Citrus Sinensis ID: 046343

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---
SSGSLFGGAVNITGAKRKFDSLASPVKTITSPLSPHHSSTSKMVVTPVSTAMTTAKWLRTIICPLPSKPSADLQGANLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPALSAEINLGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDYRSVLVERNNFTSLVKDCLLGLNNLKSKPLPPPLYPTRSNPGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNRDSEVNHNNDASVFPALPDMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSNRRVRGALNFDDVDVDVGLVSDSMVVNSLYLQNGSAAASTCAVLKPEQLDP
ccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHcccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHEEEccccccHHHHHHHHHcccccccccEEEEEccccEEEEEcccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccEEEEEEccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccc
ccccccccccccccHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHcccccHHHcccHcccccccHccccccccccccccccccccccccccccccEEEEEEcccccccccccccHHHHHHHHHHccccccccHHHHHccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccHHHHHHHHcccEEEEEcHEEHHHHHHHHHHHcccccccccccccccccccccccccccccccccEEcccccEEEEcccccccccccccccEEEEEEEcccccccccHHHHHHHHHHHHccccccEEEEEccccccccccccccccccccccccccccccccccccccccc
ssgslfggavnitgakrkfdslaspvktitsplsphhsstskmvvtPVSTAMTTAKWLRTiicplpskpsadlqganLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPALSAEINLGFTDILFQDSQDSWEEFTSiltvpptdsptrqhyenlpwwkepftevdsifllipmpsldAIAMHInfssgglspvhslhkhetspvcsifnfqFYANCYGELVTDDYRSVLVERNNFTSLVKDCLLglnnlkskplppplyptrsnpggggepcaetginicfCKINKLAAVRINAMVERLQLSQQIRESVYclcpkrtlnqrtslffnchidQIILCCFYGVAKISQLNLTFKEIIYnygkqpqckpqvfrsvfDHVDIITfynkifaptvkpllvelgpvgtamktnrdsevnhnndasvfpalpdmspkkvsathsvyvsplrtsEMDALISHSsksyyacvgesthayspfkdltdinhrlnsnrrvrgalnfddvdvdvGLVSDSMVVNSLYlqngsaaastcavlkpeqldp
ssgslfggavnitgakrkfdslasPVKTitsplsphhsstskmvvTPVSTAMTTAKWLRTIICPLPSKPSADLQGANLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFirheeslpreLRRHLNSLEERLLESMVWEKGSSMYNSLTVARPALSAEINLGFTDILFQDSQDSWEEFTSILtvpptdsptrQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDYRSVLVERNNFTSLVKDCLLGLnnlkskplpppLYPTRSNPGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYnkifaptvkPLLVELGPVGTAMKTNRDSEVNHNNDASVFPALPDMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSNRRVRGALNFDDVDVDVGLVSDSMVVNSLYLQngsaaastcavlkpeqldp
SSGSLFGGAVNITGAKRKFDSLASPVKTItsplsphhsstsKMVVTPVSTAMTTAKWLRTIICPLPSKPSADLQGANLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPALSAEINLGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDYRSVLVERNNFTSLVKDCllglnnlkskplppplyptrsnpGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNRDSEVNHNNDASVFPALPDMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSNRRVRGALNFddvdvdvglvsdsmvvNSLYLQNGSAAASTCAVLKPEQLDP
*******************************************VVTPVSTAMTTAKWLRTIICPLPSKPSADLQGANLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEE********HLNSLEERLLESMVWEKGSSMYNSLTVARPALSAEINLGFTDILFQDSQDSWEEFTSILTVPP****TRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDYRSVLVERNNFTSLVKDCLLGLNNL**********************CAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYNKIFAPTVKPLLVELGPVGT***********************************************ALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSNRRVRGALNFDDVDVDVGLVSDSMVVNSLYLQNGSAAASTCAV********
***********************************************VSTAMTTAKWLRTII**************NLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPA*********************************************************************************************************************************************************************GINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYN*********************************************************************************************************************************************************
SSGSLFGGAVNITGAKRKFDSLASPVKTITS***********MVVTPVSTAMTTAKWLRTIICPLPSKPSADLQGANLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPALSAEINLGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDYRSVLVERNNFTSLVKDCLLGLNNLKSKPLPPPLYPTRSNPGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNRDSEVNHNNDASVFPALPDMSP********VYVSPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSNRRVRGALNFDDVDVDVGLVSDSMVVNSLYLQNGSAAASTCAVLKPEQLDP
******************************S*LSPHHSSTSKMVVTPVSTAMTTAKWLRTIICPLPSKPSADLQGANLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPALSAEINLGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSP*******QFYANCYGELV***YRSVLVERNNFTSLVK*********************************ETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYNKIFAPTVKPLLVELGP******************ASVFPALPDMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSNRRVRGALNFDDV**************************************
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SSGSLFGGAVNITGAKRKFDSLASPVKTITSPLSPHHSSTSKMVVTPVSTAMTTAKWLRTIICPLPSKPSADLQGANLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSLFHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPALSAEINLGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDYRSVLVERNNFTSLVKDCLLGLNNLKSKPLPPPLYPTRSNPGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNRDSEVNHNNDASVFPALPDMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSNRRVRGALNFDDVDVDVGLVSDSMVVNSLYLQNGSAAASTCAVLKPEQLDP
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 ?
Query633 2.2.26 [Sep-21-2011]
B9SVG91020 Retinoblastoma-related pr N/A no 0.887 0.550 0.622 0.0
A7P5141007 Retinoblastoma-related pr yes no 0.884 0.556 0.624 0.0
B9GLX81035 Retinoblastoma-related pr yes no 0.895 0.547 0.607 0.0
Q4JF751006 Retinoblastoma-related pr N/A no 0.884 0.556 0.605 0.0
Q66WV01003 Retinoblastoma-related pr N/A no 0.879 0.555 0.605 0.0
Q9SLZ41026 Retinoblastoma-related pr N/A no 0.905 0.558 0.6 0.0
A9UL141025 Retinoblastoma-related pr N/A no 0.883 0.545 0.602 0.0
B1ABR61005 Retinoblastoma-related pr N/A no 0.865 0.545 0.59 0.0
B1ABS01008 Retinoblastoma-related pr N/A no 0.853 0.535 0.591 0.0
Q2ABE51025 Retinoblastoma-related pr N/A no 0.902 0.557 0.580 0.0
>sp|B9SVG9|RBR_RICCO Retinoblastoma-related protein OS=Ricinus communis GN=RBR PE=2 SV=1 Back     alignment and function desciption
 Score =  795 bits (2052), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/717 (62%), Positives = 489/717 (68%), Gaps = 155/717 (21%)

Query: 9    AVNITGAKRKFDSLASPVKTITSPLSPHHS-----------STSKMVVTPVSTAMTTAKW 57
            A+++TG KRKFD ++SP KTITSPLSPH S           + S+M  TPVSTAMTTAKW
Sbjct: 367  AISVTGTKRKFDQISSPTKTITSPLSPHRSPASHTNGILGSTNSRMAATPVSTAMTTAKW 426

Query: 58   LRTIICPLPSKPS-----------------------------------------ADLQGA 76
            LRT+I PLPSKPS                                           LQ  
Sbjct: 427  LRTVISPLPSKPSPQLERFLASCDRDVTNDVIRRAHIILEAIFPSNALGERCVTGSLQST 486

Query: 77   NLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELV 131
            NLMDNIWAEQRRLEALKL Y+VLE MCTAEAQ+LHA NLTSL     FHRCMLACSAELV
Sbjct: 487  NLMDNIWAEQRRLEALKLYYRVLEAMCTAEAQILHATNLTSLLTNERFHRCMLACSAELV 546

Query: 132  LATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
            LATHKTVTMLF AVLER GITAF+LSKVI+SFIRHEESLPRELRRHLNSLEERLLESMVW
Sbjct: 547  LATHKTVTMLFPAVLERTGITAFDLSKVIESFIRHEESLPRELRRHLNSLEERLLESMVW 606

Query: 192  EKGSSMYNSLTVARPALSAEIN-LGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYEN 250
            EKGSSMYNSLTVARP+LSAEIN LG                                   
Sbjct: 607  EKGSSMYNSLTVARPSLSAEINRLGL---------------------------------- 632

Query: 251  LPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFY 310
                           L  PMPSLDAIA+HINFSSGGL P+ S+ KHE SP          
Sbjct: 633  ---------------LAEPMPSLDAIAVHINFSSGGLPPLSSVSKHEISP---------- 667

Query: 311  ANCYGELVT-----DDYRSVLVERNNFTSLVKDCLLGLNNLKSKPLPPPLY-----PTRS 360
                G++ +      DYRSVLVERN+FTS VKD LL   NLKSK  PPPL      PTR 
Sbjct: 668  -GQNGDIRSPKRPCTDYRSVLVERNSFTSPVKDRLLAFTNLKSKLPPPPLQSAFASPTRP 726

Query: 361  NPGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQ-IRESVYCLCPKRTLNQRT 419
            NPGGGGE CAETGINI F KINKLAAVRIN MVERLQ SQQ IRE+VY L  ++ L+Q+T
Sbjct: 727  NPGGGGETCAETGINIFFSKINKLAAVRINGMVERLQQSQQHIRENVYRLF-QQVLSQQT 785

Query: 420  SLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF--------- 470
            SLFFN HIDQIILCCFYGVAKIS++NLTF+EIIYNY KQPQCKPQVFRSVF         
Sbjct: 786  SLFFNRHIDQIILCCFYGVAKISKVNLTFREIIYNYRKQPQCKPQVFRSVFVDWSSARHN 845

Query: 471  -----DHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNRDSEVNHNNDA--------SV 517
                 DHVDIITFYN+IF P  KPLLVE+G  G  +K ++  EVN+N D         S 
Sbjct: 846  GRTGQDHVDIITFYNEIFIPAAKPLLVEVGSAGITVKGSQVPEVNNNKDGQCPASPKVSP 905

Query: 518  FPALPDMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAY-SPFKDLTDI 576
            FP+LPDMSPKKVSA H+VYVSPLRTS+MDALISHSSKSYYACVGESTHAY SP KDLT I
Sbjct: 906  FPSLPDMSPKKVSAAHNVYVSPLRTSKMDALISHSSKSYYACVGESTHAYQSPSKDLTAI 965

Query: 577  NHRLNSNRRVRGALNFDDVDVDVGLVSDSMVVNSLYLQNGSAAASTCAVLKPEQLDP 633
            N+RLN NR +RG+LNFD  DVDVGLVSDSMV  SLYLQNGS A+++ A LK EQ DP
Sbjct: 966  NNRLNGNRNIRGSLNFD--DVDVGLVSDSMVAKSLYLQNGSCASTSGAPLKTEQPDP 1020
Regulator of biological processes that recruits a histone deacetylase to control gene transcription. May play a role in the entry into mitosis, negatively regulating the cell proliferation. Formation of stable complexes with geminiviridae replication-associated proteins may create a cellular environment which favors viral DNA replication.
Ricinus communis (taxid: 3988)
>sp|A7P514|RBR_VITVI Retinoblastoma-related protein OS=Vitis vinifera GN=RBR PE=2 SV=1 Back     alignment and function description
>sp|B9GLX8|RBR_POPTR Retinoblastoma-related protein OS=Populus trichocarpa GN=RBL901 PE=2 SV=1 Back     alignment and function description
>sp|Q4JF75|RBR_SCUBA Retinoblastoma-related protein OS=Scutellaria baicalensis GN=RB PE=2 SV=1 Back     alignment and function description
>sp|Q66WV0|RBR1_NICBE Retinoblastoma-related protein 1 OS=Nicotiana benthamiana GN=RBR1 PE=2 SV=1 Back     alignment and function description
>sp|Q9SLZ4|RBR1_PEA Retinoblastoma-related protein 1 OS=Pisum sativum GN=RBR1 PE=2 SV=1 Back     alignment and function description
>sp|A9UL14|RBR_MEDSA Retinoblastoma-related protein OS=Medicago sativa GN=RBR PE=2 SV=1 Back     alignment and function description
>sp|B1ABR6|RBR_HIEPI Retinoblastoma-related protein OS=Hieracium piloselloides GN=RBR PE=2 SV=1 Back     alignment and function description
>sp|B1ABS0|RBR_HIEPL Retinoblastoma-related protein OS=Hieracium pilosella GN=RBR PE=2 SV=1 Back     alignment and function description
>sp|Q2ABE5|RBR_CAMSI Retinoblastoma-related protein OS=Camellia sinensis GN=pRB PE=2 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 ?
Query633
255578241 1020 conserved hypothetical protein [Ricinus 0.887 0.550 0.622 0.0
356556778 1002 PREDICTED: retinoblastoma-related protei 0.873 0.551 0.634 0.0
6984231 801 retinoblastoma-like protein [Euphorbia e 0.903 0.714 0.607 0.0
359476005 1007 PREDICTED: retinoblastoma-related protei 0.884 0.556 0.624 0.0
296081790 1006 unnamed protein product [Vitis vinifera] 0.884 0.556 0.624 0.0
224053236 1035 hypothetical protein POPTRDRAFT_547794 [ 0.895 0.547 0.607 0.0
356507327 1014 PREDICTED: retinoblastoma-related protei 0.876 0.547 0.619 0.0
7381060 1035 retinoblastoma-related protein 1 [Populu 0.895 0.547 0.605 0.0
449449453 1024 PREDICTED: retinoblastoma-related protei 0.895 0.553 0.588 0.0
449487265 1125 PREDICTED: retinoblastoma-related protei 0.895 0.504 0.589 0.0
>gi|255578241|ref|XP_002529988.1| conserved hypothetical protein [Ricinus communis] gi|254789790|sp|B9SVG9.1|RBR_RICCO RecName: Full=Retinoblastoma-related protein gi|223530511|gb|EEF32393.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
 Score =  795 bits (2052), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/717 (62%), Positives = 489/717 (68%), Gaps = 155/717 (21%)

Query: 9    AVNITGAKRKFDSLASPVKTITSPLSPHHS-----------STSKMVVTPVSTAMTTAKW 57
            A+++TG KRKFD ++SP KTITSPLSPH S           + S+M  TPVSTAMTTAKW
Sbjct: 367  AISVTGTKRKFDQISSPTKTITSPLSPHRSPASHTNGILGSTNSRMAATPVSTAMTTAKW 426

Query: 58   LRTIICPLPSKPS-----------------------------------------ADLQGA 76
            LRT+I PLPSKPS                                           LQ  
Sbjct: 427  LRTVISPLPSKPSPQLERFLASCDRDVTNDVIRRAHIILEAIFPSNALGERCVTGSLQST 486

Query: 77   NLMDNIWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELV 131
            NLMDNIWAEQRRLEALKL Y+VLE MCTAEAQ+LHA NLTSL     FHRCMLACSAELV
Sbjct: 487  NLMDNIWAEQRRLEALKLYYRVLEAMCTAEAQILHATNLTSLLTNERFHRCMLACSAELV 546

Query: 132  LATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
            LATHKTVTMLF AVLER GITAF+LSKVI+SFIRHEESLPRELRRHLNSLEERLLESMVW
Sbjct: 547  LATHKTVTMLFPAVLERTGITAFDLSKVIESFIRHEESLPRELRRHLNSLEERLLESMVW 606

Query: 192  EKGSSMYNSLTVARPALSAEIN-LGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYEN 250
            EKGSSMYNSLTVARP+LSAEIN LG                                   
Sbjct: 607  EKGSSMYNSLTVARPSLSAEINRLGL---------------------------------- 632

Query: 251  LPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFY 310
                           L  PMPSLDAIA+HINFSSGGL P+ S+ KHE SP          
Sbjct: 633  ---------------LAEPMPSLDAIAVHINFSSGGLPPLSSVSKHEISP---------- 667

Query: 311  ANCYGELVT-----DDYRSVLVERNNFTSLVKDCLLGLNNLKSKPLPPPLY-----PTRS 360
                G++ +      DYRSVLVERN+FTS VKD LL   NLKSK  PPPL      PTR 
Sbjct: 668  -GQNGDIRSPKRPCTDYRSVLVERNSFTSPVKDRLLAFTNLKSKLPPPPLQSAFASPTRP 726

Query: 361  NPGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQ-IRESVYCLCPKRTLNQRT 419
            NPGGGGE CAETGINI F KINKLAAVRIN MVERLQ SQQ IRE+VY L  ++ L+Q+T
Sbjct: 727  NPGGGGETCAETGINIFFSKINKLAAVRINGMVERLQQSQQHIRENVYRLF-QQVLSQQT 785

Query: 420  SLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF--------- 470
            SLFFN HIDQIILCCFYGVAKIS++NLTF+EIIYNY KQPQCKPQVFRSVF         
Sbjct: 786  SLFFNRHIDQIILCCFYGVAKISKVNLTFREIIYNYRKQPQCKPQVFRSVFVDWSSARHN 845

Query: 471  -----DHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNRDSEVNHNNDA--------SV 517
                 DHVDIITFYN+IF P  KPLLVE+G  G  +K ++  EVN+N D         S 
Sbjct: 846  GRTGQDHVDIITFYNEIFIPAAKPLLVEVGSAGITVKGSQVPEVNNNKDGQCPASPKVSP 905

Query: 518  FPALPDMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAY-SPFKDLTDI 576
            FP+LPDMSPKKVSA H+VYVSPLRTS+MDALISHSSKSYYACVGESTHAY SP KDLT I
Sbjct: 906  FPSLPDMSPKKVSAAHNVYVSPLRTSKMDALISHSSKSYYACVGESTHAYQSPSKDLTAI 965

Query: 577  NHRLNSNRRVRGALNFDDVDVDVGLVSDSMVVNSLYLQNGSAAASTCAVLKPEQLDP 633
            N+RLN NR +RG+LNFD  DVDVGLVSDSMV  SLYLQNGS A+++ A LK EQ DP
Sbjct: 966  NNRLNGNRNIRGSLNFD--DVDVGLVSDSMVAKSLYLQNGSCASTSGAPLKTEQPDP 1020

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356556778|ref|XP_003546699.1| PREDICTED: retinoblastoma-related protein 1-like [Glycine max] Back     alignment and taxonomy information
>gi|6984231|gb|AAF34803.1|AF230739_1 retinoblastoma-like protein [Euphorbia esula] Back     alignment and taxonomy information
>gi|359476005|ref|XP_002280874.2| PREDICTED: retinoblastoma-related protein-like [Vitis vinifera] gi|254789791|sp|A7P514.1|RBR_VITVI RecName: Full=Retinoblastoma-related protein gi|359392418|gb|AEV45768.1| RBR protein [Vitis pseudoreticulata] Back     alignment and taxonomy information
>gi|296081790|emb|CBI20795.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224053236|ref|XP_002297730.1| hypothetical protein POPTRDRAFT_547794 [Populus trichocarpa] gi|254789789|sp|B9GLX8.1|RBR_POPTR RecName: Full=Retinoblastoma-related protein gi|222844988|gb|EEE82535.1| hypothetical protein POPTRDRAFT_547794 [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356507327|ref|XP_003522419.1| PREDICTED: retinoblastoma-related protein 1-like [Glycine max] Back     alignment and taxonomy information
>gi|7381060|gb|AAF61377.1|AF133675_1 retinoblastoma-related protein 1 [Populus tremula x Populus tremuloides] Back     alignment and taxonomy information
>gi|449449453|ref|XP_004142479.1| PREDICTED: retinoblastoma-related protein-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449487265|ref|XP_004157544.1| PREDICTED: retinoblastoma-related protein-like [Cucumis sativus] 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 ?
Query633
UNIPROTKB|Q66WV01003 RBR1 "Retinoblastoma-related p 0.567 0.357 0.555 1.5e-173
TAIR|locus:20821941013 RBR1 "retinoblastoma-related 1 0.492 0.307 0.492 3.7e-140
UNIPROTKB|E1BQ591064 RBL1 "Uncharacterized protein" 0.238 0.141 0.331 5.9e-32
UNIPROTKB|P287491068 RBL1 "Retinoblastoma-like prot 0.248 0.147 0.337 1.1e-29
UNIPROTKB|E2RQ781068 RBL1 "Uncharacterized protein" 0.238 0.141 0.331 2.7e-29
UNIPROTKB|F1PBK31068 RBL1 "Uncharacterized protein" 0.238 0.141 0.331 2.7e-29
RGD|15955111063 Rbl1 "retinoblastoma-like 1 (p 0.238 0.142 0.331 3.1e-29
MGI|MGI:1033001063 Rbl1 "retinoblastoma-like 1 (p 0.238 0.142 0.318 4.6e-29
UNIPROTKB|E1BMR31068 RBL1 "Uncharacterized protein" 0.238 0.141 0.325 9.4e-29
ZFIN|ZDB-GENE-030131-81791058 rbl1 "retinoblastoma-like 1 (p 0.238 0.142 0.362 1.6e-28
UNIPROTKB|Q66WV0 RBR1 "Retinoblastoma-related protein 1" [Nicotiana benthamiana (taxid:4100)] Back     alignment and assigned GO terms
 Score = 917 (327.9 bits), Expect = 1.5e-173, Sum P(3) = 1.5e-173
 Identities = 220/396 (55%), Positives = 247/396 (62%)

Query:   260 EVDSIFLLI-PMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELV 318
             E++ + LL  PMPSLDAIAMHIN SSG L P+ SLHK+  +P   I + +       + V
Sbjct:   617 EINRMGLLAEPMPSLDAIAMHINLSSGSLPPLPSLHKNNLAPNGQIGDIRS-----PKKV 671

Query:   319 TDDYRSVLVERNNFTSLVKDCXXXXXXXXX-----XXXXXXXXXXXXXXGGGGEPCAETG 373
               +YRSVLVERN+FTS VKD                             GGGGE CAET 
Sbjct:   672 CSEYRSVLVERNSFTSPVKDRFLALNNIKSKFPPPALHSAFASPTRPNPGGGGETCAETA 731

Query:   374 INICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILC 433
             IN+ F KI KLAAVRIN M+ERLQLSQQIRE+VYCL  K  L+QRTSLFFN HIDQIILC
Sbjct:   732 INVFFGKIVKLAAVRINGMIERLQLSQQIRETVYCLFQK-ILSQRTSLFFNRHIDQIILC 790

Query:   434 CFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF--------------DHVDIITFY 479
              FYGVAKISQLNLTFKEII NY KQPQCKPQVFRSVF              DHVDIITFY
Sbjct:   791 SFYGVAKISQLNLTFKEIICNYRKQPQCKPQVFRSVFVDWTLARHNVRTGADHVDIITFY 850

Query:   480 NKIFAPTVKPLLVELGPVGTAMKTN--RDSEVNHNNDASVFPALPDMSPKKVSATHSVYV 537
             N++F P+VKPLLVEL P G   + N   D +   +   S FP LPDMSPKKVSA H+VYV
Sbjct:   851 NEMFIPSVKPLLVELAPAGNNSEKNDHNDGQGPASPKPSPFPKLPDMSPKKVSAVHNVYV 910

Query:   538 SPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSNRRVRGALNFXXXXX 597
             SPLR S+MDALISHSSKSYYACVGESTHAY       D+      N R+ G         
Sbjct:   911 SPLRASKMDALISHSSKSYYACVGESTHAYQSPSKDLDV-----INNRLNGNRKLRGALN 965

Query:   598 XXXXX---XXXXXXNSLYLQNGSAAASTCAVLKPEQ 630
                           NSLYLQNG+   S  A +K EQ
Sbjct:   966 FDVDAGLVSDSIVANSLYLQNGNCR-SPVAHVKTEQ 1000
GO:0032875 "regulation of DNA endoreduplication" evidence=IMP
GO:0051782 "negative regulation of cell division" evidence=IMP
TAIR|locus:2082194 RBR1 "retinoblastoma-related 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|E1BQ59 RBL1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|P28749 RBL1 "Retinoblastoma-like protein 1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E2RQ78 RBL1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1PBK3 RBL1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
RGD|1595511 Rbl1 "retinoblastoma-like 1 (p107)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
MGI|MGI:103300 Rbl1 "retinoblastoma-like 1 (p107)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E1BMR3 RBL1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-8179 rbl1 "retinoblastoma-like 1 (p107)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
RBR
SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence;; Regulator of biological processes that recruits a histone deacetylase to control gene transcription. May play a role in the entry into mitosis, negatively regulating the cell proliferation. Formation of stable complexes with geminiviridae replication-associated proteins may create a cellular environment which favors viral DNA replication (By similarity) (1007 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00027417001
SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (370 aa)
    • • 0.519
GSVIVG00037279001
SubName- Full=Chromosome undetermined scaffold_87, whole genome shotgun sequence; (428 aa)
    • • 0.495
GSVIVG00024137001
SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (490 aa)
     •• 0.483
GSVIVG00021527001
SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (459 aa)
    • • 0.478

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 ?
Query633
pfam01858192 pfam01858, RB_A, Retinoblastoma-associated protein 4e-61
pfam01857130 pfam01857, RB_B, Retinoblastoma-associated protein 9e-47
smart0038583 smart00385, CYCLIN, domain present in cyclins, TFI 3e-04
>gnl|CDD|202014 pfam01858, RB_A, Retinoblastoma-associated protein A domain Back     alignment and domain information 
 Score =  201 bits (513), Expect = 4e-61
 Identities = 77/192 (40%), Positives = 103/192 (53%), Gaps = 36/192 (18%)

Query: 46  TPVSTAMTTAKWLRTIICPLPSKPSADLQGA------NLMDNI----------------- 82
           TPV TAM T   LR ++  L   PS  L         N  + I                 
Sbjct: 1   TPVRTAMNTVSQLREVLSSLSDAPSETLLQYLNSCDRNPTEAIIKRVKIIGEEIFETFAE 60

Query: 83  --------WAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAE 129
                    A QR   ALKL Y+VLE++  AE + LH  +L++L     FHR +LAC  E
Sbjct: 61  AEDQSPKEIASQRFKLALKLYYRVLESILKAEEKRLHDMDLSNLLEQEAFHRSLLACCLE 120

Query: 130 LVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESM 189
           LVLAT+KT  + F  +LE  GITAF+  KVI+SFIRHE  L RE+ +HLNS+EE++LES+
Sbjct: 121 LVLATYKTTDLSFPWILEVFGITAFDFYKVIESFIRHEGGLSREMVKHLNSIEEQILESL 180

Query: 190 VWEKGSSMYNSL 201
            W+  S ++  +
Sbjct: 181 AWKSDSPLWEMI 192

This domain has the cyclin fold as predicted. Length = 192
>gnl|CDD|216744 pfam01857, RB_B, Retinoblastoma-associated protein B domain Back     alignment and domain information
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 633
KOG1010920 consensus Rb (Retinoblastoma tumor suppressor)-rel 100.0
PF01858194 RB_A: Retinoblastoma-associated protein A domain; 100.0
PF01857135 RB_B: Retinoblastoma-associated protein B domain; 100.0
PF08934155 Rb_C: Rb C-terminal domain; InterPro: IPR015030 Th 99.76
PRK00423310 tfb transcription initiation factor IIB; Reviewed 97.5
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 97.31
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 96.64
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 96.58
KOG1597308 consensus Transcription initiation factor TFIIB [T 95.9
PRK00423310 tfb transcription initiation factor IIB; Reviewed 94.96
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 90.37
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 82.55
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information 
Probab=100.00  E-value=3.8e-122  Score=1026.12  Aligned_cols=494  Identities=35%  Similarity=0.479  Sum_probs=403.1

Q ss_pred             cccccccccccccccCCcccccCCCCCCCCCC---------CCCCCChHHHHHHHHHHHHHHhCCCCCCCCcccc-----
Q 046343            9 AVNITGAKRKFDSLASPVKTITSPLSPHHSST---------SKMVVTPVSTAMTTAKWLRTIICPLPSKPSADLQ-----   74 (633)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~TPVs~Am~s~~~L~~~la~l~~~PS~~l~-----   74 (633)
                      .++.++.++|.+...+++++--.+.| +.+|.         .+...|||++||++++||++++.|+.++||+++.     
T Consensus       353 ~~~~s~~~~r~~~~~~~~~~~~~~~s-~~~p~~~~~~y~~e~~~~~tPvsta~~sik~l~t~i~g~~~~psdkLe~~~~t  431 (920)
T KOG1010|consen  353 KSSDSFESERLAVKSSLAQEFLKTQS-KKSPPHTGVRYNLELGNYPTPVSTATNSIKQLMTILNGLKKEPSDKLEQYLNT  431 (920)
T ss_pred             ccCCccchhccccccccchhhccccc-ccCCCCcccccccccccCCCcchhHHHHHHHHHHHHhccccCCcHHHHHHHhh
Confidence            55778889999999999998888777 55551         3567899999999999999999999999999943     


Q ss_pred             C-CCCCCh---------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCchHHH-----HHH
Q 046343           75 G-ANLMDN---------------------------IWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHR  121 (633)
Q Consensus        75 ~-~~~~d~---------------------------~~a~qR~~~a~~LYYkvLE~Il~~E~krl~~~~ls~L-----FHr  121 (633)
                      | .+.+++                           .+|.|||++|++|||||||+||++|.+|++..||+.|     ||+
T Consensus       432 c~r~p~e~Il~r~~~i~e~~~q~f~~~~~~g~~~~e~~~~r~k~a~~LYykvLE~il~aE~~rl~~~dl~~LL~q~~Fh~  511 (920)
T KOG1010|consen  432 CSRDPTESILKRLKEIFEIFEQKFSAAEGSGNSCIEIASQRFKLAERLYYKVLEKILKAELKRLPDMDLSKLLEQEIFHR  511 (920)
T ss_pred             cccChHHHHHHHHHHHHHHHHHHhhhhccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence            1 112211                           1578999999999999999999999999999999998     999


Q ss_pred             HHHHHHHHHHHHHhCCCccchHHHHHhhCCCcchhhchhhhhhhcCCCCCHHHHHHHHHHHHHHHHhhhcCCCCchhHhH
Q 046343          122 CMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSL  201 (633)
Q Consensus       122 sLlACclEiVl~sy~~~~~~FPwILe~~~l~aFdf~KVIE~fIRae~~LpRelvKHLn~IEEqILEslAW~~~SpLw~~L  201 (633)
                      ||||||+|+||++|++ ++.||||||+|||+|||||||||+|||||++|+||||||||+|||+|||||||++|||||++|
T Consensus       512 sLlACclElVL~ty~~-~l~FPwvle~~~l~aFdF~KVIE~~IRhE~~L~RemiKHLn~iEE~iLEslaW~~dS~Lw~~i  590 (920)
T KOG1010|consen  512 SLLACCLELVLATYKT-DLSFPWVLECFGLKAFDFYKVIESFIRHEGGLSREMIKHLNSIEERILESLAWKSDSPLWEMI  590 (920)
T ss_pred             HHHHHHHHHHHHHhCC-CCCCchhhhhcCCcHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccCCcHHHHH
Confidence            9999999999999997 599999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhCCcchhhhccCcccccccccccchhhhccccCCCCCCCCCccccCCCCCCCCCCccccchhhcCCCCchhhhhhhcc
Q 046343          202 TVARPALSAEINLGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHIN  281 (633)
Q Consensus       202 ~~a~p~~~~ev~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~~~~k~~~~~~~~~~l~~~~~s~~~ia~~~~  281 (633)
                      +++++.++-|.+            ..|.+.                                    .  ++ +.|+.  +
T Consensus       591 ~~~~~~~~~~~~------------~~~~~~------------------------------------l--e~-~~~~~--~  617 (920)
T KOG1010|consen  591 KQAKPRLPTEEG------------VDPPDN------------------------------------L--ES-ACIAG--L  617 (920)
T ss_pred             Hhcccccccccc------------cccccc------------------------------------c--cc-ccccc--c
Confidence            999876533322            111100                                    0  00 00100  0


Q ss_pred             ccCCCCCCCcccccccCCCcccccccccccccCCcccccccccchhccccccccccccccccCCCCCCCCCCCCCCCCCC
Q 046343          282 FSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDYRSVLVERNNFTSLVKDCLLGLNNLKSKPLPPPLYPTRSN  361 (633)
Q Consensus       282 ~s~~~l~p~ps~~~~~ssp~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~sP~k~~~~~~~~~~~k~~~~~l~p~~~~  361 (633)
                      ++ .+.-+   ...++++|+         .  .|++.+            .|+|+++...              .++..+
T Consensus       618 ~p-~~~~~---~~~~~~sp~---------~--~Pk~~~------------~t~pv~~~an--------------~~qe~~  656 (920)
T KOG1010|consen  618 LP-LRVNH---VRARYSSPV---------L--EPKDKG------------TTIPVNGTAN--------------AGQEVT  656 (920)
T ss_pred             CC-ccccc---cccccCCCC---------C--Cccccc------------cccccccccc--------------ccccCC
Confidence            00 00001   122566665         1  255432            3788876321              123344


Q ss_pred             CCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhh
Q 046343          362 PGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKI  441 (633)
Q Consensus       362 p~~~~~~~~~t~L~lFfRKVy~LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV  441 (633)
                      +.+.++++++++|+||||||||||++||+|||+||+++++++++||||| ||+|+|+|+||||||||||||||||+||||
T Consensus       657 ~~~~~~~~~stsLsIF~rKvY~LAavRL~~Lc~rL~l~~e~r~~IWtlF-ehsl~~et~Lm~dRHLDQillCaiy~i~KV  735 (920)
T KOG1010|consen  657 AFGVNKPRKSTSLSIFLRKVYHLAAVRLNDLCERLSLSDELREQIWTLF-EHSLTNETELMRDRHLDQILLCAIYGIAKV  735 (920)
T ss_pred             cccCCCcccccchHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHH-HHHHhccHHHHHhhhHHHHHHHHHHhheeh
Confidence            5566788889999999999999999999999999999999999999999 999999999999999999999999999999


Q ss_pred             ccCccCHHHHHHHHhcCCCCCCcceeeec----------------cccceeehhhhcchhhhHHHHHHhcCCCcccccCC
Q 046343          442 SQLNLTFKEIIYNYGKQPQCKPQVFRSVF----------------DHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNR  505 (633)
Q Consensus       442 ~k~~~tFk~Ii~~YR~QPQa~s~VyRsVl----------------ergDII~FYN~VFvp~mK~F~l~~~~~~~~~~~~~  505 (633)
                      +++++||++||++||+||||.++|||+|+                +++|||+|||.|||+.||+|+++|....+      
T Consensus       736 ~~~~ltF~eIm~~YR~QPqa~~~vyRsV~i~~~~~~~~~~~~P~~~~~diI~fyN~iyV~~~k~~~i~~~~~~~------  809 (920)
T KOG1010|consen  736 KKEDLTFSEIMRAYRRQPQAVSLVYRSVLIKDKTNRDQGPSGPKEERSDIITFYNNIYVPPMKTFAIEYGLATT------  809 (920)
T ss_pred             hcccchHHHHHHHHhcCchhhhhhhhheeecccccccccCCCCcccccceeccccceehhhhhhhhhhhccCCC------
Confidence            99999999999999999999999999999                37899999999999999999999998732      


Q ss_pred             CcccCCCCCCCCCCCCC--CCCCCccccCCcEEEecCCCCcccccCCCCCceEEEEeCCcccCCCCccchHHHHHHhhcC
Q 046343          506 DSEVNHNNDASVFPALP--DMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSN  583 (633)
Q Consensus       506 ~~~~~~~~~lSP~P~~~--~~SP~rvs~~hnVyVSPlk~~~~~~~lsP~s~~ly~~~gest~a~SPsKdL~~IN~~i~~~  583 (633)
                          .+.++++|.|++.  ..+|+++|++||||||||+++   ..+.+++.+.|||++      ||+|+|++||.|++++
T Consensus       810 ----~~~~~lsp~~~i~~~~~e~~~~S~~h~v~is~~~~~---~~l~s~s~~~y~~~~------spsk~L~ain~~i~~s  876 (920)
T KOG1010|consen  810 ----MDAKPLSPSPSIKVSIGEPRRLSQRHNVYISPHKNS---DRLQSRSTAEYYFCN------SPSKDLPAINNLIRGS  876 (920)
T ss_pred             ----CCCCCCCCCccccccCCCCcchhhhcceeecCCCch---hhhcCcchhhccccC------CCCcchHHHHHHhhcC
Confidence                1257899999876  468999999999999999987   445556655566666      8999999999999985


Q ss_pred             cCcccceeccCCCCcccccccchhhccccc------cCCCCCCCCC
Q 046343          584 RRVRGALNFDDVDVDVGLVSDSMVVNSLYL------QNGSAAASTC  623 (633)
Q Consensus       584 ~~~kr~l~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~  623 (633)
                      ....+..++.+   |  .+++++++|.+-.      |+++.+.++.
T Consensus       877 s~~~~~~~~~~---e--s~~Es~~ani~~~~~~~~~~r~~D~~~~~  917 (920)
T KOG1010|consen  877 SERTKKKHIPG---E--SKSESKRANILQERTRMQLQRLQDAMSTR  917 (920)
T ss_pred             cccccccCCCc---c--chhhhhHhhhhhhhhHHHHhhhhhhhhcc
Confidence            44344445554   3  7899999998865      5666666553

>PF01858 RB_A: Retinoblastoma-associated protein A domain; InterPro: IPR002720 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation Back     alignment and domain information
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation Back     alignment and domain information
>PF08934 Rb_C: Rb C-terminal domain; InterPro: IPR015030 The Rb C-terminal domain is required for high-affinity binding to E2F-DP complexes and for maximal repression of E2F-responsive promoters, thereby acting as a growth suppressor by blocking the G1-S transition of the cell cycle Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) 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 ?
Query633
3pom_A352 Crystal Structure Of The Unliganded Retinoblastoma 2e-14
3pom_A352 Crystal Structure Of The Unliganded Retinoblastoma 9e-12
4elj_A656 Crystal Structure Of The Inactive Retinoblastoma Pr 2e-14
4elj_A656 Crystal Structure Of The Inactive Retinoblastoma Pr 1e-12
1gux_A218 Rb Pocket Bound To E7 Lxcxe Motif Length = 218 3e-14
2r7g_A347 Structure Of The Retinoblastoma Protein Pocket Doma 4e-14
2r7g_A347 Structure Of The Retinoblastoma Protein Pocket Doma 9e-12
1n4m_A345 Structure Of Rb Tumor Suppressor Bound To The Trans 4e-14
1n4m_A345 Structure Of Rb Tumor Suppressor Bound To The Trans 9e-12
4ell_A411 Structure Of The Inactive Retinoblastoma Protein Po 5e-14
4ell_A411 Structure Of The Inactive Retinoblastoma Protein Po 1e-12
1gh6_B333 Retinoblastoma Pocket Complexed With Sv40 Large T A 5e-14
1gh6_B333 Retinoblastoma Pocket Complexed With Sv40 Large T A 3e-12
1ad6_A185 Domain A Of Human Retinoblastoma Tumor Suppressor L 2e-12
1gux_B152 Rb Pocket Bound To E7 Lxcxe Motif Length = 152 3e-12
>pdb|3POM|A Chain A, Crystal Structure Of The Unliganded Retinoblastoma Protein Pocket Domain Length = 352 Back     alignment and structure 
Iteration: 1

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 48/152 (31%), Positives = 83/152 (54%), Gaps = 18/152 (11%)
Query: 86  QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT- 139
           QR    ++L Y+V+E+M  +E + L  +N + L     FH  +LAC+ E+V+AT+   T 
Sbjct: 68  QRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTS 127
Query: 140 --------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
                   + F  +L  + + AF+  KVI+SFI+ E +L RE+ +HL   E R++ES+ W
Sbjct: 128 QNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAW 187
Query: 192 EKGSSMYN----SLTVARPALSAEINLGFTDI 219
              S +++    S  V R + S  ++L +  +
Sbjct: 188 LSDSPLFDLIKQSKLVPRGSKSTSLSLFYKKV 219
>pdb|3POM|A Chain A, Crystal Structure Of The Unliganded Retinoblastoma Protein Pocket Domain Length = 352 Back     alignment and structure
>pdb|4ELJ|A Chain A, Crystal Structure Of The Inactive Retinoblastoma Protein Phosphorylated At T373 Length = 656 Back     alignment and structure
>pdb|4ELJ|A Chain A, Crystal Structure Of The Inactive Retinoblastoma Protein Phosphorylated At T373 Length = 656 Back     alignment and structure
>pdb|1GUX|A Chain A, Rb Pocket Bound To E7 Lxcxe Motif Length = 218 Back     alignment and structure
>pdb|2R7G|A Chain A, Structure Of The Retinoblastoma Protein Pocket Domain In Complex With Adenovirus E1a Cr1 Domain Length = 347 Back     alignment and structure
>pdb|2R7G|A Chain A, Structure Of The Retinoblastoma Protein Pocket Domain In Complex With Adenovirus E1a Cr1 Domain Length = 347 Back     alignment and structure
>pdb|1N4M|A Chain A, Structure Of Rb Tumor Suppressor Bound To The Transactivation Domain Of E2f-2 Length = 345 Back     alignment and structure
>pdb|1N4M|A Chain A, Structure Of Rb Tumor Suppressor Bound To The Transactivation Domain Of E2f-2 Length = 345 Back     alignment and structure
>pdb|4ELL|A Chain A, Structure Of The Inactive Retinoblastoma Protein Pocket Domain Length = 411 Back     alignment and structure
>pdb|4ELL|A Chain A, Structure Of The Inactive Retinoblastoma Protein Pocket Domain Length = 411 Back     alignment and structure
>pdb|1GH6|B Chain B, Retinoblastoma Pocket Complexed With Sv40 Large T Antigen Length = 333 Back     alignment and structure
>pdb|1GH6|B Chain B, Retinoblastoma Pocket Complexed With Sv40 Large T Antigen Length = 333 Back     alignment and structure
>pdb|1AD6|A Chain A, Domain A Of Human Retinoblastoma Tumor Suppressor Length = 185 Back     alignment and structure
>pdb|1GUX|B Chain B, Rb Pocket Bound To E7 Lxcxe Motif Length = 152 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 ?
Query633
4elj_A656 Retinoblastoma-associated protein; cyclin fold, tu 1e-47
4elj_A656 Retinoblastoma-associated protein; cyclin fold, tu 1e-40
4ell_A411 Retinoblastoma-associated protein; cyclin fold, tu 3e-45
4ell_A411 Retinoblastoma-associated protein; cyclin fold, tu 2e-40
2r7g_A347 PP110, retinoblastoma-associated protein, P105-RB, 5e-42
2r7g_A347 PP110, retinoblastoma-associated protein, P105-RB, 7e-41
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-11
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Length = 656 Back     alignment and structure
 Score =  176 bits (448), Expect = 1e-47
 Identities = 58/239 (24%), Positives = 101/239 (42%), Gaps = 50/239 (20%)

Query: 13  TGAKRKFDSLASPVKTITSPLSPHHSSTSKMVVTPVSTAMTTAKWLRTIICPLPSKPSAD 72
           T +   F++  +P K+                 TPV T M T + L  I+     +PS +
Sbjct: 273 TDSIDSFETQRTPRKSNLDEEVNVIPP-----HTPVRTVMNTIQQLMMILNSASDQPSEN 327

Query: 73  L-------------------------------QGANLMDNIWAEQRRLEALKLNYKVLET 101
           L                               +           QR    ++L Y+V+E+
Sbjct: 328 LISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVEIGSQRYKLGVRLYYRVMES 387

Query: 102 MCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT---------MLFLAVLE 147
           M  +E + L  +N + L     FH  +LAC+ E+V+AT+   T         + F  +L 
Sbjct: 388 MLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQNLDSGTDLSFPWILN 447

Query: 148 RIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARP 206
            + + AF+  KVI+SFI+ E +L RE+ +HL   E R++ES+ W   S +++ +  ++ 
Sbjct: 448 VLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQSKD 506
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Length = 656 Back     alignment and structure
>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens} Length = 411 Back     alignment and structure
>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens} Length = 411 Back     alignment and structure
>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B Length = 347 Back     alignment and structure
>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B Length = 347 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 ?
Query633
4ell_A411 Retinoblastoma-associated protein; cyclin fold, tu 100.0
2r7g_A347 PP110, retinoblastoma-associated protein, P105-RB, 100.0
4elj_A656 Retinoblastoma-associated protein; cyclin fold, tu 100.0
1ais_B200 TFB TFIIB, protein (transcription initiation facto 97.12
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 97.12
1c9b_A207 General transcription factor IIB; protein-DNA comp 97.07
2aze_C46 Retinoblastoma-associated protein; coiled coil, be 96.74
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 96.43
1ais_B200 TFB TFIIB, protein (transcription initiation facto 94.88
4elj_A 656 Retinoblastoma-associated protein; cyclin fold, tu 94.27
2qdj_A304 Retinoblastoma-associated protein; cyclin fold, cy 93.8
1c9b_A207 General transcription factor IIB; protein-DNA comp 93.63
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 92.3
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 91.27
2ivx_A257 Cyclin-T2; transcription regulation, cell division 90.12
1jkw_A323 Cyclin H; cell cycle, cell division, nuclear prote 89.37
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 88.71
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 86.01
>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens} Back     alignment and structure
Probab=100.00  E-value=2.5e-110  Score=895.21  Aligned_cols=359  Identities=26%  Similarity=0.461  Sum_probs=268.7

Q ss_pred             HHHHHHHHHHHHhCCCCCCCCcccc-----CC-CCCC-------------------------hHHHHHHHHHHHHHHHHH
Q 046343           50 TAMTTAKWLRTIICPLPSKPSADLQ-----GA-NLMD-------------------------NIWAEQRRLEALKLNYKV   98 (633)
Q Consensus        50 ~Am~s~~~L~~~la~l~~~PS~~l~-----~~-~~~d-------------------------~~~a~qR~~~a~~LYYkv   98 (633)
                      .||+|++|||++|+|++++||++|.     |. ++++                         ..++++|+++|++||||+
T Consensus         1 ~~~~s~~~L~~~l~~~~~~PS~~L~~~f~sC~~dp~~~I~~rv~~l~~~F~~~~~~~~~~~~~~~a~~R~~la~~LYY~~   80 (411)
T 4ell_A            1 GEFNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVEIGSQRYKLGVRLYYRV   80 (411)
T ss_dssp             ------CHHHHHHHHSCSSCCHHHHHHHHTSSSCCHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHhcCCCCCCCHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhhcccCccchhHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999943     22 1111                         126899999999999999


Q ss_pred             HHHHHHHHHHhhccCchHHH-----HHHHHHHHHHHHHHHHhCC---------CccchHHHHHhhCCCcchhhchhhhhh
Q 046343           99 LETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKT---------VTMLFLAVLERIGITAFNLSKVIQSFI  164 (633)
Q Consensus        99 LE~Il~~E~krl~~~~ls~L-----FHrsLlACclEiVl~sy~~---------~~~~FPwILe~~~l~aFdf~KVIE~fI  164 (633)
                      ||+||.+|++|+++.||+.|     ||+||||||+|||+|+|++         .++.|||||++|+|+|||||||||+||
T Consensus        81 LE~Il~~E~~rl~~~~~s~LL~~~~Fh~sLlACclEvVl~~y~~~~~~~~~~~~~~~FPwiL~~~~i~afdf~KVIE~fv  160 (411)
T 4ell_A           81 MESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFI  160 (411)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHTC------------CCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccchHHHHhhhHHHHHHHHHHHHHHHHHHhccccccccccccCcCChHHHHhcCCChhhhhhhhHHhh
Confidence            99999999999999999998     9999999999999999986         359999999999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHHHHHHHHhhhcCCCCchhHhHhhhCCcc--hhhhccCcccccccccccchhhhccccCCCCCCC
Q 046343          165 RHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPAL--SAEINLGFTDILFQDSQDSWEEFTSILTVPPTDS  242 (633)
Q Consensus       165 Rae~~LpRelvKHLn~IEEqILEslAW~~~SpLw~~L~~a~p~~--~~ev~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~  242 (633)
                      |||++||||||||||+|||||||+|||++|||||++|+.+++..  .+++.++                           
T Consensus       161 r~e~~L~r~lvkHL~~iEe~iLEslaW~~~S~Lw~~l~~~~~~~~~~~~~~~~---------------------------  213 (411)
T 4ell_A          161 KAEGNLTREMIKHLERCEHRIMESFAWLSDSPLFDLIKQSKDREGPTDHLESA---------------------------  213 (411)
T ss_dssp             HHCTTCCHHHHHHHHHHHHHHHHTGGGSTTCHHHHHHHHC----------------------------------------
T ss_pred             hccCCCCHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHhccccCCcccccCCc---------------------------
Confidence            99999999999999999999999999999999999998764321  1111110                           


Q ss_pred             CCccccCCCCCCCCCCccccchhhcCCCCchhhhhhhccccCCCCCCCcccccccCCCcccccccccccccCCccccccc
Q 046343          243 PTRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHINFSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDY  322 (633)
Q Consensus       243 p~~~~~~~~~~~k~~~~~~~~~~l~~~~~s~~~ia~~~~~s~~~l~p~ps~~~~~ssp~~~~~~~~~~~~~~p~~~~~~~  322 (633)
                                                  ++++. ..+.++         ++.+.+.||..+. +++.|+++.        
T Consensus       214 ----------------------------~~~~~-p~~~~~---------t~~~~~~SP~~~~-~~~~~~~~~--------  246 (411)
T 4ell_A          214 ----------------------------CPLNL-PLQNNH---------TAADMYLEPVRAP-KKKGSTTRV--------  246 (411)
T ss_dssp             ---------------------------------------C---------CHHHHHHCCC---------------------
T ss_pred             ----------------------------ccccc-cccCCc---------cchhcccCCCCcc-cccccCCcc--------
Confidence                                        00000 001110         0112222332211 122222111        


Q ss_pred             ccchhccccccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHhCCC-hH
Q 046343          323 RSVLVERNNFTSLVKDCLLGLNNLKSKPLPPPLYPTRSNPGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLS-QQ  401 (633)
Q Consensus       323 ~~~~~~~~~~~sP~k~~~~~~~~~~~k~~~~~l~p~~~~p~~~~~~~~~t~L~lFfRKVy~LAa~RL~dLC~rL~ls-~e  401 (633)
                             .++++|.                    +..+.|++++++++.++|++||||||+||++||++||++|+++ ++
T Consensus       247 -------~~~~~~~--------------------~~~~~~~~~~~~~~~~sl~lFfrKvy~LAa~Rl~~LC~~L~~~~~~  299 (411)
T 4ell_A          247 -------NSTANAE--------------------TQATSAFQTQKPLKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPE  299 (411)
T ss_dssp             ------------------------------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHCTTSTT
T ss_pred             -------ccccCcc--------------------ccCCCCCCCCCCccccHHHHHHHHHHHHHHHHHHHHHHHhCCCcHH
Confidence                   0111111                    0011122344566788999999999999999999999999986 48


Q ss_pred             HHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHHhcCCCCCCcceeeec----cccceee
Q 046343          402 IRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF----DHVDIIT  477 (633)
Q Consensus       402 l~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~YR~QPQa~s~VyRsVl----ergDII~  477 (633)
                      ++++||||| ||+|+|+|+||+|||||||||||||+||||++++++|+|||++||+||||+++|||+|+    ++||||+
T Consensus       300 l~~~IWt~f-e~~l~~~teLm~dRHLDQiiLCsiY~i~Kv~~~~~tFk~Ii~~Yr~qPqa~~~vyr~Vli~~g~~gDII~  378 (411)
T 4ell_A          300 LEHIIWTLF-QHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIV  378 (411)
T ss_dssp             HHHHHHHHH-HHHHHHCGGGGTTSCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHTTSTTCCTHHHHSEECSSSCEECHHH
T ss_pred             HHHHHHHHH-HHHHHhhhHhhccccHHHHHHHHHHHHHhhccCCCCHHHHHHHHHhCcCCCCceeEEEEeCCCCcccHHH
Confidence            999999999 99999999999999999999999999999999999999999999999999999999999    7899999


Q ss_pred             hhhhcchhhhHHHHHHhcCCCcccccCCCcccCCCCCCCCCCCCCC
Q 046343          478 FYNKIFAPTVKPLLVELGPVGTAMKTNRDSEVNHNNDASVFPALPD  523 (633)
Q Consensus       478 FYN~VFvp~mK~F~l~~~~~~~~~~~~~~~~~~~~~~lSP~P~~~~  523 (633)
                      |||+||||+||+|+++|+++          +   .|+|||+|++|.
T Consensus       379 FYN~Vfv~~mK~f~l~~~~~----------~---~~~lsp~p~~~~  411 (411)
T 4ell_A          379 FYNSVFMQRLKTNILQYAST----------R---PPTLAPIPHIPR  411 (411)
T ss_dssp             HHHHTHHHHHHHHHHGGGSS----------S---CCCCCCCC----
T ss_pred             HHHHHHHHHHHHHHHHhcCC----------C---CCCCCCCCCCCC
Confidence            99999999999999999976          1   489999999873
>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B Back     alignment and structure
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Back     alignment and structure
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Back     alignment and structure
>2aze_C Retinoblastoma-associated protein; coiled coil, beta sandwich, cell cycle, transcription; 2.55A {Homo sapiens} SCOP: j.119.1.1 Back     alignment and structure
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Back     alignment and structure
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Back     alignment and structure
>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens} Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B* Back     alignment and structure
>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Back     alignment and structure
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C 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 633
d2r7ga1199 a.74.1.3 (A:380-578) Retinoblastoma tumor suppress 1e-54
d2r7ga2142 a.74.1.3 (A:644-785) Retinoblastoma tumor suppress 8e-48
>d2r7ga1 a.74.1.3 (A:380-578) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]} Length = 199 Back     information, alignment and structure

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Retinoblastoma tumor suppressor domains
domain: Retinoblastoma tumor suppressor domains
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  182 bits (463), Expect = 1e-54
 Identities = 49/197 (24%), Positives = 87/197 (44%), Gaps = 45/197 (22%)

Query: 54  TAKWLRTIICPLPSKPSADL-------------------------------QGANLMDNI 82
           T + L  I+     +PS +L                               +        
Sbjct: 2   TIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVE 61

Query: 83  WAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKT 137
              QR    ++L Y+V+E+M  +E + L  +N + L     FH  +LAC+ E+V+AT+  
Sbjct: 62  IGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSR 121

Query: 138 VT---------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLES 188
            T         + F  +L  + + AF+  KVI+SFI+ E +L RE+ +HL   E R++ES
Sbjct: 122 STSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMES 181

Query: 189 MVWEKGSSMYNSLTVAR 205
           + W   S +++ +  ++
Sbjct: 182 LAWLSDSPLFDLIKQSK 198
>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]} Length = 142 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 ?
Query633
d2r7ga2142 Retinoblastoma tumor suppressor domains {Human (Ho 100.0
d2r7ga1199 Retinoblastoma tumor suppressor domains {Human (Ho 100.0
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 97.5
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 97.44
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 96.61
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 96.05
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 92.62
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 88.74
>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Retinoblastoma tumor suppressor domains
domain: Retinoblastoma tumor suppressor domains
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.8e-59  Score=435.34  Aligned_cols=137  Identities=28%  Similarity=0.578  Sum_probs=130.1

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHhCCC-hHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHH
Q 046343          371 ETGINICFCKINKLAAVRINAMVERLQLS-QQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFK  449 (633)
Q Consensus       371 ~t~L~lFfRKVy~LAa~RL~dLC~rL~ls-~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk  449 (633)
                      +++|++||||||+||++||++||++|+++ ++++++||||| ||+|.|+|+||+||||||||||||||+|||++.+++|+
T Consensus         1 stsl~iFfrKvy~La~~Rl~~LC~~L~~~~~~l~~~Iw~~f-e~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~~F~   79 (142)
T d2r7ga2           1 STSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLF-QHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFK   79 (142)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHH-HHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHCcCcHHHHHHHHHHH-HHHHHHhHHHHhccchhHHHHHHHHHHHHhccCCCCHH
Confidence            36899999999999999999999999875 68999999999 99999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCCCCcceeeec----cccceeehhhhcchhhhHHHHHHhcCCCcccccCCCcccCCCCCCCCCCCC
Q 046343          450 EIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNRDSEVNHNNDASVFPAL  521 (633)
Q Consensus       450 ~Ii~~YR~QPQa~s~VyRsVl----ergDII~FYN~VFvp~mK~F~l~~~~~~~~~~~~~~~~~~~~~~lSP~P~~  521 (633)
                      |||++||+||||+++|||+|+    |+||||+|||+||||+||+|++++.+..             +|++||+|++
T Consensus        80 ~Ii~~Yr~qPq~~~~vyR~V~i~~~e~~DII~FYN~vfv~~~K~f~~~~~s~~-------------~p~lsP~P~~  142 (142)
T d2r7ga2          80 IIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVFMQRLKTNILQYASTR-------------PPTLSPIPHI  142 (142)
T ss_dssp             HHHHHHTTSTTCCTHHHHSEECSSSCEECHHHHHHHTHHHHHHHHHHHTTSSS-------------CCCCCCCCCC
T ss_pred             HHHHHHHhCCccchhHhheeeeCCCCCCcHHHHHHHHHHHHHHHHHHHhCCCC-------------CCCCCCCCCC
Confidence            999999999999999999999    9999999999999999999999997651             4789999974
>d2r7ga1 a.74.1.3 (A:380-578) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure