Citrus Sinensis ID: 016321

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-
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLKFDLSSSLPKKGSKFEQIGVLLSSICKLLMYLVFAYEK
ccccccHHccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHccccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHcccccccccHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHccccccHHHHHHHHHHHHcc
ccccHHHEEcccccHHHcccccccccccccccccccccccccccccccEEEEEcccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHccHHHHHcccccccccccccHHHHHHHccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHcc
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYIndlgsansqvgsTKNVVAAkkssnynpsfpssnrqtqpiKALKEhvdtnfastaepwaeppnsieeesseLDYSVEALLLLQKSMLEKQWNLSFertvltdspskkthkkvpvtcsgvsARQRRLNSKKKILSQNKSILQQNGSkqlrsmisPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIktglslddHKLRLkerlgcepSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIekfdsskgfkisTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQlkfdlssslpkkgskfEQIGVLLSSICKLLMYLVFAYEK
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnrqTQPIKALKEHVDTNFAstaepwaeppnSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERtvltdspskkthkkvpvtcsgvsarqrrlnskkkilsqnksilqqngskqlrsMISPELIQNRLKGYVKGVVSEELLTHAEVVRlskkiktglslddhKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGiekfdsskgfkISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLKFdlssslpkkgskfEQIGVLLSSICKLLMYLVFAYEK
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnRQTQPIKALKEHVDTNFASTAEPWAEPPNsieeesseLDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLKFDLSSSLPKKGSKFEQIGVLLSSICKLLMYLVFAYEK
*****AVIGLSAGKRLLSSSFYYSDISEKFSYINDL*********************************************************************YSVEALLLLQKSMLEKQWNLSFERTVL******************************************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGC**********LRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLKFDLSSSL**KGSKFEQIGVLLSSICKLLMYLVFAY**
***TAAV*GLSAGKRLLSSSFYYSDISEKF******************************************************************************************************************************************************************LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE**G*EPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQ*******************GVLLSSICKLLMYLVFAYE*
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNY************PIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVL*****************GVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLKFDLSSSLPKKGSKFEQIGVLLSSICKLLMYLVFAYEK
*MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNY*******************************************SELDYSVEALLLLQKSMLEKQWNLSF***********************************************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLKFDLSSSLPKKGSKFEQIGVLLSSICKLLMYLVFAYEK
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHii
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SSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
SSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHii
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MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLKFDLSSSLPKKGSKFEQIGVLLSSICKLLMYLVFAYEK
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 ?
Query391 2.2.26 [Sep-21-2011]
O24629 502 RNA polymerase sigma fact yes no 0.790 0.615 0.647 1e-116
Q31ME3 320 RNA polymerase sigma fact yes no 0.358 0.437 0.388 3e-24
O22056 572 RNA polymerase sigma fact no no 0.445 0.304 0.363 4e-23
Q9LD95 547 RNA polymerase sigma fact no no 0.345 0.246 0.392 2e-22
P26683 390 RNA polymerase sigma fact no no 0.355 0.356 0.381 2e-20
Q03065 332 RNA polymerase sigma-B fa no no 0.337 0.397 0.348 3e-20
Q31QG5 320 RNA polymerase sigma fact no no 0.347 0.425 0.379 4e-20
P38023 399 RNA polymerase sigma fact no no 0.355 0.348 0.381 2e-18
P27785 317 RNA polymerase sigma fact N/A no 0.309 0.381 0.382 2e-18
Q03066 416 RNA polymerase sigma-C fa no no 0.250 0.235 0.391 5e-18
>sp|O24629|SIGA_ARATH RNA polymerase sigma factor sigA OS=Arabidopsis thaliana GN=SIGA PE=1 SV=1 Back     alignment and function desciption
 Score =  420 bits (1079), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 219/338 (64%), Positives = 261/338 (77%), Gaps = 29/338 (8%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVD--VASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQ
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQ 321
Essential protein. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Controls the transcription of the psaA gene and thus modulates photosystem stoichiometry. Thereby maintains an harmonious electron flow and photosynthetic efficiency.
Arabidopsis thaliana (taxid: 3702)
>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|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB PE=2 SV=2 Back     alignment and function description
>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis thaliana GN=SIGF PE=1 SV=1 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|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|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|P27785|RPOD_STRAU RNA polymerase sigma factor RpoD OS=Streptomyces aureofaciens GN=rpoD 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

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 ?
Query391
255566078 508 RNA polymerase sigma factor rpoD, putati 0.833 0.641 0.767 1e-139
224146103 509 predicted protein [Populus trichocarpa] 0.836 0.642 0.737 1e-134
449468291 508 PREDICTED: RNA polymerase sigma factor s 0.833 0.641 0.719 1e-129
356543070 503 PREDICTED: RNA polymerase sigma factor r 0.815 0.634 0.708 1e-127
356531599 503 PREDICTED: RNA polymerase sigma factor r 0.815 0.634 0.705 1e-127
224124068 499 predicted protein [Populus trichocarpa] 0.810 0.635 0.701 1e-116
2565297 502 RNA polymerase sigma subunit 1 [Arabidop 0.790 0.615 0.650 1e-115
15217767 502 sigma factor A [Arabidopsis thaliana] gi 0.790 0.615 0.647 1e-115
334183639 498 sigma factor A [Arabidopsis thaliana] gi 0.790 0.620 0.647 1e-114
11762220 502 At1g64860 [Arabidopsis thaliana] 0.790 0.615 0.644 1e-114
>gi|255566078|ref|XP_002524027.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223536754|gb|EEF38395.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  501 bits (1291), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 251/327 (76%), Positives = 283/327 (86%), Gaps = 1/327 (0%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGLSAGKRLLSS+FYYSD++EK S  N+ G  + Q+ STK ++ AKKSSNY PS
Sbjct: 1   MATAAVIGLSAGKRLLSSTFYYSDLTEKLSSANEHGLTHYQITSTKTLIVAKKSSNYGPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFA-STAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLE 120
           FPSSNR TQ IKALKEHVDT  A STA    +  N +EEESS+LDYSVEALLLLQKSMLE
Sbjct: 61  FPSSNRNTQSIKALKEHVDTASAPSTAATQFKTFNDMEEESSDLDYSVEALLLLQKSMLE 120

Query: 121 KQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQL 180
           KQWNLSFERT  +DSPS+K+ KK+PVTCSGVSARQRR+N ++K LSQ+K  +Q N  KQL
Sbjct: 121 KQWNLSFERTDSSDSPSRKSQKKIPVTCSGVSARQRRINIRRKNLSQSKFTVQANVFKQL 180

Query: 181 RSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPS 240
           +S +SPEL+QNRLKGYVKGVVSEELL+HAEVVRLS+ IK GLSL+DHK RLKERLGC+PS
Sbjct: 181 KSAVSPELLQNRLKGYVKGVVSEELLSHAEVVRLSRIIKAGLSLEDHKSRLKERLGCDPS 240

Query: 241 MEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLI 300
            EQ+A SL+ISR ELQS  + CSLAREKL MSNVRLVMSIAQRYDNMGA+MADLVQGGLI
Sbjct: 241 DEQVATSLKISRAELQSKSIACSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLI 300

Query: 301 GLLRGIEKFDSSKGFKISTYVYWWIRQ 327
           GLLRGIEKFDSSKGF+ISTYVYWWIRQ
Sbjct: 301 GLLRGIEKFDSSKGFRISTYVYWWIRQ 327

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224146103|ref|XP_002325882.1| predicted protein [Populus trichocarpa] gi|222862757|gb|EEF00264.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449468291|ref|XP_004151855.1| PREDICTED: RNA polymerase sigma factor sigA-like [Cucumis sativus] gi|449514942|ref|XP_004164521.1| PREDICTED: RNA polymerase sigma factor sigA-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356543070|ref|XP_003539986.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max] Back     alignment and taxonomy information
>gi|356531599|ref|XP_003534364.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max] Back     alignment and taxonomy information
>gi|224124068|ref|XP_002319237.1| predicted protein [Populus trichocarpa] gi|222857613|gb|EEE95160.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|2565297|gb|AAB81958.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|15217767|ref|NP_176666.1| sigma factor A [Arabidopsis thaliana] gi|75098242|sp|O24629.1|SIGA_ARATH RecName: Full=RNA polymerase sigma factor sigA; Short=Sigma factor A; Short=Sigma-A; AltName: Full=RNA polymerase sigma factor sig1; Short=Atsig1; Short=Sigma factor 1; AltName: Full=RNA polymerase sigma factor sig2; Short=Atsig2; Short=Sigma factor 2; AltName: Full=RNA polymerase sigma factor sigB; Short=Sigma factor B; Short=Sigma-B; Flags: Precursor gi|5042421|gb|AAD38260.1|AC006193_16 RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|2353171|gb|AAB69384.1| sigma factor 1 [Arabidopsis thaliana] gi|2443408|dbj|BAA22421.1| SigA [Arabidopsis thaliana] gi|2558514|emb|CAA74640.1| plastid RNA polymerase sigma factor [Arabidopsis thaliana] gi|5478439|dbj|BAA82448.1| sigma factor SigA [Arabidopsis thaliana] gi|17064900|gb|AAL32604.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|20259916|gb|AAM13305.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|222423019|dbj|BAH19492.1| AT1G64860 [Arabidopsis thaliana] gi|332196177|gb|AEE34298.1| sigma factor A [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|334183639|ref|NP_001185314.1| sigma factor A [Arabidopsis thaliana] gi|332196178|gb|AEE34299.1| sigma factor A [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|11762220|gb|AAG40388.1|AF325036_1 At1g64860 [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 ?
Query391
TAIR|locus:2010871 502 SIGA "AT1G64860" [Arabidopsis 0.795 0.619 0.613 2.6e-95
UNIPROTKB|O48655 519 rsigA "Plastid RNA polymerase 0.813 0.612 0.455 2.3e-62
TAIR|locus:2025650 572 SIG2 "AT1G08540" [Arabidopsis 0.442 0.302 0.365 1.2e-25
TAIR|locus:2057996 547 SIGF "AT2G36990" [Arabidopsis 0.345 0.246 0.392 1.6e-20
UNIPROTKB|Q84LK8 572 SIG6 "Sig6" [Oryza sativa Japo 0.552 0.377 0.303 2.1e-19
UNIPROTKB|Q59563 323 mysB "RNA polymerase sigma fac 0.304 0.368 0.424 9.4e-19
UNIPROTKB|P0A602 528 rpoD "RNA polymerase sigma fac 0.322 0.238 0.392 2.1e-16
TAIR|locus:2173249 419 SIG4 "AT5G13730" [Arabidopsis 0.342 0.319 0.386 6.3e-15
TIGR_CMR|SO_3432 326 SO_3432 "RNA polymerase sigma 0.276 0.331 0.387 1.9e-14
TIGR_CMR|APH_0576 627 APH_0576 "RNA polymerase sigma 0.401 0.250 0.315 1.8e-13
TAIR|locus:2010871 SIGA "AT1G64860" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 948 (338.8 bits), Expect = 2.6e-95, P = 2.6e-95
 Identities = 206/336 (61%), Positives = 244/336 (72%)

Query:     2 MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKXXXXXXX 61
             MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK       
Sbjct:     1 MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query:    62 XXXXXRQTQPIKALKEHVDTNFASTAEPWA------EPPNXXXXXXXXLDYSVEALLLLQ 115
                  R TQ  KALKE VD   AST +PW       E           + +SVEA+LLLQ
Sbjct:    61 FPSSNRHTQSAKALKESVDV--ASTEKPWLPNGTDKELEEECYDDDDLISHSVEAILLLQ 118

Query:   116 KSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNKSI 171
             KSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K++
Sbjct:   119 KSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVKAV 178

Query:   172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
                +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK RL
Sbjct:   179 SDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKSRL 225

Query:   232 KERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 291
             K+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA+M
Sbjct:   226 KDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEM 285

Query:   292 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327
             +DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQ
Sbjct:   286 SDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQ 321
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:0006355 "regulation of transcription, DNA-dependent" evidence=ISS;IDA
GO:0009507 "chloroplast" evidence=IDA
GO:0071482 "cellular response to light stimulus" evidence=IEP
GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS
GO:0005515 "protein binding" evidence=IPI
GO:0001053 "plastid sigma factor activity" evidence=IMP
GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP
GO:0071461 "cellular response to redox state" evidence=IDA
GO:0080005 "photosystem stoichiometry adjustment" evidence=IDA
GO:0006833 "water transport" evidence=RCA
GO:0009651 "response to salt stress" evidence=RCA
GO:0009750 "response to fructose stimulus" evidence=RCA
GO:0016987 "sigma factor activity" evidence=ISS
UNIPROTKB|O48655 rsigA "Plastid RNA polymerase sigma factor" [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
TAIR|locus:2057996 SIGF "AT2G36990" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q84LK8 SIG6 "Sig6" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
UNIPROTKB|Q59563 mysB "RNA polymerase sigma factor" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
UNIPROTKB|P0A602 rpoD "RNA polymerase sigma factor RpoD" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
TAIR|locus:2173249 SIG4 "AT5G13730" [Arabidopsis thaliana (taxid:3702)] 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|APH_0576 APH_0576 "RNA polymerase sigma factor RpoD" [Anaplasma phagocytophilum HZ (taxid:212042)] 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) ?
O24629SIGA_ARATHNo assigned EC number0.64790.79020.6155yesno

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:
grail3.0065010301
hypothetical protein (510 aa)
(Populus trichocarpa)
Predicted Functional Partners:
gw1.XIV.2894.1
hypothetical protein (684 aa)
  •     0.431
fgenesh4_pg.C_LG_XVII000398
hypothetical protein (677 aa)
  •     0.430
eugene3.17410001
annotation not avaliable (472 aa)
  •     0.429
estExt_fgenesh4_pg.C_3210002
hypothetical protein (472 aa)
  •     0.426
gw1.321.23.1
annotation not avaliable (657 aa)
  •     0.420
eugene3.00001972
hypothetical protein (485 aa)
  •     0.411

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 ?
Query391
TIGR02997298 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f 5e-40
PRK07405 317 PRK07405, PRK07405, RNA polymerase sigma factor Si 4e-33
PRK07406 373 PRK07406, PRK07406, RNA polymerase sigma factor Rp 1e-29
PRK05949 327 PRK05949, PRK05949, RNA polymerase sigma factor; V 2e-29
PRK07921 324 PRK07921, PRK07921, RNA polymerase sigma factor Si 2e-26
COG0568 342 COG0568, RpoD, DNA-directed RNA polymerase, sigma 2e-24
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 1e-23
PRK07598 415 PRK07598, PRK07598, RNA polymerase sigma factor Si 2e-23
TIGR02393 238 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor 6e-23
TIGR02394 285 TIGR02394, rpoS_proteo, RNA polymerase sigma facto 2e-19
PRK05657 325 PRK05657, PRK05657, RNA polymerase sigma factor Rp 3e-19
PRK09210 367 PRK09210, PRK09210, RNA polymerase sigma factor Rp 3e-18
pfam0454271 pfam04542, Sigma70_r2, Sigma-70 region 2 1e-17
PRK05658 619 PRK05658, PRK05658, RNA polymerase sigma factor Rp 4e-16
PRK07500 289 PRK07500, rpoH2, RNA polymerase factor sigma-32; R 1e-14
TIGR02980227 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, 2e-13
TIGR02392 270 TIGR02392, rpoH_proteo, alternative sigma factor R 3e-13
PRK08215258 PRK08215, PRK08215, sporulation sigma factor SigG; 6e-13
PRK06596 284 PRK06596, PRK06596, RNA polymerase factor sigma-32 3e-12
PRK05803233 PRK05803, PRK05803, sporulation sigma factor SigK; 4e-12
TIGR02885231 TIGR02885, spore_sigF, RNA polymerase sigma-F fact 8e-12
TIGR02850254 TIGR02850, spore_sigG, RNA polymerase sigma-G fact 1e-11
PRK05572252 PRK05572, PRK05572, sporulation sigma factor SigF; 1e-11
TIGR02846227 TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa 5e-11
COG1191247 COG1191, FliA, DNA-directed RNA polymerase special 4e-09
TIGR02937158 TIGR02937, sigma70-ECF, RNA polymerase sigma facto 4e-08
TIGR02835234 TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa 4e-08
PRK08301234 PRK08301, PRK08301, sporulation sigma factor SigE; 3e-07
TIGR02941255 TIGR02941, Sigma_B, RNA polymerase sigma-B factor 2e-05
PRK07408 256 PRK07408, PRK07408, RNA polymerase sigma factor Si 2e-05
TIGR02479224 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, 9e-05
PRK08583 257 PRK08583, PRK08583, RNA polymerase sigma factor Si 1e-04
PRK06288 268 PRK06288, PRK06288, RNA polymerase sigma factor Wh 0.001
PRK07122264 PRK07122, PRK07122, RNA polymerase sigma factor Si 0.001
>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information 
 Score =  143 bits (363), Expect = 5e-40
 Identities = 54/123 (43%), Positives = 88/123 (71%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LLT  E + L+++++  + L++ +  L+E+LG EPS E+ AA+  +S  EL+  L +   
Sbjct: 15  LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQR 74

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+EK++ +N+RLV+S+A++Y N G ++ DL+Q G +GL R +EKFD ++G+K STY YWW
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWW 134

Query: 325 IRQ 327
           IRQ
Sbjct: 135 IRQ 137

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|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>gnl|CDD|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated Back     alignment and domain information
>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed 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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional Back     alignment and domain information
>gnl|CDD|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; 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|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|236413 PRK09210, PRK09210, 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|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|236033 PRK07500, rpoH2, 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|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH Back     alignment and domain information
>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed Back     alignment and domain information
>gnl|CDD|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed Back     alignment and domain information
>gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor Back     alignment and domain information
>gnl|CDD|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor Back     alignment and domain information
>gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated Back     alignment and domain information
>gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor 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|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>gnl|CDD|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor Back     alignment and domain information
>gnl|CDD|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>gnl|CDD|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor 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
>gnl|CDD|236306 PRK08583, PRK08583, RNA polymerase sigma factor SigB; Validated Back     alignment and domain information
>gnl|CDD|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed Back     alignment and domain information
>gnl|CDD|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; 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 391
PRK07598 415 RNA polymerase sigma factor SigC; Validated 100.0
TIGR02997298 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
PRK05901 509 RNA polymerase sigma factor; Provisional 99.98
PRK07405 317 RNA polymerase sigma factor SigD; Validated 99.98
PRK07921 324 RNA polymerase sigma factor SigB; Reviewed 99.96
COG0568 342 RpoD DNA-directed RNA polymerase, sigma subunit (s 99.96
PRK09210 367 RNA polymerase sigma factor RpoD; Validated 99.94
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 99.93
PRK06596 284 RNA polymerase factor sigma-32; Reviewed 99.92
TIGR02392 270 rpoH_proteo alternative sigma factor RpoH. A sigma 99.92
PRK07122264 RNA polymerase sigma factor SigF; Reviewed 99.91
PRK07500 289 rpoH2 RNA polymerase factor sigma-32; Reviewed 99.9
COG1191247 FliA DNA-directed RNA polymerase specialized sigma 99.87
TIGR02393 238 RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter 99.86
PRK05657 325 RNA polymerase sigma factor RpoS; Validated 99.86
PRK07408256 RNA polymerase sigma factor SigF; Reviewed 99.84
TIGR02394 285 rpoS_proteo RNA polymerase sigma factor RpoS. A si 99.81
PRK05911 257 RNA polymerase sigma factor sigma-28; Reviewed 99.8
TIGR02850254 spore_sigG RNA polymerase sigma-G factor. Members 99.79
PRK08215258 sporulation sigma factor SigG; Reviewed 99.78
PRK06288 268 RNA polymerase sigma factor WhiG; Reviewed 99.72
TIGR02941255 Sigma_B RNA polymerase sigma-B factor. This sigma 99.69
TIGR02980227 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G 99.67
PRK12427231 flagellar biosynthesis sigma factor; Provisional 99.65
TIGR02885231 spore_sigF RNA polymerase sigma-F factor. Members 99.65
PRK08583 257 RNA polymerase sigma factor SigB; Validated 99.62
PRK05803233 sporulation sigma factor SigK; Reviewed 99.61
PRK05572252 sporulation sigma factor SigF; Validated 99.61
TIGR02895218 spore_sigI RNA polymerase sigma-I factor. Members 99.59
PRK07670251 RNA polymerase sigma factor SigD; Validated 99.57
TIGR02479224 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f 99.55
PRK06986236 fliA flagellar biosynthesis sigma factor; Validate 99.48
TIGR02846227 spore_sigmaK RNA polymerase sigma-K factor. The sp 99.3
PRK08301234 sporulation sigma factor SigE; Reviewed 99.28
PF0454271 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762 99.22
TIGR02835234 spore_sigmaE RNA polymerase sigma-E factor. Member 99.17
PRK08311237 putative RNA polymerase sigma factor SigI; Reviewe 99.12
PRK08295208 RNA polymerase factor sigma-70; Validated 99.04
TIGR02937158 sigma70-ECF RNA polymerase sigma factor, sigma-70 98.97
TIGR02859198 spore_sigH RNA polymerase sigma-H factor. Members 98.94
PRK09652182 RNA polymerase sigma factor RpoE; Provisional 98.81
PRK09648189 RNA polymerase sigma factor SigD; Reviewed 98.8
PRK11922231 RNA polymerase sigma factor; Provisional 98.76
PRK09646194 RNA polymerase sigma factor SigK; Reviewed 98.76
PRK05602186 RNA polymerase sigma factor; Reviewed 98.7
PRK06759154 RNA polymerase factor sigma-70; Validated 98.68
PRK09641187 RNA polymerase sigma factor SigW; Provisional 98.67
TIGR02948187 SigW_bacill RNA polymerase sigma-W factor. This si 98.67
PRK12513194 RNA polymerase sigma factor; Provisional 98.64
PRK09640188 RNA polymerase sigma factor SigX; Reviewed 98.63
PRK11923193 algU RNA polymerase sigma factor AlgU; Provisional 98.6
PRK13919186 putative RNA polymerase sigma E protein; Provision 98.59
PRK06811189 RNA polymerase factor sigma-70; Validated 98.57
PRK12519194 RNA polymerase sigma factor; Provisional 98.55
PRK09638176 RNA polymerase sigma factor SigY; Reviewed 98.53
TIGR02952170 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02 98.46
PRK12526206 RNA polymerase sigma factor; Provisional 98.45
PRK11924179 RNA polymerase sigma factor; Provisional 98.44
PRK12524196 RNA polymerase sigma factor; Provisional 98.44
PRK12514179 RNA polymerase sigma factor; Provisional 98.41
PRK12534187 RNA polymerase sigma factor; Provisional 98.4
TIGR02985161 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba 98.39
TIGR02939190 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s 98.39
PRK12531194 RNA polymerase sigma factor; Provisional 98.38
PRK12536181 RNA polymerase sigma factor; Provisional 98.32
TIGR02989159 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop 98.3
TIGR02954169 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02 98.28
TIGR02984189 Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl 98.27
PRK12538233 RNA polymerase sigma factor; Provisional 98.22
PRK12512184 RNA polymerase sigma factor; Provisional 98.18
PRK12522173 RNA polymerase sigma factor; Provisional 98.17
PRK09643192 RNA polymerase sigma factor SigM; Reviewed 98.14
PRK12515189 RNA polymerase sigma factor; Provisional 98.1
PRK12539184 RNA polymerase sigma factor; Provisional 98.07
PRK12537182 RNA polymerase sigma factor; Provisional 98.06
PRK12518175 RNA polymerase sigma factor; Provisional 97.99
PRK12543179 RNA polymerase sigma factor; Provisional 97.98
PRK09415179 RNA polymerase factor sigma C; Reviewed 97.94
PRK12542185 RNA polymerase sigma factor; Provisional 97.93
PRK09639166 RNA polymerase sigma factor SigX; Provisional 97.88
PRK09649185 RNA polymerase sigma factor SigC; Reviewed 97.87
TIGR02999183 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f 97.86
COG1595182 RpoE DNA-directed RNA polymerase specialized sigma 97.83
TIGR02983162 SigE-fam_strep RNA polymerase sigma-70 factor, sig 97.78
PF0014037 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr 97.73
PRK12547164 RNA polymerase sigma factor; Provisional 97.72
PRK09644165 RNA polymerase sigma factor SigM; Provisional 97.68
PRK08241 339 RNA polymerase factor sigma-70; Validated 97.65
PRK12528161 RNA polymerase sigma factor; Provisional 97.59
PRK12541161 RNA polymerase sigma factor; Provisional 97.58
PRK09645173 RNA polymerase sigma factor SigL; Provisional 97.57
TIGR02947193 SigH_actino RNA polymerase sigma-70 factor, TIGR02 97.53
PRK09647203 RNA polymerase sigma factor SigE; Reviewed 97.5
TIGR03001244 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco 97.48
TIGR02950154 SigM_subfam RNA polymerase sigma factor, SigM fami 97.47
PRK12520191 RNA polymerase sigma factor; Provisional 97.46
PRK12516187 RNA polymerase sigma factor; Provisional 97.42
PRK12535196 RNA polymerase sigma factor; Provisional 97.39
TIGR02943188 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02 97.37
PRK12532195 RNA polymerase sigma factor; Provisional 97.33
TIGR02960 324 SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa 97.32
PRK09637181 RNA polymerase sigma factor SigZ; Provisional 97.32
PRK09642160 RNA polymerase sigma factor SigW; Reviewed 97.29
PRK12529178 RNA polymerase sigma factor; Provisional 97.24
PRK12533216 RNA polymerase sigma factor; Provisional 97.21
TIGR02959170 SigZ RNA polymerase sigma factor, SigZ family. Thi 97.18
PRK09651172 RNA polymerase sigma factor FecI; Provisional 97.16
PRK12523172 RNA polymerase sigma factor; Reviewed 97.13
PRK12546188 RNA polymerase sigma factor; Provisional 97.04
PRK12540182 RNA polymerase sigma factor; Provisional 97.03
PRK12517188 RNA polymerase sigma factor; Provisional 96.96
PRK07037163 extracytoplasmic-function sigma-70 factor; Validat 96.86
PRK12544206 RNA polymerase sigma factor; Provisional 96.84
PRK12545201 RNA polymerase sigma factor; Provisional 96.83
PRK12530189 RNA polymerase sigma factor; Provisional 96.54
PF0453978 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 96.35
PRK12511182 RNA polymerase sigma factor; Provisional 96.34
PRK12525168 RNA polymerase sigma factor; Provisional 96.03
PRK12527159 RNA polymerase sigma factor; Reviewed 95.96
PRK09636 293 RNA polymerase sigma factor SigJ; Provisional 95.92
TIGR02957 281 SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa 95.75
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 95.73
PRK09191 261 two-component response regulator; Provisional 95.52
PF1264565 HTH_16: Helix-turn-helix domain; InterPro: IPR0247 95.32
PRK06704228 RNA polymerase factor sigma-70; Validated 95.24
PF07638185 Sigma70_ECF: ECF sigma factor 94.5
PRK09635 290 sigI RNA polymerase sigma factor SigI; Provisional 94.29
TIGR03209142 P21_Cbot clostridium toxin-associated regulator Bo 93.8
PHA02547179 55 RNA polymerase sigma factor; Provisional 93.04
COG0568342 RpoD DNA-directed RNA polymerase, sigma subunit (s 92.21
PRK09047161 RNA polymerase factor sigma-70; Validated 91.0
COG1191247 FliA DNA-directed RNA polymerase specialized sigma 87.59
PRK07122264 RNA polymerase sigma factor SigF; Reviewed 84.76
PRK05911257 RNA polymerase sigma factor sigma-28; Reviewed 82.0
PRK07500289 rpoH2 RNA polymerase factor sigma-32; Reviewed 81.39
TIGR02850254 spore_sigG RNA polymerase sigma-G factor. Members 80.82
>PRK07598 RNA polymerase sigma factor SigC; Validated Back     alignment and domain information 
Probab=100.00  E-value=5.5e-36  Score=304.13  Aligned_cols=194  Identities=31%  Similarity=0.491  Sum_probs=165.1

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCc--------------------chhHHHHHHHhhCCCCchHHHHHHhcC
Q 016321          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI  250 (391)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~--------------------L~~~~~~l~~~~g~ePs~~e~A~a~~~  250 (391)
                      |.++.||++|++.|+||++||++|+++||.+..                    |++++.+|++.+|++||.++||+++|+
T Consensus        60 d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~  139 (415)
T PRK07598         60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADI  139 (415)
T ss_pred             ChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence            689999999999999999999999999999988                    899999999999999999999966655


Q ss_pred             ----------------------ChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHh
Q 016321          251 ----------------------SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK  308 (391)
Q Consensus       251 ----------------------s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIek  308 (391)
                                            +.++|.+.+..|..|+++||.+|+++|+++|++|.++|++++||||||+|||++|+++
T Consensus       140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravek  219 (415)
T PRK07598        140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK  219 (415)
T ss_pred             cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence                                  5555556667888999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhhhhc---ccc---cccCCCCCChhHHhhHHHHHHHHHH
Q 016321          309 FDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLK---FDL---SSSLPKKGSKFEQIGVLLSSICKLL  382 (391)
Q Consensus       309 FDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~~~l~---~dl---~~~~~k~ge~~e~ig~~ls~v~~~L  382 (391)
                      |||++|++|+|||+||||++|.++|+++.|.||....-....+.+.   ..+   ..+.++..++++.+|+..+.+..++
T Consensus       220 FDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l  299 (415)
T PRK07598        220 FDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVL  299 (415)
T ss_pred             cCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            9999999999999999999999999999988884432211111111   111   1244667778889999888888877


Q ss_pred             HH
Q 016321          383 MY  384 (391)
Q Consensus       383 ~~  384 (391)
                      ..
T Consensus       300 ~~  301 (415)
T PRK07598        300 LR  301 (415)
T ss_pred             HH
Confidence            64

>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
>PRK05901 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK07405 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>PRK07921 RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] 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
>PRK06596 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>TIGR02392 rpoH_proteo alternative sigma factor RpoH 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
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>PRK05657 RNA polymerase sigma factor RpoS; Validated Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed 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
>PRK06288 RNA polymerase sigma factor WhiG; 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
>PRK12427 flagellar biosynthesis sigma factor; Provisional Back     alignment and domain information
>TIGR02885 spore_sigF RNA polymerase sigma-F factor Back     alignment and domain information
>PRK08583 RNA polymerase sigma factor SigB; Validated Back     alignment and domain information
>PRK05803 sporulation sigma factor SigK; Reviewed Back     alignment and domain information
>PRK05572 sporulation sigma factor SigF; Validated Back     alignment and domain information
>TIGR02895 spore_sigI RNA polymerase sigma-I factor 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
>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
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor Back     alignment and domain information
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed Back     alignment and domain information
>PRK08295 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>TIGR02859 spore_sigH RNA polymerase sigma-H factor Back     alignment and domain information
>PRK09652 RNA polymerase sigma factor RpoE; Provisional 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
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>PRK05602 RNA polymerase sigma factor; Reviewed 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
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor 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
>PRK11923 algU RNA polymerase sigma factor AlgU; 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
>PRK12519 RNA polymerase sigma factor; 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
>PRK12526 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK11924 RNA polymerase sigma factor; Provisional 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
>PRK12534 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1 Back     alignment and domain information
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE Back     alignment and domain information
>PRK12531 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12536 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family Back     alignment and domain information
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family Back     alignment and domain information
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1 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
>PRK12522 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09643 RNA polymerase sigma factor SigM; Reviewed Back     alignment and domain information
>PRK12515 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12539 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12518 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12543 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
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>PRK09649 RNA polymerase sigma factor SigC; Reviewed Back     alignment and domain information
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family Back     alignment and domain information
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription] Back     alignment and domain information
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family Back     alignment and domain information
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1 Back     alignment and domain information
>PRK12547 RNA polymerase sigma factor; 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
>PRK12528 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12541 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09645 RNA polymerase sigma factor SigL; Provisional Back     alignment and domain information
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family Back     alignment and domain information
>PRK09647 RNA polymerase sigma factor SigE; Reviewed Back     alignment and domain information
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1 Back     alignment and domain information
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family Back     alignment and domain information
>PRK12520 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12516 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12535 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family 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
>PRK09637 RNA polymerase sigma factor SigZ; Provisional 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
>PRK12533 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family Back     alignment and domain information
>PRK09651 RNA polymerase sigma factor FecI; Provisional Back     alignment and domain information
>PRK12523 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK12546 RNA polymerase sigma factor; Provisional 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
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated Back     alignment and domain information
>PRK12544 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12545 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12530 RNA polymerase sigma factor; Provisional 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
>PRK12511 RNA polymerase sigma factor; 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
>PRK09636 RNA polymerase sigma factor SigJ; Provisional Back     alignment and domain information
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family Back     alignment and domain information
>PRK05658 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK09191 two-component response regulator; Provisional 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
>PF07638 Sigma70_ECF: ECF sigma factor Back     alignment and domain information
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional Back     alignment and domain information
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR Back     alignment and domain information
>PHA02547 55 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
>PRK09047 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>PRK07122 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Back     alignment and domain information
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>TIGR02850 spore_sigG RNA polymerase sigma-G factor 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 ?
Query391
1l9u_H 332 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 6e-15
3iyd_F 613 Three-Dimensional Em Structure Of An Intact Activat 1e-14
4igc_X 613 X-ray Crystal Structure Of Escherichia Coli Sigma70 1e-14
3ugo_A245 Crystal Structure Of Rna-Polymerase Sigma Subunit D 1e-14
1sig_A339 Crystal Structure Of A Sigma70 Subunit Fragment Fro 1e-14
3dxj_F 423 Crystal Structure Of Thermus Thermophilus Rna Polym 2e-14
1iw7_F 423 Crystal Structure Of The Rna Polymerase Holoenzyme 2e-14
4g7h_F 443 Crystal Structure Of Thermus Thermophilus Transcrip 2e-14
1l9z_H 438 Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun 2e-14
3les_A179 2f5 Epitope Scaffold Es2 Length = 179 2e-14
1ku2_A241 Crystal Structure Of Thermus Aquaticus Rna Polymera 3e-14
1l0o_C243 Crystal Structure Of The Bacillus Stearothermophilu 2e-08
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332 Back     alignment and structure 
Iteration: 1

 Score = 78.6 bits (192), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 49/151 (32%), Positives = 81/151 (53%), Gaps = 15/151 (9%)
Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGL----------SLDDHKLR--LKERLGCEPS 240
           ++ Y+  +    LLT  E + L++K++ G+           LD   +R  ++ ++     
Sbjct: 5   VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAR 64
Query: 241 MEQLAASLRISRPELQ---SILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297
           +E++   L+    EL+    I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q 
Sbjct: 65  VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQE 124
Query: 298 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQV 328
           G  GL+R +EKF+  + FK STY  WWIRQ 
Sbjct: 125 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQA 155
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613 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|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|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339 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|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|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179 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|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 ?
Query391
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 1e-22
1l0o_C243 Sigma factor; bergerat fold, helix-turn-helix, pro 2e-22
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 3e-22
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 3e-21
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 2e-18
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 4e-17
1rp3_A239 RNA polymerase sigma factor sigma-28 (FLIA); trans 6e-17
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-11
3mzy_A164 RNA polymerase sigma-H factor; PSI, MCSG, structur 1e-05
>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 = 94.6 bits (235), Expect = 1e-22
 Identities = 46/161 (28%), Positives = 80/161 (49%), Gaps = 5/161 (3%)

Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGV--VSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           L + G   L ++     +  +++  ++ +  +SE      E++R   + K   +    K+
Sbjct: 13  LHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKI 72

Query: 230 RLKERLGCEPSMEQLAASLRISRPE---LQSILMECSLAREKLVMSNVRLVMSIAQRYDN 286
              +      ++E++   L+    E      I  E   AR+ L+ +N+RLV+SIA++Y  
Sbjct: 73  PGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 132

Query: 287 MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327
            G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ
Sbjct: 133 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQ 173
>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
>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
>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
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Length = 164 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query391
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 99.96
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 99.95
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 99.94
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 99.65
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 99.6
1rp3_A239 RNA polymerase sigma factor sigma-28 (FLIA); trans 99.36
1l0o_C243 Sigma factor; bergerat fold, helix-turn-helix, pro 99.32
1or7_A194 Sigma-24, RNA polymerase sigma-E factor; regulatio 98.83
2q1z_A184 RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc 98.65
3mzy_A164 RNA polymerase sigma-H factor; PSI, MCSG, structur 98.54
2o7g_A112 Probable RNA polymerase sigma-C factor; sigma fact 98.42
1h3l_A87 RNA polymerase sigma factor; transcription, DNA-bi 98.25
2lfw_A157 PHYR sigma-like domain; signal transduction, respo 96.99
3n0r_A 286 Response regulator; sigma factor, receiver, two-co 95.47
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 93.49
>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
Probab=99.96  E-value=1.3e-28  Score=232.05  Aligned_cols=194  Identities=29%  Similarity=0.379  Sum_probs=130.7

Q ss_pred             hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHh-----------------------------hCCCC
Q 016321          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKER-----------------------------LGCEP  239 (391)
Q Consensus       189 ~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~-----------------------------~g~eP  239 (391)
                      ..|.++.||++|+++|+||++||++|+++|+.|..+...   +...                             .+.+|
T Consensus         5 ~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~   81 (245)
T 3ugo_A            5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKK---LSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDP   81 (245)
T ss_dssp             CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHH---HHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCH
T ss_pred             CCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHH---HHhccCCcHHHHHHhhhhhhhccchhcccccccccccc
Confidence            347999999999999999999999999999998753221   2111                             14678


Q ss_pred             chHHHHHHhcCCh----HHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCC
Q 016321          240 SMEQLAASLRISR----PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGF  315 (391)
Q Consensus       240 s~~e~A~a~~~s~----~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~  315 (391)
                      +..+||.+.+++.    .+|.+.++.|..|+++|++.|.|+|+++|.+|.+.+.+.+||+|+|+|||++|+++|||++|+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~  161 (245)
T 3ugo_A           82 KTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF  161 (245)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCC
T ss_pred             hhHHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCC
Confidence            8999999999974    456667788999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhhhhc---cccc---ccCCCCCChhHHhh--HHHHHHHHHHHHH
Q 016321          316 KISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLK---FDLS---SSLPKKGSKFEQIG--VLLSSICKLLMYL  385 (391)
Q Consensus       316 rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~~~l~---~dl~---~~~~k~ge~~e~ig--~~ls~v~~~L~~~  385 (391)
                      +|+||+.||||++|.++|+++.+.++....-......+.   ..+.   ...++..++++.+|  +..+.|.+.|...
T Consensus       162 ~F~tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~a  239 (245)
T 3ugo_A          162 KFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA  239 (245)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTC-------------------------------------------------------
T ss_pred             cHHHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            999999999999999999999887663221111111111   1111   13457778999999  9999988877643
>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
>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
>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
>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
>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 391
d1siga_334 a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5 4e-22
d1ku2a2180 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq 3e-21
d1rp3a387 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A 9e-15
>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334 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: Sigma70
species: Escherichia coli [TaxId: 562]

 Score = 93.8 bits (232), Expect = 4e-22
 Identities = 46/259 (17%), Positives = 100/259 (38%)

Query: 69  TQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFE 128
           T     L +    +     E   +  ++ ++ S + + + E    L+   +  +  +  +
Sbjct: 67  THVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAK 126

Query: 129 RTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPEL 188
                 +  +            +  +Q         +  ++   Q+    +L        
Sbjct: 127 GRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMP 186

Query: 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASL 248
            +N +  +     S+     A  +      K     ++    L++    E         +
Sbjct: 187 KKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQV 246

Query: 249 RISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308
           +     +     +   A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++K
Sbjct: 247 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 306

Query: 309 FDSSKGFKISTYVYWWIRQ 327
           F+  +G+K STY  WWIRQ
Sbjct: 307 FEYRRGYKFSTYATWWIRQ 325
>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180 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 ?
Query391
d1ku2a2180 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 100.0
d1siga_334 Sigma70 {Escherichia coli [TaxId: 562]} 99.9
d1rp3a387 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 99.86
d1or7a2113 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 98.77
d1h3la_75 Sigma factor SigR {Streptomyces coelicolor a3(2) [ 97.41
d1rp3a177 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 96.77
d1l0oc_57 SigmaF {Bacillus stearothermophilus [TaxId: 1422]} 96.68
d1ku2a160 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 94.94
>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=5e-35  Score=259.26  Aligned_cols=148  Identities=32%  Similarity=0.517  Sum_probs=121.0

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHH------------------HhhCCCCc---------hHH
Q 016321          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLK------------------ERLGCEPS---------MEQ  243 (391)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~------------------~~~g~ePs---------~~e  243 (391)
                      |+++.||++|+++|+||++||++|+++|+.|..+........                  ...+..|.         ..+
T Consensus         2 DpVr~YLreig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~~   81 (180)
T d1ku2a2           2 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE   81 (180)
T ss_dssp             HHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTHHH
T ss_pred             CcHHHHHHHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHHHH
Confidence            689999999999999999999999999998865433222111                  01222222         233


Q ss_pred             HHHHhcCC---hHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhh
Q 016321          244 LAASLRIS---RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (391)
Q Consensus       244 ~A~a~~~s---~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTY  320 (391)
                      +.......   .+++.+.++.+..|+++||++|+|||++||++|.++|++++||||+|+|||++|+++|||++|++|+||
T Consensus        82 ~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~ty  161 (180)
T d1ku2a2          82 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  161 (180)
T ss_dssp             HHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            33333333   355667777899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhh
Q 016321          321 VYWWIRQVRLLLICTFKQ  338 (391)
Q Consensus       321 A~~~IR~aI~~aIre~~R  338 (391)
                      |+||||++|.++|+++.|
T Consensus       162 a~~~i~~~i~~~~~~~~r  179 (180)
T d1ku2a2         162 ATWWIRQAINRAIADQAR  179 (180)
T ss_dssp             HHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHHHHHHhCC
Confidence            999999999999988765
>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
>d1rp3a1 a.4.13.1 (A:87-163) 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
>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure