Psyllid ID: psy6664

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----

MAPTIQTTSAGTPSEKRTPSTHSTPVPPRPAERRSELVCRVKYNNTLPDIPFDCKFIAYPFESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDILTPQDSKRSRHHARSVSWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMDRDSQVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKMAREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVRLSKRRQKVGAAPNNTRLVVTHRPLNATEFRIQRLRERFLEPPNEEEEEEDEEEEEEEAEETQQGETTEAERQEGEGGEREGGGEGENDNEKRTSDAEHSSKNSSRASSRSRSRSKSKSPAKRSRSGSASSRGSNKSDRSAKSDRSAKSDRSARSDRSDKSAASNRSRSGSAASNKSRSDRSRSGSAGSDRSAASNKSVRSDKSAASNRSARSDGSDKSASNRSRSRSASSQASNNSAASNRSSNKSGSRSRSRSVSRARSNRSRSASKSGSSAASSRSGSPAGSD

ccccccccccccccccccccccccccccccccccccEEEEEEEEcccccccccccEEcccccccccccccccHHHccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccEEccccccccccccHHHHHHHcccccccccccccccccHHHHHHHHHHcHHHHccccccccccccccEEEEEccccccccccccEEEEEEcccccccccccHHHHHHHHHHHHcccccccccEEEEEEcccHHHHHHHHHHHHccccccccccccccEEEEcccccccccccccccEEEEEEcccEEEEEcccccEEEHHcccccccccccccEEEEEccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

ccccccccccccccccccccccccccccccccccccEEEEEEEccccccccccccEEcccccccHEEEccccHHHHHccccHcccccccccEcccccccccccccccccHHHHHHHHccccccccccccccccccccEEEEcEEEEccccccccccccccEEcccccHHccccHHHHHccHHHHHHHHHHHHHHHcccccccccccccEEEEEccccccHHHcccccEEEEEcccccccccccHHHHHHHHHHHHcccccccccEEEEEEcccHHHHHHHHHHHHccccccccccccEEEEEEEEEEEcccccccccccEEEEEEcccEEEEccccEEEEEEEcccccccccccEEEEEEccccHHHHHHHHHHHHHcccccHHHHHHcccHHHHHcHHcccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

maptiqttsagtpsekrtpsthstpvpprpaerrsELVCRVKynntlpdipfdckfiaypfestrfIEYKStslernykyevltehdlgvtidlinkdtyapnyniqldpadeklleediltpqdskrsrhharsvsWLRRTEYIsteqtrfqpqvMDKVEAKVGFSIkknfkednlymdrdSQVKAIEKTfadsklpiekhyskpnvtpveimpvypdfkywkypcaqvifdsdpapvgrpipAQIEEMSQAMIRGVMDESGEQFVAYFLptaetldkrkldqlsnleytdEQEYEYKMAREynwnvksksckgyeenYFLIVRDDAVYYNELETRVRLSKRRqkvgaapnntrlvvthrplnatEFRIQRLRErfleppneeeeeedeeeEEEEAEEtqqgetteaerqegeggeregggegendnekrtsdaehssknssrassrsrsrskskspakrsrsgsassrgsnksdrsaksdrsaksdrsarsdrsdksaasnrsrsgsaasnksrsdrsrsgsagsdrsaasnksvrsdksaasnrsarsdgsdksasnrsrsrsassqasnnsaasnrssnksgsrsrsrsvsrarsnrsrsasksgssaassrsgspagsd

maptiqttsagtpsekrtpsthstpvpprpaerrsELVCRVKYnntlpdipfdcKFIAYPFESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDiltpqdskrsrhharsvswlrrteyisteqtrfqpqvmdKVEAKVGFSikknfkednlymdrDSQVKAIEKtfadsklpiekhyskpnvtpveIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPtaetldkrkldqlsnleytdeQEYEYKMAReynwnvkskscKGYEENYFLIVRDDAVYYNELETRvrlskrrqkvgaapnntrlvvthrplnatefRIQRLRerfleppneeeeeedeeeeeeeaeetqqgetteaerqegeggeregggegendnekrtsdaehssknssrassrsrsrskskspakrsrsgsassrgsnksdrsaksdrsaksdrsarsdrsdksaasnrsrsgsaasnksrsdrsrsgsagsdrsaasnksvrsdksaasnrsarsdgsdksasnrsrsrsassqasnnsaasnrssnksgsrsrsrsvsrarsnrsrsasksgssaassrsgspagsd

MAPTIQTTSAGTPSEKRTPSTHSTPVPPRPAERRSELVCRVKYNNTLPDIPFDCKFIAYPFESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDILTPQDSKRSRHHARSVSWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMDRDSQVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKMAREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVRLSKRRQKVGAAPNNTRLVVTHRPLNATEFRIQRLRERFLeppneeeeeedeeeeeeeaeetqqgetteaerqegeggeregggegendneKRTSDAEHssknssrassrsrsrskskspakrsrsgsassrgsnksdrsaksdrsaksdrsarsdrsdksaasnrsrsgsaasnksrsdrsrsgsagsdrsaasnKSVRSDKSAASNRSARSDgsdksasnrsrsrsassqasnnsaasnrssnksgsrsrsrsvsrarsnrsrsasksgssaassrsgspagsD

************************************LVCRVKYNNTLPDIPFDCKFIAYPFESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLD***************************SWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMDR**QVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSD******************MIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKMAREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVRLS***********NTRLVVTHRPLNATEFRIQ*************************************************************************************************************************************************************************************************************************************************************

*************************************VCRVKYNNTLPDIPFDCKFIAYPFESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLL***********************************************************************IEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDS**************************ESGEQFVAYFLPTAET*******************YEYKMAREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVR*********************************************************************************************************************************************************************************************************************************************************************************************

*********************************RSELVCRVKYNNTLPDIPFDCKFIAYPFESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDILTP************VSWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMDRDSQVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKMAREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVRLSKRRQKVGAAPNNTRLVVTHRPLNATEFRIQRLRERFLE*****************************************************************************************************************************************************************************************************************************************************

*********************************RSELVCRVKYNNTLPDIPFDCKFIAYPFESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEED***************SVSWLRRTEYISTEQTRF*****DKVEAKVGFSIKKNFKEDNLYMDRDSQVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKMAREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVRLSKRRQKVGAAPNNTRLVVTHRPLNATEFRIQRLRE*********************************************************************************************************************************************************************************************************************************************************

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MAPTIQTTSAGTPSEKRTPSTHSTPVPPRPAERRSELVCRVKYNNTLPDIPFDCKFIAYPFESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDILTPQDSKRSRHHARSVSWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMDRDSQVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKMAREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVRLSKRRQKVGAAPNNTRLVVTHRPLNATEFRIQRLRERFLEPPxxxxxxxxxxxxxxxxxxxxxxxTTEAERQEGEGGEREGGGEGENDNEKRTSDAEHSSKNSSRASSRSRSRSKSKSPAKRSRSGSASSRGSNKSDRSAKSDRSAKSDRSARSDRSDKSAASNRSRSGSAASNKSRSDRSRSGSAGSDRSAASNKSVRSDKSAASNRSARSDGSDKSASNRSRSRSASSQASNNSAASNRSSNKSGSRSRSRSVSRARSNRSRSASKSGSSAASSRSGSPAGSD

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		624	2.2.26 [Sep-21-2011]
Q4U0S5		503	RNA polymerase II-associa	yes	N/A	0.592	0.735	0.608	1e-129
Q5RAX0		533	RNA polymerase II-associa	yes	N/A	0.663	0.776	0.543	1e-129
Q8K2T8		535	RNA polymerase II-associa	yes	N/A	0.663	0.773	0.541	1e-128
Q2KJ14		532	RNA polymerase II-associa	yes	N/A	0.663	0.778	0.543	1e-128
Q4V886		535	RNA polymerase II-associa	yes	N/A	0.663	0.773	0.541	1e-128
Q6P2Y1		520	RNA polymerase II-associa	yes	N/A	0.650	0.780	0.573	1e-127
Q8N7H5		531	RNA polymerase II-associa	yes	N/A	0.669	0.787	0.551	1e-126
A2BD83		524	RNA polymerase II-associa	N/A	N/A	0.658	0.784	0.566	1e-126
P90783		425	RNA polymerase II-associa	yes	N/A	0.520	0.764	0.320	7e-47

>sp\|Q4U0S5\|PAF1_DANRE RNA polymerase II-associated factor 1 homolog OS=Danio rerio GN=paf1 PE=1 SV=1	Back alignment and function desciption

 Score =  464 bits (1193), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 232/381 (60%), Positives = 277/381 (72%), Gaps = 11/381 (2%)

Query: 1   MAPTIQTTSAGTPSEKRTPSTHSTPVPPRPAERRSELVCRVKYNNTLPDIPFDCKFIAYP 60
           MAPTIQT +      +   S H T VP      RS +VCRVKY N+LPDIPFD KFI YP
Sbjct: 1   MAPTIQTQAQREDGHRS--SAHRT-VP-----ERSGVVCRVKYGNSLPDIPFDPKFITYP 52

Query: 61  FESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDI 120
           F+  RF++YK+TSLE+ +K+E+LTE DLGVTIDLIN DTY  + NI LDPADEKLLEE+I
Sbjct: 53  FDQHRFVQYKATSLEKQHKHELLTEPDLGVTIDLINPDTYRIDPNILLDPADEKLLEEEI 112

Query: 121 LTPQDSKRSRHHARSVSWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMD 180
             P  SKRS+ HA+ V W+R+TEYISTE  R+     +KVE K+G S+K+ F E+ +Y D
Sbjct: 113 QAPSSSKRSQQHAKVVPWMRKTEYISTEFNRYGVS-NEKVEVKIGVSVKQQFTEEEIYKD 171

Query: 181 RDSQVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVG 240
           RDSQ+ AIEKTF D++  I +HYSKP VTPVE++PV+PDFK W  PCAQVIFDSDPAP  
Sbjct: 172 RDSQIAAIEKTFEDAQKSISQHYSKPRVTPVEVLPVFPDFKMWINPCAQVIFDSDPAPKD 231

Query: 241 RPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKM 300
              PA ++ MSQAMIRG+MDE G QFVAYFLP  +T+ KRK D    L+Y  E+ YEYK+
Sbjct: 232 VSAPAGVDMMSQAMIRGMMDEEGNQFVAYFLPNEDTMRKRKRDVEEELDYMPEEVYEYKI 291

Query: 301 AREYNWNVKSKSCKGYEENYFLIVRD-DAVYYNELETRVRLSKRRQKVGA-APNNTRLVV 358
           AREYNWNVK+K+ KGYEENYF I RD D VYYNELETRVRLSKRR KVGA +  N  LV 
Sbjct: 292 AREYNWNVKNKASKGYEENYFFIFRDADGVYYNELETRVRLSKRRAKVGAQSSTNAVLVC 351

Query: 359 THRPLNATEFRIQRLRERFLE 379
            HR +N  E   Q  R+  LE
Sbjct: 352 KHRDMNEKELEAQEARKAQLE 372

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 the migration of myocardial precursors to the midline and the differentiation of the atrioventricular boundary in the developing heart.
Danio rerio (taxid: 7955)

>sp\|Q5RAX0\|PAF1_PONAB RNA polymerase II-associated factor 1 homolog OS=Pongo abelii GN=PAF1 PE=2 SV=1	Back alignment and function description

>sp\|Q8K2T8\|PAF1_MOUSE RNA polymerase II-associated factor 1 homolog OS=Mus musculus GN=Paf1 PE=2 SV=1	Back alignment and function description

>sp\|Q2KJ14\|PAF1_BOVIN RNA polymerase II-associated factor 1 homolog OS=Bos taurus GN=PAF1 PE=2 SV=1	Back alignment and function description

>sp\|Q4V886\|PAF1_RAT RNA polymerase II-associated factor 1 homolog OS=Rattus norvegicus GN=Paf1 PE=2 SV=1	Back alignment and function description

>sp\|Q6P2Y1\|PAF1_XENTR RNA polymerase II-associated factor 1 homolog OS=Xenopus tropicalis GN=paf1 PE=2 SV=1	Back alignment and function description

>sp\|Q8N7H5\|PAF1_HUMAN RNA polymerase II-associated factor 1 homolog OS=Homo sapiens GN=PAF1 PE=1 SV=2	Back alignment and function description

>sp\|A2BD83\|PAF1_XENLA RNA polymerase II-associated factor 1 homolog OS=Xenopus laevis GN=paf1 PE=2 SV=1	Back alignment and function description

>sp\|P90783\|PAF1_CAEEL RNA polymerase II-associated factor 1 homolog OS=Caenorhabditis elegans GN=C55A6.9 PE=3 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		624
332022364		581	RNA polymerase II-associated factor 1-li	0.596	0.640	0.792	0.0
307199453		530	RNA polymerase II-associated factor 1-li	0.596	0.701	0.787	0.0
307172366		428	RNA polymerase II-associated factor 1-li	0.596	0.869	0.784	1e-180
307213815		533	RNA polymerase II-associated factor 1-li	0.592	0.694	0.787	1e-180
340728168		562	PREDICTED: RNA polymerase II-associated	0.591	0.656	0.783	1e-180
380011783		548	PREDICTED: RNA polymerase II-associated	0.591	0.673	0.785	1e-179
328787903		549	PREDICTED: RNA polymerase II-associated	0.591	0.672	0.785	1e-179
383850476		554	PREDICTED: RNA polymerase II-associated	0.591	0.666	0.783	1e-179
350403064		562	PREDICTED: RNA polymerase II-associated	0.591	0.656	0.783	1e-179
156550709		583	PREDICTED: RNA polymerase II-associated	0.591	0.632	0.747	1e-170

>gi\|332022364\|gb\|EGI62676.1\| RNA polymerase II-associated factor 1-like protein [Acromyrmex echinatior]	Back alignment and taxonomy information

 Score =  647 bits (1669), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 302/381 (79%), Positives = 329/381 (86%), Gaps = 9/381 (2%)

Query: 1   MAPTIQTTSAGTPSEKRTPSTHSTPVPPRPAERRSELVCRVKYNNTLPDIPFDCKFIAYP 60
           MAPTIQT S     +KR           RPAE+RSEL+CRVKY NTLPDIPFD KFIAYP
Sbjct: 1   MAPTIQTNSNQADRDKRV---------VRPAEKRSELICRVKYCNTLPDIPFDPKFIAYP 51

Query: 61  FESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDI 120
           FE TRFI+Y  TSLERNYKYEVLTEHDLGV IDLINKDTYA + N QLDPADEKLLEED+
Sbjct: 52  FEPTRFIQYNPTSLERNYKYEVLTEHDLGVEIDLINKDTYAGDPNAQLDPADEKLLEEDV 111

Query: 121 LTPQDSKRSRHHARSVSWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMD 180
           LTPQDSKRSRHHARSVSWLRRTEYISTE TRFQPQ  DKVEAKVG+SIKKNFKE+ LYMD
Sbjct: 112 LTPQDSKRSRHHARSVSWLRRTEYISTESTRFQPQTADKVEAKVGYSIKKNFKEETLYMD 171

Query: 181 RDSQVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVG 240
           R+SQ+KAIEKTF D+K PIE+HYSKPNV P+EI+PVYPDFK WKYPCAQVIFDSDPAP G
Sbjct: 172 RESQIKAIEKTFEDNKKPIERHYSKPNVVPIEILPVYPDFKLWKYPCAQVIFDSDPAPTG 231

Query: 241 RPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKM 300
           R +PAQIEEMSQAMIRGVMDESGEQFVAYFLP  ETL+KR+ D  + ++Y DE+EYEYKM
Sbjct: 232 RSVPAQIEEMSQAMIRGVMDESGEQFVAYFLPLEETLEKRRRDFTAGIDYADEEEYEYKM 291

Query: 301 AREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVRLSKRRQKVGAAPNNTRLVVTH 360
           AREYNWNVKSK+ KGYEENYFL++R D VYYNELETRVRLSKRRQKVG  PNNTRL+V H
Sbjct: 292 AREYNWNVKSKASKGYEENYFLVIRQDGVYYNELETRVRLSKRRQKVGQQPNNTRLIVRH 351

Query: 361 RPLNATEFRIQRLRERFLEPP 381
           RPLNA EFR+QR RE+ LEPP
Sbjct: 352 RPLNANEFRMQRYREKQLEPP 372

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|307199453\|gb\|EFN80066.1\| RNA polymerase II-associated factor 1-like protein [Harpegnathos saltator]	Back alignment and taxonomy information

>gi\|307172366\|gb\|EFN63837.1\| RNA polymerase II-associated factor 1-like protein [Camponotus floridanus]	Back alignment and taxonomy information

>gi\|307213815\|gb\|EFN89122.1\| RNA polymerase II-associated factor 1-like protein [Harpegnathos saltator]	Back alignment and taxonomy information

>gi\|340728168\|ref\|XP_003402400.1\| PREDICTED: RNA polymerase II-associated factor 1 homolog [Bombus terrestris]	Back alignment and taxonomy information

>gi\|380011783\|ref\|XP_003689974.1\| PREDICTED: RNA polymerase II-associated factor 1 homolog [Apis florea]	Back alignment and taxonomy information

>gi\|328787903\|ref\|XP_624998.3\| PREDICTED: RNA polymerase II-associated factor 1 homolog isoform 1 [Apis mellifera]	Back alignment and taxonomy information

>gi\|383850476\|ref\|XP_003700821.1\| PREDICTED: RNA polymerase II-associated factor 1 homolog [Megachile rotundata]	Back alignment and taxonomy information

>gi\|350403064\|ref\|XP_003486690.1\| PREDICTED: RNA polymerase II-associated factor 1 homolog [Bombus impatiens]	Back alignment and taxonomy information

>gi\|156550709\|ref\|XP_001605818.1\| PREDICTED: RNA polymerase II-associated factor 1 homolog [Nasonia vitripennis]	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		624
FB\|FBgn0010750		538	atms "antimeros" [Drosophila m	0.591	0.685	0.656	1e-139
ZFIN\|ZDB-GENE-050506-101		503	paf1 "paf1, RNA polymerase II	0.586	0.727	0.610	6.2e-117
UNIPROTKB\|Q2KJ14		532	PAF1 "RNA polymerase II-associ	0.586	0.687	0.596	3.1e-115
UNIPROTKB\|Q8N7H5		531	PAF1 "RNA polymerase II-associ	0.586	0.689	0.596	3.1e-115
UNIPROTKB\|F1SEH0		532	PAF1 "Uncharacterized protein"	0.586	0.687	0.596	3.1e-115
UNIPROTKB\|Q5RAX0		533	PAF1 "RNA polymerase II-associ	0.586	0.686	0.596	3.1e-115
MGI\|MGI:1923988		535	Paf1 "Paf1, RNA polymerase II	0.586	0.684	0.596	3.1e-115
RGD\|1306219		535	Paf1 "Paf1, RNA polymerase II	0.586	0.684	0.596	3.1e-115
UNIPROTKB\|Q6P2Y1		520	paf1 "RNA polymerase II-associ	0.584	0.701	0.601	2.2e-114
UNIPROTKB\|G1K1Z2		355	PAF1 "RNA polymerase II-associ	0.564	0.991	0.608	3.2e-113

FB\|FBgn0010750 atms "antimeros" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 1367 (486.3 bits), Expect = 1.0e-139, P = 1.0e-139
 Identities = 248/378 (65%), Positives = 311/378 (82%)

Query:     1 MAPTIQTTSAGTPSEKRTPSTHSTPVPPRPAERRSELVCRVKYNNTLPDIPFDCKFIAYP 60
             M PTI  ++  + +EKR         P R  ER+SE++CRVKY N LPDIPFD KF+ YP
Sbjct:     1 MPPTINNSAVNSAAEKR---------PQRQTERKSEIICRVKYGNNLPDIPFDLKFLQYP 51

Query:    61 FESTRFIEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDI 120
             F+S RF++Y  TSLERN+KY+VLTEHDLGVT+DLIN++ Y  +    LDPADEKLLEE+ 
Sbjct:    52 FDSHRFVQYNPTSLERNFKYDVLTEHDLGVTVDLINRELYQADSMTLLDPADEKLLEEET 111

Query:   121 LTPQDSKRSRHHARSVSWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMD 180
             LTP DS RSR H+R+VSWLR++EYISTEQTRFQPQ ++ +EAKVG+++KK+ +E+ LY+D
Sbjct:   112 LTPTDSVRSRQHSRTVSWLRKSEYISTEQTRFQPQNLENIEAKVGYNVKKSLREETLYLD 171

Query:   181 RDSQVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVG 240
             R++Q+KAIEKTF+D+K  I KHYSKPNV PVE++P++PDF  WK+PCAQVIFDSDPAP G
Sbjct:   172 REAQIKAIEKTFSDTKSEITKHYSKPNVVPVEVLPIFPDFTNWKFPCAQVIFDSDPAPAG 231

Query:   241 RPIPAQIEEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLEYTDEQEYEYKM 300
             + +PAQ+EEMSQAMIRGVMDESGEQFVAYFLPT +TL+KR+ D ++   Y +E+EYEYK+
Sbjct:   232 KNVPAQLEEMSQAMIRGVMDESGEQFVAYFLPTEQTLEKRRTDFINGELYKEEEEYEYKI 291

Query:   301 AREYNWNVKSKSCKGYEENYFLIVRDDAVYYNELETRVRLSKRRQKVGAAPNNTRLVVTH 360
             AREYNWNVK+K+ KGYEENYF ++R D +YYNELETRVRL+KRR KVG  PNNT+LVV H
Sbjct:   292 AREYNWNVKTKASKGYEENYFFVMRQDGIYYNELETRVRLNKRRVKVGQQPNNTKLVVKH 351

Query:   361 RPLNATEFRIQRLRERFL 378
             RPL++ E R+QR RER L
Sbjct:   352 RPLDSMEHRMQRYRERQL 369

GO:0019894 "kinesin binding" evidence=IDA

GO:0016593 "Cdc73/Paf1 complex" evidence=IDA

GO:0035327 "transcriptionally active chromatin" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

ZFIN\|ZDB-GENE-050506-101 paf1 "paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q2KJ14 PAF1 "RNA polymerase II-associated factor 1 homolog" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8N7H5 PAF1 "RNA polymerase II-associated factor 1 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SEH0 PAF1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5RAX0 PAF1 "RNA polymerase II-associated factor 1 homolog" [Pongo abelii (taxid:9601)]	Back alignment and assigned GO terms

MGI\|MGI:1923988 Paf1 "Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1306219 Paf1 "Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q6P2Y1 paf1 "RNA polymerase II-associated factor 1 homolog" [Xenopus (Silurana) tropicalis (taxid:8364)]	Back alignment and assigned GO terms

UNIPROTKB\|G1K1Z2 PAF1 "RNA polymerase II-associated factor 1 homolog" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8N7H5	PAF1_HUMAN	No assigned EC number	0.5515	0.6698	0.7871	yes	N/A
Q2KJ14	PAF1_BOVIN	No assigned EC number	0.5434	0.6634	0.7781	yes	N/A
Q6P2Y1	PAF1_XENTR	No assigned EC number	0.5731	0.6506	0.7807	yes	N/A
Q8K2T8	PAF1_MOUSE	No assigned EC number	0.5412	0.6634	0.7738	yes	N/A
Q4V886	PAF1_RAT	No assigned EC number	0.5412	0.6634	0.7738	yes	N/A
Q5RAX0	PAF1_PONAB	No assigned EC number	0.5434	0.6634	0.7767	yes	N/A
Q4U0S5	PAF1_DANRE	No assigned EC number	0.6089	0.5929	0.7355	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		624
pfam03985		431	pfam03985, Paf1, Paf1	1e-128
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	1e-11
PRK12678		672	PRK12678, PRK12678, transcription termination fact	3e-11
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	3e-09
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	3e-09
PRK12678		672	PRK12678, PRK12678, transcription termination fact	1e-07
PRK12678		672	PRK12678, PRK12678, transcription termination fact	2e-07
PTZ00108		1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	6e-07
PRK12678		672	PRK12678, PRK12678, transcription termination fact	2e-06
pfam10243		506	pfam10243, MIP-T3, Microtubule-binding protein MIP	3e-06
PRK12678		672	PRK12678, PRK12678, transcription termination fact	4e-06
pfam06075		564	pfam06075, DUF936, Plant protein of unknown functi	8e-06
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-04
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	3e-04
pfam08553		794	pfam08553, VID27, VID27 cytoplasmic protein	4e-04
COG5422		1175	COG5422, ROM1, RhoGEF, Guanine nucleotide exchange	6e-04
PRK08581		619	PRK08581, PRK08581, N-acetylmuramoyl-L-alanine ami	6e-04
pfam00937		346	pfam00937, Corona_nucleoca, Coronavirus nucleocaps	6e-04
pfam00242		379	pfam00242, DNA_pol_viral_N, DNA polymerase (viral)	7e-04
pfam05110		1154	pfam05110, AF-4, AF-4 proto-oncoprotein	8e-04
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.001
pfam03344		715	pfam03344, Daxx, Daxx Family	0.001
pfam05110		1154	pfam05110, AF-4, AF-4 proto-oncoprotein	0.002
pfam05793		528	pfam05793, TFIIF_alpha, Transcription initiation f	0.002
pfam13136		301	pfam13136, DUF3984, Protein of unknown function (D	0.002
pfam04502		321	pfam04502, DUF572, Family of unknown function (DUF	0.002
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.003
PTZ00415		2849	PTZ00415, PTZ00415, transmission-blocking target a	0.003
PRK05306		746	PRK05306, infB, translation initiation factor IF-2	0.003
pfam07218		790	pfam07218, RAP1, Rhoptry-associated protein 1 (RAP	0.003
PRK09510		387	PRK09510, tolA, cell envelope integrity inner memb	0.003
pfam04484		313	pfam04484, DUF566, Family of unknown function (DUF	0.003
pfam07218		790	pfam07218, RAP1, Rhoptry-associated protein 1 (RAP	0.004

>gnl\|CDD\|217829 pfam03985, Paf1, Paf1	Back alignment and domain information

 Score =  384 bits (987), Expect = e-128
 Identities = 164/446 (36%), Positives = 240/446 (53%), Gaps = 41/446 (9%)

Query: 35  SELVCRVKYNNTLPDIPFDCKFIAYPF-ESTRFIEYKSTSLERNYKYEVLT--EHDLGVT 91
            + + +VKY N LPD PF  K I YPF +  RF     TSL R  K  VL   +HDLG+ 
Sbjct: 1   QDYIAKVKYTNNLPDPPFPPKLITYPFPDENRFSPQLITSLYRKTKVTVLIQLDHDLGMP 60

Query: 92  IDLIN---------KDTYAPNYNIQLDPADEKLLEEDILTPQDSKRSRHHARSVSWLRRT 142
           +DL+          K  Y  + N++LDP D  LL +         R++  ++ VS+LRRT
Sbjct: 61  LDLLKIPGLLQGDTKVYYGDDVNVKLDPEDRILLRDPGADK----RTKTDSKKVSFLRRT 116

Query: 143 EYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMDRDSQVKAIEKTFADSKLPIEKH 202
           EYISTE  RF  Q ++  E+KVG ++K+N +E++ Y+DR++Q++AIEKTF D K  I KH
Sbjct: 117 EYISTESARFAVQALELTESKVGRNVKQNLREEDEYLDREAQIEAIEKTFEDVKKEILKH 176

Query: 203 YSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPIPAQIEEMSQAMIRGVMDES 262
            SK NV  VE+ P+ PD         QV FD D AP G+   AQ+ + S   I G ++  
Sbjct: 177 PSKKNVKAVEVWPLLPDTASMDQQFFQVRFDGDAAPDGKEKHAQLTQASSTAIFGPVELE 236

Query: 263 GEQFVAYFLP-------TAETLDKRKLDQLSNLEYTDEQEYEYKMAREYNWNVKSKSCKG 315
            E+FV+Y+LP         +TL+KR  D     +Y +++EY++K  REY+  VKSK+ K 
Sbjct: 237 EEEFVSYYLPDEKDSEILEDTLEKRSDDL---HDYDEDEEYKFKRVREYDMKVKSKATKL 293

Query: 316 YEENYFLIVRD-DAVYYNELETRVRLSKRR-----QKVGAAPNNTRLVVTHRPLNATEFR 369
            E   F +  +   VYY  L +RV L +RR     + +    NN +L V  R  +  E +
Sbjct: 294 NELALFFVSDENGVVYYKPLRSRVELRRRRVNDVIRPLVREHNNDQLNVKLRNPSTKESK 353

Query: 370 IQRLRERFLEPPNEEEEEEDEEEEEEEAEETQQGETTEAERQEGEGGEREGGGEGENDNE 429
           ++  R   L+P + EE +EDE+EEEE+  +         E +E EG + E  G    ++ 
Sbjct: 354 MRDKRRARLDPIDFEEVDEDEDEEEEQRSD---------EHEEEEGEDSEEEGSQSREDG 404

Query: 430 KRTSDAEHSSKNSSRASSRSRSRSKS 455
              S ++  S + S+A   S S S S
Sbjct: 405 SSESSSDVGSDSESKADKESASDSDS 430

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|218883 pfam06075, DUF936, Plant protein of unknown function (DUF936)	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|219900 pfam08553, VID27, VID27 cytoplasmic protein	Back alignment and domain information

>gnl\|CDD\|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated	Back alignment and domain information

>gnl\|CDD\|216205 pfam00937, Corona_nucleoca, Coronavirus nucleocapsid protein	Back alignment and domain information

>gnl\|CDD\|215814 pfam00242, DNA_pol_viral_N, DNA polymerase (viral) N-terminal domain	Back alignment and domain information

>gnl\|CDD\|218440 pfam05110, AF-4, AF-4 proto-oncoprotein	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

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

>gnl\|CDD\|218440 pfam05110, AF-4, AF-4 proto-oncoprotein	Back alignment and domain information

>gnl\|CDD\|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)	Back alignment and domain information

>gnl\|CDD\|221931 pfam13136, DUF3984, Protein of unknown function (DUF3984)	Back alignment and domain information

>gnl\|CDD\|218115 pfam04502, DUF572, Family of unknown function (DUF572)	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>gnl\|CDD\|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional	Back alignment and domain information

>gnl\|CDD\|235401 PRK05306, infB, translation initiation factor IF-2; Validated	Back alignment and domain information

>gnl\|CDD\|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1)	Back alignment and domain information

>gnl\|CDD\|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional	Back alignment and domain information

>gnl\|CDD\|218107 pfam04484, DUF566, Family of unknown function (DUF566)	Back alignment and domain information

>gnl\|CDD\|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1)	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		624
PF03985		436	Paf1: Paf1 ; InterPro: IPR007133 Members of this f	100.0
KOG2478\|consensus		452		100.0
KOG4368\|consensus		757		96.83
KOG2478\|consensus		452		96.74
KOG4368\|consensus		757		96.26
KOG4676\|consensus		479		93.73
KOG2548\|consensus		653		92.15
KOG4207\|consensus		256		91.63
KOG2548\|consensus		653		87.62

>PF03985 Paf1: Paf1 ; InterPro: IPR007133 Members of this family are components of the RNA polymerase II associated Paf1 complex	Back alignment and domain information

Probab=100.00  E-value=6.6e-88  Score=734.53  Aligned_cols=355  Identities=45%  Similarity=0.752  Sum_probs=297.7

Q ss_pred             ccceeeccccCCCCCCCCCCceeeCCC-CCcccccccCcceeecccccccc--cccCCccccCC--------CCCCCCCC
Q psy6664          35 SELVCRVKYNNTLPDIPFDCKFIAYPF-ESTRFIEYKSTSLERNYKYEVLT--EHDLGVTIDLI--------NKDTYAPN  103 (624)
Q Consensus        35 qdfI~riRY~N~LP~PP~~PKfL~~p~-d~~r~~~Y~~tSLer~~~~~l~~--d~DLGmpIDLi--------~~~~Y~~d  103 (624)
                      |||||+|||+|+||+||||||||+||+ +..+|+.|.+|+|+++++|.|+|  |+|||||||||        |+..|..+
T Consensus         1 qd~i~~iry~N~LP~pp~~pK~L~~p~~~~~~~~~~~~tsL~~~~~~~~l~~~d~dlGmplDLi~~~g~~~~d~~~~~~~   80 (436)
T PF03985_consen    1 QDFICRIRYRNNLPPPPFPPKFLDIPFTDEQRFSPYFATSLEREYKFNILVEVDADLGMPLDLIGIPGVFEGDPSAYNAP   80 (436)
T ss_pred             CceeeeeeecCCCcccCCCCeeecCCCCchhccccchhhhHHHhcCcceecccccccCcccccccccCcccCChhhcCCC
Confidence            799999999999999999999999999 77999999999999999999977  99999999999        56666654


Q ss_pred             C-CCCCChhhHhhccccCCCCcccccccccccccccccccccccccccccCCccchhhhhhcccccccccccccccCChH
Q psy6664         104 Y-NIQLDPADEKLLEEDILTPQDSKRSRHHARSVSWLRRTEYISTEQTRFQPQVMDKVEAKVGFSIKKNFKEDNLYMDRD  182 (624)
Q Consensus       104 ~-~~~LdP~D~~LL~D~~~~p~~~krs~~~~~~VswLRRTEYIS~e~~r~~~~~~~~~Etk~g~~~kk~~~~e~~~~dre  182 (624)
                      . +++|||+|++||+|+.+.    ++++.+.++|+|||||||||+++++++ ++....+++.|+++++..+.++++.|++
T Consensus        81 ~~~~~L~p~D~~LL~d~~~~----~~~~~~~~~VswLRrTeYiS~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~d~~  155 (436)
T PF03985_consen   81 PNNPPLDPEDRALLRDPGAL----KRSKPDAKNVSWLRRTEYISSEFTRKG-QSKEKSEAKRGRNVKKKFKEEELYNDRE  155 (436)
T ss_pred             CCCCCCCHHHHHHhcCcccc----ccccCCcCCCcccccceeecccccccc-ccccchhhcccccccccccccccccCHH
Confidence            4 678999999999997654    377889999999999999999988776 5556778888998888777778899999


Q ss_pred             HHHHHHHhhhhcccC--CcccCCCCCCceeeEeeccCCCccccCCCeeEEEEcCCCCCCCCCCh-hhhhhhhhceecccc
Q psy6664         183 SQVKAIEKTFADSKL--PIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPIP-AQIEEMSQAMIRGVM  259 (624)
Q Consensus       183 sQi~aIEkTFe~akk--pllkHPtKpnLkaVev~PlLPD~~~w~~~y~~v~FD~dPa~~~~~~~-~~~~~ls~AIiRpv~  259 (624)
                      +||++||+||++|++  ++++||+|||||||++|||||||++|++.|++|+||++|+....... ....++.++|++||.
T Consensus       156 ~qi~~Ie~tF~~a~~~~~~~~HPtK~~lk~Ve~~PllPD~~~~~~~y~~v~Fd~~P~~~~~~~~~~~~~~~~~~i~~p~~  235 (436)
T PF03985_consen  156 SQIRAIEKTFEAAKKDLPRLKHPTKPNLKAVEVWPLLPDFDAWPNPYVQVKFDGDPAPDDKEKEEQEEQALQAAIFRPMD  235 (436)
T ss_pred             HHHHHHHHHHHHHhhccccccCCCCCCCeEEEEecCCCCchhcCCceEEEEECCCCccccccccchhHHHHhhhccCCCC
Confidence            999999999999999  56999999999999999999999999999999999999987665444 345677888999976


Q ss_pred             cCCCceEEEEEccChhhHHHHhhhhhc------CCCCCCCCccccceeeeecceeeccCCCCccceEEEE-EeCCeeEee
Q psy6664         260 DESGEQFVAYFLPTAETLDKRKLDQLS------NLEYTDEQEYEYKMAREYNWNVKSKSCKGYEENYFLI-VRDDAVYYN  332 (624)
Q Consensus       260 ~e~ge~fvaY~lP~~~~~~k~~~D~e~------~~d~~d~e~y~Yk~vReYd~~v~~~~~~~~ee~~~f~-fr~~~aYY~  332 (624)
                      . +|++||+||||....+.+....+..      ..++++++.|.|+|||+|+|+|++....+++.+++|+ ++.++||||
T Consensus       236 ~-~~~~fvsy~lP~~~~~~~~~~~l~~~~~d~~~~~~~~~~~~~y~~vReY~~~~~~~~~~~~e~~i~f~~~~~k~ayY~  314 (436)
T PF03985_consen  236 S-EGDQFVSYYLPDKEDAKELKEKLEKNSPDRDEEDDDDDEEYEYKRVREYEWSVQNEASKGYEENIFFVDFKQKAAYYY  314 (436)
T ss_pred             C-CCcceeeEEecChhhhhHhHHhhhcccccccccccCCCceeeccceecccceeeccCCCCccceEEEEecCCCceEEe
Confidence            5 6778899999954443333332221      2244677899999999999999977777788888888 667999999


Q ss_pred             eccceeeeccccccCCC-----CCCCceEEEEecCCCHHHHHHHHHhhhhcCCCCCCccchhHHHHHH
Q psy6664         333 ELETRVRLSKRRQKVGA-----APNNTRLVVTHRPLNATEFRIQRLRERFLEPPNEEEEEEDEEEEEE  395 (624)
Q Consensus       333 pL~tRv~LrKrR~~~~~-----~~~~d~i~V~~R~~t~~E~~~~~~R~~~~E~~~e~~eeeeee~e~e  395 (624)
                      ||.+||+|+|+|.+...     ..++++|+|+||+||++|.++|+.+..+.++...+.++|+||++++
T Consensus       315 pI~~Rv~LrkrR~~~~~~~~~~~~~~d~i~V~~R~p~e~E~~~~~~~r~~~dp~~~~~~ee~eeeee~  382 (436)
T PF03985_consen  315 PIETRVRLRKRRTNSKIRPKVREQRPDQITVKHRDPTEEEEAERDKRRAQLDPIEYEEEEEEEEEEEE  382 (436)
T ss_pred             eccccceeeeeccccccccccccCCCceEEEEeCCCCHHHHHHHHHHHhhccCCCccccCcccccccc
Confidence            99999999999944332     3468999999999999999988877777777766655555444433

The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i [, ].

>KOG2478\|consensus	Back alignment and domain information

>KOG4368\|consensus	Back alignment and domain information

>KOG2478\|consensus	Back alignment and domain information

>KOG4368\|consensus	Back alignment and domain information

>KOG4676\|consensus	Back alignment and domain information

>KOG2548\|consensus	Back alignment and domain information

>KOG4207\|consensus	Back alignment and domain information

>KOG2548\|consensus	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		624
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-07
2zjr_S		237	50S ribosomal protein L25; ribosome, large ribosom	2e-05
2zjr_S		237	50S ribosomal protein L25; ribosome, large ribosom	3e-05
2zjr_S		237	50S ribosomal protein L25; ribosome, large ribosom	2e-04
2zjr_S		237	50S ribosomal protein L25; ribosome, large ribosom	5e-04

>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 = 69.1 bits (168), Expect = 3e-12
 Identities = 72/463 (15%), Positives = 136/463 (29%), Gaps = 168/463 (36%)

Query: 22  HSTPVPPRP---AERRSELVCRVKYNNTL--------PDI--PFD--CKFIAYPFESTRF 66
           HS+ +  R          L+    Y N L              F+  CK +         
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL--------- 269

Query: 67  IEYKSTSLERNYKYEVLTEHDLGVTIDLINKDTYAPNYNIQLDPADEKLLEEDILTPQDS 126
                           LT     VT D ++  T     +I LD           LTP + 
Sbjct: 270 ----------------LTTRFKQVT-DFLSAATT---THISLDH------HSMTLTPDEV 303

Query: 127 KRSRHHARSVSWLR-RTEYISTEQTRFQPQVMDKVEA--KVGFSIKKNFKEDNLYMDRDS 183
           K     +  + +L  R + +  E     P+ +  +    + G +   N+K    +++ D 
Sbjct: 304 K-----SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK----HVNCDK 354

Query: 184 QVKAIEKTFADSKLPIEKHYSKPNVTPVEIMPVYPDFKYWKYPCAQVIFDSDPAPVGRPI 243
               IE +                + P E   ++             +F          I
Sbjct: 355 LTTIIESSLN-------------VLEPAEYRKMFDRL---------SVFPPS---A--HI 387

Query: 244 PAQI-----EEMSQAMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNL-----EYTDE 293
           P  +      ++ ++ +  V+++       Y L     ++K+  +   ++     E   +
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNK----LHKYSL-----VEKQPKESTISIPSIYLELKVK 438

Query: 294 QEYEYKMAR----EYNWNVKSKSCKGYEENYFLIVRDDAVYYN---------------EL 334
            E EY + R     YN        K ++ +  +    D  +Y+                L
Sbjct: 439 LENEYALHRSIVDHYNIP------KTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492

Query: 335 ETRVRLSKR--RQKV---GAAPNNTRLVVTHRPLNATEFRIQRLR--ERFLEP--PNEEE 385
              V L  R   QK+     A N +        +  T   +Q+L+  + ++    P  E 
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNAS------GSILNT---LQQLKFYKPYICDNDPKYER 543

Query: 386 EEED-------EEEEEEEAEET---Q---QGETT----EAERQ 411
                       EE    ++ T   +     E      EA +Q
Sbjct: 544 LVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQ 586

PyMOL of 1vt4

>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

>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

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237	Back alignment and structure

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237	Back alignment and structure

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237	Back alignment and structure

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237	Back alignment and structure

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