Citrus Sinensis ID: 018361

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Local Sequence Feature Prediction

Residue Number Marker
--------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-------
Protein Sequence
MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVETDGGGDDLELDDISLIRACERPLKDREALLECKGIDFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNLIWGCIDF
Secondary Structure (PSIPRED)
ccHHHHHHHHHHccccccEEEcccEEEEcccccccccccEEEEEccccEEEHHHHHHHHHHccccHHHHHHHHHHcccccEEcccccHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccEEEEcccccccccHHHHHHHHHccccccccHHHHccccccccEEEEEEEEcccccccEEEEEEEccccccccccccEEEEEEEccccccccccccccHHHHHHcccEEEEEEccEEccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHcccccEEEEEccEEEEcccccccccccccccccccccccHHHHHHHHHcccccHHHHHHHHHHcccccEccccHHHHHHHHcccccccHHcccccccHHHccccccccccccccccccccHHHHHHHccccccHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccHHHHHHHHHHHHHHcccEcccHHHHHHccccccccEEEEEEccccccccEEEEEEEccHHHccHHHHcEEEEEEEcccccEEcccccccHHHHHHHcccEEEEEEEEEEEEcc
Coil and Loop (DISEMBL)
mdplsalrdftirseldkvtqtgdeilfgsdytfpssiETAYrskqgnlyTLQTVVYFIKHYNLKHTDYIQRArsnklpavtlpdrkplyeyltgvtdsadQIETVIAndhvlndgkivetdgggddleldDISLIRACERPLKDREALLECKGIDFYSVLVSSTRREEERQRIESQQRKDGLVAknrlmgvdergigyggggggggggagdeayeanpkpkllqlksgkigegvpiilvpsasqTLITIYNVKefledgvyiptdvkvknmngmrpecvTVQKKFSRDRDQVVKAyevrdkpstmksedwDRVVAVFVLGkewqfkewpfkdhvEIFNKSKLIFELYNLIWGCIDF
Flexible Loop (DISEMBL)
mdplsalrdftirseldkvtqtgdeilfgsdytFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRarsnklpavtlpdrkPLYEYLTGVTDSADQIETVIandhvlndgkivetdgggddlelDDISLIRACERPLKDrealleckgidfysvlvsstrreeerqriesqqrkdglvaknrlMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTdvkvknmngmrpecvtvqkkfsrdrdqvvkayevrdkpstmksedwdrVVAVFVLGKewqfkewpfkdHVEIFNKSKLIFELYNLIWGCIDF
Low Complexity Region (SEG)
MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVETdgggddlelddISLIRACERPLKDREALLECKGIDFYSVLVsstrreeerqriesqqrKDGLVAKNRLMGVDERgigyggggggggggagDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNLIWGCIDF
Disordered region (IsUnstruct)
**********TIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLND*****************ISLIRACERPLKDREALLECKGIDFYSVLV******************************************************************GKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKF******VVKAY************DWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNLIWGCI**
Disordered Region (DISOPRED)
MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVT*************************************************************SV*****************************************************************************ILVPSASQTLITIYNVKEFLEDGVY*********************************AYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNLIWGCID*
Disordered Region (DISEMBL)
MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVETDGGGDDLELDDISLIRACERPLKDREALLECKGIDFYSVLV*****************KDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNLIWGCIDF
Disordered Region (DISPRO)
MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVT********************************LDDISLIRACERPLKDREALLECKGIDFYSVLVSSTRREEE**************************************************************EGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVK***GMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNLIWGCIDF
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVETDGGGDDLELDDISLIRACERPLKDREALLECKGIDFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNLIWGCIDF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	357	2.2.26 [Sep-21-2011]
Q5ZLM0	531	Parafibromin OS=Gallus ga	yes	no	0.610	0.410	0.294	3e-16
Q8JZM7	531	Parafibromin OS=Mus muscu	yes	no	0.610	0.410	0.294	6e-16
Q6P1J9	531	Parafibromin OS=Homo sapi	yes	no	0.610	0.410	0.294	6e-16
Q4V8C8	531	Parafibromin OS=Rattus no	yes	no	0.610	0.410	0.294	7e-16
Q06697	393	Cell division control pro	yes	no	0.767	0.697	0.232	2e-11
Q9UUE7	371	Cell division control pro	yes	no	0.677	0.652	0.223	5e-05

>sp|Q5ZLM0|CDC73_CHICK Parafibromin OS=Gallus gallus GN=CDC73 PE=2 SV=1

 Score = 86.3 bits (212), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 80/272 (29%), Positives = 116/272 (42%), Gaps = 54/272 (19%)

Query: 127 DLELDDISLIRACERPLKDREALLECKGIDF----YSVLVSSTRREEER---QRIESQQR 179
           D E+D    I + ER  + R  +L+  G +F    +++L S   REE R   QR      
Sbjct: 215 DAEVDVTRDIVSRERVWRTRTTILQSTGKNFAKNIFAILQSVKAREEGRAPEQRPAPNTA 274

Query: 180 KDGLVAKN--------------RLMG--------VDERGIGYG---GGGGGGGGGAGDEA 214
                 +N              R  G        +D  G  +G        G      + 
Sbjct: 275 PTDPTLRNKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQT 334

Query: 215 YEANPKPKLLQLK----SGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVK 270
             A P P+ +       + K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K
Sbjct: 335 PAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKK 394

Query: 271 NMNGMRPECVTVQKKFSRDRDQ---------VVKAYEVRDKPSTMKSEDWDRVVAVFVLG 321
              G + E  T+     R +DQ         V   Y V D+P  +  +DWDRVVAVFV G
Sbjct: 395 Q--GCQRENETL---IQRRKDQMQPGGTTVSVTVPYRVVDQPLKLMPQDWDRVVAVFVQG 449

Query: 322 KEWQFKEWPF----KDHVEIFNKSKLIFELYN 349
             WQFK WP+       V+IF K K     Y+
Sbjct: 450 PAWQFKGWPWLLPDGSPVDIFAKIKAFHLKYD 481

Tumor suppressor probably involved in transcriptional and post-transcriptional control pathways. May be involved in cell cycle progression through the regulation of cyclin D1/PRAD1 expression. 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).
Gallus gallus (taxid: 9031)

>sp|Q8JZM7|CDC73_MOUSE Parafibromin OS=Mus musculus GN=Cdc73 PE=2 SV=1

 Score = 85.1 bits (209), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 80/272 (29%), Positives = 118/272 (43%), Gaps = 54/272 (19%)

Query: 127 DLELDDISLIRACERPLKDREALLECKGIDF----YSVLVSSTRREEER---QRIES--- 176
           D E+D    I + ER  + R  +L+  G +F    +++L S   REE R   QR      
Sbjct: 215 DAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAA 274

Query: 177 ------QQRKDGLVAKNRL-------------MGVDERGIGYG---GGGGGGGGGAGDEA 214
                 + ++    A NR                +D  G  +G        G      + 
Sbjct: 275 PVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQT 334

Query: 215 YEANPKPKLLQLK----SGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVK 270
             A P P+ +       + K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K
Sbjct: 335 PAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKK 394

Query: 271 NMNGMRPECVTVQKKFSRDRDQ---------VVKAYEVRDKPSTMKSEDWDRVVAVFVLG 321
              G + E  T+     R +DQ         V   Y V D+P  +  +DWDRVVAVFV G
Sbjct: 395 Q--GCQRENETL---IQRRKDQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQG 449

Query: 322 KEWQFKEWPF----KDHVEIFNKSKLIFELYN 349
             WQFK WP+       V+IF K K     Y+
Sbjct: 450 PAWQFKGWPWLLPDGSPVDIFAKIKAFHLKYD 481

Tumor suppressor probably involved in transcriptional and post-transcriptional control pathways. May be involved in cell cycle progression through the regulation of cyclin D1/PRAD1 expression. Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. Connects PAF1C with the cleavage and polyadenylation specificity factor (CPSF) complex and the cleavage stimulation factor (CSTF) complex, and with Wnt signaling. Involved in polyadenylation of mRNA precursors.

Mus musculus (taxid: 10090)

>sp|Q6P1J9|CDC73_HUMAN Parafibromin OS=Homo sapiens GN=CDC73 PE=1 SV=1

 Score = 85.1 bits (209), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 80/272 (29%), Positives = 118/272 (43%), Gaps = 54/272 (19%)

Query: 127 DLELDDISLIRACERPLKDREALLECKGIDF----YSVLVSSTRREEER---QRIES--- 176
           D E+D    I + ER  + R  +L+  G +F    +++L S   REE R   QR      
Sbjct: 215 DAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAA 274

Query: 177 ------QQRKDGLVAKNRL-------------MGVDERGIGYG---GGGGGGGGGAGDEA 214
                 + ++    A NR                +D  G  +G        G      + 
Sbjct: 275 PVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQT 334

Query: 215 YEANPKPKLLQLK----SGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVK 270
             A P P+ +       + K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K
Sbjct: 335 PAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKK 394

Query: 271 NMNGMRPECVTVQKKFSRDRDQ---------VVKAYEVRDKPSTMKSEDWDRVVAVFVLG 321
              G + E  T+     R +DQ         V   Y V D+P  +  +DWDRVVAVFV G
Sbjct: 395 Q--GCQRENETL---IQRRKDQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQG 449

Query: 322 KEWQFKEWPF----KDHVEIFNKSKLIFELYN 349
             WQFK WP+       V+IF K K     Y+
Sbjct: 450 PAWQFKGWPWLLPDGSPVDIFAKIKAFHLKYD 481

Tumor suppressor probably involved in transcriptional and post-transcriptional control pathways. May be involved in cell cycle progression through the regulation of cyclin D1/PRAD1 expression. Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1; it promotes leukemogenesis though association with MLL-rearranged oncoproteins, such as MLL-MLLT3/AF9 and MLL-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Connects PAF1C with the cleavage and polyadenylation specificity factor (CPSF) complex and the cleavage stimulation factor (CSTF) complex, and with Wnt signaling. Involved in polyadenylation of mRNA precursors.

Homo sapiens (taxid: 9606)

>sp|Q4V8C8|CDC73_RAT Parafibromin OS=Rattus norvegicus GN=Cdc73 PE=2 SV=1

 Score = 85.1 bits (209), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 80/272 (29%), Positives = 118/272 (43%), Gaps = 54/272 (19%)

Query: 127 DLELDDISLIRACERPLKDREALLECKGIDF----YSVLVSSTRREEER---QRIES--- 176
           D E+D    I + ER  + R  +L+  G +F    +++L S   REE R   QR      
Sbjct: 215 DAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAA 274

Query: 177 ------QQRKDGLVAKNRL-------------MGVDERGIGYG---GGGGGGGGGAGDEA 214
                 + ++    A NR                +D  G  +G        G      + 
Sbjct: 275 PVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQT 334

Query: 215 YEANPKPKLLQLK----SGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVK 270
             A P P+ +       + K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K
Sbjct: 335 PAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKK 394

Query: 271 NMNGMRPECVTVQKKFSRDRDQ---------VVKAYEVRDKPSTMKSEDWDRVVAVFVLG 321
              G + E  T+     R +DQ         V   Y V D+P  +  +DWDRVVAVFV G
Sbjct: 395 Q--GCQRENETL---IQRRKDQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQG 449

Query: 322 KEWQFKEWPF----KDHVEIFNKSKLIFELYN 349
             WQFK WP+       V+IF K K     Y+
Sbjct: 450 PAWQFKGWPWLLPDGSPVDIFAKIKAFHLKYD 481

Tumor suppressor probably involved in transcriptional and post-transcriptional control pathways. May be involved in cell cycle progression through the regulation of cyclin D1/PRAD1 expression. Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. Connects PAF1C with the cleavage and polyadenylation specificity factor (CPSF) complex and the cleavage stimulation factor (CSTF) complex, and with Wnt signaling. Involved in polyadenylation of mRNA precursors.

Rattus norvegicus (taxid: 10116)

>sp|Q06697|CDC73_YEAST Cell division control protein 73 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CDC73 PE=1 SV=1

 Score = 70.9 bits (172), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 76/327 (23%), Positives = 141/327 (43%), Gaps = 53/327 (16%)

Query: 33  TFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEY 92
           +FP + ET      G+L  L+ +V+   + +    DY+   ++ +L  V+   R  L  +
Sbjct: 49  SFPLNEETEIEI-DGSLVQLRIIVHCWMNKDSSAADYLADCQNKQLTNVSFLQRTDLINW 107

Query: 93  LTGVTDSADQIETV-----------IANDHVLNDGKIVETDGGG---DDLELDDISLIRA 138
           L+G T+S+  ++             I N  +  +   V++       +D E+ D  ++  
Sbjct: 108 LSGNTESSQYLKAPGQKGETSDKVDIENKTLAGELSTVKSTTSASLENDSEVSDPVVVET 167

Query: 139 C--ERPLKDREALLE-CKGIDFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDER 195
              ER L D  + L   K I+F  ++     ++ E + ++S +   G +  ++L    + 
Sbjct: 168 MKHERILVDHNSALRGAKPINFGYLI-----KDAELKLVQSIK---GSLRGSKLPPGHKG 219

Query: 196 GIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKE 255
             G      G  GG   +                      PIIL+PSA+ +++T+ N+K+
Sbjct: 220 AHGRISKTNGSSGGPRKD----------------------PIILIPSAASSILTVANIKQ 257

Query: 256 FLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVV 315
           FL +  Y    V  +N+  +    V ++K F R   + ++   V +     K E WDRVV
Sbjct: 258 FLLESKY----VNPRNLPSVPNGLVNIEKNFER-ISRPIRFIIVDNTRMFTKPEYWDRVV 312

Query: 316 AVFVLGKEWQFKEWPFKDHVEIFNKSK 342
           A+F  G  WQF  + +    E+F + K
Sbjct: 313 AIFTTGHTWQFNNYQWNSPQELFQRCK 339

The PAF1 complex is a multifunctional complex. Involved in transcription initiation via genetic interactions with TATA-binding proteins. Involved in elongation. It regulates 3'-end formation of snR47 by modulating the recruitment or stable association of NRD1 and NAB3 with RNA polymerase II. Also has a role in transcription-coupled histone modification. Required for activation of RAD6 ubiquitin conjugate and the BRE1 ubiquitin ligase which ubiquitinate 'Lys-126' histone H2B. Activates the SET1 histone methyltransferase complex for methylation of 'Lys-4' of histone H3 and for methylation of 'Lys-73' of histone H3 by DOT1 and 'Lys-36' of histone H3 by SET2.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q9UUE7|CDC73_SCHPO Cell division control protein 73 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cdc73 PE=3 SV=1

 Score = 49.3 bits (116), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 67/300 (22%), Positives = 128/300 (42%), Gaps = 58/300 (19%)

Query: 50  YTLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIAN 109
           ++L++V +     +    +YIQ+     +  +T  +R  L  +L G +DS    E +I  
Sbjct: 64  FSLRSVYFAWLLRDTSIAEYIQQCSELGIQNLTFLERTDLISWLEGSSDS----EHIIGL 119

Query: 110 DHVLNDGKIVETDGGGD-DLEL----DDISLIRACERPLKDREALLE-CKGIDFYSVLVS 163
           +    +G    TD     D++L    ++++ +    R + +  ++L   K IDF S+   
Sbjct: 120 EKPKPEGS---TDAATSMDVDLHKKSEEVNWLFENTRTVSNHNSVLHGIKPIDFISL--- 173

Query: 164 STRREEERQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKL 223
                          RKD L               Y            DE          
Sbjct: 174 ---------------RKDVL--------------DYIHANKATASAHADE---------- 194

Query: 224 LQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYI-PTDVKVKNMNGMRPECVTV 282
            Q +  K     PIIL+  ++ +L+T++N+K+FLE+G+++ P +       G  PE + +
Sbjct: 195 -QERPAKKRNRDPIILLSPSASSLLTMHNIKKFLEEGIFVPPAEAAHAAGGGRGPELIAL 253

Query: 283 QKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSK 342
             K S  +   ++ + + +     K + WDRVV VF  G+ WQF+++ + +  ++F+  K
Sbjct: 254 SHKSSNSKFGTMR-FIIVEGTEKFKPDYWDRVVCVFTTGQAWQFRDYKWSEPHQLFHHVK 312

The PAF1 complex is a multifunctional complex. Involved in transcription initiation via genetic interactions with TATA-binding proteins. Involved in elongation. It regulates 3'-end formation of snR47 by modulating the recruitment or stable association of nrd1 with RNA polymerase II.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	357
449432690	407	PREDICTED: parafibromin-like [Cucumis sa	0.921	0.808	0.661	1e-130
225432718	413	PREDICTED: parafibromin-like [Vitis vini	0.924	0.799	0.649	1e-121
297830980	414	predicted protein [Arabidopsis lyrata su	0.929	0.801	0.607	1e-120
356538299	389	PREDICTED: parafibromin-like [Glycine ma	0.918	0.843	0.641	1e-120
15228799	415	RNA pol II accessory factor CDC73-like p	0.927	0.797	0.595	1e-119
255552129	409	conserved hypothetical protein [Ricinus	0.921	0.804	0.643	1e-119
224111144	405	PAF1 complex component [Populus trichoca	0.921	0.812	0.625	1e-116
357480993	398	Parafibromin [Medicago truncatula] gi|21	0.904	0.811	0.594	1e-109
297737078	312	unnamed protein product [Vitis vinifera]	0.708	0.810	0.565	2e-95
224112979	256	PAF complex protein [Populus trichocarpa	0.554	0.773	0.725	4e-76

>gi|449432690|ref|XP_004134132.1| PREDICTED: parafibromin-like [Cucumis sativus] gi|449513423|ref|XP_004164322.1| PREDICTED: parafibromin-like [Cucumis sativus]

 Score =  471 bits (1212), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 238/360 (66%), Positives = 278/360 (77%), Gaps = 31/360 (8%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPLSALRDFTIR ELDK+ +  DE  F SDY+FP S+ETAYRSKQGNLYTL+T+VY+IK
Sbjct: 1   MDPLSALRDFTIRGELDKIVRVNDEFRFASDYSFPCSVETAYRSKQGNLYTLETLVYYIK 60

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIV- 119
           ++++KHT+Y+Q AR+  + +VT PDRKPL +YLTG   S+D IE ++  +    D   V 
Sbjct: 61  NHHVKHTEYLQNARTQGITSVTFPDRKPLLDYLTGKVSSSDAIEFLVPQNPKFPDLPSVD 120

Query: 120 ------------------ETDGGGDDLELDDISLIRACERPLKDREALLECKGIDFYSVL 161
                             E DG  D   +D +++IRA ERPLKDRE+LLECK  +FY+VL
Sbjct: 121 EYRPEDPVIVGAAMDAVDEDDGFKDSTNVDYMTMIRAIERPLKDRESLLECKNRNFYNVL 180

Query: 162 VSSTRREEERQRIESQQRKDGLVAKNRLMGVDERG-IGYGGGGGGGGGGAGDEAYEANPK 220
           V ST+REEERQR+ESQQRKDGLVAK+RLMG D+RG +GYG   G          Y+ANPK
Sbjct: 181 VMSTKREEERQRLESQQRKDGLVAKSRLMGSDDRGLVGYGDDLG----------YDANPK 230

Query: 221 PKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECV 280
           PK+  LK GKIGEGVPIILVPSA QTLITIYNVKEFLEDGV+IPTDVKVK M G RP+CV
Sbjct: 231 PKM-HLKGGKIGEGVPIILVPSAFQTLITIYNVKEFLEDGVFIPTDVKVKQMKGARPDCV 289

Query: 281 TVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNK 340
           TVQKKFSRDRD+VV AYEVRDKPS +KSEDWDRVVAVFVLGKEWQFK+WPFKDHVEIFNK
Sbjct: 290 TVQKKFSRDRDRVVTAYEVRDKPSALKSEDWDRVVAVFVLGKEWQFKDWPFKDHVEIFNK 349

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225432718|ref|XP_002282888.1| PREDICTED: parafibromin-like [Vitis vinifera]

 Score =  442 bits (1136), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 237/365 (64%), Positives = 275/365 (75%), Gaps = 35/365 (9%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPLSALRDFT+R ELDK+ + GDE  FGSDYTFP S ETAYRSKQGNLYTL+T+VY++K
Sbjct: 1   MDPLSALRDFTVRGELDKIVRVGDEFRFGSDYTFPCSAETAYRSKQGNLYTLETLVYYVK 60

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVE 120
           ++++KHT+Y+Q AR+ ++PAVTLPDRKPL EYL G   S D IE V+  +  + D  +  
Sbjct: 61  NHHIKHTEYLQSARTQRIPAVTLPDRKPLLEYLQGKVASTDAIEFVVPQNPKIPDIGVDA 120

Query: 121 TD----------------GGGDDLE---------LDDISLIRACERPLKDREALLECKGI 155
            D                G  D L+         +D IS+IRA ERPLKDRE+LLECK  
Sbjct: 121 VDEYRPEDPTLLAIRDPPGSEDALDNSRVRGFDNVDYISMIRASERPLKDRESLLECKQR 180

Query: 156 DFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAY 215
           DFYSVL++STRREEER R+ES QRKDGLVAK+RLMG DERG+G+   G   G       Y
Sbjct: 181 DFYSVLMASTRREEERHRLESHQRKDGLVAKSRLMGADERGLGFWKDGDELG-------Y 233

Query: 216 EANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGM 275
           +  PKPK+L L   KIGEGVPIILVPSA QTLITIYNVKEFLEDGV+IPTDVK K M G 
Sbjct: 234 DGTPKPKML-LNRSKIGEGVPIILVPSAFQTLITIYNVKEFLEDGVFIPTDVKAKQMKGA 292

Query: 276 RPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHV 335
           +P+CVTVQKKFSRDR  VV AYEVRDKPS +K+EDWDRVVAVFVLGKEWQFK+WPFKDHV
Sbjct: 293 KPDCVTVQKKFSRDR--VVMAYEVRDKPSALKTEDWDRVVAVFVLGKEWQFKDWPFKDHV 350

Query: 336 EIFNK 340
           EIFNK
Sbjct: 351 EIFNK 355

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830980|ref|XP_002883372.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297329212|gb|EFH59631.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  437 bits (1125), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 221/364 (60%), Positives = 273/364 (75%), Gaps = 32/364 (8%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPLS L+DFTIR ++DK+ + G    FGS+Y+FP + ETAYRSK G+LYTL+ +V+++K
Sbjct: 1   MDPLSVLKDFTIRGDVDKIERVGVNYRFGSEYSFPCATETAYRSKSGSLYTLEALVHYVK 60

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVI----------AND 110
           + +LKH +Y+Q    N +PAVTLPDRKPL +YLTG   S+D I+ ++           N+
Sbjct: 61  NQHLKHGEYMQSTVKNSVPAVTLPDRKPLLDYLTGRVASSDSIDYLLLQQQNAQSQKQNE 120

Query: 111 HVLND---GKIVETDGGGDDLELDD----------ISLIRACERPLKDREALLECKGIDF 157
               D      V  +   +D+E++D          I LIR+ ERPLK R+A+L+CK  DF
Sbjct: 121 EYRPDQDNSAFVSRENAIEDMEVEDFGKSGEDVDYIMLIRSNERPLKSRDAILQCKNRDF 180

Query: 158 YSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDERGI-GYGGGGGGGGGGAGDEAYE 216
           YSVLV+ST+REEERQRIES QRKDGLVAK+RLMG +ERGI G+ GGG   G       Y+
Sbjct: 181 YSVLVNSTKREEERQRIESHQRKDGLVAKSRLMGAEERGIVGFSGGGDDNG-------YD 233

Query: 217 ANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMR 276
           ANPK KL   ++GKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIP DVK K M G++
Sbjct: 234 ANPKSKL-HFRAGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPNDVKAKEMKGLK 292

Query: 277 PECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVE 336
           P+C+TVQKKFSRDR++VV AYEVRDKPS +K +DWDRVVAVFVLGK+WQFK+WPFKDHVE
Sbjct: 293 PDCITVQKKFSRDRERVVTAYEVRDKPSALKPDDWDRVVAVFVLGKDWQFKDWPFKDHVE 352

Query: 337 IFNK 340
           IFNK
Sbjct: 353 IFNK 356

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538299|ref|XP_003537641.1| PREDICTED: parafibromin-like [Glycine max]

 Score =  436 bits (1121), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 220/343 (64%), Positives = 264/343 (76%), Gaps = 15/343 (4%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPLSALR+FT+R E++K+ +   E  FG +YTFP  +ETAYRS +GN YTL+T+V++I+
Sbjct: 1   MDPLSALREFTMRGEVEKIVRVNAEFRFGEEYTFPCWVETAYRSTKGNRYTLETLVHYIQ 60

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVE 120
           +++LKHT+YIQ   +  +P+VTLPDRKPL +YL G   S+D IE    +D          
Sbjct: 61  NHHLKHTEYIQNTFAVGIPSVTLPDRKPLLQYLQGTLSSSDSIEYRPHDDPSSFPAPKST 120

Query: 121 TDGGG---DDLELDDISLIRACERPLKDREALLECKGIDFYSVLVSSTRREEERQRIESQ 177
            +      +DL LD IS+IR+ E+PLKDR++LLECK  DFYSVLVS+T+REEERQR+ES 
Sbjct: 121 PNPPSLPPEDLNLDFISMIRSAEKPLKDRQSLLECKNRDFYSVLVSATKREEERQRMESH 180

Query: 178 QRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGKIGEGVPI 237
           QRKDGLVAK+RLMG D+RG+G+    GG         Y+  PKPK + LK  KIGEGVPI
Sbjct: 181 QRKDGLVAKSRLMGSDDRGLGFSDDMGG---------YDPTPKPK-MHLKGTKIGEGVPI 230

Query: 238 ILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAY 297
           ILVPSA QTLITIYNVKEFLEDGVYIPTDVKVK M G RP+CVTVQKK SRDR  VV AY
Sbjct: 231 ILVPSAFQTLITIYNVKEFLEDGVYIPTDVKVKQMKGARPDCVTVQKKLSRDR--VVTAY 288

Query: 298 EVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNK 340
           EVRDKPST+K +DWDRVVAVFVLGKEWQFK+WPFKDHVEIFNK
Sbjct: 289 EVRDKPSTLKPDDWDRVVAVFVLGKEWQFKDWPFKDHVEIFNK 331

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15228799|ref|NP_188898.1| RNA pol II accessory factor CDC73-like protein [Arabidopsis thaliana] gi|11994291|dbj|BAB01474.1| unnamed protein product [Arabidopsis thaliana] gi|17529302|gb|AAL38878.1| unknown protein [Arabidopsis thaliana] gi|23296828|gb|AAN13180.1| unknown protein [Arabidopsis thaliana] gi|332643135|gb|AEE76656.1| RNA pol II accessory factor CDC73-like protein [Arabidopsis thaliana]

 Score =  435 bits (1118), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 218/366 (59%), Positives = 271/366 (74%), Gaps = 35/366 (9%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPLS L++FTIR ++DK+ + G    FGS+Y+FP + ETAYRSK G+LYTL+ +V+++K
Sbjct: 1   MDPLSVLKEFTIRGDIDKIERVGANYRFGSEYSFPCATETAYRSKSGSLYTLEALVHYVK 60

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIE---------------- 104
           +  LKH +Y+Q    N +PAVTLPDRKPL +YLTG   S+D I+                
Sbjct: 61  NQQLKHGEYMQSTVKNSVPAVTLPDRKPLLDYLTGRVASSDSIDFLLLQQQNAQSQKQNE 120

Query: 105 ---------TVIANDHVLNDGKIVETDGGGDDLELDDISLIRACERPLKDREALLECKGI 155
                      ++ ++ + D ++ +    G+D+  D I LIR+ ERPLK R+A+L+CK  
Sbjct: 121 EYRPDQDNSAFVSRENAIADMEVEDFGKSGEDV--DYIMLIRSNERPLKSRDAILQCKNR 178

Query: 156 DFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDERGI-GYGGGGGGGGGGAGDEA 214
           DFYSVLV+ST+REEERQRIES QRKDGLVAK+RLMG +ERGI G+  GGG   G      
Sbjct: 179 DFYSVLVNSTKREEERQRIESHQRKDGLVAKSRLMGAEERGIVGFSSGGGDDNG------ 232

Query: 215 YEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNG 274
           Y+ANPK KL   K+GKIGEGVPIILVPSA QTLITIYNVKEFLEDGVYIP DVK K M G
Sbjct: 233 YDANPKSKL-HFKAGKIGEGVPIILVPSAFQTLITIYNVKEFLEDGVYIPNDVKAKEMKG 291

Query: 275 MRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDH 334
           ++P+C+TVQKKFSRDR++VV AYEVRDKPS +K +DWDRVVAVFVLGK+WQFK+WPFKDH
Sbjct: 292 LKPDCITVQKKFSRDRERVVTAYEVRDKPSALKPDDWDRVVAVFVLGKDWQFKDWPFKDH 351

Query: 335 VEIFNK 340
           VEIFNK
Sbjct: 352 VEIFNK 357

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552129|ref|XP_002517109.1| conserved hypothetical protein [Ricinus communis] gi|223543744|gb|EEF45272.1| conserved hypothetical protein [Ricinus communis]

 Score =  434 bits (1116), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 233/362 (64%), Positives = 279/362 (77%), Gaps = 33/362 (9%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPLSALRDFT+R+++DK+ +  DE  F ++YTFP +I+TAYRSKQGNLYTL+T+VY+I+
Sbjct: 1   MDPLSALRDFTMRNDVDKIVRINDEFRFSNEYTFPCNIKTAYRSKQGNLYTLETLVYYIQ 60

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIAN--------DHV 112
           + +LK TDY+Q AR+  LPA+T  DRKPLY+YLTG   S D I   +          D+ 
Sbjct: 61  NSHLKFTDYLQHARAAGLPAITFIDRKPLYDYLTGKVSSTDSIVFPLPQNPNPNLDLDND 120

Query: 113 LNDGKI-------------VETDGGGDDLELDD-ISLIRACERPLKDREALLECKGIDFY 158
           LN   +             V + GGG++++ D+ IS+I + ERP+KDREALLECK  DFY
Sbjct: 121 LNSNAVLDSTINNNSADADVASGGGGNNVKEDNLISIIYSMERPIKDREALLECKTKDFY 180

Query: 159 SVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEAN 218
           SVLV+STRREEERQRIESQQRKDGLVAK+RLMG ++RG  YGG   G         Y+AN
Sbjct: 181 SVLVASTRREEERQRIESQQRKDGLVAKSRLMGSEDRG--YGGDEMG---------YDAN 229

Query: 219 PKPKLLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPE 278
            KPK+L LK GK GEGVPIILVPSA QTLITIYNVKEFLEDGVYIPTDVKVK M G +P+
Sbjct: 230 SKPKMLHLKGGKFGEGVPIILVPSAFQTLITIYNVKEFLEDGVYIPTDVKVKQMKGAKPD 289

Query: 279 CVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIF 338
           CVTVQKKFS DR++V+ AYEVRDKPS +K+EDWDRVVAVFVLGKEWQFK+WPFKDHVEIF
Sbjct: 290 CVTVQKKFSTDRNRVMTAYEVRDKPSALKAEDWDRVVAVFVLGKEWQFKDWPFKDHVEIF 349

Query: 339 NK 340
           NK
Sbjct: 350 NK 351

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111144|ref|XP_002315762.1| PAF1 complex component [Populus trichocarpa] gi|222864802|gb|EEF01933.1| PAF1 complex component [Populus trichocarpa]

 Score =  424 bits (1089), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 224/358 (62%), Positives = 267/358 (74%), Gaps = 29/358 (8%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPLSALRDFTIR +LDK+ +  DE  FG++YTFP S +TAYRSKQGNLYTL+T+VY I+
Sbjct: 1   MDPLSALRDFTIRGDLDKIIRINDEFRFGNEYTFPCSTKTAYRSKQGNLYTLETLVYCIQ 60

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQI------ETVIAN----- 109
           +  +K T+Y+Q A +  +P VT  D KP+ EYL+G   S D I      E+   N     
Sbjct: 61  NTKIKFTNYLQDALALGIPPVTYIDWKPVKEYLSGKLSSTDSIVFPLPQESQNPNLNYRP 120

Query: 110 -DHVLNDGKIVET------DGGGDDLELDDISLIRACERPLKDREALLECKGIDFYSVLV 162
            D +L D +I ++      + G + +E + +SLI A ERPLKDRE+LLECK  DFY VLV
Sbjct: 121 DDPMLLDSRIDDSAAADKVNNGNEGVE-NHVSLIYANERPLKDRESLLECKNRDFYGVLV 179

Query: 163 SSTRREEERQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPK 222
           +STRREEER + ESQQRKDGLVAK+RLMG DERGIGYGG   G         Y++  KPK
Sbjct: 180 ASTRREEERHKFESQQRKDGLVAKSRLMGTDERGIGYGGDELG---------YDSAAKPK 230

Query: 223 LLQLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTV 282
           +   K GKIGEGVPIILVPSA QTLITIYNVKEFLEDG++IPTDVK K M G +PECVTV
Sbjct: 231 M-HSKGGKIGEGVPIILVPSAFQTLITIYNVKEFLEDGIFIPTDVKAKQMKGPKPECVTV 289

Query: 283 QKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNK 340
           QKKFS DR++V+ AYEVRDKPS +K +DWDRVVAVFVLGKEWQFK+WPFKDHVEIFNK
Sbjct: 290 QKKFSTDRNRVMTAYEVRDKPSALKGDDWDRVVAVFVLGKEWQFKDWPFKDHVEIFNK 347

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357480993|ref|XP_003610782.1| Parafibromin [Medicago truncatula] gi|217073460|gb|ACJ85089.1| unknown [Medicago truncatula] gi|355512117|gb|AES93740.1| Parafibromin [Medicago truncatula] gi|388521181|gb|AFK48652.1| unknown [Medicago truncatula]

 Score =  401 bits (1030), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 208/350 (59%), Positives = 253/350 (72%), Gaps = 27/350 (7%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPL+ LRDFTIR +LDK+ +      FG DYTFP S+ETAYRS +GN YTL+T+V++IK
Sbjct: 8   MDPLTLLRDFTIRGDLDKIVRLNGNFRFGEDYTFPCSLETAYRSTKGNRYTLETLVHYIK 67

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLND----- 115
           +++LKHT+Y Q   +  +P+VTLPDRKP+  YL G+  + D IE +     + ++     
Sbjct: 68  NHHLKHTEYFQNTLALGIPSVTLPDRKPILNYLQGILSTTDSIEYLPEQPSIPDEPSSHQ 127

Query: 116 --GKIVETDGGGDDLE---LDDISLIRACERPLKDREALLECKGIDFYSVLVSSTRREEE 170
              +   +D    +LE   LD IS+IR  E+PLKDRE+LLECK  DFYSVLV++T+REEE
Sbjct: 128 QHSQFPNSDEIITELESPPLDFISMIRTAEKPLKDRESLLECKNRDFYSVLVAATKREEE 187

Query: 171 RQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGK 230
           RQR ES QRKDGLVAK+RL+G  +    +GG   G             PKPK+      K
Sbjct: 188 RQRAESHQRKDGLVAKSRLLGSAD---DFGGDEMGYD--------HQTPKPKM----HLK 232

Query: 231 IGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDR 290
           IGEGVPIILVPSA QTLITIYNVK+FLEDGVY+PTDVKVK M G +P+CVTVQKK SRDR
Sbjct: 233 IGEGVPIILVPSAFQTLITIYNVKDFLEDGVYVPTDVKVKAMKGAKPDCVTVQKKLSRDR 292

Query: 291 DQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNK 340
              V AYEVRDKPS +K EDWDRVVAVFVLGK+WQFK+WPFKDHVEIFNK
Sbjct: 293 --AVTAYEVRDKPSALKPEDWDRVVAVFVLGKDWQFKDWPFKDHVEIFNK 340

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737078|emb|CBI26279.3| unnamed protein product [Vitis vinifera]

 Score =  355 bits (911), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 193/341 (56%), Positives = 220/341 (64%), Gaps = 88/341 (25%)

Query: 1   MDPLSALRDFTIRSELDKVTQTGDEILFGSDYTFPSSIETAYRSKQGNLYTLQTVVYFIK 60
           MDPLSALRDFT+R ELDK+ + GDE  FGSDYTFP S ETAYRSKQGNLYTL+T+VY++K
Sbjct: 1   MDPLSALRDFTVRGELDKIVRVGDEFRFGSDYTFPCSAETAYRSKQGNLYTLETLVYYVK 60

Query: 61  HYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVE 120
           ++++KHT+Y+Q AR+ ++PAVTLPDRKPL EYL                      GK+  
Sbjct: 61  NHHIKHTEYLQSARTQRIPAVTLPDRKPLLEYL---------------------QGKVAS 99

Query: 121 TDGGGDDLELDDISLIRACERPLKDREALLECKGIDFYSVLVSSTRREEERQRIESQQRK 180
           TD     +E D                                   REEER R+ES QRK
Sbjct: 100 TDA----IEFDPT---------------------------------REEERHRLESHQRK 122

Query: 181 DGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDE-AYEANPKPKLLQLKSGKIGEGVPIIL 239
           DGL                           GDE  Y+  PKPK+L L   KIGEGVPIIL
Sbjct: 123 DGL--------------------------DGDELGYDGTPKPKML-LNRSKIGEGVPIIL 155

Query: 240 VPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEV 299
           VPSA QTLITIYNVKEFLEDGV+IPTDVK K M G +P+CVTVQKKFSRDR  VV AYEV
Sbjct: 156 VPSAFQTLITIYNVKEFLEDGVFIPTDVKAKQMKGAKPDCVTVQKKFSRDR--VVMAYEV 213

Query: 300 RDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNK 340
           RDKPS +K+EDWDRVVAVFVLGKEWQFK+WPFKDHVEIFNK
Sbjct: 214 RDKPSALKTEDWDRVVAVFVLGKEWQFKDWPFKDHVEIFNK 254

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112979|ref|XP_002332677.1| PAF complex protein [Populus trichocarpa] gi|222836471|gb|EEE74878.1| PAF complex protein [Populus trichocarpa]

 Score =  291 bits (745), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 151/208 (72%), Positives = 166/208 (79%), Gaps = 10/208 (4%)

Query: 133 ISLIRACERPLKDREALLECKGIDFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGV 192
           +SLI A E PLKDRE+LLE K  DFY VLV+STRREEE QR ESQ RKDGLVAK+RLMG 
Sbjct: 1   MSLIYANETPLKDRESLLERKSRDFYGVLVASTRREEESQRFESQHRKDGLVAKSRLMGA 60

Query: 193 DERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYN 252
           DERGIG GG   G         Y++  KPK+  LK  KI EGV IILVPSA QTLITIYN
Sbjct: 61  DERGIGCGGDELG---------YDSAAKPKM-HLKGRKIREGVHIILVPSAFQTLITIYN 110

Query: 253 VKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWD 312
           VKEFLEDG+YIPTDVKVK M   +PECVTVQKKFS DR++V+ AYEVRDKPS +K+ DWD
Sbjct: 111 VKEFLEDGIYIPTDVKVKKMKRPKPECVTVQKKFSTDRNRVMTAYEVRDKPSALKAGDWD 170

Query: 313 RVVAVFVLGKEWQFKEWPFKDHVEIFNK 340
           RVVAVFVLGKEWQFK+WPFKD VEIFNK
Sbjct: 171 RVVAVFVLGKEWQFKDWPFKDRVEIFNK 198

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	357
TAIR|locus:2077076	415	PHP "PLANT HOMOLOGOUS TO PARAF	0.565	0.486	0.658	4.1e-100
FB|FBgn0037657	538	hyx "hyrax" [Drosophila melano	0.277	0.184	0.411	2e-29
UNIPROTKB|Q5ZLM0	531	CDC73 "Parafibromin" [Gallus g	0.324	0.218	0.393	9e-28
UNIPROTKB|E1BPQ8	531	CDC73 "Uncharacterized protein	0.324	0.218	0.393	1.9e-27
UNIPROTKB|A2SXS7	531	HRPT2 "Uncharacterized protein	0.324	0.218	0.393	1.9e-27
UNIPROTKB|Q6P1J9	531	CDC73 "Parafibromin" [Homo sap	0.324	0.218	0.393	1.9e-27
MGI|MGI:2384876	531	Cdc73 "cell division cycle 73,	0.324	0.218	0.393	1.9e-27
RGD|1311766	531	Cdc73 "cell division cycle 73"	0.324	0.218	0.393	1.9e-27
ZFIN|ZDB-GENE-040426-1309	521	cdc73 "cell division cycle 73,	0.327	0.224	0.366	1.2e-26
WB|WBGene00018064	517	F35F11.1 [Caenorhabditis elega	0.274	0.189	0.394	5.9e-24

TAIR|locus:2077076 PHP "PLANT HOMOLOGOUS TO PARAFIBROMIN" [Arabidopsis thaliana (taxid:3702)]

 Score = 693 (249.0 bits), Expect = 4.1e-100, Sum P(2) = 4.1e-100
 Identities = 137/208 (65%), Positives = 155/208 (74%)

Query:   133 ISLIRACERPLKDREALLECKGIDFYSVLVXXXXXXXXXXXXXXXXXKDGLVAKNRLMGV 192
             I LIR+ ERPLK R+A+L+CK  DFYSVLV                 KDGLVAK+RLMG 
Sbjct:   156 IMLIRSNERPLKSRDAILQCKNRDFYSVLVNSTKREEERQRIESHQRKDGLVAKSRLMGA 215

Query:   193 DERXXXXXXXXXXXXXXXXDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITIYN 252
             +ER                D  Y+ANPK KL   K+GKIGEGVPIILVPSA QTLITIYN
Sbjct:   216 EERGIVGFSSGGGD-----DNGYDANPKSKL-HFKAGKIGEGVPIILVPSAFQTLITIYN 269

Query:   253 VKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSEDWD 312
             VKEFLEDGVYIP DVK K M G++P+C+TVQKKFSRDR++VV AYEVRDKPS +K +DWD
Sbjct:   270 VKEFLEDGVYIPNDVKAKEMKGLKPDCITVQKKFSRDRERVVTAYEVRDKPSALKPDDWD 329

Query:   313 RVVAVFVLGKEWQFKEWPFKDHVEIFNK 340
             RVVAVFVLGK+WQFK+WPFKDHVEIFNK
Sbjct:   330 RVVAVFVLGKDWQFKDWPFKDHVEIFNK 357

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=IMP

GO:0009911 "positive regulation of flower development" evidence=IMP

GO:0051568 "histone H3-K4 methylation" evidence=IMP

GO:0070860 "RNA polymerase I core factor complex" evidence=ISS

FB|FBgn0037657 hyx "hyrax" [Drosophila melanogaster (taxid:7227)]

 Score = 213 (80.0 bits), Expect = 2.0e-29, Sum P(2) = 2.0e-29
 Identities = 44/107 (41%), Positives = 71/107 (66%)

Query:   236 PIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPEC-VTVQKKFSRDRDQVV 294
             PII++PSA+ +LIT+ N K+ L++  ++ T  K   + G + EC V +Q+K    R+   
Sbjct:   379 PIIIIPSANTSLITMLNAKDILQELRFMSTSDK--KLQGCQRECEVLLQRK----RNNQT 432

Query:   295 KAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDH-VEIFNK 340
              +Y V D P+ +  ++W RVVAVFV+G +WQFK WP++ + V+IF+K
Sbjct:   433 VSYRVIDNPTKLSQQEWQRVVAVFVMGPQWQFKGWPWEGNPVDIFSK 479

GO:0016055 "Wnt receptor signaling pathway" evidence=IMP

GO:0008587 "imaginal disc-derived wing margin morphogenesis" evidence=IMP

GO:0008586 "imaginal disc-derived wing vein morphogenesis" evidence=IMP

GO:0008407 "chaeta morphogenesis" evidence=IMP

GO:0001745 "compound eye morphogenesis" evidence=IMP

GO:0007480 "imaginal disc-derived leg morphogenesis" evidence=IMP

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

GO:0045880 "positive regulation of smoothened signaling pathway" evidence=IGI;IMP

GO:0008134 "transcription factor binding" evidence=IPI

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

GO:0043234 "protein complex" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|Q5ZLM0 CDC73 "Parafibromin" [Gallus gallus (taxid:9031)]

 Score = 203 (76.5 bits), Expect = 9.0e-28, Sum P(2) = 9.0e-28
 Identities = 52/132 (39%), Positives = 75/132 (56%)

Query:   230 KIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVT-VQKKFSR 288
             K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K   G + E  T +Q++  +
Sbjct:   354 KKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKKQ--GCQRENETLIQRR--K 409

Query:   289 DRDQ-------VVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFK----DHVEI 337
             D+ Q       V   Y V D+P  +  +DWDRVVAVFV G  WQFK WP+       V+I
Sbjct:   410 DQMQPGGTTVSVTVPYRVVDQPLKLMPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDI 469

Query:   338 FNKSKLIFELYN 349
             F K K     Y+
Sbjct:   470 FAKIKAFHLKYD 481

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0010390 "histone monoubiquitination" evidence=IEA

GO:0031648 "protein destabilization" evidence=IEA

GO:0033523 "histone H2B ubiquitination" evidence=IEA

GO:0048147 "negative regulation of fibroblast proliferation" evidence=IEA

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IEA

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

GO:0031442 "positive regulation of mRNA 3'-end processing" evidence=ISS

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=ISS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISS

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

GO:0000993 "RNA polymerase II core binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=ISS

GO:0019827 "stem cell maintenance" evidence=ISS

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0001711 "endodermal cell fate commitment" evidence=ISS

GO:0008285 "negative regulation of cell proliferation" evidence=ISS

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=ISS

GO:0006378 "mRNA polyadenylation" evidence=ISS

GO:0045749 "negative regulation of S phase of mitotic cell cycle" evidence=ISS

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=ISS

UNIPROTKB|E1BPQ8 CDC73 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 203 (76.5 bits), Expect = 1.9e-27, Sum P(2) = 1.9e-27
 Identities = 52/132 (39%), Positives = 75/132 (56%)

Query:   230 KIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVT-VQKKFSR 288
             K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K   G + E  T +Q++  +
Sbjct:   354 KKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKKQ--GCQRENETLIQRR--K 409

Query:   289 DRDQ-------VVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFK----DHVEI 337
             D+ Q       V   Y V D+P  +  +DWDRVVAVFV G  WQFK WP+       V+I
Sbjct:   410 DQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDI 469

Query:   338 FNKSKLIFELYN 349
             F K K     Y+
Sbjct:   470 FAKIKAFHLKYD 481

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=IEA

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IEA

GO:0048147 "negative regulation of fibroblast proliferation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045749 "negative regulation of S phase of mitotic cell cycle" evidence=IEA

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IEA

GO:0033523 "histone H2B ubiquitination" evidence=IEA

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0031648 "protein destabilization" evidence=IEA

GO:0031442 "positive regulation of mRNA 3'-end processing" evidence=IEA

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

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

GO:0010390 "histone monoubiquitination" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=IEA

GO:0001711 "endodermal cell fate commitment" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|A2SXS7 HRPT2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 203 (76.5 bits), Expect = 1.9e-27, Sum P(2) = 1.9e-27
 Identities = 52/132 (39%), Positives = 75/132 (56%)

Query:   230 KIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVT-VQKKFSR 288
             K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K   G + E  T +Q++  +
Sbjct:   354 KKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKKQ--GCQRENETLIQRR--K 409

Query:   289 DRDQ-------VVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFK----DHVEI 337
             D+ Q       V   Y V D+P  +  +DWDRVVAVFV G  WQFK WP+       V+I
Sbjct:   410 DQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDI 469

Query:   338 FNKSKLIFELYN 349
             F K K     Y+
Sbjct:   470 FAKIKAFHLKYD 481

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=IEA

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IEA

GO:0048147 "negative regulation of fibroblast proliferation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045749 "negative regulation of S phase of mitotic cell cycle" evidence=IEA

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IEA

GO:0033523 "histone H2B ubiquitination" evidence=IEA

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0031648 "protein destabilization" evidence=IEA

GO:0031442 "positive regulation of mRNA 3'-end processing" evidence=IEA

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

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

GO:0010390 "histone monoubiquitination" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=IEA

GO:0001711 "endodermal cell fate commitment" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|Q6P1J9 CDC73 "Parafibromin" [Homo sapiens (taxid:9606)]

 Score = 203 (76.5 bits), Expect = 1.9e-27, Sum P(2) = 1.9e-27
 Identities = 52/132 (39%), Positives = 75/132 (56%)

Query:   230 KIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVT-VQKKFSR 288
             K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K   G + E  T +Q++  +
Sbjct:   354 KKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKKQ--GCQRENETLIQRR--K 409

Query:   289 DRDQ-------VVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFK----DHVEI 337
             D+ Q       V   Y V D+P  +  +DWDRVVAVFV G  WQFK WP+       V+I
Sbjct:   410 DQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDI 469

Query:   338 FNKSKLIFELYN 349
             F K K     Y+
Sbjct:   470 FAKIKAFHLKYD 481

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0010390 "histone monoubiquitination" evidence=IDA

GO:0033523 "histone H2B ubiquitination" evidence=IDA

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

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IMP

GO:0048147 "negative regulation of fibroblast proliferation" evidence=IMP

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0031648 "protein destabilization" evidence=IMP

GO:0071222 "cellular response to lipopolysaccharide" evidence=ISS

GO:0031442 "positive regulation of mRNA 3'-end processing" evidence=IMP

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0000993 "RNA polymerase II core binding" evidence=IDA

GO:0045749 "negative regulation of S phase of mitotic cell cycle" evidence=IMP

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IDA

GO:0019827 "stem cell maintenance" evidence=ISS

GO:0008285 "negative regulation of cell proliferation" evidence=IDA

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=IDA

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IDA

GO:0006378 "mRNA polyadenylation" evidence=IMP

GO:0001711 "endodermal cell fate commitment" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:2384876 Cdc73 "cell division cycle 73, Paf1/RNA polymerase II complex component" [Mus musculus (taxid:10090)]

 Score = 203 (76.5 bits), Expect = 1.9e-27, Sum P(2) = 1.9e-27
 Identities = 52/132 (39%), Positives = 75/132 (56%)

Query:   230 KIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVT-VQKKFSR 288
             K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K   G + E  T +Q++  +
Sbjct:   354 KKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKKQ--GCQRENETLIQRR--K 409

Query:   289 DRDQ-------VVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFK----DHVEI 337
             D+ Q       V   Y V D+P  +  +DWDRVVAVFV G  WQFK WP+       V+I
Sbjct:   410 DQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDI 469

Query:   338 FNKSKLIFELYN 349
             F K K     Y+
Sbjct:   470 FAKIKAFHLKYD 481

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO;IMP

GO:0000993 "RNA polymerase II core binding" evidence=ISO

GO:0001711 "endodermal cell fate commitment" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=ISO

GO:0007049 "cell cycle" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=ISO

GO:0010390 "histone monoubiquitination" evidence=ISO

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

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

GO:0019827 "stem cell maintenance" evidence=IMP

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=ISO

GO:0031442 "positive regulation of mRNA 3'-end processing" evidence=ISO

GO:0031648 "protein destabilization" evidence=ISO

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=ISO

GO:0033523 "histone H2B ubiquitination" evidence=ISO

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=ISO

GO:0045749 "negative regulation of S phase of mitotic cell cycle" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0048147 "negative regulation of fibroblast proliferation" evidence=ISO

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=ISO

GO:0071222 "cellular response to lipopolysaccharide" evidence=IDA

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=ISO

RGD|1311766 Cdc73 "cell division cycle 73" [Rattus norvegicus (taxid:10116)]

 Score = 203 (76.5 bits), Expect = 1.9e-27, Sum P(2) = 1.9e-27
 Identities = 52/132 (39%), Positives = 75/132 (56%)

Query:   230 KIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVT-VQKKFSR 288
             K G   PII++P+A+ +LIT+ N K+ L+D  ++P+D K K   G + E  T +Q++  +
Sbjct:   354 KKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKKQ--GCQRENETLIQRR--K 409

Query:   289 DRDQ-------VVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFK----DHVEI 337
             D+ Q       V   Y V D+P  +  +DWDRVVAVFV G  WQFK WP+       V+I
Sbjct:   410 DQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDI 469

Query:   338 FNKSKLIFELYN 349
             F K K     Y+
Sbjct:   470 FAKIKAFHLKYD 481

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO;ISS

GO:0000993 "RNA polymerase II core binding" evidence=IEA;ISO;ISS

GO:0001711 "endodermal cell fate commitment" evidence=IEA;ISO;ISS

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO;ISS

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=IEA;ISO;ISS

GO:0007049 "cell cycle" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008285 "negative regulation of cell proliferation" evidence=ISO;ISS

GO:0010390 "histone monoubiquitination" evidence=IEA;ISO

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0016593 "Cdc73/Paf1 complex" evidence=IEA;ISO;ISS

GO:0019827 "stem cell maintenance" evidence=IEA;ISO;ISS

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IEA;ISO;ISS

GO:0031442 "positive regulation of mRNA 3'-end processing" evidence=IEA;ISO;ISS

GO:0031648 "protein destabilization" evidence=IEA;ISO

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA;ISO;ISS

GO:0033523 "histone H2B ubiquitination" evidence=IEA;ISO

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IEA;ISO;ISS

GO:0045749 "negative regulation of S phase of mitotic cell cycle" evidence=IEA;ISO;ISS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO;ISS

GO:0048147 "negative regulation of fibroblast proliferation" evidence=IEA;ISO

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IEA;ISO

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA;ISO;ISS

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=IEA;ISO;ISS

ZFIN|ZDB-GENE-040426-1309 cdc73 "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 189 (71.6 bits), Expect = 1.2e-26, Sum P(2) = 1.2e-26
 Identities = 48/131 (36%), Positives = 72/131 (54%)

Query:   230 KIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRD 289
             K G   PII++P+A+ +LIT+ N K+ L+D  ++ ++ K K     R   V +Q++  +D
Sbjct:   353 KKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVTSEEK-KKQGIQRDNEVLLQRR--KD 409

Query:   290 RDQ-------VVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFK----DHVEIF 338
             + Q       V   Y V D+P  +  +DWDRVVAVFV G  WQFK WP+       V+IF
Sbjct:   410 QVQPGGATLSVTVPYRVIDQPLKLAPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDIF 469

Query:   339 NKSKLIFELYN 349
              K +     Y+
Sbjct:   470 AKIRAFHLKYD 480

GO:0034243 "regulation of transcription elongation from RNA polymerase II promoter" evidence=IGI

GO:0030218 "erythrocyte differentiation" evidence=IGI

GO:0051301 "cell division" evidence=IEA

GO:0007507 "heart development" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

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

GO:0021529 "spinal cord oligodendrocyte cell differentiation" evidence=IMP

WB|WBGene00018064 F35F11.1 [Caenorhabditis elegans (taxid:6239)]

 Score = 200 (75.5 bits), Expect = 5.9e-24, Sum P(2) = 5.9e-24
 Identities = 41/104 (39%), Positives = 63/104 (60%)

Query:   236 PIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVK 295
             PII+VPSA  T+I +YNV++ L++  Y+P D + K  N  +P  + +Q    R ++ V  
Sbjct:   354 PIIIVPSAMNTMINLYNVRDILQNFSYVPVDQRRKETN-KKPVDLAIQ----RQKNGVTY 408

Query:   296 AYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDH-VEIF 338
                V D    + ++DWDRV+AVFV+G  WQFK W +  +  +IF
Sbjct:   409 NIRVIDNAEKLANDDWDRVIAVFVMGVAWQFKGWKWNGNPTDIF 452

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

---

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:
	Al_scaffold_0003_2421	annotation not avaliable (414 aa)
		(Arabidopsis lyrata)
Predicted Functional Partners:
	fgenesh2_kg.2__351__AT1G61040.1	annotation not avaliable (643 aa)							•		0.404

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	357
pfam05179	273	pfam05179, CDC73, RNA pol II accessory factor, Cdc	3e-63
COG5157	362	COG5157, CDC73, RNA polymerase II assessory factor	2e-18

>gnl|CDD|113931 pfam05179, CDC73, RNA pol II accessory factor, Cdc73 family

 Score =  202 bits (515), Expect = 3e-63
 Identities = 79/225 (35%), Positives = 109/225 (48%), Gaps = 17/225 (7%)

Query: 131 DDISLIRACERP------LKDREALLECKGIDFYSVLVSSTRREEERQRIESQQR--KDG 182
               LI               + A L  +G     V V + + E+ R  + S Q   K  
Sbjct: 2   RTEVLISNGTLFERLDIIASLQGASLREEGRLEKPVPVPTDKPEDMRVDLHSPQEEAKYN 61

Query: 183 LVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPK-----LLQLKSGKIGEGVPI 237
             A+ R  G +  G      G   G     ++  A PK         Q    K G   PI
Sbjct: 62  RYAQERFSGEETEGFKIDTFGSLRGSV--LKSIHAGPKATASARADKQNGPSKKGSRDPI 119

Query: 238 ILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAY 297
           IL+PSA+ +LIT+YN+K+FL++G Y+P D K +     +PE + +Q+KFSR +   V  Y
Sbjct: 120 ILIPSAASSLITMYNIKDFLQEGKYVPVDAK-RKQGCQKPELIAIQRKFSRSKFVTV-RY 177

Query: 298 EVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSK 342
            V D P  +K +DWDRVVAVFV G  WQFK WP+   V+IF+K K
Sbjct: 178 RVVDNPEKLKPDDWDRVVAVFVTGPAWQFKGWPWNSPVDIFHKIK 222

Length = 273

>gnl|CDD|227486 COG5157, CDC73, RNA polymerase II assessory factor [Transcription]

 Score = 85.1 bits (210), Expect = 2e-18
 Identities = 78/332 (23%), Positives = 126/332 (37%), Gaps = 58/332 (17%)

Query: 17  DKVTQTGDEILFGSD----YTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKHTDYIQR 72
            K       + F       YTF  + ET    +  +L  L+ V+++  + +  +  Y+  
Sbjct: 29  GKKVPPKQMVKFKGTESKEYTFEQNEET--EIEIDSLVQLRIVLFYWLNRDKSYAVYMTL 86

Query: 73  ARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKI-VETDGGGDDLELD 131
            R + +  +   DR  L E+L G T+S+  ++         +   I    D    D  + 
Sbjct: 87  CRESGIGNIYFLDRTDLIEWLEGNTESSQYLKAPGQKKETSSTTSISARIDSEVSDPVVV 146

Query: 132 DISLIRACERPLKDRE-ALLECKGIDFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLM 190
           +       ER L      L+  K I F  +L               + ++D LV      
Sbjct: 147 ETM---KHERILVGHNSRLIGLKPISFLGLL---------------KDKEDKLVQSE--- 185

Query: 191 GVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQLKSGKIGEGVPIILVPSASQTLITI 250
                     GG  G  G  G         P               IILVP ++ + +T+
Sbjct: 186 ----------GGSLGHKGAHGRPTKYYAKDP---------------IILVPQSASSPLTL 220

Query: 251 YNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSED 310
            N+KEFLE+G Y+         +G+R   ++  +K   D D   +   V D     K E 
Sbjct: 221 SNIKEFLEEGKYVNPRNLPSCSDGIR---ISEVEKVELDLDGPFRFIIV-DDTGGFKPEY 276

Query: 311 WDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSK 342
           WDRVV +F  G +WQF  + ++D  E+FN  K
Sbjct: 277 WDRVVCIFTTGSKWQFGRYNWRDPGELFNTIK 308

Length = 362

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	357
COG5157	362	CDC73 RNA polymerase II assessory factor [Transcri	100.0
KOG3786	395	consensus RNA polymerase II assessory factor Cdc73	100.0
PF05179	273	CDC73: RNA pol II accessory factor, Cdc73 family;	100.0
KOG3786	395	consensus RNA polymerase II assessory factor Cdc73	97.69

>COG5157 CDC73 RNA polymerase II assessory factor [Transcription]

Probab=100.00  E-value=1.5e-63  Score=467.40  Aligned_cols=298  Identities=25%  Similarity=0.352  Sum_probs=223.2

Q ss_pred             ChhHHHHHHHhcCCC-----------CcceecCCEEEecC----CccccCCCcceeeecCCceeeHHHHHHHHHhCCCCh
Q 018361            2 DPLSALRDFTIRSEL-----------DKVTQTGDEILFGS----DYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKH   66 (357)
Q Consensus         2 DpL~~LR~~~~~~~~-----------~~i~~~~~~i~Fg~----~~~~~k~~~T~f~~~~~~~ytL~si~f~~~~~d~~~   66 (357)
                      ..|.+||.++.+++.           .+++....++.|.+    .++|+.+..|....  +..+.|++|||||+|+|.++
T Consensus         3 n~ldllk~~l~~~d~~~l~~~E~~s~~~kv~~~q~~~f~~~~S~~~~fe~ne~~eiE~--DS~~qLR~v~f~wlnrD~s~   80 (362)
T COG5157           3 NSLDLLKKALRDPDACQLSPEEIVSGGKKVPPKQMVKFKGTESKEYTFEQNEETEIEI--DSLVQLRIVLFYWLNRDKSY   80 (362)
T ss_pred             cHHHHHHHHhcCccceecchhhccccCcccCceeEEEecCCCCceeecCcccceeecc--cchhhhhhhhhhhhhccchH
Confidence            568899999998851           11222346888843    25788888888774  58899999999999999999


Q ss_pred             HHHHHHHHhCCCCceecCchhhHHHhhcCCCCCccccccccccccccCCCCccccCCCCCCcchhhHHHHHhccccCCch
Q 018361           67 TDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVETDGGGDDLELDDISLIRACERPLKDR  146 (357)
Q Consensus        67 ~~Yv~~a~~~~i~~Vs~~DRkdLl~yL~G~~dts~~I~~~~p~~~~~~~~~~~~~~~~~d~~~~d~~~~I~~~Er~l~dR  146 (357)
                      ++||++|++.||++|+|+||+|||+||+|.+|++.+|....|..++..+.+.  .+..+.+...+++-+.+.+||.+.+|
T Consensus        81 a~Y~~~C~e~gi~ni~fl~rtdlI~wlegnteSsq~l~~~~~k~EtSs~ts~--s~~~D~~~sd~~V~~~~k~eR~l~~h  158 (362)
T COG5157          81 AVYMTLCRESGIGNIYFLDRTDLIEWLEGNTESSQYLKAPGQKKETSSTTSI--SARIDSEVSDPVVVETMKHERILVGH  158 (362)
T ss_pred             HHHHHHHHHcCcccEEEeeHHHHHHHHhCCcchhhhhcCCCCCCCCcccccc--eeecccccccHHHhhhhhcceeecCC
Confidence            9999999999999999999999999999999999999753222211111111  11122222335899999999999999


Q ss_pred             hhhhh-hcCCchHHHHhhhhHHHHHHHHHHhhhhcccccccccccCcccCCcccCCCCCCCCCCCCCCCccCCCChhhhh
Q 018361          147 EALLE-CKGIDFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQ  225 (357)
Q Consensus       147 nsvLr-~k~~dFs~vl~~~~~~e~~~~~~~~~~~k~~~~~~~r~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~p~~~~~~  225 (357)
                      |++|+ .||.+|.+++.++...     +   ++++.+.                  .|..+.+|        .|.     
T Consensus       159 ns~l~G~kpi~f~~l~kd~ed~-----l---~qs~~~s------------------~~Hk~ah~--------Rp~-----  199 (362)
T COG5157         159 NSRLIGLKPISFLGLLKDKEDK-----L---VQSEGGS------------------LGHKGAHG--------RPT-----  199 (362)
T ss_pred             CceeecccccchhhhhhhHHHH-----h---hhhcccc------------------cccccccc--------Ccc-----
Confidence            99999 4999999998766321     1   2222110                  00001111        111     


Q ss_pred             cccCCCCCCCcEEEecCCcccccchhhHHHHhhcCcccCChhhhhccCCCCCceEEEEeeecCCCCCeeeEEEEEcCCCC
Q 018361          226 LKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPST  305 (357)
Q Consensus       226 ~~~~k~~~~~PIIivPs~~tslitm~Nik~FLe~g~fv~~~~~~~~~~~~~~~~v~i~r~~~~~~~~~~~~f~VvD~~~~  305 (357)
                          |...++||||||++++|+|||+|||+|||+|+||+|.+......+  -..+.+.+...+  -..+++|++||++.+
T Consensus       200 ----k~~~kDPIIlvp~saSS~lt~~NIK~FleEgkyV~P~n~~~~~~G--~~i~~~eK~~~~--~~g~~rfIiVd~t~~  271 (362)
T COG5157         200 ----KYYAKDPIILVPQSASSPLTLSNIKEFLEEGKYVNPRNLPSCSDG--IRISEVEKVELD--LDGPFRFIIVDDTGG  271 (362)
T ss_pred             ----ccccCCceEEeccccccceeHHHHHHHHHhcCccCccccccCCCC--ceEEeeeehhhc--ccCceEEEEEcCCCC
Confidence                223679999999999999999999999999999998764332111  113444443322  255799999999999


Q ss_pred             CCCCCCCeEEEEEeeCCccccCCCCCCChHHHhccccEEEEEece
Q 018361          306 MKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNL  350 (357)
Q Consensus       306 ~~~~~W~rVVaVf~~G~~WQFk~w~~~~p~~lF~~v~gf~~~~~~  350 (357)
                      |+||||||||||||||++|||.+|+|++|.+||++|+||||+|.|
T Consensus       272 FkpeyWdRVVciFttG~~WQf~~y~w~~p~elF~~~kgfyf~~~G  316 (362)
T COG5157         272 FKPEYWDRVVCIFTTGSKWQFGRYNWRDPGELFNTIKGFYFARRG  316 (362)
T ss_pred             cChhhhceEEEEEecCCeeeecCcccCCHHHHHhhCCceEEEEcC
Confidence            999999999999999999999999999999999999999999985

>KOG3786 consensus RNA polymerase II assessory factor Cdc73p [Transcription]

Probab=100.00  E-value=9.5e-61  Score=464.51  Aligned_cols=307  Identities=34%  Similarity=0.489  Sum_probs=230.2

Q ss_pred             CChhHHHHHHHhcCCCCcceec--------------CCEEEecC---CccccCCCcceeeecCCceeeHHHHHHHHHhCC
Q 018361            1 MDPLSALRDFTIRSELDKVTQT--------------GDEILFGS---DYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYN   63 (357)
Q Consensus         1 ~DpL~~LR~~~~~~~~~~i~~~--------------~~~i~Fg~---~~~~~k~~~T~f~~~~~~~ytL~si~f~~~~~d   63 (357)
                      ||.|.+|+.++..+  ..+.+.              ..++.|-.   ..++|+...|.-.+  +.-.+|+.++++|..++
T Consensus         2 l~sll~l~kn~~~~--h~v~l~~~~~~s~~~v~~~drk~lL~~~ng~~~~~~~~e~~~~~~--d~~~~~~i~~l~~amsd   77 (395)
T KOG3786|consen    2 LDSLLLLLKNVALK--HDVYLRASAEESIPVVTRPDRKELLFYLNGPIAKKPRTEETELEN--DSVFDLRIKSLSEAMSD   77 (395)
T ss_pred             hhHHHHHHHHHhhc--CCeeeecccccCCCccccccHHHHHhhcCChhhccCCccceeeee--cccccHHHHHHHHHhcc
Confidence            68999999999999  555442              13555521   22456666665553  44799999999999999


Q ss_pred             CChHHHHHHHHhCCCCceecCchhhHHHhhcCCCCCccccccccccccccCCCCccccCCCCCCcchhhHHHHHhccccC
Q 018361           64 LKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVETDGGGDDLELDDISLIRACERPL  143 (357)
Q Consensus        64 ~~~~~Yv~~a~~~~i~~Vs~~DRkdLl~yL~G~~dts~~I~~~~p~~~~~~~~~~~~~~~~~d~~~~d~~~~I~~~Er~l  143 (357)
                      .++++|.++|.+.+..+++|.+|.|++.||+|-.++                             +.|.++.|+.+||++
T Consensus        78 ~~ia~ykak~~~~~~~~~k~~~~~d~i~~~~g~~~~-----------------------------d~d~~~~i~k~Er~~  128 (395)
T KOG3786|consen   78 ESIAEYKAKCLAKKRTNIKFLVRTDLIVWLKGNTES-----------------------------DVDLIRDILKRERPW  128 (395)
T ss_pred             HHHHHHhHHHHHhcccchhcccchHHHHHhhCCccc-----------------------------cHHHHhhhhccCCcc
Confidence            999999999999999999999999999999993221                             115778899999999


Q ss_pred             CchhhhhhhcCCchH----HHHhhhhHHHHHHHHHHhhhh----------ccc--ccccccccCcccCCcccCCCCCCCC
Q 018361          144 KDREALLECKGIDFY----SVLVSSTRREEERQRIESQQR----------KDG--LVAKNRLMGVDERGIGYGGGGGGGG  207 (357)
Q Consensus       144 ~dRnsvLr~k~~dFs----~vl~~~~~~e~~~~~~~~~~~----------k~~--~~~~~r~~~~~~~~~g~~~~~~~~~  207 (357)
                      ++|.++|++.+++|.    +++...+.+++.++..+.++.          ..+  +..|+||.+...  .+|.+++.|. 
T Consensus       129 rt~~~il~~~~~~~~k~~~s~l~~~~~~~e~~~~v~~~~~~~~~v~~~~~~~~p~~~~y~ryi~~rf--~~~~~~~~Gs-  205 (395)
T KOG3786|consen  129 RTRTTILQSTGREFVKNIFSKLQEVKAREEDRKTVEEHNPNFMPVDPAIRIDGPKPIDYNRYIQERF--LSFGIDTYGS-  205 (395)
T ss_pred             chHHHHHhhcchhhhhhHHHHhhccceeeecCcccccccccccCCCHHHhcCCccchhhhhhhhhhh--hccccccccc-
Confidence            999999999888882    344555555555554433321          112  235788853222  2333444433 


Q ss_pred             CCCCCCCccCCCChhhh------hcccCCCCCCCcEEEecCCcccccchhhHHHHhhcCcccCChhhhhccCCCCCceEE
Q 018361          208 GGAGDEAYEANPKPKLL------QLKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVT  281 (357)
Q Consensus       208 ~~~~~~~~~~~p~~~~~------~~~~~k~~~~~PIIivPs~~tslitm~Nik~FLe~g~fv~~~~~~~~~~~~~~~~v~  281 (357)
                      +|. .+    +|..+..      ...+...++++||||||+|+||||||+|||+|||||+|||...++.+++. ++++|.
T Consensus       206 ~g~-~l----~~~~e~~~~~~~~~~~~~~~prr~PIIlvPsA~sSlITm~NiK~fLeEgkyvp~~~k~~~g~~-~~~~v~  279 (395)
T KOG3786|consen  206 HGM-KL----KPVHEGARKRRKKQPGASGGPRRDPIILVPSAASSLITMLNIKEFLEEGKYVPEAAKKNQGCR-RPEEVL  279 (395)
T ss_pred             ccc-cC----CccchhhhhccccCCCCCCCCccCcEEEechhhcchhhHHhHHHHHHhcccCccchhhcCCCC-CCceee
Confidence            222 11    1111100      00011234689999999999999999999999999999995555555444 899999


Q ss_pred             EEeeecCCCCCeeeEEEEEcCCCCCCCCCCCeEEEEEeeCCccccCCCCCCChHHHhccccEEEEEecee
Q 018361          282 VQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYNLI  351 (357)
Q Consensus       282 i~r~~~~~~~~~~~~f~VvD~~~~~~~~~W~rVVaVf~~G~~WQFk~w~~~~p~~lF~~v~gf~~~~~~~  351 (357)
                      |+|++++.  ..+++|+|||||.+|+|+||||||||||+|++||||+|||+||+|||++||||||+|.|-
T Consensus       280 ve~kf~~~--~~~v~y~VVDn~~~ltPedWDRVVaVF~~G~~WQFk~wpw~dp~eIF~ki~gF~l~f~gd  347 (395)
T KOG3786|consen  280 VEKKFDNF--KVTVRYRVVDNPTKLTPEDWDRVVAVFVTGPKWQFKGWPWRDPVEIFNKIKGFHLHFRGD  347 (395)
T ss_pred             eeeccccc--ccceEEEEecCCCcCChhhhceEEEEEeecCccccCCCCCCCHHHHHhhcceeEEEecCC
Confidence            99999753  368999999999999999999999999999999999999999999999999999999964

>PF05179 CDC73: RNA pol II accessory factor, Cdc73 family; InterPro: IPR007852 Paf1 is an RNA polymerase II-associated protein in yeast, which defines a complex that is distinct from the Srb/Mediator holoenzyme

Probab=100.00  E-value=5.2e-52  Score=397.68  Aligned_cols=123  Identities=46%  Similarity=0.844  Sum_probs=84.1

Q ss_pred             CCCCCcEEEecCCcccccchhhHHHHhhcCcccCChhhhhccCCCCCceEEEEeeecCCCCCeeeEEEEEcCCCCCCCCC
Q 018361          231 IGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSED  310 (357)
Q Consensus       231 ~~~~~PIIivPs~~tslitm~Nik~FLe~g~fv~~~~~~~~~~~~~~~~v~i~r~~~~~~~~~~~~f~VvD~~~~~~~~~  310 (357)
                      ..+++||||||+++||||||+|||+|||||+||++++++..++ .++++|+|+|++.++. ..+++|+|||||.+|+|||
T Consensus       113 ~~~~~PIIiVp~s~sSlitm~NiK~FLed~~fv~~~~~~~~~~-~~~~~v~i~r~~~~~~-~~~v~f~VvD~~~~~~ped  190 (273)
T PF05179_consen  113 RRSKDPIIIVPPSASSLITMYNIKQFLEDGKFVPPDEKRKSGS-SKPNEVTIQRKFDRIK-PGPVRFRVVDNPEKFTPED  190 (273)
T ss_dssp             ---S--EEE----TT-SS-TTTHHHHHHH--------GGGS----TTSEEEEEE--TTSS-S--EEEEEESSSTT--GGG
T ss_pred             cCCCCCEEEECCcccchhHHHHHHHHHHcCeeecCccccccCC-CCCCEEEEEeccCCCC-CCceeEEEecChhhCCccc
Confidence            3478999999999999999999999999999999988877654 4889999999997542 2389999999999999999


Q ss_pred             CCeEEEEEeeCCccccCCCCCCChHHHhccccEEEEEec--------eeeeee
Q 018361          311 WDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYN--------LIWGCI  355 (357)
Q Consensus       311 W~rVVaVf~~G~~WQFk~w~~~~p~~lF~~v~gf~~~~~--------~~~~~~  355 (357)
                      |+|||||||+||+||||+|||++|++||+|||||||+|+        .+|||.
T Consensus       191 W~RVVAVF~~G~~WQFk~w~~~~P~~LF~~v~gf~~~~~~~~~p~~v~~WnV~  243 (273)
T PF05179_consen  191 WDRVVAVFVTGQAWQFKGWPWSDPVELFQKVKGFYVHYDGDKVPPNVKQWNVK  243 (273)
T ss_dssp             GGGEEEEE--S-GGGGTTSSS-SHHHHHHHSEEEEEEETTS---HHHHHSSEE
T ss_pred             CCeEEEEEeECchhhhCCCCCCCHHHHhhcCcEEEEEecCCCCChhHhcCCCe
Confidence            999999999999999999999999999999999999999        467764

The Paf1 complex, which also contains Cdc73, Ctr9, Hpr1, Ccr4, Rtf1 and Leo1, is required for full expression of a subset of yeast genes, particularly those responsive to signals from the Pkc1/MAP kinase cascade. The complex appears to play an essential role in RNA elongation []. ; PDB: 3V46_A.

>KOG3786 consensus RNA polymerase II assessory factor Cdc73p [Transcription]

Probab=97.69  E-value=1.1e-05  Score=80.24  Aligned_cols=47  Identities=38%  Similarity=0.669  Sum_probs=45.1

Q ss_pred             eHHHHHHHHHhCCCChHHHHHHHHhCCCCceecCchhhHHHhhcCCC
Q 018361           51 TLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVT   97 (357)
Q Consensus        51 tL~si~f~~~~~d~~~~~Yv~~a~~~~i~~Vs~~DRkdLl~yL~G~~   97 (357)
                      ||+||+|+.+|..++|..||++|.++.++.|+.+||++||.||+|..
T Consensus         1 tl~sll~l~kn~~~~h~v~l~~~~~~s~~~v~~~drk~lL~~~ng~~   47 (395)
T KOG3786|consen    1 TLDSLLLLLKNVALKHDVYLRASAEESIPVVTRPDRKELLFYLNGPI   47 (395)
T ss_pred             ChhHHHHHHHHHhhcCCeeeecccccCCCccccccHHHHHhhcCChh
Confidence            68999999999999999999999999999999999999999999933

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	357
3v46_A	170	Crystal Structure Of Yeast Cdc73 C-Terminal Domain		7e-11
4dm4_A	167	The Conserved Domain Of Yeast Cdc73 Length = 167		9e-11

>pdb|3V46|A Chain A, Crystal Structure Of Yeast Cdc73 C-Terminal Domain Length = 170

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 36/107 (33%), Positives = 59/107 (55%), Gaps = 5/107 (4%)
Query: 236 PIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVK 295
           PIIL+PSA+ +++T+ N+K+FL +  Y    V  +N+  +    V ++K F R   + ++
Sbjct: 15  PIILIPSAASSILTVANIKQFLLESKY----VNPRNLPSVPNGLVNIEKNFERI-SRPIR 69
Query: 296 AYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSK 342
              V +     K E WDRVVA+F  G  WQF  + +    E+F + K
Sbjct: 70  FIIVDNTRMFTKPEYWDRVVAIFTTGHTWQFNNYQWNSPQELFQRCK 116

>pdb|4DM4|A Chain A, The Conserved Domain Of Yeast Cdc73 Length = 167

Iteration: 1
 Score = 64.3 bits (155), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 36/107 (33%), Positives = 59/107 (55%), Gaps = 5/107 (4%)
Query: 236 PIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVK 295
           PIIL+PSA+ +++T+ N+K+FL +  Y    V  +N+  +    V ++K F R   + ++
Sbjct: 4   PIILIPSAASSILTVANIKQFLLESKY----VNPRNLPSVPNGLVNIEKNFERI-SRPIR 58
Query: 296 AYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKSK 342
              V +     K E WDRVVA+F  G  WQF  + +    E+F + K
Sbjct: 59  FIIVDNTRMFTKPEYWDRVVAIFTTGHTWQFNNYQWNSPQELFQRCK 105

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	357
3v46_A	170	Cell division control protein 73; RAS-like fold, n	100.0

>3v46_A Cell division control protein 73; RAS-like fold, non-GTP binding, protein interaction surface, transcription elongation factor; 1.55A {Saccharomyces cerevisiae} PDB: 4dm4_A

Probab=100.00  E-value=4.6e-47  Score=338.55  Aligned_cols=117  Identities=30%  Similarity=0.578  Sum_probs=106.7

Q ss_pred             CCCcEEEecCCcccccchhhHHHHhhcCcccCChhhhhccCCCCCceEEEEeeecCCCCCeeeEEEEEcCCCCC-CCCCC
Q 018361          233 EGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTM-KSEDW  311 (357)
Q Consensus       233 ~~~PIIivPs~~tslitm~Nik~FLe~g~fv~~~~~~~~~~~~~~~~v~i~r~~~~~~~~~~~~f~VvD~~~~~-~~~~W  311 (357)
                      +++|||||||++||||||+|||+|||||+||++++..+    +.+++|+|+|++.+  .+.+++|+||||+.+| +||||
T Consensus        12 ~~~PIIiVp~s~sSlitm~NiK~FLedg~fv~~~~~~~----~~~~~v~I~r~~~~--~~~~~~f~VVD~~~~~tkpe~W   85 (170)
T 3v46_A           12 RKDPIILIPSAASSILTVANIKQFLLESKYVNPRNLPS----VPNGLVNIEKNFER--ISRPIRFIIVDNTRMFTKPEYW   85 (170)
T ss_dssp             CSCCEEECCCCTTCSSCTTTHHHHHHHCCCCCGGGSCC----CTTSEEEEEECCTT--SSSCEEEEEESSSTTCCSGGGG
T ss_pred             CCCCEEEECCCccchhhHHHHHHHHhcCeecChhhccc----CCCCeEEEEEecCC--CCcceEEEEEEChHHcCCccCC
Confidence            67999999999999999999999999999999998643    24679999999864  2578999999999999 69999


Q ss_pred             CeEEEEEeeCCccccCCCCCCChHHHhccccEEEEEec--------eeeeee
Q 018361          312 DRVVAVFVLGKEWQFKEWPFKDHVEIFNKSKLIFELYN--------LIWGCI  355 (357)
Q Consensus       312 ~rVVaVf~~G~~WQFk~w~~~~p~~lF~~v~gf~~~~~--------~~~~~~  355 (357)
                      +|||||||+|++||||+|||++|++||++||||||+|+        .+|||.
T Consensus        86 ~RVVAVFv~G~~WQFk~w~~~~P~elF~~v~Gf~~~~~~~~~p~~v~~WnV~  137 (170)
T 3v46_A           86 DRVVAIFTTGHTWQFNNYQWNSPQELFQRCKGYYFHFAGDSVPQHVQQWNVE  137 (170)
T ss_dssp             GGEEEEECCSCGGGGTTSSSCSHHHHHHHSEEEEEEETTSCCCHHHHHSSEE
T ss_pred             ceEEEEEeECchhhcCCCCCCChHHHhccceEEEEEecCCCCChhHhhCCCE
Confidence            99999999999999999999999999999999999999        467764

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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