Citrus Sinensis ID: 008460

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----

MHDAEPDPGQSEGERDQSSQEVDVVDQREESEAKYTDSDEKEEYGQRVATSRRREVIESGSERSEENHYPDHEDEEVDQARSPRSPGGEEKDQTHISHSAAEIRDVFGDSDEEDVGEYAIRNDIDQDSNRSPMEEEGSYEKSIRPEDIVPDEDMHYESEEEHVEPKHKEKPVGPPLELEIPLRPPPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTFVTDESGAKKRIRLENNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPEREKEEKERAESQNIRANVLLNRKREKINRKYTQTVERRRQLSTGYLEDALEEDDETDYHDSRRSRRRFEEELEAEVRAEKRIINAKKPQGHRDIPRKSSTLPAAKSSRRPVDFSESEREESEYETDGEEDERSPLRKRVEGPEQDYEEEEEEEEEEQEEEPDINRASDDEEEAVEPKQKARDSGSNHKRRGIESDEDSPPRKMPTHRRMAVVYDSDEE

ccccccccccccccccccccccccccccccHHHHcccccHHHHcccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccHHHHHHccccccccEEEEEEEccccccEEcccccEEEEccccEEEEEcccccccccccccccccEEEEEccccEEEEEEEEccEEEEEcccccHHHHHHHHHHHHHHHcccccccEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccc

cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccEEEEEccccEEccccccccHHcccHHHHccccccccHHHEccccEEEEEEEEcccccEEEEcccEEEEEccccEEEEEcccEEEEEEccccccccEEEEEccccEEEEEEEEEcEEEEEccccccHHHHHHHHHHHHHccccccEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHcccccccccccccccccccccccccccHcccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHcccccHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHccHcccccccccccccccccccccccccccccccEEEEEccccc

mhdaepdpgqsegerdqssqevdVVDQreeseakytdsdekeeygqrVATSRRREVIesgserseenhypdhedeevdqarsprspggeekdqthisHSAAEIRdvfgdsdeedvgeyairndidqdsnrspmeeegsyeksirpedivpdedmhyeseeehvepkhkekpvgppleleiplrpppadptkmnmikvsnimgidpkpfdpktyveedtfvtdesgakkriRLENNIVRWRtvknkdgmtsyesnarfvrwsdgslqlqignevLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKmrfipsslssnsHRLLTALVDSrhkkvykvkncitdidpereKEEKERAESQNIRANVLLNRKREKINRKYTQTVERRRQLSTGYLedaleeddetdyhdsrrsRRRFEEELEAEVRAEKRIINakkpqghrdiprksstlpaakssrrpvdfsesereeseyetdgeedersplrkrvegpeqdyeeeeeeeeeeqeeepdinrasddeeeavepkqkardsgsnhkrrgiesdedspprkmpthrrmavvydsdee

mhdaepdpgqsegerdqssqevdvvdqreeseakytdsdekeeygqrvatsrrreviesgserseenhypdhedeevdqARSPRSPGgeekdqthishsaaeirdvfgdsdeedVGEYAirndidqdsnrspmeeegsyeksirpedivpDEDMHYESeeehvepkhkekpvgppLELEIPLRPPPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDtfvtdesgakkrirlennivrwrtvknkdgmtsyeSNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFipsslssnsHRLLTAlvdsrhkkvykvkncitdidperekeekeraesqniranvllnrkrekinrkytqtverrrqlstgyledaleeddetdyhdsrrsrrrFEEELEAEVraekriinakkpqghrdiprksstlpaakssrrpvdfsesereeseyetdgeedersplrkrvegpeqdyeeeeeeeeeeqeeepdinrasddeeeavepkqkardsgsnhkrrgiesdedspprkmpthrrmavvydsdee

MHDAEPDPGQSEGERDQSSQEVDVVDQREESEAKYTDSDEKEEYGQRVATSRRREVIESGSERSEENHYPDHEDEEVDQARSPRSPGGEEKDQTHISHSAAEIRDVFGDSDEEDVGEYAIRNDIDQDSNRSPMEEEGSYEKSIRPEDIVPDEDMHYESeeehvepkhkekpvGppleleiplrpppADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTFVTDESGAKKRIRLENNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPerekeekeraeSQNIRANVLLNRKREKINRKYTQTVERRRQLSTGYledaleeddetdYHDSrrsrrrfeeeleaevraekrIINAKKPQGHRDIPRKSSTLPAAKSSRRPVDFsesereeseyetdgeedersPLRKRVEGPEQDYeeeeeeeeeeqeeePDINRASDDEEEAVEPKQKARDSGSNHKRRGIESDEDSPPRKMPTHRRMAVVYDSDEE

*******************************************************************************************************************************************************************************************************IMG*********TYVEEDTFVTD***AKKRIRLENNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFIPS*****SHRLLTALVDSRHKKVYKVKNCITDI*****************************************************************************************************************************************************************************************************************************

*********************************************************************************************************************************************************************************LEIPLRPP*ADPTKMNMIKVSNIMGIDPKPFDPKTYV*******************NNIVRW***************ARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFIPSSLSSNS***********************************************************************************************************************************************************************************************************************************************V******

************************************************************************************************SHSAAEIRDVFGDSDEEDVGEYAIRNDIDQDS*************SIRPEDIVPDEDM********************PLELEIPLRPPPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTFVTDESGAKKRIRLENNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPE***********QNIRANVLLNRKREKINRKYTQTVERRRQLSTGYLEDAL***********************AEVRAEKRIINA************************************************************************************************************************HRRMAVVYDSDEE

**************************************************************************************************************************************************************************PVGPPLELEIPLRPPPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTFV***SGAKKRIRLENNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPEREKEEKERAESQNIRANVLLN********************************************RRFEEELEAEVRAEKRIINA**************************************************************************************************************************R**********

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MHDAEPDPGQSEGERDQSSQEVDVVDQREESEAKYTDSDEKEEYGQRVATSRRREVIESGSERSEENHYPDHEDEEVDQARSPRSPGGEEKDQTHISHSAAEIRDVFGDSDEEDVGEYAIRNDIDQDSNRSPMEEEGSYEKSIRPEDIVPDEDMHYESEEEHVEPKHKEKPVGPPLELEIPLRPPPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTFVTDESGAKKRIRLENNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPEREKEExxxxxxxxxxxxxxxxxxxxxINRKYTQTVERRRQLSTGYLEDALEEDDETDYHDSRRSRRRFEEELEAEVRAEKRIINAKKPQGHRDIPRKSSTLPAAKSSRRPVDFSESEREESEYETDGEEDERSPLRKRxxxxxxxxxxxxxxxxxxxxxxxxxxxxSDDEEEAVEPKQKARDSGSNHKRRGIESDEDSPPRKMPTHRRMAVVYDSDEE

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
Query		564	2.2.26 [Sep-21-2011]
Q6NYV9		696	RNA polymerase-associated	yes	no	0.388	0.314	0.343	3e-29
Q52KV5		703	RNA polymerase-associated	N/A	no	0.374	0.300	0.343	6e-29
Q641X2		678	RNA polymerase-associated	yes	no	0.374	0.311	0.339	7e-28
Q5XJE5		667	RNA polymerase-associated	yes	no	0.374	0.316	0.339	7e-28
Q8WVC0		666	RNA polymerase-associated	yes	no	0.374	0.316	0.339	8e-28
Q5R4D6		666	RNA polymerase-associated	yes	no	0.372	0.315	0.342	3e-27
Q94546		725	Another transcription uni	yes	no	0.289	0.224	0.394	3e-24
Q54MB8		487	RNA polymerase-associated	yes	no	0.265	0.308	0.380	1e-21
P38439		464	RNA polymerase-associated	yes	no	0.306	0.372	0.331	7e-18
Q9P6R2		429	Uncharacterized protein C	yes	no	0.329	0.433	0.282	2e-13

>sp\|Q6NYV9\|LEO1_DANRE RNA polymerase-associated protein LEO1 OS=Danio rerio GN=leo1 PE=1 SV=1	Back alignment and function desciption

 Score =  130 bits (326), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 129/230 (56%), Gaps = 11/230 (4%)

Query: 176 LELEIPLRPPPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTFVTDESG-AKKRIRLE- 233
           +E+EIP +      + +  +K+ N + ++P+PFDP+ Y +E           + R++L+ 
Sbjct: 336 IEVEIP-KVSTDLGSDLYFVKLPNFLSVEPRPFDPQYYEDEFEDEEMLDEEGRTRLKLKV 394

Query: 234 NNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHG 293
            N +RWR+ ++++G    ESNAR V+WSDGS+ L +GNEV D+     Q D  HLF+R G
Sbjct: 395 ENTIRWRSRRDEEGNEVKESNARIVKWSDGSMSLHLGNEVFDVYKAPLQGDHNHLFIRQG 454

Query: 294 KGILQSQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNC-ITDIDPEREKEEK 352
            G LQ Q     K+ F P S  S +HR +T  +  R  K  K++   +   DPE ++ E 
Sbjct: 455 TG-LQGQAVFKTKLTFRPHSTDSATHRKMTLSLADRCSKTQKIRILPMAGRDPESQRNEM 513

Query: 353 ERAESQNIRANVLLNRKREKINRKYTQTVERRRQLSTGYLE-DALEEDDE 401
            + E + +RA++    +RE   R+  +  + +R L+ GYLE D  +ED+E
Sbjct: 514 IKKEEERLRASI----RRESQQRRMREK-QHQRGLNAGYLEPDRYDEDEE 558

Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II. PAF1C associates with RNA polymerase II, is involved in transcriptional elongation and in histone modifications including methylation on histone H3 'Lys-4' (H3K4me3) (By similarity). PAF1C seems to be required for multiple steps in cardiac formation. Involved in heart development and required for differentiation of the atrioventricular boundary. Required for neural crest cell development.
Danio rerio (taxid: 7955)

>sp\|Q52KV5\|LEO1_XENLA RNA polymerase-associated protein LEO1 OS=Xenopus laevis GN=leo1 PE=2 SV=1	Back alignment and function description

>sp\|Q641X2\|LEO1_RAT RNA polymerase-associated protein LEO1 OS=Rattus norvegicus GN=Leo1 PE=2 SV=1	Back alignment and function description

>sp\|Q5XJE5\|LEO1_MOUSE RNA polymerase-associated protein LEO1 OS=Mus musculus GN=Leo1 PE=1 SV=2	Back alignment and function description

>sp\|Q8WVC0\|LEO1_HUMAN RNA polymerase-associated protein LEO1 OS=Homo sapiens GN=LEO1 PE=1 SV=1	Back alignment and function description

>sp\|Q5R4D6\|LEO1_PONAB RNA polymerase-associated protein LEO1 OS=Pongo abelii GN=LEO1 PE=2 SV=1	Back alignment and function description

>sp\|Q94546\|ATU_DROME Another transcription unit protein OS=Drosophila melanogaster GN=Atu PE=1 SV=2	Back alignment and function description

>sp\|Q54MB8\|LEO1_DICDI RNA polymerase-associated protein LEO1 OS=Dictyostelium discoideum GN=leo1 PE=3 SV=1	Back alignment and function description

>sp\|P38439\|LEO1_YEAST RNA polymerase-associated protein LEO1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LEO1 PE=1 SV=1	Back alignment and function description

>sp\|Q9P6R2\|YOH8_SCHPO Uncharacterized protein C13E7.08c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC13E7.08c PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		564
297733888		622	unnamed protein product [Vitis vinifera]	0.984	0.892	0.781	0.0
359491648		623	PREDICTED: uncharacterized protein LOC10	0.985	0.892	0.776	0.0
224121454		620	PAF1 complex component [Populus trichoca	0.975	0.887	0.75	0.0
147820590		718	hypothetical protein VITISV_003891 [Viti	0.985	0.774	0.680	0.0
449439305		623	PREDICTED: uncharacterized protein LOC10	0.975	0.882	0.753	0.0
255547219		629	RNA polymerase-associated protein LEO1,	0.987	0.885	0.737	0.0
356508502		629	PREDICTED: uncharacterized protein LOC10	0.987	0.885	0.718	0.0
356516855		631	PREDICTED: uncharacterized protein LOC10	0.978	0.874	0.716	0.0
297797071		720	hypothetical protein ARALYDRAFT_358320 [	0.984	0.770	0.611	1e-169
30697488		623	leo1-like family protein [Arabidopsis th	0.964	0.873	0.631	1e-163

>gi\|297733888\|emb\|CBI15135.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  785 bits (2027), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 441/564 (78%), Positives = 490/564 (86%), Gaps = 9/564 (1%)

Query: 1   MHDAEPDPGQSEGERDQSSQEVDVVDQREESEAKYTDSDEKEEYGQRVATSRRREVIESG 60
           + D +PDPG+SE ERDQSS++V+V DQREESE + T SDEKE YGQRV TSRRR+VIESG
Sbjct: 68  LRDVDPDPGESEAERDQSSEDVEVGDQREESEGRETGSDEKEGYGQRVVTSRRRDVIESG 127

Query: 61  SERSEENHYPDHEDEEVDQARSPRSPGGEEKDQTHISHSAAEIRDVFGDSDEEDVGEYAI 120
           SERSEENHY DHEDEEVDQARSPRSPG EEKDQTH SHS AEIRDVFG+SD+E+  EYA+
Sbjct: 128 SERSEENHYADHEDEEVDQARSPRSPG-EEKDQTHNSHSVAEIRDVFGESDDEEAAEYAV 186

Query: 121 RNDIDQDSNRSPMEEEGSYEKSIRPEDIVPDEDMHYESEEEHVEPKHKEKPVGPPLELEI 180
            NDI+Q+S RSPMEEEGSYEK++RPEDI+PDED  Y SEEE+VE K KEKPVGPPL LE+
Sbjct: 187 DNDIEQNSIRSPMEEEGSYEKNLRPEDILPDEDAQYGSEEENVEIKSKEKPVGPPLVLEV 246

Query: 181 PLRPPPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTFVTDESGAKKRIRLENNIVRWR 240
           PLR PPA P KMNMIKVSNIMGI+PKPFDPKTYVEEDTFVTDESG+KKRIRLENNIVRWR
Sbjct: 247 PLRRPPAHPDKMNMIKVSNIMGIEPKPFDPKTYVEEDTFVTDESGSKKRIRLENNIVRWR 306

Query: 241 TVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQ 300
            VKN DG TSYESNARFVRWSDGSLQL IGNEVLDI+VQDAQHDQ+HLFLRHGKGILQSQ
Sbjct: 307 NVKNPDGTTSYESNARFVRWSDGSLQLLIGNEVLDISVQDAQHDQSHLFLRHGKGILQSQ 366

Query: 301 GRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPEREKEEKERAESQNI 360
           GRIL+KMRF+PSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPEREKEEKE+A SQ I
Sbjct: 367 GRILRKMRFMPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPEREKEEKEKAVSQTI 426

Query: 361 RANVLLNRKREKINRKYTQTVERRRQLSTGYLEDALEEDDETDYHDSRRSRRRFEEELEA 420
           RAN LLNRKREK+NRKYTQTV+R RQLS G+LE+AL+EDDE DYHDSRR RRRFE++LE 
Sbjct: 427 RANQLLNRKREKVNRKYTQTVDRGRQLSPGFLEEALDEDDEPDYHDSRRHRRRFEDDLEM 486

Query: 421 EVRAEKRIINAKKPQGHRDIPRKSSTLPAAKSSRRPVDFSESEREESEYETDGEEDERSP 480
           + RAEKRI N KK  GH+DIPRKSS L A KSSRRPVDFS+SEREESEYE+DGEEDERS 
Sbjct: 487 DTRAEKRIFNVKK--GHKDIPRKSS-LSAIKSSRRPVDFSDSEREESEYESDGEEDERSF 543

Query: 481 LRKRVEGPEQDYEEEEEEEEEEQEEEPDINRASDDEEEAVEPKQKARDSGSNHKRRGIES 540
            RKR E  E + E  EE+EEE++ +E +     + EEE  EPKQK ++     KR+GIES
Sbjct: 544 SRKRAE--EPEEEYAEEDEEEDERDEEEAEANEESEEEVEEPKQKGKEYA---KRKGIES 598

Query: 541 DEDSPPRKMPTHRRMAVVYDSDEE 564
           DEDSPPRK  +HRRMA VY+SDEE
Sbjct: 599 DEDSPPRKTASHRRMAFVYESDEE 622

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359491648\|ref\|XP_002280975.2\| PREDICTED: uncharacterized protein LOC100248444 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224121454\|ref\|XP_002318586.1\| PAF1 complex component [Populus trichocarpa] gi\|222859259\|gb\|EEE96806.1\| PAF1 complex component [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|147820590\|emb\|CAN72101.1\| hypothetical protein VITISV_003891 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449439305\|ref\|XP_004137426.1\| PREDICTED: uncharacterized protein LOC101221752 [Cucumis sativus] gi\|449486962\|ref\|XP_004157455.1\| PREDICTED: uncharacterized protein LOC101229895 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255547219\|ref\|XP_002514667.1\| RNA polymerase-associated protein LEO1, putative [Ricinus communis] gi\|223546271\|gb\|EEF47773.1\| RNA polymerase-associated protein LEO1, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|356508502\|ref\|XP_003522995.1\| PREDICTED: uncharacterized protein LOC100791454 [Glycine max]	Back alignment and taxonomy information

>gi\|356516855\|ref\|XP_003527108.1\| PREDICTED: uncharacterized protein LOC100810965 [Glycine max]	Back alignment and taxonomy information

>gi\|297797071\|ref\|XP_002866420.1\| hypothetical protein ARALYDRAFT_358320 [Arabidopsis lyrata subsp. lyrata] gi\|297312255\|gb\|EFH42679.1\| hypothetical protein ARALYDRAFT_358320 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|30697488\|ref\|NP_200923.2\| leo1-like family protein [Arabidopsis thaliana] gi\|332010045\|gb\|AED97428.1\| leo1-like family protein [Arabidopsis thaliana]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		564
TAIR\|locus:2159466		625	VIP4 "VERNALIZATION INDEPENDEN	0.964	0.870	0.524	5.2e-136
ZFIN\|ZDB-GENE-040426-2435		696	leo1 "Leo1, Paf1/RNA polymeras	0.336	0.272	0.348	2e-32
UNIPROTKB\|Q52KV5		703	leo1 "RNA polymerase-associate	0.652	0.523	0.256	2.7e-32
UNIPROTKB\|E1BV70		657	LOC769405 "Uncharacterized pro	0.336	0.289	0.348	1e-31
UNIPROTKB\|Q8WVC0		666	LEO1 "RNA polymerase-associate	0.336	0.285	0.348	1.8e-31
MGI\|MGI:2685031		667	Leo1 "Leo1, Paf1/RNA polymeras	0.336	0.284	0.348	2.3e-31
RGD\|1549772		678	Leo1 "Leo1, Paf1/RNA polymeras	0.336	0.280	0.348	3.2e-31
UNIPROTKB\|Q641X2		678	Leo1 "RNA polymerase-associate	0.336	0.280	0.348	3.2e-31
UNIPROTKB\|Q5R4D6		666	LEO1 "RNA polymerase-associate	0.336	0.285	0.343	2.3e-30
UNIPROTKB\|F1RZB7		666	LEO1 "Uncharacterized protein"	0.336	0.285	0.348	2.4e-30

TAIR\|locus:2159466 VIP4 "VERNALIZATION INDEPENDENCE 4" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1332 (473.9 bits), Expect = 5.2e-136, P = 5.2e-136
 Identities = 300/572 (52%), Positives = 363/572 (63%)

Query:     3 DAEPDPGQSEGERDQSSQEVDVVDQREESEAKYTDSDEKEE-YGQRVATSRRREVIESGS 61
             D E DPG+SEGER+QSSQE D    +EESEA+ +DSD KEE +G RVA  RR+EV+ESGS
Sbjct:    72 DVELDPGESEGEREQSSQEAD---PQEESEARDSDSDNKEEEHGGRVAKKRRQEVVESGS 128

Query:    62 ERSEENHYPDHEDEEVDQARSPRSPGGEEKDQTHISHSAAEIRDVFGDSDEEDVGEYAIR 121
             ERS E HY + EDEEVDQ RSPRSP  EEK++  ++ S   IR+VFG SD+ED  EY +R
Sbjct:   129 ERSGEKHY-ESEDEEVDQTRSPRSPS-EEKEEVQVAQSDVNIRNVFGSSDDEDAEEY-VR 185

Query:   122 NDIDQDSNRSPMEEEGSYEKSIRPED-----IVPDEDMHYESXXXXXXXXXXXXXXGXXX 176
             ND++QD +RSP+E+E   EK +RP+D     I+P+ED  YES              G   
Sbjct:   186 NDVEQDEHRSPIEDEEGSEKDLRPDDMVLDDIIPEEDPQYESEAEHVEARYRERPVGPPL 245

Query:   177 XXXXXXXXXXADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTFVTDESGAKKRIRLENNI 236
                        DP KMNMIKVSNIMGIDPKPFD KT+VEEDTF+TDE GAK RIRL+NNI
Sbjct:   246 EVEVPFRPPPGDPVKMNMIKVSNIMGIDPKPFDAKTFVEEDTFMTDEPGAKNRIRLDNNI 305

Query:   237 VRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGI 296
             VR R VK++DG T  ESNARFVRWSDGSLQL IGNEVL+IT QDA+ DQ HLF++H KGI
Sbjct:   306 VRHRFVKSRDGKTYSESNARFVRWSDGSLQLLIGNEVLNITEQDAKEDQNHLFIKHEKGI 365

Query:   297 LQSQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPXXXXXXXXXXX 356
             LQSQGRILKKMRF PSSL+SNSHRLLTA+V+SR KK +KVKNC+TDIDP           
Sbjct:   366 LQSQGRILKKMRFTPSSLTSNSHRLLTAIVESRQKKAFKVKNCVTDIDPEREKEKREKAE 425

Query:   357 SQNIRANVLLNRKREKINRKYTQTVERRRQLSTGYXXXXXXXXXXXXYHDSXXXXXXXXX 416
             SQN++A+  L++ REKI RKY   VERR QLSTGY            Y  +         
Sbjct:   426 SQNLKASTKLSQAREKIKRKYPLPVERR-QLSTGYLEDALDEDDED-YRSNRGYEEDLEA 483

Query:   417 XXXXXXXXXXXIINAKKPQGHRDIPRKSSTLPAAKSSRRPVDFXXXXXXXXXXXXXXXXX 476
                        I+NAKK   H+ IP +SS + +A+ SRR +++                 
Sbjct:   484 EAQRERR----ILNAKK--SHKGIPGRSS-MTSARPSRRQMEYSESEREESEYETEEEEE 536

Query:   477 XXXPLRKRVEGPEQDYXXXXXXXXXXXXXXPDINRASDD--EEEAVEPKQKARDS-GSNH 533
                P R R +  E +Y                 NR SD+  EEE V   +  +D  GS  
Sbjct:   537 EKSPARGRGKDSEDEYEEDAEEDEEERGKS---NRYSDEDEEEEEVAGGRAEKDHRGSGR 593

Query:   534 KRRGIESDED-SPPRKMPTHRRMAVVYDSDEE 564
             KR+GIESDE+ SPPRK PTHRR AV+ DSDE+
Sbjct:   594 KRKGIESDEEESPPRKAPTHRRKAVIDDSDED 625

GO:0005634 "nucleus" evidence=ISM

GO:0009910 "negative regulation of flower development" evidence=IMP

GO:0010048 "vernalization response" evidence=RCA;IMP

GO:0005829 "cytosol" evidence=IDA

GO:0000226 "microtubule cytoskeleton organization" evidence=RCA

GO:0000911 "cytokinesis by cell plate formation" evidence=RCA

GO:0008284 "positive regulation of cell proliferation" evidence=RCA

ZFIN\|ZDB-GENE-040426-2435 leo1 "Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q52KV5 leo1 "RNA polymerase-associated protein LEO1" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BV70 LOC769405 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8WVC0 LEO1 "RNA polymerase-associated protein LEO1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:2685031 Leo1 "Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1549772 Leo1 "Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q641X2 Leo1 "RNA polymerase-associated protein LEO1" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5R4D6 LEO1 "RNA polymerase-associated protein LEO1" [Pongo abelii (taxid:9601)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RZB7 LEO1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	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:
	PAFB901	PAF1 complex component (620 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	PAFC901	PAF1 complex component (1056 aa)	•	•	0.603
	eugene3.00060987	SubName- Full=Putative uncharacterized protein; (321 aa)	•	•	0.498

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
Query		564
pfam04004		312	pfam04004, Leo1, Leo1-like protein	1e-62
TIGR00927		1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-05
pfam03344		715	pfam03344, Daxx, Daxx Family	2e-04
COG5271		4600	COG5271, MDN1, AAA ATPase containing von Willebran	6e-04

>gnl\|CDD\|217838 pfam04004, Leo1, Leo1-like protein	Back alignment and domain information

 Score =  207 bits (529), Expect = 1e-62
 Identities = 109/313 (34%), Positives = 153/313 (48%), Gaps = 13/313 (4%)

Query: 123 DIDQDSNRSPMEEEGSYEKSIRPEDI-----VPDEDMHYESEEEHVEPKHKEKPVGPPLE 177
           D +QDS+RS      S +  +          +  ED    SE E       EK V    +
Sbjct: 1   DREQDSHRSNDRNSLSGDDDLSRGGNGDDGEINGEDPSQFSEIEEATETFPEKDVAVKFQ 60

Query: 178 LEIPLRP--PPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTF----VTDESGAKKRIR 231
            E+P +    PA        K+ N + ++PKPFDP+T+  E T        E+  ++RI+
Sbjct: 61  TEVPTQNFGLPAGSNPSFFAKIPNFLSVEPKPFDPETFEAEMTKEDAKDEHEAHWRQRIK 120

Query: 232 LE-NNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFL 290
           L   N VRWR  K+KDG T+ ESNA+ VRWSDGS  L IGNE+ DI  Q    +Q HL +
Sbjct: 121 LRVENTVRWRENKSKDGKTTKESNAQIVRWSDGSYSLHIGNEIFDIMHQPLSVNQNHLTV 180

Query: 291 RHGKGILQSQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKKVYKVKNCITDIDPEREKE 350
            H + +LQ QG I KK+ F PSS +S +HR LT  + +R +K   VK  I   DPE EK 
Sbjct: 181 SHEQTLLQPQGVIKKKLTFRPSSTNSFTHRKLTRNLATRQRKSGGVKITIVGKDPEHEKR 240

Query: 351 EKERAESQNIRANVLLNRKREKINRKYTQTVERRRQLSTGYLEDALEEDDETDYHDSRRS 410
           E+E+ E Q +RA     + REK+  K            +   + A    ++ D      +
Sbjct: 241 EREKKEEQKLRARR-RRQNREKMKNKPPNRPGHGSGSDSNVAKAATTYSEDEDEGSDCET 299

Query: 411 RRRFEEELEAEVR 423
           R+  E + E   R
Sbjct: 300 RKAKEVKKEGAGR 312

Members of this family are part of the Paf1/RNA polymerase II complex. The Paf1 complex probably functions during the elongation phase of transcription. The Leo1 subunit of the yeast Paf1-complex binds RNA and contributes to complex recruitment. The subunit acts by co-ordinating co-transcriptional chromain modifications and helping recruitment of mRNA 3prime-end processing factors. Length = 312

>gnl\|CDD\|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	Back alignment and domain information

>gnl\|CDD\|217503 pfam03344, Daxx, Daxx Family	Back alignment and domain information

>gnl\|CDD\|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		564
KOG2428		443	consensus Uncharacterized conserved protein [Funct	100.0
PF04004		171	Leo1: Leo1-like protein; InterPro: IPR007149 Membe	100.0

>KOG2428 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

Probab=100.00  E-value=6.5e-64  Score=523.11  Aligned_cols=323  Identities=36%  Similarity=0.528  Sum_probs=258.7

Q ss_pred             cccC-CcCCCCCCCCCeeeecc-CCCCCCCCCceeEeecCCcccccCCCCCCCCCcccCCc--ccccch-hccccccccc
Q 008460          161 EHVE-PKHKEKPVGPPLELEIP-LRPPPADPTKMNMIKVSNIMGIDPKPFDPKTYVEEDTF--VTDESG-AKKRIRLENN  235 (564)
Q Consensus       161 e~~E-~~~~ek~~~~~ldlelP-~~~~p~~~~~l~~lKmPNFLsIeP~PFDPeTFe~e~~~--~~dE~g-~~~rl~~eeN  235 (564)
                      +.++ +..++.++.++|++.|| +.+++.....+||+||||||+|+|+||||+||+.+..+  .+++.| .+.++++ +|
T Consensus       113 ~~~e~~~e~e~~~e~v~evevp~~~n~~~~~~~~~fvkiPNFLsVep~PfDPetyede~~~~~~~Dee~r~r~klkv-eN  191 (443)
T KOG2428|consen  113 EEQEEAQEKEPPVETVLEVEVPIFVNPDLGKNPSFFVKIPNFLSVEPKPFDPETYEDEFEDEALLDEEGRQRLKLKV-EN  191 (443)
T ss_pred             cchhhccccccCCCcceEeecccccCCccCCCccceeecCcccccCCcCCChhhhhhhhhhhhhcccchhhhhhhhh-cc
Confidence            3444 66788899999999999 55554455678999999999999999999999986432  335544 4566665 69


Q ss_pred             eEEEeeecCCCCCceecccccEEEeCCCceeeeeccceeeeeccccccCCceEEEeccCceeEEeeeecceEEeecCCCC
Q 008460          236 IVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQDAQHDQAHLFLRHGKGILQSQGRILKKMRFIPSSLS  315 (564)
Q Consensus       236 TIRWR~~~d~dG~~~kESNARIVRWSDGSlSL~IGnE~FDI~~~~l~~~d~hLyvrh~s~lLQ~qg~It~kLtfrPtSt~  315 (564)
                      |||||+.++.+|..++||||||||||||||||+||||+|||+.+||..+++|||++++++ ||.||+|+++|||+|+||+
T Consensus       192 TVRWR~~~d~~g~~~kESNAriVrWSDGS~SL~lGNEvfDv~~~pl~~~~nhl~vrq~t~-l~~Q~~ik~kltFrP~S~~  270 (443)
T KOG2428|consen  192 TVRWRERRDKDGNKIKESNARIVRWSDGSMSLHLGNEVFDVYKQPLSGNQNHLFVRQGTG-LQGQAVIKKKLTFRPHSTD  270 (443)
T ss_pred             eeeEeeeecCCCCcceeccceEEEecCCceeEeechhHHHhhhcccccCcceeEEecccc-cchhheeeceeEeeccccc
Confidence            999999999999999999999999999999999999999999999999999999999864 8899999999999999999


Q ss_pred             cHHHHHHHHHHHhhhccccccc-ceeccCChhhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhccccccccCCCcccccc
Q 008460          316 SNSHRLLTALVDSRHKKVYKVK-NCITDIDPEREKEEKERAESQNIRANVLLNRKREKINRKYTQTVERRRQLSTGYLED  394 (564)
Q Consensus       316 S~tHrrLt~ava~r~~K~~kik-~~it~~DPEleKke~EkaEeErlRa~~kl~RKREk~~rr~~~~~~Rr~gLS~g~LE~  394 (564)
                      |.||++||+.|+.+.+|+.+|+ +++++.|||.+|.+++|+|.++|||+.+++.++.               +..++++.
T Consensus       271 S~tHrklt~~~a~r~~k~skvk~~~~vg~DPE~~k~~~~KkEee~LRa~~R~~~~~~---------------~~~~~r~~  335 (443)
T KOG2428|consen  271 SATHRKLTLNRADRSQKTSKVKILTIVGKDPEHEKREREKKEEERLRASRRREQRAL---------------MNPKQREK  335 (443)
T ss_pred             hHHHHHHHHHHhhcccccccceeeeeccCCccchhHHHHHHHHHHHHHHHHHHHHHh---------------hcccccCc
Confidence            9999999999999999999999 5689999999999999999999997665332221               12344445


Q ss_pred             ccccCCCCCccchhhhHHHhHHHHHHHHHHhHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCcchhcccccccccc
Q 008460          395 ALEEDDETDYHDSRRSRRRFEEELEAEVRAEKRIINAKKPQGHRDIPRKSSTLPAAKSSRRPVDFSESEREESEYETDGE  474 (564)
Q Consensus       395 gldeDDe~d~~~~~r~~~~~~~~~~~~~~~e~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~  474 (564)
                      ++.+++....|+     ..|..+++.|...+.+|.++|+..  +.   ... |-.........+++++..++.+++...+
T Consensus       336 ~~~~e~~~~~~n-----~~~~~~~~~e~e~~~~~~a~k~~~--~~---~~~-~~~~~~d~~~~d~de~sd~e~e~~~~~~  404 (443)
T KOG2428|consen  336 RYAEEDSDSAYN-----SPTTYDEEEEGEDEIRLAALKNRY--KE---AGQ-SEEETADIEESDEDESSDEEAEKEKREE  404 (443)
T ss_pred             ccccCccccccC-----CCCccccccccchhhhhhhhhhhh--cc---ccc-cccccccccccccccccchhHHHHHHHH
Confidence            555555555465     456778899999999999999853  32   122 5677778888899999999999998888


Q ss_pred             ccccCcccccCCCCCccchhhHHHHhhhhccccccCCCCchhHhh
Q 008460          475 EDERSPLRKRVEGPEQDYEEEEEEEEEEQEEEPDINRASDDEEEA  519 (564)
Q Consensus       475 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  519 (564)
                      ..+.+|..++.++...+|.+..+.+        ..+.++.+++|.
T Consensus       405 kee~~~~~~~~~ees~~~~~~s~~d--------~~~~as~e~~Ed  441 (443)
T KOG2428|consen  405 KEEKLPADGEGREESDEGKDESESD--------KSNRASIEDEED  441 (443)
T ss_pred             hhhcccccccccCcccccccccccc--------cccccccccccc
Confidence            8888888887766665444332221        355566665553

>PF04004 Leo1: Leo1-like protein; InterPro: IPR007149 Members of this family are part of the Paf1/RNA polymerase II complex [, ]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		564
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-06

>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

 Score = 48.3 bits (114), Expect = 6e-06
 Identities = 56/458 (12%), Positives = 127/458 (27%), Gaps = 100/458 (21%)

Query: 18  SSQEVD-VVDQREESEAKYTDSDEKEEYGQRVATSRRREVIESG-----SERSEENHYPD 71
           S +E+D ++  ++                + +      EV+        S    E   P 
Sbjct: 47  SKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPS 106

Query: 72  HEDEEVDQARSPRSPGGEEKDQTHIS--HSAAEIRD-VFGDSDEEDV--------GEYAI 120
                  + R       +   + ++S      ++R  +      ++V        G+  +
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWV 166

Query: 121 RNDIDQDSNRSPMEEEGSY----EKSIRPEDIV-PDEDMHYESEEEHVEPKHKEKPVGPP 175
             D+          +   +    +    PE ++   + + Y      ++P    +     
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY-----QIDPNWTSRSDHSS 221

Query: 176 LELEIPLRPPPADPTKMNMIK-------------VSNIMGIDPKPFDP--KTYV-EEDTF 219
               I LR          ++K             V N    +   F+   K  +      
Sbjct: 222 ---NIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA--FNLSCKILLTTRFKQ 276

Query: 220 VTDESGAKKRIRLENNIVRWRTVKNKDGMTSYESNARFVRWSDGSLQLQIGNEVLDITVQ 279
           VTD   A     +           +   +T  E  +  +++        +     D+  +
Sbjct: 277 VTDFLSAATTTHI-------SLDHHSMTLTPDEVKSLLLKY--------LDCRPQDLPRE 321

Query: 280 DAQHDQAHL-----FLRHGKGILQ--SQGRILKKMRFIPSSLSSNSHRLLTALVDSRHKK 332
               +   L      +R G             K    I SSL+         L  + ++K
Sbjct: 322 VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN--------VLEPAEYRK 373

Query: 333 VYK-----VKNCITDIDPEREKE----EKERAESQNIRANVLLNRKREKINRKYTQTVER 383
           ++        +    I P         +  +++   +  N L      +   K     E 
Sbjct: 374 MFDRLSVFPPS--AHI-PTILLSLIWFDVIKSDVMVV-VNKLHKYSLVEKQPK-----ES 424

Query: 384 RRQLSTGYLEDALEEDDETDYH----DSRRSRRRFEEE 417
              + + YLE  ++ ++E   H    D     + F+ +
Sbjct: 425 TISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462

PyMOL of 1vt4

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00