32
Q03065 332 RNA polymerase sigma-B fa no no 0.357 0.460 0.428 1e-29
Q03066 416 RNA polymerase sigma-C fa no no 0.378 0.389 0.371 7e-27
Q59996 404 Probable RNA polymerase s N/A no 0.378 0.400 0.364 2e-26
P74565 425 RNA polymerase sigma fact N/A no 0.390 0.392 0.344 6e-26
>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis thaliana GN=SIGF PE=1 SV=1 Back     alignment and function desciption
 Score =  360 bits (923), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 213/421 (50%), Positives = 274/421 (65%), Gaps = 39/421 (9%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K     S+ SS SS V++H++ + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK-----SSYSSPSSVVMLHDQTTTPVVNSRHLNSLSRHFP 55

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E RPL H  ++D+TSQ T + R                 D+LV     + 
Sbjct: 56  ASVLSQEPREESRPLSHALRDDRTSQLTLERRQ---------------FDELVSSREDEK 100

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P+V   +           DAE  D VALA+KALSA
Sbjct: 101 FEQQLLHSTGLWNLLISPLTSETKLPAVVSPL----------ADAELCDVVALAQKALSA 150

Query: 174 SKEAASLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
           SK+AA L ++ + N ++   D   TSS     E+       R LERR+K R+  K    +
Sbjct: 151 SKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKRQLERRAKNRRAPKSNDVD 210

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
            E Y  +K S KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K
Sbjct: 211 DEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVK 270

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+G+S   LKS++H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 271 TKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRG 330

Query: 353 ISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFN 411
           ++  DLLQ GSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLP   + 
Sbjct: 331 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYM 390

Query: 412 L 412
           L
Sbjct: 391 L 391
Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Regulates transcription in chloroplast in a DG1-dependent manner. Involved in light-dependent chloroplast development. Required during early plant development and primary leaf formation.
Arabidopsis thaliana (taxid: 3702)
>sp|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB PE=2 SV=2 Back     alignment and function description
>sp|P26683|RPOD_NOSS1 RNA polymerase sigma factor RpoD OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rpoD PE=3 SV=1 Back     alignment and function description
>sp|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD2 PE=1 SV=1 Back     alignment and function description
>sp|Q31QG5|RPOD3_SYNE7 RNA polymerase sigma factor rpoD3 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD3 PE=3 SV=1 Back     alignment and function description
>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD1 PE=3 SV=2 Back     alignment and function description
>sp|Q03065|RPSB_NOSS1 RNA polymerase sigma-B factor OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=sigB PE=3 SV=1 Back     alignment and function description
>sp|Q03066|RPSC_NOSS1 RNA polymerase sigma-C factor OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=sigC PE=3 SV=2 Back     alignment and function description
>sp|Q59996|RPSC_SYNY3 Probable RNA polymerase sigma-C factor OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=sigC PE=3 SV=1 Back     alignment and function description
>sp|P74565|RPOD_SYNY3 RNA polymerase sigma factor RpoD OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rpoD PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query428
224068757 535 predicted protein [Populus trichocarpa] 0.883 0.706 0.583 1e-130
297741628 561 unnamed protein product [Vitis vinifera] 0.929 0.709 0.589 1e-129
359481391 572 PREDICTED: RNA polymerase sigma factor r 0.950 0.711 0.584 1e-127
255556952 548 RNA polymerase sigma factor rpoD, putati 0.897 0.700 0.588 1e-127
356536959 571 PREDICTED: RNA polymerase sigma factor r 0.948 0.711 0.551 1e-110
356548319 574 PREDICTED: RNA polymerase sigma factor r 0.950 0.709 0.527 1e-109
449451030 562 PREDICTED: RNA polymerase sigma factor s 0.929 0.708 0.526 1e-103
312282671 547 unnamed protein product [Thellungiella h 0.892 0.698 0.517 1e-100
297827203 546 RNA polymerase sigma-70 factor [Arabidop 0.890 0.697 0.513 3e-99
18404292 547 RNApolymerase sigma-subunit F [Arabidops 0.892 0.698 0.505 1e-96
>gi|224068757|ref|XP_002326192.1| predicted protein [Populus trichocarpa] gi|222833385|gb|EEE71862.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  469 bits (1208), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 241/413 (58%), Positives = 302/413 (73%), Gaps = 35/413 (8%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEAGR LLSS PSFP+RT +K+SL+SS        VL+  EQ+ PAV+S+PT+S A+HFP
Sbjct: 1   MEAGRTLLSSSPSFPTRTHLKNSLTSS--------VLILREQATPAVSSIPTTSTAQHFP 52

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
           TSVLLQEQRDE+RPL ++FKED+ SQAT D R  E      E K+S +LDQLV++ E+Q 
Sbjct: 53  TSVLLQEQRDEFRPLQNIFKEDRASQATLDRRKTEIGTSGHEGKDSDELDQLVENFEYQL 112

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
            HWP  WNL                      T++ +D EP + + LA++ALSASK AA L
Sbjct: 113 HHWPAYWNL----------------------TDKLIDVEPTNVINLAKRALSASKHAAFL 150

Query: 181 AENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRK 240
           A+N      +  +++ TSS  + LEEVK     R L R+S  R+  K +    ETY+S+ 
Sbjct: 151 ADN----NTDLDNLASTSSSSFSLEEVKIVRSRRHLARQSLNRRAPKTKDLIFETYDSKS 206

Query: 241 ASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300
           A ++K+LS+GFD NDPLRLFLWGPET++LLTA EEFELIAQIQDL+ LE  K++L+SQFG
Sbjct: 207 ADIQKRLSQGFDPNDPLRLFLWGPETKQLLTAKEEFELIAQIQDLMNLEGVKNRLESQFG 266

Query: 301 REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           REPTL+EWA+A+GLSC  LK +LHSGN SREKLINANLR+VVH+AK+YQ RG+ L DLLQ
Sbjct: 267 REPTLVEWAQAVGLSCHVLKLQLHSGNRSREKLINANLRMVVHIAKRYQNRGLGLQDLLQ 326

Query: 361 -GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNL 412
            G++GLMKS+EKFKPQAGCRFA+YAYWW+RQTI KAIFQHSRTIRLP   + L
Sbjct: 327 EGTVGLMKSIEKFKPQAGCRFATYAYWWIRQTITKAIFQHSRTIRLPENVYGL 379

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297741628|emb|CBI32760.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|359481391|ref|XP_002276710.2| PREDICTED: RNA polymerase sigma factor rpoD [Vitis vinifera] Back     alignment and taxonomy information
>gi|255556952|ref|XP_002519509.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223541372|gb|EEF42923.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356536959|ref|XP_003536999.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max] Back     alignment and taxonomy information
>gi|356548319|ref|XP_003542550.1| PREDICTED: RNA polymerase sigma factor rpoD [Glycine max] Back     alignment and taxonomy information
>gi|449451030|ref|XP_004143265.1| PREDICTED: RNA polymerase sigma factor sigF, chloroplastic-like [Cucumis sativus] gi|449482444|ref|XP_004156283.1| PREDICTED: RNA polymerase sigma factor sigF, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|312282671|dbj|BAJ34201.1| unnamed protein product [Thellungiella halophila] Back     alignment and taxonomy information
>gi|297827203|ref|XP_002881484.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata] gi|297327323|gb|EFH57743.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|18404292|ref|NP_565856.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana] gi|75173811|sp|Q9LD95.1|SIGF_ARATH RecName: Full=RNA polymerase sigma factor sigF, chloroplastic; Short=Sigma factor F; Short=Sigma-F; AltName: Full=Protein SINGLET OXYGEN-LINKED DEATH ACTIVATOR 8; AltName: Full=RNA polymerase sigma factor sig6; Short=Atsig6; Short=Sigma factor 6; Flags: Precursor gi|7209640|dbj|BAA92288.1| SigF [Arabidopsis thaliana] gi|7688083|emb|CAB89775.1| sigma factor-like protein [Arabidopsis thaliana] gi|16604647|gb|AAL24116.1| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana] gi|20197948|gb|AAD31584.2| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana] gi|20259557|gb|AAM14121.1| putative RNA polymerase sigma-70 factor protein [Arabidopsis thaliana] gi|330254238|gb|AEC09332.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query428
TAIR|locus:2057996 547 SIGF "AT2G36990" [Arabidopsis 0.733 0.574 0.480 9.2e-68
UNIPROTKB|Q84LK8 572 SIG6 "Sig6" [Oryza sativa Japo 0.464 0.347 0.465 1.4e-46
TAIR|locus:2025650 572 SIG2 "AT1G08540" [Arabidopsis 0.450 0.337 0.394 3.9e-37
UNIPROTKB|O48655 519 rsigA "Plastid RNA polymerase 0.348 0.287 0.38 1.9e-26
TIGR_CMR|GSU_1525 328 GSU_1525 "RNA polymerase sigma 0.212 0.277 0.494 8.9e-26
TIGR_CMR|SO_3432 326 SO_3432 "RNA polymerase sigma 0.334 0.438 0.381 1.6e-22
TIGR_CMR|VC_0534 335 VC_0534 "RNA polymerase sigma 0.385 0.492 0.356 7.4e-22
TIGR_CMR|CPS_1079 296 CPS_1079 "RNA polymerase sigma 0.221 0.320 0.479 5.1e-21
TIGR_CMR|CBU_1669 352 CBU_1669 "RNA polymerase sigma 0.418 0.508 0.343 6.8e-21
UNIPROTKB|P13445 330 rpoS "RNA polymerase, sigma S 0.320 0.415 0.381 8.9e-21
TAIR|locus:2057996 SIGF "AT2G36990" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 688 (247.2 bits), Expect = 9.2e-68, P = 9.2e-68
 Identities = 161/335 (48%), Positives = 207/335 (61%)

Query:    85 SQATSDSRNIETEAFFVEEKNSGDLDQLVQD--LEHQFLHWPDLWNL--SPPMKRGEDPS 140
             S A  D R   T    +E +   +L    +D   E Q LH   LWNL  SP     + P+
Sbjct:    71 SHALRDDR---TSQLTLERRQFDELVSSREDEKFEQQLLHSTGLWNLLISPLTSETKLPA 127

Query:   141 VSLTMQSLSNDTEESVDAEPFDXXXXXXXXXXXXXXXXXXXXNPKLNGAE-FTD-ISLTS 198
             V   +  L+       DAE  D                    + + N ++   D +S +S
Sbjct:   128 V---VSPLA-------DAELCDVVALAQKALSASKQAALLVDDTEANPSDNIKDSLSTSS 177

Query:   199 SLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLR 258
             S+  P E+       R LERR+K R+  K    + E Y  +K S KKK  +G D +D L+
Sbjct:   178 SMSLP-EKGNIVRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYKQGADNDDALQ 236

Query:   259 LFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRD 318
             LFLWGPET++LLTA EE ELI+ IQ L++LEK K+KL+SQ G EPT+ EWA+A+G+S   
Sbjct:   237 LFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPV 296

Query:   319 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAG 377
             LKS++H G SSREKLI ANLRLVVH+AKQYQ RG++  DLLQ GSMGLMKSVEKFKPQ+G
Sbjct:   297 LKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSG 356

Query:   378 CRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNL 412
             CRFA+YAYWW+RQ+IRK+IFQ+SRTIRLP   + L
Sbjct:   357 CRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYML 391
GO:0003677 "DNA binding" evidence=ISS
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS
GO:0006352 "DNA-dependent transcription, initiation" evidence=TAS
GO:0009507 "chloroplast" evidence=IDA
GO:0009536 "plastid" evidence=IDA
GO:0016987 "sigma factor activity" evidence=ISS;IDA
GO:0071483 "cellular response to blue light" evidence=IEP
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IMP
GO:0071482 "cellular response to light stimulus" evidence=IMP
GO:0090351 "seedling development" evidence=IMP
GO:0001053 "plastid sigma factor activity" evidence=IMP
GO:0005515 "protein binding" evidence=IPI
GO:0009902 "chloroplast relocation" evidence=RCA
GO:0009965 "leaf morphogenesis" evidence=RCA
GO:0010027 "thylakoid membrane organization" evidence=RCA
GO:0016117 "carotenoid biosynthetic process" evidence=RCA
GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA
GO:0030154 "cell differentiation" evidence=RCA
GO:0034660 "ncRNA metabolic process" evidence=RCA
UNIPROTKB|Q84LK8 SIG6 "Sig6" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2025650 SIG2 "AT1G08540" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|O48655 rsigA "Plastid RNA polymerase sigma factor" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_1525 GSU_1525 "RNA polymerase sigma-70 factor family" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|SO_3432 SO_3432 "RNA polymerase sigma factor RpoS" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
TIGR_CMR|VC_0534 VC_0534 "RNA polymerase sigma factor RpoS" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_1079 CPS_1079 "RNA polymerase sigma factor RpoS" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_1669 CBU_1669 "RNA polymerase sigma factor RpoS" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
UNIPROTKB|P13445 rpoS "RNA polymerase, sigma S (sigma 38) factor" [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9LD95SIGF_ARATHNo assigned EC number0.50590.89250.6983yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
fgenesh4_pm.C_scaffold_28000088
hypothetical protein (535 aa)
(Populus trichocarpa)
Predicted Functional Partners:
eugene3.28720003
Predicted protein (152 aa)
  •   • 0.574
gw1.XIV.2894.1
hypothetical protein (684 aa)
  •     0.452
fgenesh4_pm.C_LG_X000986
hypothetical protein (932 aa)
      • 0.441
fgenesh4_pg.C_LG_XVII000398
hypothetical protein (677 aa)
  •     0.439
eugene3.17410001
annotation not avaliable (472 aa)
  •     0.439
gw1.321.23.1
annotation not avaliable (657 aa)
  •     0.438
estExt_fgenesh4_pg.C_3210002
hypothetical protein (472 aa)
  •     0.438
eugene3.00001972
hypothetical protein (485 aa)
  •     0.426
eugene3.29520003
annotation not avaliable (742 aa)
    • • 0.425
gw1.XIV.2088.1
hypothetical protein (955 aa)
  ••  • 0.420

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query428
TIGR02997 298 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f 9e-54
PRK07406 373 PRK07406, PRK07406, RNA polymerase sigma factor Rp 3e-45
PRK07405 317 PRK07405, PRK07405, RNA polymerase sigma factor Si 4e-45
PRK05949 327 PRK05949, PRK05949, RNA polymerase sigma factor; V 9e-42
PRK07598 415 PRK07598, PRK07598, RNA polymerase sigma factor Si 3e-36
COG0568 342 COG0568, RpoD, DNA-directed RNA polymerase, sigma 5e-34
TIGR02394 285 TIGR02394, rpoS_proteo, RNA polymerase sigma facto 1e-28
PRK05657 325 PRK05657, PRK05657, RNA polymerase sigma factor Rp 3e-28
TIGR02393 238 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor 3e-28
PRK07921 324 PRK07921, PRK07921, RNA polymerase sigma factor Si 1e-27
PRK09210 367 PRK09210, PRK09210, RNA polymerase sigma factor Rp 3e-27
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 2e-26
PRK05658 619 PRK05658, PRK05658, RNA polymerase sigma factor Rp 3e-20
pfam0454271 pfam04542, Sigma70_r2, Sigma-70 region 2 4e-17
TIGR02392 270 TIGR02392, rpoH_proteo, alternative sigma factor R 2e-16
PRK06596 284 PRK06596, PRK06596, RNA polymerase factor sigma-32 3e-15
TIGR02980 227 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, 3e-13
PRK08215 258 PRK08215, PRK08215, sporulation sigma factor SigG; 1e-11
PRK07500 289 PRK07500, rpoH2, RNA polymerase factor sigma-32; R 2e-11
COG1191 247 COG1191, FliA, DNA-directed RNA polymerase special 5e-11
TIGR02850 254 TIGR02850, spore_sigG, RNA polymerase sigma-G fact 3e-10
TIGR02846227 TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa 7e-10
PRK05803233 PRK05803, PRK05803, sporulation sigma factor SigK; 2e-09
PRK05572 252 PRK05572, PRK05572, sporulation sigma factor SigF; 9e-09
PRK08301234 PRK08301, PRK08301, sporulation sigma factor SigE; 9e-09
TIGR02885 231 TIGR02885, spore_sigF, RNA polymerase sigma-F fact 1e-08
TIGR02835234 TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa 2e-08
TIGR02937158 TIGR02937, sigma70-ECF, RNA polymerase sigma facto 2e-08
PRK07122 264 PRK07122, PRK07122, RNA polymerase sigma factor Si 2e-06
PRK07408 256 PRK07408, PRK07408, RNA polymerase sigma factor Si 1e-05
TIGR02479 224 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, 9e-04
>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information 
 Score =  180 bits (460), Expect = 9e-54
 Identities = 76/140 (54%), Positives = 102/140 (72%), Gaps = 1/140 (0%)

Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328
           LLT +EE EL  Q+Q ++ LE+ + +L+ Q GREP+  EWA A GLS  +L+  L  G  
Sbjct: 15  LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQR 74

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWW 387
           ++EK+I ANLRLVV VAK+YQ RG+ L DL+Q GS+GL ++VEKF P  G +F++YAYWW
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWW 134

Query: 388 VRQTIRKAIFQHSRTIRLPV 407
           +RQ I +AI   SRTIRLP+
Sbjct: 135 IRQGITRAIANQSRTIRLPI 154

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). Length = 298
>gnl|CDD|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated Back     alignment and domain information
>gnl|CDD|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated Back     alignment and domain information
>gnl|CDD|223642 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Back     alignment and domain information
>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS Back     alignment and domain information
>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated Back     alignment and domain information
>gnl|CDD|213709 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>gnl|CDD|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional Back     alignment and domain information
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|218138 pfam04542, Sigma70_r2, Sigma-70 region 2 Back     alignment and domain information
>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH Back     alignment and domain information
>gnl|CDD|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>gnl|CDD|234078 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G subfamily Back     alignment and domain information
>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed Back     alignment and domain information
>gnl|CDD|236033 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>gnl|CDD|224112 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>gnl|CDD|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor Back     alignment and domain information
>gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor Back     alignment and domain information
>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed Back     alignment and domain information
>gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated Back     alignment and domain information
>gnl|CDD|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor Back     alignment and domain information
>gnl|CDD|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor Back     alignment and domain information
>gnl|CDD|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>gnl|CDD|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>gnl|CDD|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>gnl|CDD|233885 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG family Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 428
PRK07598 415 RNA polymerase sigma factor SigC; Validated 100.0
TIGR02997 298 Sig70-cyanoRpoD RNA polymerase sigma factor, cyano 100.0
PRK07406 373 RNA polymerase sigma factor RpoD; Validated 100.0
PRK05949 327 RNA polymerase sigma factor; Validated 100.0
PRK07405 317 RNA polymerase sigma factor SigD; Validated 100.0
PRK05901 509 RNA polymerase sigma factor; Provisional 100.0
COG0568 342 RpoD DNA-directed RNA polymerase, sigma subunit (s 100.0
PRK07921 324 RNA polymerase sigma factor SigB; Reviewed 100.0
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 99.96
PRK09210 367 RNA polymerase sigma factor RpoD; Validated 99.96
PRK07122 264 RNA polymerase sigma factor SigF; Reviewed 99.94
TIGR02392 270 rpoH_proteo alternative sigma factor RpoH. A sigma 99.93
PRK06596 284 RNA polymerase factor sigma-32; Reviewed 99.93
PRK07500 289 rpoH2 RNA polymerase factor sigma-32; Reviewed 99.91
TIGR02393 238 RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter 99.9
PRK07408 256 RNA polymerase sigma factor SigF; Reviewed 99.89
PRK05657 325 RNA polymerase sigma factor RpoS; Validated 99.89
COG1191 247 FliA DNA-directed RNA polymerase specialized sigma 99.88
TIGR02394 285 rpoS_proteo RNA polymerase sigma factor RpoS. A si 99.85
PRK05911 257 RNA polymerase sigma factor sigma-28; Reviewed 99.83
TIGR02850 254 spore_sigG RNA polymerase sigma-G factor. Members 99.82
PRK08215 258 sporulation sigma factor SigG; Reviewed 99.81
TIGR02941 255 Sigma_B RNA polymerase sigma-B factor. This sigma 99.76
TIGR02980 227 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G 99.76
PRK06288 268 RNA polymerase sigma factor WhiG; Reviewed 99.75
PRK08583 257 RNA polymerase sigma factor SigB; Validated 99.73
TIGR02885 231 spore_sigF RNA polymerase sigma-F factor. Members 99.72
TIGR02895 218 spore_sigI RNA polymerase sigma-I factor. Members 99.69
PRK05572 252 sporulation sigma factor SigF; Validated 99.66
PRK12427 231 flagellar biosynthesis sigma factor; Provisional 99.66
PRK07670 251 RNA polymerase sigma factor SigD; Validated 99.62
TIGR02479 224 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f 99.59
PRK05803233 sporulation sigma factor SigK; Reviewed 99.52
PRK06986 236 fliA flagellar biosynthesis sigma factor; Validate 99.51
TIGR02846227 spore_sigmaK RNA polymerase sigma-K factor. The sp 99.15
PRK08301234 sporulation sigma factor SigE; Reviewed 99.11
PF0454271 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762 99.08
PRK08311 237 putative RNA polymerase sigma factor SigI; Reviewe 99.04
TIGR02835234 spore_sigmaE RNA polymerase sigma-E factor. Member 99.0
PRK08295208 RNA polymerase factor sigma-70; Validated 98.98
TIGR02859198 spore_sigH RNA polymerase sigma-H factor. Members 98.87
TIGR02937158 sigma70-ECF RNA polymerase sigma factor, sigma-70 98.83
PRK09652182 RNA polymerase sigma factor RpoE; Provisional 98.7
PRK05602186 RNA polymerase sigma factor; Reviewed 98.61
PRK12513194 RNA polymerase sigma factor; Provisional 98.53
PRK06759154 RNA polymerase factor sigma-70; Validated 98.52
PRK09641187 RNA polymerase sigma factor SigW; Provisional 98.51
PRK09640188 RNA polymerase sigma factor SigX; Reviewed 98.49
TIGR02948187 SigW_bacill RNA polymerase sigma-W factor. This si 98.49
PRK09648189 RNA polymerase sigma factor SigD; Reviewed 98.48
PRK11922 231 RNA polymerase sigma factor; Provisional 98.46
PRK06811189 RNA polymerase factor sigma-70; Validated 98.45
PRK09646194 RNA polymerase sigma factor SigK; Reviewed 98.4
PRK13919186 putative RNA polymerase sigma E protein; Provision 98.39
PRK09638176 RNA polymerase sigma factor SigY; Reviewed 98.34
TIGR02952170 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02 98.29
PRK12519194 RNA polymerase sigma factor; Provisional 98.29
PRK11924179 RNA polymerase sigma factor; Provisional 98.27
PRK11923193 algU RNA polymerase sigma factor AlgU; Provisional 98.21
TIGR02939190 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s 98.18
PRK12524196 RNA polymerase sigma factor; Provisional 98.17
PRK12514179 RNA polymerase sigma factor; Provisional 98.15
TIGR02954169 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02 98.15
PRK12526206 RNA polymerase sigma factor; Provisional 98.12
TIGR02984189 Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl 98.08
TIGR02985161 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba 98.06
TIGR02989159 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop 98.02
PRK12531194 RNA polymerase sigma factor; Provisional 98.02
PRK09643192 RNA polymerase sigma factor SigM; Reviewed 98.0
PRK12538233 RNA polymerase sigma factor; Provisional 97.97
PRK12536181 RNA polymerase sigma factor; Provisional 97.97
PF0014037 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr 97.95
PRK12515189 RNA polymerase sigma factor; Provisional 97.95
PRK12537182 RNA polymerase sigma factor; Provisional 97.93
PRK12534187 RNA polymerase sigma factor; Provisional 97.93
PRK12512184 RNA polymerase sigma factor; Provisional 97.89
PRK12522173 RNA polymerase sigma factor; Provisional 97.84
PRK12539184 RNA polymerase sigma factor; Provisional 97.79
PRK12543179 RNA polymerase sigma factor; Provisional 97.77
PRK12518175 RNA polymerase sigma factor; Provisional 97.67
PRK09415179 RNA polymerase factor sigma C; Reviewed 97.65
PRK12542185 RNA polymerase sigma factor; Provisional 97.62
TIGR02999183 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f 97.53
TIGR02983162 SigE-fam_strep RNA polymerase sigma-70 factor, sig 97.5
COG1595182 RpoE DNA-directed RNA polymerase specialized sigma 97.44
PRK09639166 RNA polymerase sigma factor SigX; Provisional 97.34
PRK09644165 RNA polymerase sigma factor SigM; Provisional 97.24
PRK08241 339 RNA polymerase factor sigma-70; Validated 97.2
PRK12541161 RNA polymerase sigma factor; Provisional 97.2
TIGR03001244 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco 97.18
PRK09647203 RNA polymerase sigma factor SigE; Reviewed 97.13
PRK12547164 RNA polymerase sigma factor; Provisional 97.09
PRK09649185 RNA polymerase sigma factor SigC; Reviewed 97.03
TIGR02947193 SigH_actino RNA polymerase sigma-70 factor, TIGR02 97.02
PRK09645173 RNA polymerase sigma factor SigL; Provisional 97.01
TIGR02943188 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02 96.97
TIGR02950154 SigM_subfam RNA polymerase sigma factor, SigM fami 96.96
PRK12528161 RNA polymerase sigma factor; Provisional 96.96
TIGR02959170 SigZ RNA polymerase sigma factor, SigZ family. Thi 96.93
PRK12520191 RNA polymerase sigma factor; Provisional 96.9
PRK09637181 RNA polymerase sigma factor SigZ; Provisional 96.88
PRK12532195 RNA polymerase sigma factor; Provisional 96.85
TIGR02960 324 SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa 96.84
PRK12535196 RNA polymerase sigma factor; Provisional 96.82
PRK12516187 RNA polymerase sigma factor; Provisional 96.76
PRK12533216 RNA polymerase sigma factor; Provisional 96.7
PRK12544206 RNA polymerase sigma factor; Provisional 96.67
PRK12546188 RNA polymerase sigma factor; Provisional 96.53
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 96.45
PRK09642160 RNA polymerase sigma factor SigW; Reviewed 96.41
PRK12529178 RNA polymerase sigma factor; Provisional 96.4
PRK12523172 RNA polymerase sigma factor; Reviewed 96.4
PRK12540182 RNA polymerase sigma factor; Provisional 96.27
PRK12517188 RNA polymerase sigma factor; Provisional 96.24
PRK12545201 RNA polymerase sigma factor; Provisional 96.11
PRK07037163 extracytoplasmic-function sigma-70 factor; Validat 96.04
PF0453978 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 95.85
PRK09651172 RNA polymerase sigma factor FecI; Provisional 95.6
PRK12530189 RNA polymerase sigma factor; Provisional 95.54
PRK12511182 RNA polymerase sigma factor; Provisional 95.33
PRK09636 293 RNA polymerase sigma factor SigJ; Provisional 94.38
PRK12525168 RNA polymerase sigma factor; Provisional 94.31
PRK12527159 RNA polymerase sigma factor; Reviewed 94.2
PF1264565 HTH_16: Helix-turn-helix domain; InterPro: IPR0247 94.1
PRK06704 228 RNA polymerase factor sigma-70; Validated 93.94
TIGR02957 281 SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa 93.43
PF07638185 Sigma70_ECF: ECF sigma factor 92.88
PRK09191 261 two-component response regulator; Provisional 92.58
TIGR03209142 P21_Cbot clostridium toxin-associated regulator Bo 90.87
PRK09635 290 sigI RNA polymerase sigma factor SigI; Provisional 89.99
PHA02547179 55 RNA polymerase sigma factor; Provisional 86.64
PRK09047161 RNA polymerase factor sigma-70; Validated 83.73
COG0568 342 RpoD DNA-directed RNA polymerase, sigma subunit (s 81.01
>PRK07598 RNA polymerase sigma factor SigC; Validated Back     alignment and domain information 
Probab=100.00  E-value=2.2e-40  Score=340.03  Aligned_cols=172  Identities=42%  Similarity=0.683  Sum_probs=162.1

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhhCCCCcHHHHHHHh
Q 014241          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI  312 (428)
Q Consensus       253 ~~d~l~~YL~ei~~~~LLT~EEE~eL~~~Iq~l~~--------------------Le~~~~~L~~~lGr~Pt~~ewA~a~  312 (428)
                      .+|+++.||++|++.||||++||++|+++||+++.                    |++++.+|++++|++||..|||.++
T Consensus        58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~  137 (415)
T PRK07598         58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA  137 (415)
T ss_pred             CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence            57999999999999999999999999999999999                    9999999999999999999999555


Q ss_pred             c----------------------CCHHHHHHHhhccHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHH-HHHHHHHHH
Q 014241          313 G----------------------LSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSV  369 (428)
Q Consensus       313 g----------------------~s~~eL~~~l~~G~~Are~LI~~nLrLV~sIAkrY~~rGld~eDLIQ-G~IGLikAV  369 (428)
                      |                      |++++|.+.++.|..|+++||.+|+++|+++|++|.++|++++|||| |++||++|+
T Consensus       138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav  217 (415)
T PRK07598        138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV  217 (415)
T ss_pred             CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence            5                      55666666678899999999999999999999999999999999999 999999999


Q ss_pred             HhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCCcccchhHHHhhHHHHHHHHHhh
Q 014241          370 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVFS  424 (428)
Q Consensus       370 ekFDpskG~rFSTYA~~wIR~aI~raIr~qsr~IRlP~~~~e~l~ri~r~~~~Ls  424 (428)
                      ++|||++|++|+|||+||||++|.+++++++++||+|.|+.+.+++++++...|.
T Consensus       218 ekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~  272 (415)
T PRK07598        218 EKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKIS  272 (415)
T ss_pred             HHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999887654

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information
>PRK07406 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK05949 RNA polymerase sigma factor; Validated Back     alignment and domain information
>PRK07405 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>PRK05901 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Back     alignment and domain information
>PRK07921 RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>PRK05658 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK09210 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK07122 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>TIGR02392 rpoH_proteo alternative sigma factor RpoH Back     alignment and domain information
>PRK06596 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PRK05657 RNA polymerase sigma factor RpoS; Validated Back     alignment and domain information
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS Back     alignment and domain information
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Back     alignment and domain information
>TIGR02850 spore_sigG RNA polymerase sigma-G factor Back     alignment and domain information
>PRK08215 sporulation sigma factor SigG; Reviewed Back     alignment and domain information
>TIGR02941 Sigma_B RNA polymerase sigma-B factor Back     alignment and domain information
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily Back     alignment and domain information
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed Back     alignment and domain information
>PRK08583 RNA polymerase sigma factor SigB; Validated Back     alignment and domain information
>TIGR02885 spore_sigF RNA polymerase sigma-F factor Back     alignment and domain information
>TIGR02895 spore_sigI RNA polymerase sigma-I factor Back     alignment and domain information
>PRK05572 sporulation sigma factor SigF; Validated Back     alignment and domain information
>PRK12427 flagellar biosynthesis sigma factor; Provisional Back     alignment and domain information
>PRK07670 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family Back     alignment and domain information
>PRK05803 sporulation sigma factor SigK; Reviewed Back     alignment and domain information
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated Back     alignment and domain information
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor Back     alignment and domain information
>PRK08301 sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed Back     alignment and domain information
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor Back     alignment and domain information
>PRK08295 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02859 spore_sigH RNA polymerase sigma-H factor Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>PRK05602 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK12513 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK09641 RNA polymerase sigma factor SigW; Provisional Back     alignment and domain information
>PRK09640 RNA polymerase sigma factor SigX; Reviewed Back     alignment and domain information
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor Back     alignment and domain information
>PRK09648 RNA polymerase sigma factor SigD; Reviewed Back     alignment and domain information
>PRK11922 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK06811 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>PRK13919 putative RNA polymerase sigma E protein; Provisional Back     alignment and domain information
>PRK09638 RNA polymerase sigma factor SigY; Reviewed Back     alignment and domain information
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family Back     alignment and domain information
>PRK12519 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK11924 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Back     alignment and domain information
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE Back     alignment and domain information
>PRK12524 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family Back     alignment and domain information
>PRK12526 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1 Back     alignment and domain information
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1 Back     alignment and domain information
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family Back     alignment and domain information
>PRK12531 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09643 RNA polymerase sigma factor SigM; Reviewed Back     alignment and domain information
>PRK12538 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12536 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1 Back     alignment and domain information
>PRK12515 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12534 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12512 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12522 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12539 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12543 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12518 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09415 RNA polymerase factor sigma C; Reviewed Back     alignment and domain information
>PRK12542 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family Back     alignment and domain information
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family Back     alignment and domain information
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription] Back     alignment and domain information
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>PRK09644 RNA polymerase sigma factor SigM; Provisional Back     alignment and domain information
>PRK08241 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK12541 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1 Back     alignment and domain information
>PRK09647 RNA polymerase sigma factor SigE; Reviewed Back     alignment and domain information
>PRK12547 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09649 RNA polymerase sigma factor SigC; Reviewed Back     alignment and domain information
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family Back     alignment and domain information
>PRK09645 RNA polymerase sigma factor SigL; Provisional Back     alignment and domain information
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family Back     alignment and domain information
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family Back     alignment and domain information
>PRK12528 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family Back     alignment and domain information
>PRK12520 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09637 RNA polymerase sigma factor SigZ; Provisional Back     alignment and domain information
>PRK12532 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family Back     alignment and domain information
>PRK12535 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12516 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12533 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12544 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12546 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK05658 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK09642 RNA polymerase sigma factor SigW; Reviewed Back     alignment and domain information
>PRK12529 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12523 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK12540 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12517 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12545 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated Back     alignment and domain information
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK09651 RNA polymerase sigma factor FecI; Provisional Back     alignment and domain information
>PRK12530 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12511 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09636 RNA polymerase sigma factor SigJ; Provisional Back     alignment and domain information
>PRK12525 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12527 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein Back     alignment and domain information
>PRK06704 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family Back     alignment and domain information
>PF07638 Sigma70_ECF: ECF sigma factor Back     alignment and domain information
>PRK09191 two-component response regulator; Provisional Back     alignment and domain information
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR Back     alignment and domain information
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional Back     alignment and domain information
>PHA02547 55 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09047 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query428
1l9u_H 332 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 1e-23
1l9z_H 438 Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun 3e-22
3ugo_A245 Crystal Structure Of Rna-Polymerase Sigma Subunit D 1e-21
1ku2_A241 Crystal Structure Of Thermus Aquaticus Rna Polymera 1e-21
3dxj_F 423 Crystal Structure Of Thermus Thermophilus Rna Polym 3e-21
1iw7_F 423 Crystal Structure Of The Rna Polymerase Holoenzyme 3e-21
4g7h_F 443 Crystal Structure Of Thermus Thermophilus Transcrip 4e-21
4igc_X 613 X-ray Crystal Structure Of Escherichia Coli Sigma70 1e-19
3iyd_F 613 Three-Dimensional Em Structure Of An Intact Activat 1e-19
3les_A179 2f5 Epitope Scaffold Es2 Length = 179 8e-19
1sig_A339 Crystal Structure Of A Sigma70 Subunit Fragment Fro 7e-16
1l0o_C 243 Crystal Structure Of The Bacillus Stearothermophilu 8e-06
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332 Back     alignment and structure 
Iteration: 1

 Score =  107 bits (268), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 103/173 (59%), Gaps = 22/173 (12%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 311 AIGLS------------CRDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 355
            +G +             ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S 
Sbjct: 59  ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 356 HDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
            DL+Q G+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +RTIR+PV
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPV 171
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438 Back     alignment and structure
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245 Back     alignment and structure
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment Containing Regions 1.2 To 3.1 Length = 241 Back     alignment and structure
>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423 Back     alignment and structure
>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423 Back     alignment and structure
>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443 Back     alignment and structure
>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613 Back     alignment and structure
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613 Back     alignment and structure
>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179 Back     alignment and structure
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339 Back     alignment and structure
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti- Sigma Factor Spoiiab With The Sporulation Sigma Factor Sigmaf Length = 243 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query428
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 4e-31
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 3e-29
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 3e-28
1l0o_C 243 Sigma factor; bergerat fold, helix-turn-helix, pro 6e-26
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 1e-24
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 2e-21
1rp3_A 239 RNA polymerase sigma factor sigma-28 (FLIA); trans 1e-16
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-04
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A* 3les_A* Length = 245 Back     alignment and structure
 Score =  118 bits (297), Expect = 4e-31
 Identities = 59/187 (31%), Positives = 96/187 (51%), Gaps = 35/187 (18%)

Query: 254 NDPLRLFLWGPETRK--LLTADEEFELIAQI------------------QDLIRLEKEKS 293
           +DP+R +L   E  +  LLT +EE +L  ++                  + +  + + K 
Sbjct: 6   SDPVRQYLH--EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKI 63

Query: 294 KLQSQFGREPTLIEWAKAIGLS------------CRDLKSELHSGNSSREKLINANLRLV 341
              ++  + P L E      +              +        G ++R+ LI ANLRLV
Sbjct: 64  LGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLV 123

Query: 342 VHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 400
           V +AK+Y GRG+S  DL+Q G+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +
Sbjct: 124 VSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQA 183

Query: 401 RTIRLPV 407
           RTIR+PV
Sbjct: 184 RTIRIPV 190
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Length = 423 Back     alignment and structure
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Length = 438 Back     alignment and structure
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Length = 243 Back     alignment and structure
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 613 Back     alignment and structure
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Length = 339 Back     alignment and structure
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query428
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 99.97
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 99.97
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 99.97
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 99.67
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 99.6
1l0o_C 243 Sigma factor; bergerat fold, helix-turn-helix, pro 99.43
1rp3_A 239 RNA polymerase sigma factor sigma-28 (FLIA); trans 99.36
1or7_A194 Sigma-24, RNA polymerase sigma-E factor; regulatio 98.64
2q1z_A184 RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc 98.61
3mzy_A164 RNA polymerase sigma-H factor; PSI, MCSG, structur 98.32
2o7g_A112 Probable RNA polymerase sigma-C factor; sigma fact 98.1
1h3l_A87 RNA polymerase sigma factor; transcription, DNA-bi 97.84
2lfw_A157 PHYR sigma-like domain; signal transduction, respo 96.11
3n0r_A 286 Response regulator; sigma factor, receiver, two-co 95.0
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 94.63
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Back     alignment and structure
Probab=99.97  E-value=3.5e-31  Score=272.33  Aligned_cols=172  Identities=34%  Similarity=0.558  Sum_probs=150.6

Q ss_pred             CCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHhhhCCCCcHHHHHH---
Q 014241          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAK---  310 (428)
Q Consensus       252 ~~~d~l~~YL~ei~~~~LLT~EEE~eL~~~Iq~l~~Le~~~~------------------~L~~~lGr~Pt~~ewA~---  310 (428)
                      ...|+++.||++|+++|+||++||++|+++|+.++.++....                  .....+|+.|+..+|+.   
T Consensus        91 ~~~d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (438)
T 1l9z_H           91 STSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT  170 (438)
T ss_pred             CCCChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchh
Confidence            456899999999999999999999999999999765443221                  12234567888888743   


Q ss_pred             ---------HhcCCHHHHHHHhhccHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHH-HHHHHHHHHHhcCCCCCCch
Q 014241          311 ---------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRF  380 (428)
Q Consensus       311 ---------a~g~s~~eL~~~l~~G~~Are~LI~~nLrLV~sIAkrY~~rGld~eDLIQ-G~IGLikAVekFDpskG~rF  380 (428)
                               +.|++..+|...+.+|..|+++||.+|+++|++||++|.++|.+++|||| |+||||+|+++|||++|++|
T Consensus       171 ~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rF  250 (438)
T 1l9z_H          171 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  250 (438)
T ss_pred             hhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCh
Confidence                     23567788999999999999999999999999999999999999999999 99999999999999999999


Q ss_pred             hcHHHHHHHHHHHHHHHhcCCCcccchhHHHhhHHHHHHHHHh
Q 014241          381 ASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYIFKFYVF  423 (428)
Q Consensus       381 STYA~~wIR~aI~raIr~qsr~IRlP~~~~e~l~ri~r~~~~L  423 (428)
                      +|||+||||++|.++|+++.+.+|+|.|+.+.++++.+....|
T Consensus       251 sTYA~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l  293 (438)
T 1l9z_H          251 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL  293 (438)
T ss_pred             HHHHHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999887765543
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Back     alignment and structure
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A* Back     alignment and structure
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Back     alignment and structure
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Back     alignment and structure
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Back     alignment and structure
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Back     alignment and structure
>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A Back     alignment and structure
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Back     alignment and structure
>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis} Back     alignment and structure
>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1 Back     alignment and structure
>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP} Back     alignment and structure
>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A Back     alignment and structure
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 428
d1ku2a2180 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq 5e-28
d1siga_334 a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5 2e-26
d1rp3a387 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A 3e-18
d1rp3a177 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) { 0.003
>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180 Back     information, alignment and structure

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score =  107 bits (267), Expect = 5e-28
 Identities = 56/179 (31%), Positives = 91/179 (50%), Gaps = 31/179 (17%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIR------------------LEKEKSKLQ 296
           DP+R +L       LLT +EE +L  ++++ +                   + + K    
Sbjct: 2   DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGT 61

Query: 297 SQFGREPTLIEWAKAIGLSCRDLKSE------------LHSGNSSREKLINANLRLVVHV 344
           ++  + P L E      +   D K +               G ++R+ LI ANLRLVV +
Sbjct: 62  ARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSI 121

Query: 345 AKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 402
           AK+Y GRG+S  DL+Q G+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +RT
Sbjct: 122 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 180
>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334 Back     information, alignment and structure
>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 87 Back     information, alignment and structure
>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query428
d1ku2a2180 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 100.0
d1siga_334 Sigma70 {Escherichia coli [TaxId: 562]} 99.91
d1rp3a387 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 99.86
d1or7a2113 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 98.53
d1h3la_75 Sigma factor SigR {Streptomyces coelicolor a3(2) [ 96.64
d1l0oc_57 SigmaF {Bacillus stearothermophilus [TaxId: 1422]} 96.58
d1rp3a177 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 96.2
d1ku2a160 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 94.77
d1l0oc_57 SigmaF {Bacillus stearothermophilus [TaxId: 1422]} 82.38
d1ku2a160 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 80.23
>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure
class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=100.00  E-value=2.6e-37  Score=277.61  Aligned_cols=149  Identities=37%  Similarity=0.629  Sum_probs=122.9

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------hhhCCCCcHHHH-------
Q 014241          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPTLIEW-------  308 (428)
Q Consensus       254 ~d~l~~YL~ei~~~~LLT~EEE~eL~~~Iq~l~~Le~~~~~L~------------------~~lGr~Pt~~ew-------  308 (428)
                      +||++.||++|+++||||+|||++|+++|+.++.+.+...+..                  ...+..|...+|       
T Consensus         1 tDpVr~YLreig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~   80 (180)
T d1ku2a2           1 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE   80 (180)
T ss_dssp             CHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTHH
T ss_pred             CCcHHHHHHHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHHH
Confidence            5899999999999999999999999999998876554432221                  112233333333       


Q ss_pred             --HHHhcCC---HHHHHHHhhccHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHH-HHHHHHHHHHhcCCCCCCchhc
Q 014241          309 --AKAIGLS---CRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFAS  382 (428)
Q Consensus       309 --A~a~g~s---~~eL~~~l~~G~~Are~LI~~nLrLV~sIAkrY~~rGld~eDLIQ-G~IGLikAVekFDpskG~rFST  382 (428)
                        .......   .+.+.+.+..|..|+++||++|+|||++||++|.++|++++|||| |+||||+||++|||++|++|+|
T Consensus        81 ~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~t  160 (180)
T d1ku2a2          81 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  160 (180)
T ss_dssp             HHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHHH
Confidence              2222222   355667778899999999999999999999999999999999999 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCC
Q 014241          383 YAYWWVRQTIRKAIFQHSRT  402 (428)
Q Consensus       383 YA~~wIR~aI~raIr~qsr~  402 (428)
                      ||+||||++|.++|++++|+
T Consensus       161 ya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         161 YATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHhCCC
Confidence            99999999999999999875
>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1h3la_ a.177.1.1 (A:) Sigma factor SigR {Streptomyces coelicolor a3(2) [TaxId: 100226]} Back     information, alignment and structure
>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure
>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure