Citrus Sinensis ID: 006477

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640---
MADLENLLLEAAGRTNSAGRNRHSASSSKRRREGSYSGSDSRDDDSDDNRGYGSRKPSGSQVPLKKRLDPAERDDDQGSQEEGDYDGGASEHEGDSSNESDDDNHGQMTELEREMMIFERDDKKVDKNLRDKFRSRREERSTRSTKETPPLPSSRSARLAARSADRAAAKDDALNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVKRKAFTPAGLSSSSQSESESRSHSDDEGSTGDGGMADSDDDGAPGSGRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDSKVKDAKAIRLAEMNRKNRVENFKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVGMAATEAALEAAAGAGKLVDTNAPLDLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIEATVGCQVPENDGRRHALTLTVGDYKRRRGLL
ccccHHHHHHHccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccHHHHHHHHcccHHHHHccccEEEEEEccccccccEEEEEEEEEEEcccccccccccEEEEEEEEEEEcccccccEEEcEEcccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccHHHHHHHcccc
cccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcEEcHHHHHHHHccccHHHHccccEEEEEEcccccccEEEEEEEEEEEEEccccEEEEcccEccEEEEEEEccccEEEEEEEEEEccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccHcccccccEEEEcccccccccccccccccccHHcccccccccccccccccccccEEcHHHHHHHcccc
MADLENLLLEAAGrtnsagrnrhsassskrrregsysgsdsrdddsddnrgygsrkpsgsqvplkkrldpaerdddqgsqeegdydggasehegdssnesdddnhgQMTELEREMMIFERDDKKVDKNLRDKFRSrreerstrstketpplpssrsARLAARSADRAAAKDDALNELRAKRLKQQDPEAHRRlrdasrggsgsrvlspvkrkaftpaglssssqsesesrshsddegstgdggmadsdddgapgsgrptyddikEITIRRSKLAKWFMEPFFEELIVGCFVrvgigrskngpiyrlcmvrnvdatepdrsyklenrtTCKYLNVTWGNESSAARWQMamvsdsppleEEFKQWLREVErnsgrmpskqdvlEKKESIQKINTFVYSAATVKQMLQEKksassrplnvaaEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDSKVKDAKAIRLAEMNRKNRVENFKNASELKRVNtslkageagydpfsrrwtrsrnyyiskpgeevtaeangdkngvpggangeegatgevGMAATEAALEAAAGagklvdtnapldlgtesnmlhdfELDISLNALKkfggpqgvlaGFMARKQRIEAtvgcqvpendgrrhaltLTVGDYKRRRGLL
MADLENLLLEaagrtnsagrnrhsassskrrregsysgsdsrdddsddnrgygsrkpsgsqvplkkrldpaerdddqgsqeegdydggasehegdssnesdddnHGQMTELEREmmiferddkkvdknlrdkfrsrreerstrstketpplpssrsarLAARSADRAAAKDDALNELRakrlkqqdpeahrrlrdasrggsgsrvlspvkrkaftpaglssssqsesesrshsddegstgdggmadsdddgapgsgrptyddikeITIRRSKLAKWFMEPFFEELIVGCFVRVGigrskngpiyrlcmvrnvdatepdrsyklenrttckylNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVErnsgrmpskqdvlekkesIQKINTFVYSAATVKQMLqekksassrplnvaaekdrLRRELevaqsrhdevdmeRIKKRLqeleasrdskvkdakairlaemnrknrvenfknaselkrvntslkageagydpfsrrwtrSRNYYISKpgeevtaeangdkngvpgGANGEEGATGEVGMAATEAALEAAAGAGKLVDTNAPLDLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIEATvgcqvpendgrrhaltltvgdykrrrgll
MADLENLLLEAAGRTNSAGRNRHSASSSKrrregsysgsdsrdddsddnrgygsrKPSGSQVPLKKRLDPAERDDDQGSQEEGDYDGGAsehegdssnesdddnhgQMTELEREMMIFERDDKKVDKNLRDKFrsrreerstrstketpplpssrsarlaarsadraaakddalNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVKRKAFTPAGLssssqsesesrshsddegstgdggmadsdddgapgsgRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDSKVKDAKAIRLAEMNRKNRVENFKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPggangeegatgevgMaateaaleaaagagKLVDTNAPLDLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIEATVGCQVPENDGRRHALTLTVGDYKRRRGLL
*********************************************************************************************************************************************************************************************************************************************************************DIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQ******************************************KINTFVYSAA*********************************************************************************************************RWTRSRNYYI************************************************KLVDTNAPLDLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIEATVGCQVPENDGRRHALTLTVG*********
MADLENLLL*************************************************************************************DSSNES*********ELEREMMIFERD********************************************************************************************************************************************DIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATV*********************DRLRR******************************************************************************WTR*******************************************************************ESNMLHDFELDISLNAL****************************************TVGDYKRRRGLL
MADLENLLLEAAGRT******************************************************************************************GQMTELEREMMIFERDDKKVDKNLRDKF**************************************DALNELRAKRLK*********************VLSPVKRKA*****************************GMADSDDDGAPGSGRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVE***************KESIQKINTFVYSAATVKQ**************VAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELE********DAKAIRLAEMNRKNRVENFKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVGMAATEAALEAAAGAGKLVDTNAPLDLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIEATVGCQVPENDGRRHALTLTVGDYKRRRGLL
*****N**LE******************************************************************************ASEHEGDSSNESDDDNHGQMTELEREMMIFERDDKKVDKNLRDKFRSRREERS*******************************************************************************************************************RPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDSKVKDAKAIRLAEMNRKNRVENFKNASELKRVNTSL*******DPFSR**TRS*NYYIS************************************************************ESNMLHDFELDISLNALKKFG********************************ALTLTV*DYKRRR***
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MADLENLLLEAAGRTNSAGRNRHSASSSKRRREGSYSGSDSRDDDSDDNRGYGSRKPSGSQVPLKKRLDPAERDDDQGSQEEGDYDGGASEHEGDSSNESDDDNHGQMTELEREMMIFERDDKKVDKNLRDKFRSRREERSTRSTKETPPLPSSRSARLAARSADRAAAKDDALNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVKRKAFTPAGLSSSSQSESESRSHSDDEGSTGDGGMADSDDDGAPGSGRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAKAIRLAEMNRKNRVENFKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVGMAATEAALEAAAGAGKLVDTNAPLDLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIEATVGCQVPENDGRRHALTLTVGDYKRRRGLL
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 ?
Query643 2.2.26 [Sep-21-2011]
A2AQ19715 RNA polymerase-associated yes no 0.538 0.483 0.265 7e-23
Q92541710 RNA polymerase-associated yes no 0.550 0.498 0.264 1e-22
Q5RAD5665 RNA polymerase-associated yes no 0.491 0.475 0.267 6e-21
P53064558 RNA polymerase-associated yes no 0.623 0.718 0.259 4e-20
O94667560 RNA polymerase-associated yes no 0.640 0.735 0.259 2e-19
Q9W261775 RNA polymerase-associated yes no 0.528 0.438 0.240 2e-18
>sp|A2AQ19|RTF1_MOUSE RNA polymerase-associated protein RTF1 homolog OS=Mus musculus GN=Rtf1 PE=2 SV=1 Back     alignment and function desciption
 Score =  109 bits (272), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 104/391 (26%), Positives = 180/391 (46%), Gaps = 45/391 (11%)

Query: 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRS 320
           +++  + + R KL +W   PFF + + GCFVR+GIG   + P+YR+  +  V   E  + 
Sbjct: 362 EELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGV--VETAKV 419

Query: 321 YKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDV 380
           Y+L    T K L +  GN+    R  +  VS+    E EF +W   +     ++P+  ++
Sbjct: 420 YQLGGTRTNKGLQLRHGNDQRVFR--LEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEI 477

Query: 381 LEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDM 440
            +K+ SI++   + ++   ++++++EK+     P N A +K +L +E  +A+   D+   
Sbjct: 478 NKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKTQLLKEKAMAEDLGDQDKA 537

Query: 441 ERIKKRLQELEASRDS----KVKDAKAIRLAEMNRKNRVENFKNASELKRVNTSLKAGEA 496
           ++I+ +L ELE   ++    + K+  AI  + +N++NR  N    SE   V  S      
Sbjct: 538 KQIQDQLNELEERAEALDRQRTKNISAI--SYINQRNREWNIVE-SEKALVAESHNMRNQ 594

Query: 497 GYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVGMAATEAALEA 556
             DPF+RR          KP    T  +N     V      +  A    G+   +A  E 
Sbjct: 595 QMDPFTRRQC--------KP----TIVSNSRDPAVQAAILAQLNAKYGSGVLP-DAPKEM 641

Query: 557 AAGAGKLVDTNAPL--DLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIEAT 614
           + G GK  D N+    DL  +   +HDF++ I L                 + + +  A 
Sbjct: 642 SKGQGKDKDLNSKTASDLSEDLFKVHDFDVKIDLQV--------------PSSESKALAI 687

Query: 615 VGCQVPENDG--RRHALTLTVGDYKRRRGLL 643
                P  DG  RR   +L + DYK+RRGL+
Sbjct: 688 TSKAPPAKDGAPRR---SLNLEDYKKRRGLI 715
Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. Binds single-stranded DNA (By similarity). Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex.
Mus musculus (taxid: 10090)
>sp|Q92541|RTF1_HUMAN RNA polymerase-associated protein RTF1 homolog OS=Homo sapiens GN=RTF1 PE=1 SV=4 Back     alignment and function description
>sp|Q5RAD5|RTF1_PONAB RNA polymerase-associated protein RTF1 homolog (Fragment) OS=Pongo abelii GN=RTF1 PE=2 SV=2 Back     alignment and function description
>sp|P53064|RTF1_YEAST RNA polymerase-associated protein RTF1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RTF1 PE=1 SV=2 Back     alignment and function description
>sp|O94667|RTF1_SCHPO RNA polymerase-associated protein C651.09c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC651.09c PE=1 SV=1 Back     alignment and function description
>sp|Q9W261|RTF1_DROME RNA polymerase-associated protein Rtf1 OS=Drosophila melanogaster GN=Rtf1 PE=1 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 ?
Query643
255555987660 RNA polymerase-associated protein RTF1, 0.998 0.972 0.747 0.0
356521329656 PREDICTED: RNA polymerase-associated pro 0.993 0.974 0.739 0.0
224113965664 PAF1 complex component [Populus trichoca 1.0 0.968 0.713 0.0
356548759656 PREDICTED: RNA polymerase-associated pro 0.993 0.974 0.727 0.0
224078932662 PAF1 complex component [Populus trichoca 0.996 0.968 0.722 0.0
449462844660 PREDICTED: RNA polymerase-associated pro 0.996 0.971 0.717 0.0
297840459643 At1g61040/T7P1_17 [Arabidopsis lyrata su 0.959 0.959 0.650 0.0
15219855643 plus-3 domain-containing protein [Arabid 0.967 0.967 0.665 0.0
20147193643 At1g61040/T7P1_17 [Arabidopsis thaliana] 0.967 0.967 0.664 0.0
356572305646 PREDICTED: RNA polymerase-associated pro 0.979 0.975 0.641 0.0
>gi|255555987|ref|XP_002519028.1| RNA polymerase-associated protein RTF1, putative [Ricinus communis] gi|223541691|gb|EEF43239.1| RNA polymerase-associated protein RTF1, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  867 bits (2241), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 494/661 (74%), Positives = 551/661 (83%), Gaps = 19/661 (2%)

Query: 1   MADLENLLLEAAGRTNSAGRNRHSASSSKRRREGSYSGSDSRDDDSDDNRGYGS--RKPS 58
           MADLENLLLEAAGRT ++GRNR++   S+RRREGSYS   S   D D +   G   RKPS
Sbjct: 1   MADLENLLLEAAGRTGTSGRNRNALPPSRRRREGSYSDGGSDSRDDDSDDDRGYSSRKPS 60

Query: 59  GSQVPLKKRLDPAERDDDQGSQEEGDYDGGASEHEGDSS-----------NESDDDNHGQ 107
           GSQVPLKKRLDP ERDDDQGSQ+EGDYD G S+ EGDSS           NE D     Q
Sbjct: 61  GSQVPLKKRLDPTERDDDQGSQDEGDYDDGNSDREGDSSDGSDVGEDLYKNEDDRRKLAQ 120

Query: 108 MTELEREMMIFERDDKKVDKNLRDKFRSRRE-ERSTRSTKETPPLPSSRSARLAARSADR 166
           M+ELEREM++ ER DKK DKNL ++ RS+RE ER+TRS KETPPLPSSR  R +ARSADR
Sbjct: 121 MSELEREMILSERADKKGDKNLTERIRSKRESERTTRSRKETPPLPSSRGVRTSARSADR 180

Query: 167 AAAKDDALNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVKRKAFTPAGLSSSSQSE 226
           AAAKDDALNEL+A+RLKQQDPEAHR+LRDASR GSGSR  SP+KRK FT +   SSS SE
Sbjct: 181 AAAKDDALNELKARRLKQQDPEAHRKLRDASRRGSGSRGFSPIKRKRFT-SASLSSSSSE 239

Query: 227 SESRSHSDDEGSTGDGGMADSDDDGAPGSGRPTYDDIKEITIRRSKLAKWFMEPFFEELI 286
           SESRSHS+DEGSTGDGGMADSDDDG PGS  PT+DDI+EITIRRSKLAKWFMEP+FEELI
Sbjct: 240 SESRSHSEDEGSTGDGGMADSDDDGEPGSQGPTFDDIREITIRRSKLAKWFMEPWFEELI 299

Query: 287 VGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQ 346
           VGCFVRVGIGRSK+GPIYRLC+VRNVDA +PDR YKLEN+TT KYLNV WGNESSAARWQ
Sbjct: 300 VGCFVRVGIGRSKSGPIYRLCLVRNVDAADPDRPYKLENKTTYKYLNVIWGNESSAARWQ 359

Query: 347 MAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQE 406
           MAM+SDS P E+E+KQW+REVER+ GRMP+KQD+LEKKE+I+K NTFVYSAATVKQMLQE
Sbjct: 360 MAMISDSAPTEDEYKQWVREVERSGGRMPTKQDILEKKEAIRKSNTFVYSAATVKQMLQE 419

Query: 407 KKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDSKVKDAKAIRL 466
           KKSASSRPLNVAAEKDRLRRELEVAQS+ D+ ++ERI+ R+QELEASR ++ KDAKAIRL
Sbjct: 420 KKSASSRPLNVAAEKDRLRRELEVAQSKQDDAEVERIRARIQELEASRQTQGKDAKAIRL 479

Query: 467 AEMNRKNRVENFKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKP-GEEVTAEAN 525
           AEMNRKNR ENF+NASELK VNTSLKAGEAGYDPFSRRWTRSRNYY+SKP G +  A  N
Sbjct: 480 AEMNRKNRAENFRNASELKPVNTSLKAGEAGYDPFSRRWTRSRNYYVSKPAGGDAAAATN 539

Query: 526 GDKNGVPGGANGEEGATG---EVGMAATEAALEAAAGAGKLVDTNAPLDLGTESNMLHDF 582
            + +G    AN  E A G   E GMAAT AALEAAA AGKLVDT AP+D GTESN LH+F
Sbjct: 540 NEASGTVAVANKTESAAGVSAEAGMAATAAALEAAADAGKLVDTAAPVDQGTESNTLHNF 599

Query: 583 ELDISLNALKKFGGPQGVLAGFMARKQRIEATVGCQVPENDGRRHALTLTVGDYKRRRGL 642
           EL ISL AL+KFGG QG  AGFMARKQRIEAT+GC+V END +RH LTLTV DYKRRRGL
Sbjct: 600 ELPISLTALQKFGGAQGAQAGFMARKQRIEATIGCRVSENDEKRHVLTLTVSDYKRRRGL 659

Query: 643 L 643
           L
Sbjct: 660 L 660

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356521329|ref|XP_003529309.1| PREDICTED: RNA polymerase-associated protein RTF1 homolog [Glycine max] Back     alignment and taxonomy information
>gi|224113965|ref|XP_002316628.1| PAF1 complex component [Populus trichocarpa] gi|222859693|gb|EEE97240.1| PAF1 complex component [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356548759|ref|XP_003542767.1| PREDICTED: RNA polymerase-associated protein RTF1 homolog [Glycine max] Back     alignment and taxonomy information
>gi|224078932|ref|XP_002305685.1| PAF1 complex component [Populus trichocarpa] gi|222848649|gb|EEE86196.1| PAF1 complex component [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449462844|ref|XP_004149150.1| PREDICTED: RNA polymerase-associated protein RTF1 homolog [Cucumis sativus] gi|449517636|ref|XP_004165851.1| PREDICTED: RNA polymerase-associated protein RTF1 homolog [Cucumis sativus] Back     alignment and taxonomy information
>gi|297840459|ref|XP_002888111.1| At1g61040/T7P1_17 [Arabidopsis lyrata subsp. lyrata] gi|297333952|gb|EFH64370.1| At1g61040/T7P1_17 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|15219855|ref|NP_176299.1| plus-3 domain-containing protein [Arabidopsis thaliana] gi|12323334|gb|AAG51642.1|AC018908_8 unknown protein; 78902-80833 [Arabidopsis thaliana] gi|332195649|gb|AEE33770.1| plus-3 domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|20147193|gb|AAM10312.1| At1g61040/T7P1_17 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356572305|ref|XP_003554309.1| PREDICTED: RNA polymerase-associated protein RTF1 homolog [Glycine max] 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 ?
Query643
TAIR|locus:2205996643 VIP5 "vernalization independen 0.981 0.981 0.526 5.2e-168
ZFIN|ZDB-GENE-030131-6778739 rtf1 "Rtf1, Paf1/RNA polymeras 0.367 0.319 0.293 4.8e-25
UNIPROTKB|Q92541710 RTF1 "RNA polymerase-associate 0.367 0.332 0.285 7.9e-24
UNIPROTKB|E2RPD2714 RTF1 "Uncharacterized protein" 0.367 0.330 0.285 8.1e-24
MGI|MGI:1309480715 Rtf1 "Rtf1, Paf1/RNA polymeras 0.367 0.330 0.285 8.2e-24
WB|WBGene00009103613 F25B3.6 [Caenorhabditis elegan 0.362 0.380 0.303 8.4e-24
UNIPROTKB|D4A6Z3715 Rtf1 "Protein Rtf1" [Rattus no 0.367 0.330 0.285 1.3e-23
UNIPROTKB|F1NY87701 RTF1 "Uncharacterized protein" 0.367 0.336 0.281 1.4e-23
UNIPROTKB|F1SSV6701 RTF1 "Uncharacterized protein" 0.367 0.336 0.281 3e-23
UNIPROTKB|F1N6E9714 RTF1 "Uncharacterized protein" 0.367 0.330 0.281 3.3e-23
TAIR|locus:2205996 VIP5 "vernalization independence 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1634 (580.3 bits), Expect = 5.2e-168, P = 5.2e-168
 Identities = 345/655 (52%), Positives = 408/655 (62%)

Query:     1 MADLENLLLEAAGRTNSAGRNRHSASSSKXXXXXXXXXXXXXXXXXXXXXXXXXXKPSGS 60
             M DLENLLLEAAGRTNSAGR+RH  SS +                          KPSGS
Sbjct:     1 MGDLENLLLEAAGRTNSAGRSRHPPSSRRREGSYSDGSSDSRDDSDEDRGYASR-KPSGS 59

Query:    61 QVPLKKRLDPAERDD----------DQGSQEEGDYDGGAXXXXXXXXXXXXXXXXXQMTE 110
             QVPLKKRL+ AER+D          D  S  EGD    +                  MTE
Sbjct:    60 QVPLKKRLE-AEREDRAARVEGGYGDGPSDREGDSSEESDFGDDLYKNEEDRQKLAGMTE 118

Query:   111 LEREMMIFERDDKKVDKNLRDKFXXXXXXXXXXXXXXXXXXX-XXXXXXXXXXXXXXXXX 169
              +REM++ ER DKK DKN  +K                                      
Sbjct:   119 FQREMILSERADKKGDKNFTEKLRSKRESEKTPVSKKETQPLPASRGVRSSARSADRAAA 178

Query:   170 XXXXXNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVKRKAFTPAGLXXXXXXXXXX 229
                  NELRAKR+KQQDP A R+LRDAS+GGSGSR  S  KRK    + L          
Sbjct:   179 KDDALNELRAKRMKQQDPAALRKLRDASKGGSGSRDFSSTKRKPLASSNLSSSSQSDSDS 238

Query:   230 XXXXXXXXXXXXXXXXXXXXXXXXXXXRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGC 289
                                         PT++D+KE+TIRRSKLAKW MEPFFEELIVGC
Sbjct:   239 RSQSDDEGSNGGMLDSDDDRSDV-----PTFEDVKEVTIRRSKLAKWLMEPFFEELIVGC 293

Query:   290 FVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAM 349
             FVRVGIGRSK+GPIYRLC V+NVDAT+PD++YKLEN+TT KYLNV WGNE+SAARWQMAM
Sbjct:   294 FVRVGIGRSKSGPIYRLCWVKNVDATDPDKTYKLENKTTHKYLNVVWGNETSAARWQMAM 353

Query:   350 VSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKS 409
             +SD  PLEEE++QW+REVER +GRMP+KQD+ EKKE+IQ+ N+FVYSA TVKQMLQEKKS
Sbjct:   354 ISDGHPLEEEYRQWIREVERTNGRMPTKQDISEKKEAIQRTNSFVYSAETVKQMLQEKKS 413

Query:   410 ASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDSKVKDAKAIRLAEM 469
             AS RP+NVAAEKDRLR+ELE+AQS++DE  +ERIK ++++L+ASR+ K  D KA++LAEM
Sbjct:   414 ASVRPMNVAAEKDRLRKELEIAQSKNDEAGVERIKSKIKQLDASRNKKGVDKKALKLAEM 473

Query:   470 NRKNRVENFKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKN 529
             N+KNR ENFKNASE+K +  SLKAGEAGYDPFSRRWTRS NYY  K         +G++N
Sbjct:   474 NKKNRAENFKNASEVKSITASLKAGEAGYDPFSRRWTRSSNYYNGK-----NKGKDGEEN 528

Query:   530 -GVPXXXXXXXXXXXXXXMXXXXXXXXXXXXXXKLVDTNAPLDLGTESNMLHDFELDISL 588
                               +              KL+DT AP+  G E N LH+FEL +SL
Sbjct:   529 EAAVAAAVETNGADAGAGVEATEAALEAAAEAGKLIDTRAPIGQGAEHNQLHNFELSLSL 588

Query:   589 NALKKFGGPQGVLAGFMARKQRIEATVGCQVPENDGRRHALTLTVGDYKRRRGLL 643
              AL+K+GGPQGV   FMARKQ  EATVGC+V ENDG+RH LTLTV DYKRRRGLL
Sbjct:   589 TALQKYGGPQGVQKAFMARKQLTEATVGCRVAENDGKRHGLTLTVSDYKRRRGLL 643
GO:0003677 "DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA
GO:0016570 "histone modification" evidence=IEA
GO:0009910 "negative regulation of flower development" evidence=IMP
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IMP
GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA
GO:0008284 "positive regulation of cell proliferation" evidence=RCA
GO:0009630 "gravitropism" evidence=RCA
GO:0030244 "cellulose biosynthetic process" evidence=RCA
GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA
GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA
GO:0043687 "post-translational protein modification" evidence=RCA
GO:0048193 "Golgi vesicle transport" evidence=RCA
GO:0048573 "photoperiodism, flowering" evidence=RCA
GO:0051276 "chromosome organization" evidence=RCA
ZFIN|ZDB-GENE-030131-6778 rtf1 "Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q92541 RTF1 "RNA polymerase-associated protein RTF1 homolog" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E2RPD2 RTF1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:1309480 Rtf1 "Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
WB|WBGene00009103 F25B3.6 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|D4A6Z3 Rtf1 "Protein Rtf1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1NY87 RTF1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1SSV6 RTF1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|F1N6E9 RTF1 "Uncharacterized protein" [Bos taurus (taxid:9913)] 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 ?
Query643
pfam03126105 pfam03126, Plus-3, Plus-3 domain 1e-34
COG5296521 COG5296, COG5296, Transcription factor involved in 1e-30
smart00719109 smart00719, Plus3, Short conserved domain in trans 2e-30
PRK12678672 PRK12678, PRK12678, transcription termination fact 0.002
>gnl|CDD|190531 pfam03126, Plus-3, Plus-3 domain Back     alignment and domain information 
 Score =  126 bits (319), Expect = 1e-34
 Identities = 47/109 (43%), Positives = 61/109 (55%), Gaps = 6/109 (5%)

Query: 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPI--YRLCMVRNVDATEPD 318
           DDI  I + RS LAK    P FE  +VGCFVRV IG  K      YRL  +  V      
Sbjct: 1   DDINRIRLGRSLLAKLLFYPGFESTVVGCFVRVNIGPDKETGQQSYRLAQITGVKEG--K 58

Query: 319 RSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREV 367
           + Y+L  +TT KYL VT G   S   ++++ VS+SP  EEEF++WL+  
Sbjct: 59  KPYQLGGKTTDKYLKVTHGK--SERVFRISFVSNSPFTEEEFERWLQSC 105

This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor. Length = 105
>gnl|CDD|227615 COG5296, COG5296, Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription] Back     alignment and domain information
>gnl|CDD|197843 smart00719, Plus3, Short conserved domain in transcriptional regulators Back     alignment and domain information
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 643
KOG2402525 consensus Paf1/RNA polymerase II complex, RTF1 com 100.0
COG5296521 Transcription factor involved in TATA site selecti 100.0
smart00719109 Plus3 Short conserved domain in transcriptional re 100.0
PF03126108 Plus-3: Plus-3 domain; InterPro: IPR004343 The yea 99.97
KOG2402525 consensus Paf1/RNA polymerase II complex, RTF1 com 83.61
>KOG2402 consensus Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription] Back     alignment and domain information 
Probab=100.00  E-value=3.9e-82  Score=686.98  Aligned_cols=462  Identities=36%  Similarity=0.517  Sum_probs=346.1

Q ss_pred             CCCCCCCCCCCCCCCCCCChhhhHhhccCChhHHHHHHhhhHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCchhhhh
Q 006477           80 QEEGDYDGGASEHEGDSSNESDDDNHGQMTELEREMMIFERDDKKVDKNLRDKFRSRREERSTRSTKETPPLPSSRSARL  159 (643)
Q Consensus        80 ~~~~~~~~~~~p~EgkykDe~DR~~L~~MtElERE~iLaeR~ee~e~~~~r~~l~~~~~k~k~~~rk~~~~~~ssr~~Rs  159 (643)
                      +++++.-.+||++| +|++++||.+|+.|+|++||+|||+|. .++.+.- +.+...          +...+..+++.|+
T Consensus        62 ~e~e~e~e~~~r~E-~yk~~~~R~ki~~~~e~~re~~~~er~-~~q~e~~-rk~~~~----------e~Q~~~~~~~~rs  128 (525)
T KOG2402|consen   62 DEEEDEQENPTRLE-KYKDEADREKIALMLELERETILFERS-KKQKEKR-RKSDVR----------EMQQLSDSRKERS  128 (525)
T ss_pred             chhhhhhccccHHH-HHHHHHHHHHHhhhHHHHHHHHHHHHH-HHHHHHH-Hhccch----------hhhcccchhhhhh
Confidence            44455568899999 999999999999999999999999999 2222211 112111          1112234677888


Q ss_pred             hhhcccccchhHHHHHHHHHHHhhcCCHHHHHhhhcccCCCCCCcccCccccccCCCCCCCCCCccccccCCCCCCCCCC
Q 006477          160 AARSADRAAAKDDALNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVKRKAFTPAGLSSSSQSESESRSHSDDEGST  239 (643)
Q Consensus       160 S~R~~~~~~~K~~AL~eLK~kRekk~~r~~~rr~~d~s~~~s~s~~~sp~~r~~~~s~~~ss~s~~d~e~rs~sdee~~~  239 (643)
                      +.|+..+.+.+++||+.|+++|++......+....+..  .+-+.++.+    ..-++++++++.+...++..+.+..  
T Consensus       129 s~R~~~~s~~~~~a~s~lk~kR~~~~~~~k~~~e~~~e--~~~sev~~k----~~~~se~~~~~~s~e~s~~~~~~~~--  200 (525)
T KOG2402|consen  129 SVRSSVRSDKKKSAMSLLKAKRERLEEVKKRNAEKDLE--RSLSEVTYK----RSPSSELGSEDESKEFSRRSSYDQS--  200 (525)
T ss_pred             hhccccccccchhhhHhhhcccchHHHHHHHhhhccch--hchhhhccC----CCCCCCccccccccccchhhccccc--
Confidence            88854455789999999999999543211111111100  111222222    2111222222111111111111111  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCHhhhhcceechHHHHHhhcCccccccccccEEEEeecCCCCCCceEEEEEEEeecCCCCC
Q 006477          240 GDGGMADSDDDGAPGSGRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDR  319 (643)
Q Consensus       240 ~~~~~~d~~de~~~~~~~atledl~~irLsRs~L~k~~~~P~Fee~V~GCFVRV~IG~~~~g~vYRm~qI~gV~~~e~~K  319 (643)
                         ......+++.+..+.++++||+.|||+|++|++|||+|||+++|+||||||+||.+.++|+||||+|+||.  ++.|
T Consensus       201 ---~s~~~~~e~~p~~~v~~~~dln~~rlsR~~vak~~~~P~Fe~~V~gCfvRv~ig~~~~~p~YRv~~I~gV~--es~k  275 (525)
T KOG2402|consen  201 ---SSEEEDEEKDPDARVPSISDLNALRLSRHKVAKWLFSPFFESTVTGCFVRVGIGGEGSKPVYRVAEIVGVL--ESDK  275 (525)
T ss_pred             ---cCcchhcccCcccCCCCHHHHHHHHhhHHHHHHHHhhhHHHHHhhhheEEeeecCcCCCCceeEEEEeeec--ccCc
Confidence               11111222234568899999999999999999999999999999999999999998667999999999997  5999


Q ss_pred             ccccCCceeeeEEEEEeCCCccceeeeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHhcCCCCHHH
Q 006477          320 SYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAAT  399 (643)
Q Consensus       320 ~Y~l~~~~Tnk~L~L~~G~~~~~r~f~m~~VSNspfTe~Ef~rw~~~~~~~~~~lPT~~~v~~K~~~I~ka~n~~~Teed  399 (643)
                      ||.|+++.||+||.|.||..  .++|+|++|||++||+.||++|+.+|...++.+||++.|..|+.+|.++++|+|++.+
T Consensus       276 ~Y~l~~~~Tnk~l~~~~G~s--~r~f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~~a~~~~~sd~~  353 (525)
T KOG2402|consen  276 PYKLEGVKTNKYLRVRHGRS--ERVFRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIVKALNYRLSDKE  353 (525)
T ss_pred             cccccceeecceeeeecCcc--hhhcchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHhcCccCccc
Confidence            99999999999999999986  4899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCchhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccc--ccchHHHHHHHHHHHhhHHHH
Q 006477          400 VKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDS--KVKDAKAIRLAEMNRKNRVEN  477 (643)
Q Consensus       400 I~~ml~~K~~~~~~~~N~a~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~~~~~--~~~~~~~~~la~IN~RNRk~N  477 (643)
                      |.+||++|..+...|.|+||||++|++++++|...||...|+.|+.||.+||+.+..  ....+.+..|++||+|||++ 
T Consensus       354 v~~~v~~k~~~~~~p~N~ameK~~l~k~r~~A~~~~d~~~a~~~~~qi~elE~~a~~~~~~~~s~i~~~~~lN~rNR~~-  432 (525)
T KOG2402|consen  354 VDQMVAEKFEASPRPRNVAMEKTGLRKERDLAQLLGDAKSAEEIQRQINELEARAEELDKARASPILKLAELNRRNRRR-  432 (525)
T ss_pred             HHHHHHhhhhcCcCcchHHHHHHhHHHHHHHHHhcccHhHHHHHHHHHHHHHHHHhhhccccccccccccccchhHHHH-
Confidence            999999999999999999999999999999999999999999999999999998732  22345578899999999999 


Q ss_pred             HHHHHHHHHHhhhhhcCCCCCCCCcccccccceeccCCCCCccccccCCCCCCCCCCCCCCCCCccccchhhhHHHHHHH
Q 006477          478 FKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVGMAATEAALEAA  557 (643)
Q Consensus       478 ~~~a~e~k~~~~~~k~ge~~~DPFsRrkTr~k~~y~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  557 (643)
                      ++.+.  ....+.++.+..+ |||||+||++++||+++++.+++-++.+..              ++.++.++.++..++
T Consensus       433 ~~~a~--~~~~~~~~~~~~~-dpfTRr~~~~~v~~~s~~k~~~~ls~~~~~--------------~~~~~~~~~~~~~~~  495 (525)
T KOG2402|consen  433 IAKAE--LSGGAVAKNLSAP-DPFTRRKTRTSVLYGSKYKPEGALSAEIAR--------------AGKKLEASEAAEKAA  495 (525)
T ss_pred             hhhhh--hhhhhhhhcCCCC-CCccccccccceeecccCCCCchhhccccc--------------cccccCccccccccc
Confidence            54542  1122223344444 999999999999999999998655433221              122222222222221


Q ss_pred             hhcCCCcCCCCCCCCCcccccccccccccchhhhhhc
Q 006477          558 AGAGKLVDTNAPLDLGTESNMLHDFELDISLNALKKF  594 (643)
Q Consensus       558 a~~gk~~~~~~~~~~~~~~~~~h~f~l~i~l~~l~~~  594 (643)
                             +..+++|++++++.||+|+++|||.+|++|
T Consensus       496 -------~~~s~~~~~~~l~~lh~f~~~ldl~~~~~~  525 (525)
T KOG2402|consen  496 -------EKRSLIDQSQDLMSLHDFDLDLDLKVLQKF  525 (525)
T ss_pred             -------ccccchhhhhhhhhhcccceeecccccCCC
Confidence                   234788999999999999999999999876

>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription] Back     alignment and domain information
>smart00719 Plus3 Short conserved domain in transcriptional regulators Back     alignment and domain information
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1 Back     alignment and domain information
>KOG2402 consensus Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query643
2bze_A153 Nmr Structure Of Human Rtf1 Plus3 Domain Length = 1 5e-12
2db9_A149 Solution Structure Of The Plus-3 Domain Of Human Ki 8e-12
3u1u_A137 Crystal Structure Of Rna Polymerase-Associated Prot 2e-11
>pdb|2BZE|A Chain A, Nmr Structure Of Human Rtf1 Plus3 Domain Length = 153 Back     alignment and structure 
Iteration: 1

 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 68/129 (52%), Gaps = 4/129 (3%)
Query: 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRS 320
           +++  + + R KL +W   PFF + + GCFVR+GIG   + P+YR+  +  V   E  + 
Sbjct: 26  EELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGV--VETAKV 83
Query: 321 YKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDV 380
           Y+L    T K L +  GN+    R  +  VS+    E EF +W   +     ++P+  ++
Sbjct: 84  YQLGGTRTNKGLQLRHGNDQRVFR--LEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEI 141
Query: 381 LEKKESIQK 389
            +K+ SI++
Sbjct: 142 NKKELSIKE 150
>pdb|2DB9|A Chain A, Solution Structure Of The Plus-3 Domain Of Human Kiaa0252 Protein Length = 149 Back     alignment and structure
>pdb|3U1U|A Chain A, Crystal Structure Of Rna Polymerase-Associated Protein Rtf1 Homolog Plus-3 Domain Length = 137 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 ?
Query643
3u1u_A137 RNA polymerase-associated protein RTF1 homolog; pl 3e-40
2bze_A153 KIAA0252 protein; human RTF1 PLUS3 domain, transcr 6e-38
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-04
>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3, transcription elongation, structural genomics, struc genomics consortium, SGC; 1.80A {Homo sapiens} PDB: 2db9_A Length = 137 Back     alignment and structure
 Score =  142 bits (360), Expect = 3e-40
 Identities = 37/132 (28%), Positives = 69/132 (52%), Gaps = 4/132 (3%)

Query: 258 PTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEP 317
              +++  + + R KL +W   PFF + + GCFVR+GIG   + P+YR+  +  V   E 
Sbjct: 9   SLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGV--VET 66

Query: 318 DRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSK 377
            + Y+L    T K L +  GN+     +++  VS+    E EF +W   +     ++P+ 
Sbjct: 67  AKVYQLGGTRTNKGLQLRHGNDQRV--FRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTL 124

Query: 378 QDVLEKKESIQK 389
            ++ +K+ SI++
Sbjct: 125 DEINKKELSIKE 136
>2bze_A KIAA0252 protein; human RTF1 PLUS3 domain, transcription, elongation, PAF1 complex, histone H3 methylation, H2B ubiquitination, CDC73, LEO1, CTR9; NMR {Homo sapiens} SCOP: b.34.21.1 Length = 153 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 ?
Query643
3u1u_A137 RNA polymerase-associated protein RTF1 homolog; pl 100.0
2bze_A153 KIAA0252 protein; human RTF1 PLUS3 domain, transcr 100.0
>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3, transcription elongation, structural genomics, struc genomics consortium, SGC; 1.80A {Homo sapiens} PDB: 2db9_A Back     alignment and structure
Probab=100.00  E-value=6.9e-41  Score=313.26  Aligned_cols=132  Identities=28%  Similarity=0.582  Sum_probs=122.9

Q ss_pred             CCCCCHhhhhcceechHHHHHhhcCccccccccccEEEEeecCCCCCCceEEEEEEEeecCCCCCccccCCceeeeEEEE
Q 006477          255 SGRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNV  334 (643)
Q Consensus       255 ~~~atledl~~irLsRs~L~k~~~~P~Fee~V~GCFVRV~IG~~~~g~vYRm~qI~gV~~~e~~K~Y~l~~~~Tnk~L~L  334 (643)
                      .+.++|+||++|+|+|++|++||++|+|+++|+||||||+||++.+.++||||+|+||.  +++++|+|+++.||+||.|
T Consensus         6 ~~v~~l~dl~~i~L~R~~l~~~~~~P~Fe~~V~GcFVRv~ig~~~~~~~Yrl~qI~gv~--~~~k~Y~l~~~~T~~~L~l   83 (137)
T 3u1u_A            6 QPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVV--ETAKVYQLGGTRTNKGLQL   83 (137)
T ss_dssp             SBCCSHHHHHTTBCCHHHHHHHTTSTTHHHHHTTCEEEEEEEC----CEEEEEEEEEEE--EEEEEEEETTEEEEEEEEE
T ss_pred             CCCCCHHHhcceEEEHHHHHHHhcCCChhHheEEEEEEEEeCCCCCCccEEEEEEEEEE--ecCcccccCCceeeEEEEE
Confidence            57889999999999999999999999999999999999999998755999999999996  4799999999999999999


Q ss_pred             EeCCCccceeeeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Q 006477          335 TWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKI  390 (643)
Q Consensus       335 ~~G~~~~~r~f~m~~VSNspfTe~Ef~rw~~~~~~~~~~lPT~~~v~~K~~~I~ka  390 (643)
                      +||+.  .+.|+|++|||+|||++||++|+++|++.++++||+.+|++|+++|++|
T Consensus        84 ~~g~~--~r~~~~~~vSN~~fte~E~~~w~~~~~~~~~~~Pt~~~l~~K~~~i~~a  137 (137)
T 3u1u_A           84 RHGND--QRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEA  137 (137)
T ss_dssp             EETTE--EEEEEGGGBCSSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHTCCC
T ss_pred             EeCCc--ceEEEeeeecCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhhC
Confidence            99986  4789999999999999999999999999999999999999999999754
>2bze_A KIAA0252 protein; human RTF1 PLUS3 domain, transcription, elongation, PAF1 complex, histone H3 methylation, H2B ubiquitination, CDC73, LEO1, CTR9; NMR {Homo sapiens} SCOP: b.34.21.1 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 643
d2bzea1132 b.34.21.1 (A:345-476) RNA polymerase-associated pr 2e-42
>d2bzea1 b.34.21.1 (A:345-476) RNA polymerase-associated protein RTF1 homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 132 Back     information, alignment and structure

class: All beta proteins
fold: SH3-like barrel
superfamily: Plus3-like
family: Plus3
domain: RNA polymerase-associated protein RTF1 homolog
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  147 bits (372), Expect = 2e-42
 Identities = 36/129 (27%), Positives = 68/129 (52%), Gaps = 4/129 (3%)

Query: 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRS 320
           +++  + + R KL +W   PFF + + GCFVR+GIG   + P+YR+  +      E  + 
Sbjct: 5   EELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEI--TGVVETAKV 62

Query: 321 YKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDV 380
           Y+L    T K L +  GN+     +++  VS+    E EF +W   +     ++P+  ++
Sbjct: 63  YQLGGTRTNKGLQLRHGNDQRV--FRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEI 120

Query: 381 LEKKESIQK 389
            +K+ SI++
Sbjct: 121 NKKELSIKE 129

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query643
d2bzea1132 RNA polymerase-associated protein RTF1 homolog {Hu 100.0
>d2bzea1 b.34.21.1 (A:345-476) RNA polymerase-associated protein RTF1 homolog {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: SH3-like barrel
superfamily: Plus3-like
family: Plus3
domain: RNA polymerase-associated protein RTF1 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.7e-41  Score=308.51  Aligned_cols=131  Identities=28%  Similarity=0.589  Sum_probs=124.4

Q ss_pred             CCHhhhhcceechHHHHHhhcCccccccccccEEEEeecCCCCCCceEEEEEEEeecCCCCCccccCCceeeeEEEEEeC
Q 006477          258 PTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWG  337 (643)
Q Consensus       258 atledl~~irLsRs~L~k~~~~P~Fee~V~GCFVRV~IG~~~~g~vYRm~qI~gV~~~e~~K~Y~l~~~~Tnk~L~L~~G  337 (643)
                      .+.+||++|+|+|++|++|||+|+|+++|+||||||+||++.+.++||||+|+||.  +++++|+++++.||+||.|+||
T Consensus         2 ~~~e~l~~irL~R~~l~~~~~~P~Fe~~v~GcFVRv~ig~~~~~~~Yrl~~I~gv~--~~~k~Y~~~~~~T~~~L~l~~g   79 (132)
T d2bzea1           2 SLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVV--ETAKVYQLGGTRTNKGLQLRHG   79 (132)
T ss_dssp             CCHHHHHHSEECHHHHHHHSSSSSCHHHHTTCEEEEESSTTSSSCCEEEEEEEEEE--EEEEEEEETTEEEEEEEEEESS
T ss_pred             CChHHhhheEEeHHHHHHHHcCCchHHhheeeEEEEEeCCCCCCCceEEEEEEeee--ecCcccccCCCcccEEEEEEEC
Confidence            57899999999999999999999999999999999999976666999999999997  4899999999999999999999


Q ss_pred             CCccceeeeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHhc
Q 006477          338 NESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINT  392 (643)
Q Consensus       338 ~~~~~r~f~m~~VSNspfTe~Ef~rw~~~~~~~~~~lPT~~~v~~K~~~I~ka~n  392 (643)
                      +.  .+.|+|++|||+|||++||++|+++|.+.++++||+.+|++|+++|++|+|
T Consensus        80 ~~--~~~~~l~~vSn~~fte~E~~~w~~~~~~~~~~~Pt~~~l~~K~~~i~~a~n  132 (132)
T d2bzea1          80 ND--QRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEALN  132 (132)
T ss_dssp             SC--EEEECGGGBCCSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHHHHHC-
T ss_pred             Cc--eeEEEeEEEeCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence            87  479999999999999999999999999999999999999999999999976