Citrus Sinensis ID: 017616

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-------37
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVASAN
cccccEEccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHcHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHccccccccccccccccccHHHHHHHHHHHccHHHHHHccccccHHHHHHccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccEEEEHHHHcccccccHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHcc
ccccEEEccEEccccccccccccccccccccccccEcccccEEEcccccccccccHHccccccEEEEccccccccccccccccccccccccEcccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHccccccccccccccccccccccccccccEEEEcccHHHHHHHHHHcHHHHccccccccccccHHccccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHcc
mgmgfrlnlkwvspvqshffttsscrlsstsvrgregsfnsARLSFLSTISedsasyfqdpvkayTCSFVntqtvendyseTEEIRQKstscigqdassrsDFRLLMENLDVlestfadsDALRLEREILQQLGKLGALKLFNSHLSRIvktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktaRVSEESIETSLlslpsealqeglkqptiFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEkesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNyrglgipfsdllqagnvgvlqgaerfdhtrgykfsTYVQYWIRKSISKMVASAN
MGMGFRLNLKWVSPVQSHFfttsscrlsstsvrgregsfNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEirqkstscigqdassRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRivktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktarvseesietsllslpsealqeglkqptifsaeralnsRGRRLtiarneaemskgvqvvaNLERIKTTLekesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQgaerfdhtrgykfSTYVQYWIRKSISKMVASAN
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREIlqqlgklgalklFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVseesietsllslpseALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVASAN
****FRLNLKWVSPVQSHFFTTSSCR*****************LSFLSTISEDSASYFQDPVKAYTCSFVNTQTV***************************FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDL******************************************************************************************VQVVANLERIKTTL*****KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI********
**MGFRLNLKWVSPV****************************LS*****************K*YTCSFVNTQTVENDYSE********************DFRLLMENLDVLE**********LEREILQQLGKLGALKLFNS**********************************************************************************RALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLE********LNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA***
MGMGFRLNLKWVSPVQSHFFTTSS**************FNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVE********************ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSK*******************SLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVASAN
*GMGFRLNLKWVSPVQS**********SSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVK*********************************************************************TIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVASA*
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
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MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVASAN
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 ?
Query368 2.2.26 [Sep-21-2011]
O24621 571 RNA polymerase sigma fact yes no 0.872 0.562 0.476 2e-69
O22056 572 RNA polymerase sigma fact no no 0.347 0.223 0.421 9e-28
Q9LD95 547 RNA polymerase sigma fact no no 0.355 0.239 0.381 5e-22
P26683 390 RNA polymerase sigma fact yes no 0.375 0.353 0.330 2e-19
P38023 399 RNA polymerase sigma fact yes no 0.375 0.345 0.345 6e-17
Q31QG5 320 RNA polymerase sigma fact no no 0.339 0.390 0.349 7e-17
P52322 416 RNA polymerase sigma fact no no 0.309 0.274 0.359 6e-16
Q03065 332 RNA polymerase sigma-B fa no no 0.355 0.394 0.330 3e-15
P0A602 528 RNA polymerase sigma fact yes no 0.195 0.136 0.435 3e-15
P0A603 528 RNA polymerase sigma fact yes no 0.195 0.136 0.435 3e-15
>sp|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC PE=2 SV=1 Back     alignment and function desciption
 Score =  263 bits (671), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 163/342 (47%), Positives = 224/342 (65%), Gaps = 21/342 (6%)

Query: 32  VRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVEND-YSETEEIRQKST 90
           VR    S  + R SFLS++ E+S  Y  D +KA  C+ V+  T +N+ Y E ++ ++   
Sbjct: 73  VRIPMTSVVATRWSFLSSVKEESRIYQNDSLKACGCASVSPYTAQNNVYVELKDPKEN-- 130

Query: 91  SCIGQDASSRS-------DFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFN 143
             IG  ++ RS        + LL +NL  LE TF   D++R+ER+I+ Q+GKLGA +LF 
Sbjct: 131 --IGVGSAERSYSSRSMLQYNLLAKNLLALEETFVALDSVRMERDIMLQMGKLGAAELFK 188

Query: 144 SHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIET 203
           + LSR   +S    LSD  TE      ++     ++ V S+RK K+K + + V+ E+ + 
Sbjct: 189 TCLSRYRGSSITSCLSDT-TELVDTTPNQ-----QVFVSSRRKVKKKARRSSVTAENGDQ 242

Query: 204 SLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLE 263
           S L +        +  P +    R    R +R  I+RNE EMS GV++VA++ERI+T LE
Sbjct: 243 SSLPIGLRTTWNNIDVPRV---RRPPKYRKKRERISRNETEMSTGVKIVADMERIRTQLE 299

Query: 264 KESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFS 323
           +ESGK ASL+CWA AAG++E++L ++L +GWYCR+EL+KSTR LVLFLARNYRGLGI   
Sbjct: 300 EESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHE 359

Query: 324 DLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365
           DL+QAG VGVLQGAERFDHTRGYKFSTYVQYWIRKS+S MV+
Sbjct: 360 DLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVS 401
Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released.
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|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|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|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa GN=rpoD1 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|P0A602|RPOD_MYCTU RNA polymerase sigma factor RpoD OS=Mycobacterium tuberculosis GN=rpoD PE=1 SV=1 Back     alignment and function description
>sp|P0A603|RPOD_MYCBO RNA polymerase sigma factor RpoD OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) GN=rpoD PE=3 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query368
225429414 561 PREDICTED: RNA polymerase sigma factor r 0.991 0.650 0.525 1e-109
147865632 611 hypothetical protein VITISV_036980 [Viti 0.907 0.546 0.520 1e-98
224088962 559 predicted protein [Populus trichocarpa] 0.980 0.645 0.494 2e-93
255550882 560 RNA polymerase sigma factor rpoD, putati 0.989 0.65 0.505 2e-89
39840783 548 sigma factor [Spinacia oleracea] 0.980 0.658 0.479 5e-87
449461399 559 PREDICTED: RNA polymerase sigma factor s 0.978 0.644 0.453 1e-81
356565804 551 PREDICTED: RNA polymerase sigma factor r 0.956 0.638 0.460 2e-75
7363220 567 sigma factor 3 [Sinapis alba] 0.845 0.548 0.476 3e-73
357436347 549 RNA polymerase sigma-B factor [Medicago 0.983 0.659 0.458 2e-70
297820128 568 predicted protein [Arabidopsis lyrata su 0.926 0.600 0.467 2e-68
>gi|225429414|ref|XP_002275831.1| PREDICTED: RNA polymerase sigma factor rpoD [Vitis vinifera] gi|296081598|emb|CBI20603.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  402 bits (1033), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 206/392 (52%), Positives = 268/392 (68%), Gaps = 27/392 (6%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQD 60
           MGMGFRLNLKW  P+     T S  RL ++SV+G+E SF+S R SF S  SED  S ++D
Sbjct: 1   MGMGFRLNLKWDFPISCPTLTNSPSRLCTSSVQGKEASFDSTRFSFPSVTSEDCESLYKD 60

Query: 61  PVKAYTCSFVNTQTVENDYSETEEIRQKSTSC---------------IGQD--------- 96
           P K + CS    QT ENDYS  E ++ K   C               IG+D         
Sbjct: 61  PFKPFACSSGALQTFENDYSAMEAMKMKIGKCSHGDLFKIVNASQAPIGEDISASVAGLQ 120

Query: 97  ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVL 156
           AS  S F LL+ENLD+LE  FADS+ +RLER+I+ QLG+LGALKLF   LSR +KTS   
Sbjct: 121 ASKASQFSLLLENLDILEEMFADSNMVRLERDIMVQLGRLGALKLFQICLSRTLKTSTSF 180

Query: 157 DLSDVHTE---EQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEAL 213
           DL    TE   E + N + D H+ K++V S +K +RK K  R  E++       LPS+ +
Sbjct: 181 DLFSAPTEHIRECQTNGTVDDHLDKVVVRSGKKEERKSKRERALEKADNIYAFPLPSKTI 240

Query: 214 QEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLN 273
           ++G  +P++ + +R LNSR +RL  A+NEAEMSKGV++VANLERI+ TLE+E G  ASL+
Sbjct: 241 RKGPGRPSVSTVKRTLNSRRKRLMNAKNEAEMSKGVKLVANLERIRATLEEEIGHVASLS 300

Query: 274 CWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGV 333
            WA+AAGV ++VL+Q L FGWYCR+EL++ST  LVL++ARNYRG+G+ F D+LQAGN+GV
Sbjct: 301 NWAEAAGVDKKVLQQQLQFGWYCRDELLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGV 360

Query: 334 LQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365
           LQGAERFDHT+GY+FSTYVQYWIRKS+S +VA
Sbjct: 361 LQGAERFDHTKGYRFSTYVQYWIRKSMSTLVA 392

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|147865632|emb|CAN83254.1| hypothetical protein VITISV_036980 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224088962|ref|XP_002308586.1| predicted protein [Populus trichocarpa] gi|222854562|gb|EEE92109.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255550882|ref|XP_002516489.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223544309|gb|EEF45830.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|39840783|emb|CAD20832.1| sigma factor [Spinacia oleracea] Back     alignment and taxonomy information
>gi|449461399|ref|XP_004148429.1| PREDICTED: RNA polymerase sigma factor sigC-like [Cucumis sativus] gi|449507267|ref|XP_004162982.1| PREDICTED: RNA polymerase sigma factor sigC-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356565804|ref|XP_003551127.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max] Back     alignment and taxonomy information
>gi|7363220|emb|CAB83107.1| sigma factor 3 [Sinapis alba] Back     alignment and taxonomy information
>gi|357436347|ref|XP_003588449.1| RNA polymerase sigma-B factor [Medicago truncatula] gi|355477497|gb|AES58700.1| RNA polymerase sigma-B factor [Medicago truncatula] Back     alignment and taxonomy information
>gi|297820128|ref|XP_002877947.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297323785|gb|EFH54206.1| predicted protein [Arabidopsis lyrata subsp. lyrata] 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 ?
Query368
TAIR|locus:2084420 571 SIGC "AT3G53920" [Arabidopsis 0.858 0.553 0.458 1.1e-64
TAIR|locus:2025650 572 SIG2 "AT1G08540" [Arabidopsis 0.375 0.241 0.410 2.1e-26
TAIR|locus:2057996 547 SIGF "AT2G36990" [Arabidopsis 0.355 0.239 0.381 2.6e-21
UNIPROTKB|Q84LK8 572 SIG6 "Sig6" [Oryza sativa Japo 0.342 0.220 0.341 1.7e-16
TAIR|locus:2173249 419 SIG4 "AT5G13730" [Arabidopsis 0.298 0.262 0.380 2.3e-13
UNIPROTKB|O48655 519 rsigA "Plastid RNA polymerase 0.396 0.281 0.288 1.2e-12
TIGR_CMR|GSU_3089 577 GSU_3089 "RNA polymerase sigma 0.336 0.214 0.335 2.4e-12
UNIPROTKB|P0A602 528 rpoD "RNA polymerase sigma fac 0.195 0.136 0.435 4.7e-12
UNIPROTKB|Q59563 323 mysB "RNA polymerase sigma fac 0.198 0.226 0.438 6.1e-12
TIGR_CMR|APH_0576 627 APH_0576 "RNA polymerase sigma 0.187 0.110 0.420 2.5e-11
TAIR|locus:2084420 SIGC "AT3G53920" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 659 (237.0 bits), Expect = 1.1e-64, P = 1.1e-64
 Identities = 151/329 (45%), Positives = 204/329 (62%)

Query:    41 SARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVEND-YSETEEIRQK-STSCIGQDAS 98
             + R SFLS++ E+S  Y  D +KA  C+ V+  T +N+ Y E ++ ++        +  S
Sbjct:    82 ATRWSFLSSVKEESRIYQNDSLKACGCASVSPYTAQNNVYVELKDPKENIGVGSAERSYS 141

Query:    99 SRS--DFRLLMENLDVLESTFADSDALRLEREIXXXXXXXXXXXXFNSHLSRIVKTSNVL 156
             SRS   + LL +NL  LE TF   D++R+ER+I            F + LSR   +S   
Sbjct:   142 SRSMLQYNLLAKNLLALEETFVALDSVRMERDIMLQMGKLGAAELFKTCLSRYRGSSITS 201

Query:   157 DLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVXXXXXXXXXXXXXXXALQEG 216
              LSD  TE   + D+      ++ V S+RK K+K + + V                    
Sbjct:   202 CLSDT-TE---LVDTTPNQ--QVFVSSRRKVKKKARRSSVTAENGDQSSLPIGLRTTWNN 255

Query:   217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWA 276
             +  P +    R    R +R  I+RNE EMS GV++VA++ERI+T LE+ESGK ASL+CWA
Sbjct:   256 IDVPRV---RRPPKYRKKRERISRNETEMSTGVKIVADMERIRTQLEEESGKVASLSCWA 312

Query:   277 QAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQG 336
              AAG++E++L ++L +GWYCR+EL+KSTR LVLFLARNYRGLGI   DL+QAG VGVLQG
Sbjct:   313 AAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQG 372

Query:   337 AERFDHTRGYKFSTYVQYWIRKSISKMVA 365
             AERFDHTRGYKFSTYVQYWIRKS+S MV+
Sbjct:   373 AERFDHTRGYKFSTYVQYWIRKSMSTMVS 401
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;IMP
GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS
GO:0009507 "chloroplast" evidence=ISM;IDA
GO:0019685 "photosynthesis, dark reaction" evidence=NAS
GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS
GO:0071482 "cellular response to light stimulus" evidence=IEP
GO:0001053 "plastid sigma factor activity" evidence=IMP
GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP
GO:0016987 "sigma factor activity" evidence=ISS
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
TAIR|locus:2173249 SIG4 "AT5G13730" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|O48655 rsigA "Plastid RNA polymerase sigma factor" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_3089 GSU_3089 "RNA polymerase sigma factor RpoD" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
UNIPROTKB|P0A602 rpoD "RNA polymerase sigma factor RpoD" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
UNIPROTKB|Q59563 mysB "RNA polymerase sigma factor" [Mycobacterium tuberculosis (taxid:1773)] 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

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

Fail to connect to STRING server

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 ?
Query368
TIGR02997 298 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f 2e-25
PRK07406 373 PRK07406, PRK07406, RNA polymerase sigma factor Rp 7e-23
PRK05949 327 PRK05949, PRK05949, RNA polymerase sigma factor; V 9e-22
PRK07405 317 PRK07405, PRK07405, RNA polymerase sigma factor Si 1e-20
COG0568 342 COG0568, RpoD, DNA-directed RNA polymerase, sigma 1e-18
TIGR02393 238 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor 1e-18
PRK07921 324 PRK07921, PRK07921, RNA polymerase sigma factor Si 7e-16
PRK07598 415 PRK07598, PRK07598, RNA polymerase sigma factor Si 2e-15
TIGR02394 285 TIGR02394, rpoS_proteo, RNA polymerase sigma facto 5e-15
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 8e-15
PRK09210 367 PRK09210, PRK09210, RNA polymerase sigma factor Rp 3e-14
pfam0454271 pfam04542, Sigma70_r2, Sigma-70 region 2 1e-12
PRK07500 289 PRK07500, rpoH2, RNA polymerase factor sigma-32; R 4e-12
TIGR02392 270 TIGR02392, rpoH_proteo, alternative sigma factor R 1e-11
PRK05657 325 PRK05657, PRK05657, RNA polymerase sigma factor Rp 2e-11
PRK05658 619 PRK05658, PRK05658, RNA polymerase sigma factor Rp 7e-11
TIGR02980 227 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, 2e-10
PRK06596 284 PRK06596, PRK06596, RNA polymerase factor sigma-32 2e-10
COG1191 247 COG1191, FliA, DNA-directed RNA polymerase special 3e-06
TIGR02937158 TIGR02937, sigma70-ECF, RNA polymerase sigma facto 2e-05
TIGR02479 224 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, 1e-04
TIGR02850 254 TIGR02850, spore_sigG, RNA polymerase sigma-G fact 9e-04
PRK07408 256 PRK07408, PRK07408, RNA polymerase sigma factor Si 9e-04
PRK07122 264 PRK07122, PRK07122, RNA polymerase sigma factor Si 0.001
PRK08215 258 PRK08215, PRK08215, sporulation sigma factor SigG; 0.001
PRK06288 268 PRK06288, PRK06288, RNA polymerase sigma factor Wh 0.001
TIGR02885 231 TIGR02885, spore_sigF, RNA polymerase sigma-F fact 0.003
>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information 
 Score =  103 bits (260), Expect = 2e-25
 Identities = 55/138 (39%), Positives = 86/138 (62%), Gaps = 1/138 (0%)

Query: 229 LNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287
           L   GR  L     E E+++ VQ +  LE ++  LE++ G+  S   WA AAG+SE  L+
Sbjct: 7   LQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELR 66

Query: 288 QHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           Q L  G   +E++IK+   LV+ +A+ Y+  G+   DL+Q G++G+ +  E+FD TRGYK
Sbjct: 67  QRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYK 126

Query: 348 FSTYVQYWIRKSISKMVA 365
           FSTY  +WIR+ I++ +A
Sbjct: 127 FSTYAYWWIRQGITRAIA 144

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|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated Back     alignment and domain information
>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; 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|213709 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>gnl|CDD|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated Back     alignment and domain information
>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS Back     alignment and domain information
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional 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|236033 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH 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|234078 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G subfamily Back     alignment and domain information
>gnl|CDD|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>gnl|CDD|224112 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>gnl|CDD|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family 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|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor Back     alignment and domain information
>gnl|CDD|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>gnl|CDD|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed Back     alignment and domain information
>gnl|CDD|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed Back     alignment and domain information
>gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 368
PRK07598 415 RNA polymerase sigma factor SigC; Validated 100.0
TIGR02997 298 Sig70-cyanoRpoD RNA polymerase sigma factor, cyano 100.0
PRK07406 373 RNA polymerase sigma factor RpoD; Validated 99.98
PRK05949 327 RNA polymerase sigma factor; Validated 99.97
PRK07405 317 RNA polymerase sigma factor SigD; Validated 99.97
PRK05901 509 RNA polymerase sigma factor; Provisional 99.96
COG0568 342 RpoD DNA-directed RNA polymerase, sigma subunit (s 99.96
PRK07921 324 RNA polymerase sigma factor SigB; Reviewed 99.94
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 99.89
PRK07122 264 RNA polymerase sigma factor SigF; Reviewed 99.88
PRK09210 367 RNA polymerase sigma factor RpoD; Validated 99.86
TIGR02392 270 rpoH_proteo alternative sigma factor RpoH. A sigma 99.83
TIGR02393 238 RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter 99.82
PRK07500 289 rpoH2 RNA polymerase factor sigma-32; Reviewed 99.81
PRK06596 284 RNA polymerase factor sigma-32; Reviewed 99.81
COG1191 247 FliA DNA-directed RNA polymerase specialized sigma 99.78
PRK07408 256 RNA polymerase sigma factor SigF; Reviewed 99.78
PRK05911 257 RNA polymerase sigma factor sigma-28; Reviewed 99.76
TIGR02850 254 spore_sigG RNA polymerase sigma-G factor. Members 99.67
PRK05657 325 RNA polymerase sigma factor RpoS; Validated 99.66
PRK08215 258 sporulation sigma factor SigG; Reviewed 99.66
TIGR02895 218 spore_sigI RNA polymerase sigma-I factor. Members 99.63
TIGR02980 227 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G 99.6
TIGR02394 285 rpoS_proteo RNA polymerase sigma factor RpoS. A si 99.59
TIGR02885 231 spore_sigF RNA polymerase sigma-F factor. Members 99.58
PRK06288 268 RNA polymerase sigma factor WhiG; Reviewed 99.56
PRK12427 231 flagellar biosynthesis sigma factor; Provisional 99.55
TIGR02941 255 Sigma_B RNA polymerase sigma-B factor. This sigma 99.54
TIGR02479 224 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f 99.49
PRK07670 251 RNA polymerase sigma factor SigD; Validated 99.49
PRK05803 233 sporulation sigma factor SigK; Reviewed 99.45
PRK08583 257 RNA polymerase sigma factor SigB; Validated 99.44
PRK06986 236 fliA flagellar biosynthesis sigma factor; Validate 99.44
PRK05572 252 sporulation sigma factor SigF; Validated 99.39
TIGR02846 227 spore_sigmaK RNA polymerase sigma-K factor. The sp 99.2
PF0454271 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762 99.2
PRK08311 237 putative RNA polymerase sigma factor SigI; Reviewe 99.19
PRK08295 208 RNA polymerase factor sigma-70; Validated 99.12
PRK08301 234 sporulation sigma factor SigE; Reviewed 99.12
TIGR02835 234 spore_sigmaE RNA polymerase sigma-E factor. Member 99.04
TIGR02859 198 spore_sigH RNA polymerase sigma-H factor. Members 99.03
TIGR02937158 sigma70-ECF RNA polymerase sigma factor, sigma-70 98.97
PRK09652 182 RNA polymerase sigma factor RpoE; Provisional 98.84
PRK05602186 RNA polymerase sigma factor; Reviewed 98.83
PRK09641187 RNA polymerase sigma factor SigW; Provisional 98.74
TIGR02948187 SigW_bacill RNA polymerase sigma-W factor. This si 98.72
PRK09646194 RNA polymerase sigma factor SigK; Reviewed 98.72
PRK12513194 RNA polymerase sigma factor; Provisional 98.72
PRK06811189 RNA polymerase factor sigma-70; Validated 98.71
PRK09648189 RNA polymerase sigma factor SigD; Reviewed 98.71
PRK13919186 putative RNA polymerase sigma E protein; Provision 98.69
PRK09640188 RNA polymerase sigma factor SigX; Reviewed 98.65
PRK06759154 RNA polymerase factor sigma-70; Validated 98.65
PRK09638176 RNA polymerase sigma factor SigY; Reviewed 98.6
PRK12519194 RNA polymerase sigma factor; Provisional 98.56
TIGR02952170 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02 98.55
PRK11923 193 algU RNA polymerase sigma factor AlgU; Provisional 98.53
PRK11922 231 RNA polymerase sigma factor; Provisional 98.52
PRK11924179 RNA polymerase sigma factor; Provisional 98.49
TIGR02939190 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s 98.49
PRK12524196 RNA polymerase sigma factor; Provisional 98.48
PRK12514179 RNA polymerase sigma factor; Provisional 98.48
PRK12526206 RNA polymerase sigma factor; Provisional 98.46
TIGR02954169 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02 98.45
PRK12534187 RNA polymerase sigma factor; Provisional 98.34
PRK12538233 RNA polymerase sigma factor; Provisional 98.33
PRK12531194 RNA polymerase sigma factor; Provisional 98.33
PRK09643192 RNA polymerase sigma factor SigM; Reviewed 98.31
PRK12515189 RNA polymerase sigma factor; Provisional 98.31
TIGR02985161 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba 98.3
PRK12536181 RNA polymerase sigma factor; Provisional 98.3
TIGR02984 189 Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl 98.29
TIGR02989159 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop 98.28
PRK12537182 RNA polymerase sigma factor; Provisional 98.27
PRK12539184 RNA polymerase sigma factor; Provisional 98.17
PRK12512184 RNA polymerase sigma factor; Provisional 98.15
PRK12522173 RNA polymerase sigma factor; Provisional 98.12
PRK12518175 RNA polymerase sigma factor; Provisional 98.09
PRK12543 179 RNA polymerase sigma factor; Provisional 98.01
PRK12542 185 RNA polymerase sigma factor; Provisional 97.89
TIGR02999183 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f 97.87
PRK09415179 RNA polymerase factor sigma C; Reviewed 97.85
COG1595182 RpoE DNA-directed RNA polymerase specialized sigma 97.79
TIGR02983162 SigE-fam_strep RNA polymerase sigma-70 factor, sig 97.79
PRK09639166 RNA polymerase sigma factor SigX; Provisional 97.72
TIGR03001 244 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco 97.68
PRK08241 339 RNA polymerase factor sigma-70; Validated 97.65
PRK09649185 RNA polymerase sigma factor SigC; Reviewed 97.64
PRK12541161 RNA polymerase sigma factor; Provisional 97.59
PRK12547164 RNA polymerase sigma factor; Provisional 97.59
PRK09644165 RNA polymerase sigma factor SigM; Provisional 97.55
PRK12535 196 RNA polymerase sigma factor; Provisional 97.47
PRK09647 203 RNA polymerase sigma factor SigE; Reviewed 97.47
TIGR02947 193 SigH_actino RNA polymerase sigma-70 factor, TIGR02 97.46
PRK12528161 RNA polymerase sigma factor; Provisional 97.46
TIGR02950154 SigM_subfam RNA polymerase sigma factor, SigM fami 97.45
PRK09645173 RNA polymerase sigma factor SigL; Provisional 97.44
PRK09637 181 RNA polymerase sigma factor SigZ; Provisional 97.38
PRK12532 195 RNA polymerase sigma factor; Provisional 97.37
PRK12520 191 RNA polymerase sigma factor; Provisional 97.36
TIGR02943 188 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02 97.34
PRK12533 216 RNA polymerase sigma factor; Provisional 97.24
TIGR02959 170 SigZ RNA polymerase sigma factor, SigZ family. Thi 97.24
PRK12516 187 RNA polymerase sigma factor; Provisional 97.21
TIGR02960 324 SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa 97.21
PRK09642160 RNA polymerase sigma factor SigW; Reviewed 97.16
PRK12523172 RNA polymerase sigma factor; Reviewed 97.01
PRK12546 188 RNA polymerase sigma factor; Provisional 96.95
PRK12544 206 RNA polymerase sigma factor; Provisional 96.94
PRK12540 182 RNA polymerase sigma factor; Provisional 96.94
PRK07037163 extracytoplasmic-function sigma-70 factor; Validat 96.83
PRK12529178 RNA polymerase sigma factor; Provisional 96.8
PRK12545 201 RNA polymerase sigma factor; Provisional 96.79
PRK12517188 RNA polymerase sigma factor; Provisional 96.77
PF0014037 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr 96.57
PRK12530 189 RNA polymerase sigma factor; Provisional 96.56
PRK09651172 RNA polymerase sigma factor FecI; Provisional 96.53
PRK12511 182 RNA polymerase sigma factor; Provisional 96.5
PRK12527159 RNA polymerase sigma factor; Reviewed 96.14
PRK12525168 RNA polymerase sigma factor; Provisional 95.98
PRK09636 293 RNA polymerase sigma factor SigJ; Provisional 95.81
TIGR02957 281 SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa 95.72
PF1264565 HTH_16: Helix-turn-helix domain; InterPro: IPR0247 95.68
PF0453978 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 95.25
PRK06704 228 RNA polymerase factor sigma-70; Validated 94.92
TIGR03209142 P21_Cbot clostridium toxin-associated regulator Bo 94.38
PRK09191 261 two-component response regulator; Provisional 94.32
PRK09635 290 sigI RNA polymerase sigma factor SigI; Provisional 94.11
PF07638185 Sigma70_ECF: ECF sigma factor 94.11
PHA02547179 55 RNA polymerase sigma factor; Provisional 91.02
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 86.57
>PRK07598 RNA polymerase sigma factor SigC; Validated Back     alignment and domain information 
Probab=100.00  E-value=4e-35  Score=295.74  Aligned_cols=145  Identities=33%  Similarity=0.549  Sum_probs=131.3

Q ss_pred             HHHHHHhhccCC-CCCCcHHHHHHHhhchHHHH--------------------HHHHHHHHHHHhCCCCchhHHHHHc--
Q 017616          223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWAQAA--  279 (368)
Q Consensus       223 ~~v~~~~~~~~~-~LLtaeEE~eL~~~Iq~~~~--------------------Le~ir~~L~~~~gr~pt~~ewA~a~--  279 (368)
                      +.|+-|++.+++ ||||++||++|+++||.++.                    |++++..|++++|++||..+||.++  
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            334555556664 99999999999999999999                    8999999999999999999999554  


Q ss_pred             --------------------CCCHHHHHHHHHhcHHHHHHHHHHchHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHh
Q 017616          280 --------------------GVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER  339 (368)
Q Consensus       280 --------------------g~~~eeL~~~l~~G~~Are~LI~~nlrLV~~IAkrY~~rg~d~eDLiQEG~iGLirAVek  339 (368)
                                          ||++++|.+.++.|..|+++||++|+++|+++|++|.++|++++||+|||++|||+|+++
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                                556666667778898999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCccccHHHHHHHHHHHHHHHhc
Q 017616          340 FDHTRGYKFSTYVQYWIRKSISKMVASA  367 (368)
Q Consensus       340 FDpskG~rFSTYA~~wIRqaI~r~Lrr~  367 (368)
                      |||++|++|+|||+||||++|.++++++
T Consensus       220 FDp~rG~rFSTYa~wwIRqaI~r~i~~~  247 (415)
T PRK07598        220 FDPTKGYRFSTYAYWWIRQGITRAIATQ  247 (415)
T ss_pred             cCcccCCCHHHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999999999753

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information
>PRK07406 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK05949 RNA polymerase sigma factor; Validated Back     alignment and domain information
>PRK07405 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>PRK05901 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Back     alignment and domain information
>PRK07921 RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>PRK05658 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK07122 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PRK09210 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>TIGR02392 rpoH_proteo alternative sigma factor RpoH Back     alignment and domain information
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>PRK06596 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
>PRK07408 RNA polymerase sigma factor SigF; Reviewed 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
>PRK05657 RNA polymerase sigma factor RpoS; Validated Back     alignment and domain information
>PRK08215 sporulation sigma factor SigG; Reviewed Back     alignment and domain information
>TIGR02895 spore_sigI RNA polymerase sigma-I factor Back     alignment and domain information
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily Back     alignment and domain information
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS Back     alignment and domain information
>TIGR02885 spore_sigF RNA polymerase sigma-F factor Back     alignment and domain information
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed Back     alignment and domain information
>PRK12427 flagellar biosynthesis sigma factor; Provisional Back     alignment and domain information
>TIGR02941 Sigma_B RNA polymerase sigma-B factor Back     alignment and domain information
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family Back     alignment and domain information
>PRK07670 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>PRK05803 sporulation sigma factor SigK; Reviewed Back     alignment and domain information
>PRK08583 RNA polymerase sigma factor SigB; Validated Back     alignment and domain information
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated Back     alignment and domain information
>PRK05572 sporulation sigma factor SigF; Validated Back     alignment and domain information
>TIGR02846 spore_sigmaK RNA polymerase sigma-K 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
>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
>PRK08301 sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor Back     alignment and domain information
>TIGR02859 spore_sigH RNA polymerase sigma-H factor Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>PRK05602 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>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
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>PRK12513 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK06811 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK09648 RNA polymerase sigma factor SigD; Reviewed Back     alignment and domain information
>PRK13919 putative RNA polymerase sigma E protein; Provisional Back     alignment and domain information
>PRK09640 RNA polymerase sigma factor SigX; Reviewed Back     alignment and domain information
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK09638 RNA polymerase sigma factor SigY; Reviewed Back     alignment and domain information
>PRK12519 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
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Back     alignment and domain information
>PRK11922 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK11924 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE Back     alignment and domain information
>PRK12524 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12526 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
>PRK12534 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12538 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12531 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09643 RNA polymerase sigma factor SigM; Reviewed Back     alignment and domain information
>PRK12515 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
>PRK12536 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1 Back     alignment and domain information
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12539 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
>PRK12518 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12543 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12542 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family Back     alignment and domain information
>PRK09415 RNA polymerase factor sigma C; Reviewed 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
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1 Back     alignment and domain information
>PRK08241 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK09649 RNA polymerase sigma factor SigC; Reviewed Back     alignment and domain information
>PRK12541 RNA polymerase sigma factor; Provisional 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
>PRK12535 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09647 RNA polymerase sigma factor SigE; Reviewed Back     alignment and domain information
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family Back     alignment and domain information
>PRK12528 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family Back     alignment and domain information
>PRK09645 RNA polymerase sigma factor SigL; Provisional Back     alignment and domain information
>PRK09637 RNA polymerase sigma factor SigZ; Provisional Back     alignment and domain information
>PRK12532 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12520 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
>PRK12533 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family Back     alignment and domain information
>PRK12516 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family Back     alignment and domain information
>PRK09642 RNA polymerase sigma factor SigW; Reviewed 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
>PRK12544 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12540 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated Back     alignment and domain information
>PRK12529 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12545 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12517 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1 Back     alignment and domain information
>PRK12530 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09651 RNA polymerase sigma factor FecI; Provisional Back     alignment and domain information
>PRK12511 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12527 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK12525 RNA polymerase sigma factor; Provisional 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
>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
>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
>PRK06704 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR Back     alignment and domain information
>PRK09191 two-component response regulator; Provisional Back     alignment and domain information
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional Back     alignment and domain information
>PF07638 Sigma70_ECF: ECF sigma factor Back     alignment and domain information
>PHA02547 55 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK05658 RNA polymerase sigma factor RpoD; Validated 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 ?
Query368
3iyd_F 613 Three-Dimensional Em Structure Of An Intact Activat 7e-14
4igc_X 613 X-ray Crystal Structure Of Escherichia Coli Sigma70 8e-14
1sig_A339 Crystal Structure Of A Sigma70 Subunit Fragment Fro 8e-14
1l9z_H 438 Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun 2e-13
3les_A179 2f5 Epitope Scaffold Es2 Length = 179 2e-13
3dxj_F 423 Crystal Structure Of Thermus Thermophilus Rna Polym 3e-13
1iw7_F 423 Crystal Structure Of The Rna Polymerase Holoenzyme 3e-13
1ku2_A241 Crystal Structure Of Thermus Aquaticus Rna Polymera 3e-13
1l9u_H 332 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 4e-13
4g7h_F 443 Crystal Structure Of Thermus Thermophilus Transcrip 4e-13
3ugo_A245 Crystal Structure Of Rna-Polymerase Sigma Subunit D 4e-13
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613 Back     alignment and structure 
Iteration: 1

 Score = 74.7 bits (182), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 52/71 (73%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +W
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 356 IRKSISKMVAS 366
           IR++I++ +A 
Sbjct: 435 IRQAITRSIAD 445
>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613 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|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|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|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|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332 Back     alignment and structure
>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query368
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 3e-17
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 1e-16
1l0o_C 243 Sigma factor; bergerat fold, helix-turn-helix, pro 3e-16
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 3e-16
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 1e-15
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 5e-15
1rp3_A 239 RNA polymerase sigma factor sigma-28 (FLIA); trans 3e-13
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-04
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A* 3les_A* Length = 245 Back     alignment and structure
 Score = 79.2 bits (195), Expect = 3e-17
 Identities = 29/69 (42%), Positives = 50/69 (72%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WI
Sbjct: 112 RQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWI 171

Query: 357 RKSISKMVA 365
           R++I++ +A
Sbjct: 172 RQAINRAIA 180
>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
>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
>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
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 613 Back     alignment and structure
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Length = 339 Back     alignment and structure
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query368
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 99.93
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 99.93
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 99.93
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 99.65
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 99.56
1rp3_A 239 RNA polymerase sigma factor sigma-28 (FLIA); trans 99.31
1l0o_C 243 Sigma factor; bergerat fold, helix-turn-helix, pro 99.24
1or7_A 194 Sigma-24, RNA polymerase sigma-E factor; regulatio 98.86
2q1z_A184 RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc 98.78
2o7g_A112 Probable RNA polymerase sigma-C factor; sigma fact 98.32
1h3l_A87 RNA polymerase sigma factor; transcription, DNA-bi 98.18
2lfw_A157 PHYR sigma-like domain; signal transduction, respo 97.06
3n0r_A 286 Response regulator; sigma factor, receiver, two-co 95.7
>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=99.93  E-value=2.9e-26  Score=214.55  Aligned_cols=146  Identities=25%  Similarity=0.415  Sum_probs=122.8

Q ss_pred             HHHHHHHhhccCC-CCCCcHHHHHHHhhchHHHHHH-HHHHHH--HHH-----------------------hCCCCchhH
Q 017616          222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLE-RIKTTL--EKE-----------------------SGKAASLNC  274 (368)
Q Consensus       222 ~~~v~~~~~~~~~-~LLtaeEE~eL~~~Iq~~~~Le-~ir~~L--~~~-----------------------~gr~pt~~e  274 (368)
                      .|.|+-|++..++ ||||++||++|+++|+.++.+. .+....  +..                       .+.+|+..+
T Consensus         6 ~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~~   85 (245)
T 3ugo_A            6 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE   85 (245)
T ss_dssp             CHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHHH
T ss_pred             CCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhHH
Confidence            3456777777775 9999999999999999987733 332210  000                       146888999


Q ss_pred             HHHHcCCC----HHHHHHHHHhcHHHHHHHHHHchHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHhcCCCCCCcccc
Q 017616          275 WAQAAGVS----ERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFST  350 (368)
Q Consensus       275 wA~a~g~~----~eeL~~~l~~G~~Are~LI~~nlrLV~~IAkrY~~rg~d~eDLiQEG~iGLirAVekFDpskG~rFST  350 (368)
                      ||.+.|++    ..+|.+.++.|+.|+++|+..|.|+|.++|++|.+.+.+.+||+|||++||++|+++|||++|++|+|
T Consensus        86 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~t  165 (245)
T 3ugo_A           86 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  165 (245)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHH
T ss_pred             HHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHHH
Confidence            99998875    34566677788889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 017616          351 YVQYWIRKSISKMVASA  367 (368)
Q Consensus       351 YA~~wIRqaI~r~Lrr~  367 (368)
                      |++||||++|.++++++
T Consensus       166 ya~~~ir~~i~~~ir~~  182 (245)
T 3ugo_A          166 YATWWIRQAINRAIADQ  182 (245)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999999999999864
>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
>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

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 368
d1siga_334 a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5 9e-21
d1ku2a2180 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq 1e-14
d1rp3a387 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A 1e-14
>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 = 89.6 bits (221), Expect = 9e-21
 Identities = 27/71 (38%), Positives = 52/71 (73%)

Query: 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY 354
             ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 321

Query: 355 WIRKSISKMVA 365
           WIR++I++ +A
Sbjct: 322 WIRQAITRSIA 332
>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 ?
Query368
d1ku2a2180 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 100.0
d1siga_334 Sigma70 {Escherichia coli [TaxId: 562]} 99.92
d1rp3a387 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 99.87
d1or7a2113 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 98.77
d1h3la_75 Sigma factor SigR {Streptomyces coelicolor a3(2) [ 97.21
d1l0oc_57 SigmaF {Bacillus stearothermophilus [TaxId: 1422]} 96.45
d1rp3a177 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 95.72
d1ku2a160 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 93.48
>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=1.5e-34  Score=254.48  Aligned_cols=147  Identities=24%  Similarity=0.388  Sum_probs=115.0

Q ss_pred             CCchHHHHHHHhhccCCCCCCcHHHHHHHhhchHHHHHHHHHHHHH------------------HHhCCCCchhHHHHHc
Q 017616          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLE------------------KESGKAASLNCWAQAA  279 (368)
Q Consensus       218 ~~~~~~~v~~~~~~~~~~LLtaeEE~eL~~~Iq~~~~Le~ir~~L~------------------~~~gr~pt~~ewA~a~  279 (368)
                      +||++.|+++   .+..||||++||++|+++|+.+..+.+...+..                  ...+..|...+|....
T Consensus         1 tDpVr~YLre---ig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~   77 (180)
T d1ku2a2           1 SDPVRQYLHE---IGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPK   77 (180)
T ss_dssp             CHHHHHHHHH---HTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTT
T ss_pred             CCcHHHHHHH---hcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHH
Confidence            3566555542   344699999999999999998877554432221                  0123344443332211


Q ss_pred             C---------C---CHHHHHHHHHhcHHHHHHHHHHchHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHhcCCCCCCc
Q 017616          280 G---------V---SERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK  347 (368)
Q Consensus       280 g---------~---~~eeL~~~l~~G~~Are~LI~~nlrLV~~IAkrY~~rg~d~eDLiQEG~iGLirAVekFDpskG~r  347 (368)
                      .         .   ....+.+.++.|+.|+++||++|+|||.+||++|.++|++++||+|||+||||+||++|||++|++
T Consensus        78 ~~~~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~  157 (180)
T d1ku2a2          78 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFK  157 (180)
T ss_dssp             THHHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSC
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCC
Confidence            1         1   134566777889999999999999999999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHHHHHHHhc
Q 017616          348 FSTYVQYWIRKSISKMVASA  367 (368)
Q Consensus       348 FSTYA~~wIRqaI~r~Lrr~  367 (368)
                      |+|||+||||++|.++|+++
T Consensus       158 f~tya~~~i~~~i~~~~~~~  177 (180)
T d1ku2a2         158 FSTYATWWIRQAINRAIADQ  177 (180)
T ss_dssp             HHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999875
>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1h3la_ a.177.1.1 (A:) Sigma factor SigR {Streptomyces coelicolor a3(2) [TaxId: 100226]} Back     information, alignment and structure
>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure