Citrus Sinensis ID: 017044

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-------38
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKWLLLFQYH
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccHHHHHcccccHHHHHHHHcccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHccccHHHHHHHHHHHHccccccccccccccHHHHHHHHHccccccccHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHccccccccHHHHHHHHHcccc
ccccHHcccccccccccccccccccccccccccccccccccccccEEccccccHHHccccccEEcccccccccccccccHccccHHHHHcccccccEEEcccccccccHHHHHHHHHHHHHccccHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHccHHHHHHcccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHccHHHccccccccccccccHcccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcHHHHHHHcc
meagrnllssppsfpsrtrvkhslsssasssssssVLMHneqsapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQyqgrgislhDLLQVNQATFNFGKWLLLFQYH
meagrnllssppsfpsrtrVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKWLLLFQYH
MEAGRNLLSSPPSFPSRTRVKHslsssasssssssVLMHNEQsapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKWLLLFQYH
**************************************************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDLK***********KLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKWLLLFQY*
***********P****************************EQS********TSSVARHFPTSVLL***********************************************VQDLEHQFLH****************************************************************************************************************************************LFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS**GREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKWLLLFQYH
******************************************************VARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKWLLLFQYH
********************************************P*VASV*TSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPP*************************AEPFDAVALARKALSASKEAASLAENPKLN*A*F**I**********EEVKQFSQPRFLERRSKKR*****************************RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKWLLLFQYH
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKWLLLFQYH
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 ?
Query378 2.2.26 [Sep-21-2011]
Q9LD95 547 RNA polymerase sigma fact yes no 0.873 0.603 0.467 8e-71
O22056 572 RNA polymerase sigma fact no no 0.388 0.256 0.378 5e-23
P26683 390 RNA polymerase sigma fact yes no 0.375 0.364 0.354 3e-17
Q31ME3 320 RNA polymerase sigma fact yes no 0.280 0.331 0.396 3e-14
P38023 399 RNA polymerase sigma fact no no 0.280 0.265 0.415 3e-14
Q31QG5 320 RNA polymerase sigma fact no no 0.306 0.362 0.393 1e-13
Q03065 332 RNA polymerase sigma-B fa no no 0.280 0.319 0.358 2e-10
P74565 425 RNA polymerase sigma fact N/A no 0.309 0.275 0.293 2e-08
Q59996 404 Probable RNA polymerase s N/A no 0.283 0.264 0.302 3e-08
P52322 416 RNA polymerase sigma fact no no 0.280 0.254 0.296 5e-08
>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 =  267 bits (683), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 172/368 (46%), Positives = 226/368 (61%), Gaps = 38/368 (10%)

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 360
           ++  DLLQ
Sbjct: 331 LNFQDLLQ 338
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|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|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|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|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
>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|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa GN=rpoD1 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 ?
Query378
224068757 535 predicted protein [Populus trichocarpa] 0.862 0.609 0.555 1e-102
297741628 561 unnamed protein product [Vitis vinifera] 0.915 0.616 0.560 1e-101
359481391 572 PREDICTED: RNA polymerase sigma factor r 0.939 0.620 0.554 1e-100
255556952 548 RNA polymerase sigma factor rpoD, putati 0.880 0.607 0.549 2e-98
356536959 571 PREDICTED: RNA polymerase sigma factor r 0.936 0.619 0.527 1e-85
356548319 574 PREDICTED: RNA polymerase sigma factor r 0.939 0.618 0.502 1e-84
449451030 562 PREDICTED: RNA polymerase sigma factor s 0.920 0.619 0.490 2e-77
312282671 547 unnamed protein product [Thellungiella h 0.873 0.603 0.480 8e-73
297827203 546 RNA polymerase sigma-70 factor [Arabidop 0.870 0.602 0.475 1e-71
18404292 547 RNApolymerase sigma-subunit F [Arabidops 0.873 0.603 0.467 5e-69
>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 =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 200/360 (55%), Positives = 255/360 (70%), Gaps = 34/360 (9%)

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

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 ?
Query378
TAIR|locus:2057996 547 SIGF "AT2G36990" [Arabidopsis 0.693 0.478 0.425 1.5e-44
UNIPROTKB|Q84LK8 572 SIG6 "Sig6" [Oryza sativa Japo 0.388 0.256 0.422 8e-28
TAIR|locus:2025650 572 SIG2 "AT1G08540" [Arabidopsis 0.388 0.256 0.378 1.5e-23
UNIPROTKB|O48655 519 rsigA "Plastid RNA polymerase 0.272 0.198 0.359 7.5e-11
TAIR|locus:2084420 571 SIGC "AT3G53920" [Arabidopsis 0.428 0.283 0.282 6.3e-06
TAIR|locus:2010871 502 SIGA "AT1G64860" [Arabidopsis 0.275 0.207 0.307 1.9e-05
UNIPROTKB|Q59563 323 mysB "RNA polymerase sigma fac 0.148 0.173 0.473 0.00011
TAIR|locus:2167413 517 SIGE "AT5G24120" [Arabidopsis 0.351 0.257 0.273 0.00025
TIGR_CMR|GSU_1525 328 GSU_1525 "RNA polymerase sigma 0.116 0.134 0.4 0.00026
TAIR|locus:2057996 SIGF "AT2G36990" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 469 (170.2 bits), Expect = 1.5e-44, P = 1.5e-44
 Identities = 120/282 (42%), Positives = 159/282 (56%)

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 360
             LKS++H G SSREKLI ANLRLVVH+AKQYQ RG++  DLLQ
Sbjct:   297 LKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQ 338
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
TAIR|locus:2084420 SIGC "AT3G53920" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010871 SIGA "AT1G64860" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q59563 mysB "RNA polymerase sigma factor" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
TAIR|locus:2167413 SIGE "AT5G24120" [Arabidopsis thaliana (taxid:3702)] 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

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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 ?
Query378
TIGR02997 298 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f 2e-26
PRK07406 373 PRK07406, PRK07406, RNA polymerase sigma factor Rp 3e-24
PRK07405 317 PRK07405, PRK07405, RNA polymerase sigma factor Si 1e-21
PRK05949 327 PRK05949, PRK05949, RNA polymerase sigma factor; V 6e-19
PRK07598 415 PRK07598, PRK07598, RNA polymerase sigma factor Si 1e-13
COG0568 342 COG0568, RpoD, DNA-directed RNA polymerase, sigma 5e-11
PRK07921 324 PRK07921, PRK07921, RNA polymerase sigma factor Si 4e-09
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 8e-09
TIGR02393 238 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor 1e-06
PRK09210 367 PRK09210, PRK09210, RNA polymerase sigma factor Rp 4e-06
PRK08215 258 PRK08215, PRK08215, sporulation sigma factor SigG; 2e-05
TIGR02980 227 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, 4e-05
TIGR02850 254 TIGR02850, spore_sigG, RNA polymerase sigma-G fact 5e-05
TIGR02394 285 TIGR02394, rpoS_proteo, RNA polymerase sigma facto 2e-04
PRK05657 325 PRK05657, PRK05657, RNA polymerase sigma factor Rp 2e-04
PRK05658 619 PRK05658, PRK05658, RNA polymerase sigma factor Rp 0.001
TIGR02392 270 TIGR02392, rpoH_proteo, alternative sigma factor R 0.002
PRK08301 234 PRK08301, PRK08301, sporulation sigma factor SigE; 0.002
pfam0454271 pfam04542, Sigma70_r2, Sigma-70 region 2 0.003
PRK05803 233 PRK05803, PRK05803, sporulation sigma factor SigK; 0.004
>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information 
 Score =  106 bits (268), Expect = 2e-26
 Identities = 48/92 (52%), Positives = 65/92 (70%)

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 360
           ++EK+I ANLRLVV VAK+YQ RG+ L DL+Q
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQ 106

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|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional 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|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; 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|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor 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|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH Back     alignment and domain information
>gnl|CDD|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>gnl|CDD|218138 pfam04542, Sigma70_r2, Sigma-70 region 2 Back     alignment and domain information
>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 378
PRK07598 415 RNA polymerase sigma factor SigC; Validated 99.97
TIGR02997 298 Sig70-cyanoRpoD RNA polymerase sigma factor, cyano 99.95
PRK07406 373 RNA polymerase sigma factor RpoD; Validated 99.94
PRK05949 327 RNA polymerase sigma factor; Validated 99.93
PRK07405 317 RNA polymerase sigma factor SigD; Validated 99.92
PRK05901 509 RNA polymerase sigma factor; Provisional 99.89
COG0568 342 RpoD DNA-directed RNA polymerase, sigma subunit (s 99.88
PRK07921 324 RNA polymerase sigma factor SigB; Reviewed 99.83
PRK09210 367 RNA polymerase sigma factor RpoD; Validated 99.67
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 99.66
TIGR02392 270 rpoH_proteo alternative sigma factor RpoH. A sigma 99.58
PRK06596 284 RNA polymerase factor sigma-32; Reviewed 99.58
PRK07122 264 RNA polymerase sigma factor SigF; Reviewed 99.49
PRK07500 289 rpoH2 RNA polymerase factor sigma-32; Reviewed 99.45
PRK05657 325 RNA polymerase sigma factor RpoS; Validated 99.32
TIGR02394 285 rpoS_proteo RNA polymerase sigma factor RpoS. A si 99.27
PRK07408 256 RNA polymerase sigma factor SigF; Reviewed 99.2
COG1191 247 FliA DNA-directed RNA polymerase specialized sigma 99.13
TIGR02850 254 spore_sigG RNA polymerase sigma-G factor. Members 99.1
PRK08215 258 sporulation sigma factor SigG; Reviewed 99.07
PRK05911 257 RNA polymerase sigma factor sigma-28; Reviewed 99.0
PRK06288 268 RNA polymerase sigma factor WhiG; Reviewed 98.9
PRK05803 233 sporulation sigma factor SigK; Reviewed 98.8
TIGR02941 255 Sigma_B RNA polymerase sigma-B factor. This sigma 98.7
PRK08583 257 RNA polymerase sigma factor SigB; Validated 98.6
TIGR02885 231 spore_sigF RNA polymerase sigma-F factor. Members 98.47
PRK05572 252 sporulation sigma factor SigF; Validated 98.44
PRK07670 251 RNA polymerase sigma factor SigD; Validated 98.35
PRK12427 231 flagellar biosynthesis sigma factor; Provisional 98.34
PF0014037 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr 98.1
TIGR02846 227 spore_sigmaK RNA polymerase sigma-K factor. The sp 97.98
PRK08301 234 sporulation sigma factor SigE; Reviewed 97.82
TIGR02835 234 spore_sigmaE RNA polymerase sigma-E factor. Member 97.54
PF0454271 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762 97.47
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 97.18
PRK08295 208 RNA polymerase factor sigma-70; Validated 97.01
TIGR02859 198 spore_sigH RNA polymerase sigma-H factor. Members 96.81
PRK08311 237 putative RNA polymerase sigma factor SigI; Reviewe 96.8
PF0453978 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 96.6
PRK09652 182 RNA polymerase sigma factor RpoE; Provisional 96.22
PRK05602 186 RNA polymerase sigma factor; Reviewed 96.1
PRK11922 231 RNA polymerase sigma factor; Provisional 95.93
TIGR02895 218 spore_sigI RNA polymerase sigma-I factor. Members 95.93
TIGR02948 187 SigW_bacill RNA polymerase sigma-W factor. This si 95.84
PRK09641 187 RNA polymerase sigma factor SigW; Provisional 95.54
PRK09648 189 RNA polymerase sigma factor SigD; Reviewed 95.41
PRK12519 194 RNA polymerase sigma factor; Provisional 95.28
PRK09646 194 RNA polymerase sigma factor SigK; Reviewed 95.26
PRK06759154 RNA polymerase factor sigma-70; Validated 94.8
PRK06986 236 fliA flagellar biosynthesis sigma factor; Validate 94.67
PRK11923 193 algU RNA polymerase sigma factor AlgU; Provisional 94.62
PRK12513 194 RNA polymerase sigma factor; Provisional 94.61
PRK09640 188 RNA polymerase sigma factor SigX; Reviewed 94.23
PRK11924 179 RNA polymerase sigma factor; Provisional 94.0
PRK13919 186 putative RNA polymerase sigma E protein; Provision 93.48
PRK06811 189 RNA polymerase factor sigma-70; Validated 93.15
TIGR02939 190 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s 92.58
PRK12534 187 RNA polymerase sigma factor; Provisional 92.18
PRK12531 194 RNA polymerase sigma factor; Provisional 92.17
TIGR02952 170 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02 91.99
PRK12514 179 RNA polymerase sigma factor; Provisional 91.8
PRK09638 176 RNA polymerase sigma factor SigY; Reviewed 91.74
PRK12526 206 RNA polymerase sigma factor; Provisional 90.53
PRK12524 196 RNA polymerase sigma factor; Provisional 90.17
PRK12538 233 RNA polymerase sigma factor; Provisional 89.51
PRK12512 184 RNA polymerase sigma factor; Provisional 87.78
TIGR02954 169 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02 86.92
PRK12536 181 RNA polymerase sigma factor; Provisional 85.61
PRK12537 182 RNA polymerase sigma factor; Provisional 85.59
COG1191247 FliA DNA-directed RNA polymerase specialized sigma 84.87
PRK12515 189 RNA polymerase sigma factor; Provisional 83.75
PRK12518 175 RNA polymerase sigma factor; Provisional 83.15
PRK07408256 RNA polymerase sigma factor SigF; Reviewed 82.11
PRK09643 192 RNA polymerase sigma factor SigM; Reviewed 81.95
PRK12539 184 RNA polymerase sigma factor; Provisional 80.18
>PRK07598 RNA polymerase sigma factor SigC; Validated Back     alignment and domain information 
Probab=99.97  E-value=1.2e-30  Score=263.29  Aligned_cols=126  Identities=38%  Similarity=0.572  Sum_probs=118.6

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhcCCCcchHHHHHHh
Q 017044          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI  312 (378)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~--------------------LEkik~~Le~~lGrePT~~EWA~Aa  312 (378)
                      .+|+++.||++||+.+|||++||++|+++||.+++                    |++++.+|++++|++||..|||.++
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                    9999999999999999999999887


Q ss_pred             ccchhhhhhhc----------------------cccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-----
Q 017044          313 GLSCRDLKSEL----------------------HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-----  365 (378)
Q Consensus       313 G~s~~eLr~~L----------------------~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-----  365 (378)
                      |+++.+|+.+|                      ..|+.|+++||++|+|||++||++|.|+|+.++||||||+||     
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            77766666665                      578899999999999999999999999999999999999999     


Q ss_pred             --cccCCCccccccC
Q 017044          366 --FNFGKWLLLFQYH  378 (378)
Q Consensus       366 --FDpsRG~rFstY~  378 (378)
                        |||+||++|+||.
T Consensus       218 ekFDp~rG~rFSTYa  232 (415)
T PRK07598        218 EKFDPTKGYRFSTYA  232 (415)
T ss_pred             HHcCcccCCCHHHHH
Confidence              9999999999994

>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
>PRK09210 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK05658 RNA polymerase sigma factor RpoD; Validated 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
>PRK07122 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>PRK05657 RNA polymerase sigma factor RpoS; Validated Back     alignment and domain information
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] 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
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Back     alignment and domain information
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed Back     alignment and domain information
>PRK05803 sporulation sigma factor SigK; Reviewed Back     alignment and domain information
>TIGR02941 Sigma_B RNA polymerase sigma-B factor 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
>PRK05572 sporulation sigma factor SigF; Validated Back     alignment and domain information
>PRK07670 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>PRK12427 flagellar biosynthesis sigma factor; Provisional Back     alignment and domain information
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1 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
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor 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
>PRK05658 RNA polymerase sigma factor RpoD; Validated 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
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed 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
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>PRK05602 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK11922 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02895 spore_sigI RNA polymerase sigma-I factor Back     alignment and domain information
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor Back     alignment and domain information
>PRK09641 RNA polymerase sigma factor SigW; Provisional Back     alignment and domain information
>PRK09648 RNA polymerase sigma factor SigD; Reviewed Back     alignment and domain information
>PRK12519 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated Back     alignment and domain information
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Back     alignment and domain information
>PRK12513 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09640 RNA polymerase sigma factor SigX; Reviewed Back     alignment and domain information
>PRK11924 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK13919 putative RNA polymerase sigma E protein; Provisional Back     alignment and domain information
>PRK06811 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE Back     alignment and domain information
>PRK12534 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12531 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09638 RNA polymerase sigma factor SigY; Reviewed Back     alignment and domain information
>PRK12526 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12524 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12538 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12512 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
>PRK12536 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>PRK12515 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12518 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PRK09643 RNA polymerase sigma factor SigM; Reviewed Back     alignment and domain information
>PRK12539 RNA polymerase sigma factor; Provisional 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 ?
Query378
1l9u_H 332 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 2e-08
1l9z_H 438 Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun 5e-07
1ku2_A241 Crystal Structure Of Thermus Aquaticus Rna Polymera 9e-07
3ugo_A245 Crystal Structure Of Rna-Polymerase Sigma Subunit D 9e-07
3les_A179 2f5 Epitope Scaffold Es2 Length = 179 1e-06
3dxj_F 423 Crystal Structure Of Thermus Thermophilus Rna Polym 4e-06
1iw7_F 423 Crystal Structure Of The Rna Polymerase Holoenzyme 4e-06
4g7h_F 443 Crystal Structure Of Thermus Thermophilus Transcrip 4e-06
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332 Back     alignment and structure 
Iteration: 1

 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/125 (34%), Positives = 67/125 (53%), Gaps = 21/125 (16%)
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 360
            DL+Q
Sbjct: 119 LDLIQ 123
>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|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|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|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query378
1l0o_C 243 Sigma factor; bergerat fold, helix-turn-helix, pro 2e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-08
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 3e-09
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 9e-09
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 5e-08
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 3e-06
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 8e-06
1rp3_A 239 RNA polymerase sigma factor sigma-28 (FLIA); trans 6e-04
>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
 Score = 56.4 bits (137), Expect = 2e-09
 Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 317 RDLKSELHSGNSS-REKLINANLRLVVHVAKQYQGRGISLHDLLQV 361
           ++L      G+   R+++I  N+RLV  V +++  RG    DL Q+
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQI 61
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query378
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 99.86
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 99.86
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 99.83
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 98.84
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 98.48
1l0o_C 243 Sigma factor; bergerat fold, helix-turn-helix, pro 98.14
1rp3_A 239 RNA polymerase sigma factor sigma-28 (FLIA); trans 97.96
2q1z_A 184 RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc 96.04
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 95.85
1or7_A 194 Sigma-24, RNA polymerase sigma-E factor; regulatio 95.27
2o7g_A112 Probable RNA polymerase sigma-C factor; sigma fact 82.95
>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=99.86  E-value=8e-22  Score=198.95  Aligned_cols=127  Identities=30%  Similarity=0.466  Sum_probs=107.9

Q ss_pred             CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHhhcCCCcchHHHHHH--
Q 017044          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAKA--  311 (378)
Q Consensus       252 ~~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~------------------~Le~~lGrePT~~EWA~A--  311 (378)
                      ...|+++.||++|+++||||++||++|+++|+.++.++....                  .....+|+.|+..+|+..  
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            467899999999999999999999999999999865443221                  122345678888887532  


Q ss_pred             ----------hccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccc
Q 017044          312 ----------IGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLL  374 (378)
Q Consensus       312 ----------aG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rF  374 (378)
                                .|++..+|..++..|..|+++||.+|+|+|++||++|.|+|++++||||||+||       |||++|++|
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                      355667888888889999999999999999999999999999999999999999       999999999


Q ss_pred             cccC
Q 017044          375 FQYH  378 (378)
Q Consensus       375 stY~  378 (378)
                      +||.
T Consensus       251 sTYA  254 (438)
T 1l9z_H          251 STYA  254 (438)
T ss_pred             HHHH
Confidence            9983
>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
>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
>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
>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
>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
>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
>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
>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

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 378
d1ku2a2180 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq 5e-09
d1siga_334 a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5 6e-08
d1rp3a387 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A 2e-06
>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 = 52.9 bits (126), Expect = 5e-09
 Identities = 37/137 (27%), Positives = 60/137 (43%), Gaps = 30/137 (21%)

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 AKQYQGRGISLHDLLQV 361
           AK+Y GRG+S  DL+Q 
Sbjct: 122 AKKYTGRGLSFLDLIQE 138
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query378
d1ku2a2180 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 99.95
d1siga_334 Sigma70 {Escherichia coli [TaxId: 562]} 99.67
d1rp3a387 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 99.32
d1l0oc_57 SigmaF {Bacillus stearothermophilus [TaxId: 1422]} 96.99
d1rp3a177 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 96.86
d1ku2a160 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 96.15
d1or7a2113 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 91.5
>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=99.95  E-value=1.1e-29  Score=222.44  Aligned_cols=125  Identities=30%  Similarity=0.485  Sum_probs=99.6

Q ss_pred             CcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------hhcCCCcchHHHH------
Q 017044          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPTLIEWA------  309 (378)
Q Consensus       254 ~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le------------------~~lGrePT~~EWA------  309 (378)
                      +|||++||++||+++|||++||++|+++|+.++.+.+...+..                  ...+..|...+|+      
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            5899999999999999999999999999999887654432221                  1122333333332      


Q ss_pred             ---HHhcc---chhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccc
Q 017044          310 ---KAIGL---SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQ  376 (378)
Q Consensus       310 ---~AaG~---s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFst  376 (378)
                         .....   ..+.+.+.+..|..||++||.+|+|||++||++|.++|++|+||||||+||       |||+||++|+|
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               22222   234556677789999999999999999999999999999999999999999       99999999999


Q ss_pred             cC
Q 017044          377 YH  378 (378)
Q Consensus       377 Y~  378 (378)
                      |.
T Consensus       161 ya  162 (180)
T d1ku2a2         161 YA  162 (180)
T ss_dssp             HH
T ss_pred             HH
Confidence            93
>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
>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