Psyllid ID: psy14634

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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-------360-------370-------380-------39
Protein Sequence
MENGFYLENWSTLETFVFQKSKQIFPMGGLFLIPSAFQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKIGESQPFRDGNLSSLPRAGIEPEIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMVSCCCCCSGFSYRSVKSSASRKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHcccccccccccccccccHHHHHHHccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHcccccccccEEEEEEEEEccccccccccEEEEEEEEEEEcccEEEcccEEEcEEEEEEEcccEEEEEEEEEccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHccHHHHHcccccHHHHHccEEEEEEccccccccEEEEEccc
Secondary Structure Prediction (SSPRO)
ccccEEEEccccHHHHHEcccccccccccHHHcccHHHHHHHHHHccccccccccccccccccccccHHccccccccccccHHHHHHcEEcHHHHHHHHccccccHHEEcccEEEEEEcccccccEEEEEEEEEEEEcccEEEEccccccEEEEEEEcccEEEEEEEEEccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHcccccccEEEEEccHHHHHHHHHcHHHHHHHHHcHHHHHHEcccEEEEEEcccccccEEEEEEccc
Coil and Loop (DISEMBL)
MENGFYLENWSTLETFVFQkskqifpmgglflipsaFQIVREkerfkptpynyamKKTQLMKERDMAQskigesqpfrdgnlsslpragiepeIVEVVYKKDLissamfygsvcdltswhifsshpqeigeisgvcetgkiyslgktrtnkglklrhgnserVFRLEFisnqeftesefirwkdqcmtegvalptkdeVERKSKEIQNGMMYQWKEEDVEQIVREKerfkptpynyaMKKTQLMKERDmaqskgddeEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMVSCccccsgfsyrsvkssaSRKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVrigignntgiplyrvsenfc
Flexible Loop (DISEMBL)
MENGFYLENWSTLETFVFQKSKQIFPMGGLFLIPSAFQIVREkerfkptpynyaMKKTQLMKERDMAQSKigesqpfrdgnlsslpragiePEIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSlgktrtnkglklrhgnservfrlefisnqeftesefirwkdqcmtegvalptkdeverKSKEiqngmmyqwkeedVEQIVRekerfkptpynyamkktqlMKERDMAqskgddeeasILQRKIDDLEERANeldkartstissisyinnrnrrKNVEEAEKAIMVSCCCCCSGfsyrsvkssasrkvIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGnntgiplyrvsenfc
Low Complexity Region (SEG)
MENGFYLENWSTLETFVFQKSKQIFPMGGLFLIPSAFQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKIGESQPFRDGNLSSLPRAGIEPEIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTissisyinnrnrrKNVEEAEKAIMVSCCCCCSGFSYRSVKSSASRKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC
Disordered region (IsUnstruct)
***GFYLENWSTLETFVFQKSKQIFPMGGLFLIPSAFQIVREKERFKPTPYNY***********************************GIEPEIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGVAL******************YQW***************************************************************************************AEKAIMVSCCCCCSGFSYRSVKSSASRKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRV*****
Disordered Region (DISOPRED)
**NGFYLENWSTLETFVFQKSKQIFPMGGLFLIPS************************************************SLPRAGIEPEIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEE*********************KKTQLMKERDM***********ILQ******************************NRRKNVEE****************************************************VHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC
Disordered Region (DISEMBL)
MENGFYLENWSTLETFVFQKSKQIFPMGGLFLIPSAFQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKIGESQPFRDGNLSSLPRAGIEPEIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQL****************SILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMVSCCCCCSGFSYRSVKSSASRKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC
Disordered Region (DISPRO)
**NGFYLENWSTLETFVFQKSKQIFPMGGLFLIPSAFQIVREKERF********************************DGNLSSLPRAGIEPEIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMVSCCCCCSGFSYRSVKSSASRKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MENGFYLENWSTLETFVFQKSKQIFPMGGLFLIPSAFQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKIGESQPFRDGNLSSLPRAGIEPEIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQxxxxxxxxxxxxxxxxxxxxxxxxxxxxRTSTISSISYINNRNRRKNVEEAEKAIMVSCCCCCSGFSYRSVKSSASRKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC
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	388	2.2.26 [Sep-21-2011]
Q5RAD5	665	RNA polymerase-associated	yes	N/A	0.463	0.270	0.561	3e-56
Q92541	710	RNA polymerase-associated	yes	N/A	0.463	0.253	0.561	3e-56
A2AQ19	715	RNA polymerase-associated	yes	N/A	0.463	0.251	0.561	3e-56
Q9W261	775	RNA polymerase-associated	yes	N/A	0.461	0.230	0.597	2e-55
O94667	560	RNA polymerase-associated	yes	N/A	0.440	0.305	0.298	3e-18

>sp|Q5RAD5|RTF1_PONAB RNA polymerase-associated protein RTF1 homolog (Fragment) OS=Pongo abelii GN=RTF1 PE=2 SV=2

 Score =  219 bits (558), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 101/180 (56%), Positives = 140/180 (77%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++WK+   +
Sbjct: 397 VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 456

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
            G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKTQL+KE+ 
Sbjct: 457 AGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKTQLLKEKA 516

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMV 308
           MA+  GD ++A  +Q ++++LEERA  LD+ RT  IS+ISYIN RNR  N+ E+EKA++ 
Sbjct: 517 MAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVESEKALVA 576

Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex.
Pongo abelii (taxid: 9601)

>sp|Q92541|RTF1_HUMAN RNA polymerase-associated protein RTF1 homolog OS=Homo sapiens GN=RTF1 PE=1 SV=4

 Score =  219 bits (558), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 101/180 (56%), Positives = 140/180 (77%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++WK+   +
Sbjct: 402 VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 461

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
            G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKTQL+KE+ 
Sbjct: 462 AGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKTQLLKEKA 521

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMV 308
           MA+  GD ++A  +Q ++++LEERA  LD+ RT  IS+ISYIN RNR  N+ E+EKA++ 
Sbjct: 522 MAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVESEKALVA 581

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. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex.

Homo sapiens (taxid: 9606)

>sp|A2AQ19|RTF1_MOUSE RNA polymerase-associated protein RTF1 homolog OS=Mus musculus GN=Rtf1 PE=2 SV=1

 Score =  219 bits (557), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 101/180 (56%), Positives = 140/180 (77%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++WK+   +
Sbjct: 407 VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 466

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
            G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKTQL+KE+ 
Sbjct: 467 AGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKTQLLKEKA 526

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMV 308
           MA+  GD ++A  +Q ++++LEERA  LD+ RT  IS+ISYIN RNR  N+ E+EKA++ 
Sbjct: 527 MAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVESEKALVA 586

Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. Binds single-stranded DNA (By similarity). Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex.

Mus musculus (taxid: 10090)

>sp|Q9W261|RTF1_DROME RNA polymerase-associated protein Rtf1 OS=Drosophila melanogaster GN=Rtf1 PE=1 SV=1

 Score =  216 bits (550), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 107/179 (59%), Positives = 138/179 (77%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI GV ETGKIYSLG TRTN+GL+L+HG  ERVFRLEFISNQEFTE+EF +W + C  
Sbjct: 477 VAEIVGVVETGKIYSLGTTRTNRGLRLKHGTQERVFRLEFISNQEFTENEFNKWNEVCQQ 536

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
             V +PT D +  K  +I+  + Y++K+EDV++IV EK RF+  P NYAMKKT LMKERD
Sbjct: 537 SHVQMPTIDLIAIKQNDIKKALNYEFKDEDVDKIVEEKNRFRNRPTNYAMKKTCLMKERD 596

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GD + A  L ++ID+LE RA+ELDK R+ T++ ISYIN+RNR+KNVE+AEKAI+
Sbjct: 597 AAMLRGDYDIAQDLGQQIDELENRASELDKRRSHTLNLISYINDRNRKKNVEDAEKAIL 655

Plays a role in transcription-coupled histone modification. Required for methylation of 'Lys-4' of histone H3. Plays a role in regulation of transcription. Required for maximal induction of heat-shock genes. Plays a role in Notch signaling in the wing margins.

Drosophila melanogaster (taxid: 7227)

>sp|O94667|RTF1_SCHPO RNA polymerase-associated protein C651.09c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC651.09c PE=1 SV=1

 Score = 92.8 bits (229), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 51/171 (29%), Positives = 95/171 (55%)

Query: 131 EISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEG 190
           ++ G+ E+ K Y +    T   L+  HG S+RVF +  +SN+ F++ +F RW  Q M + 
Sbjct: 265 QVKGILESRKPYRVDGVLTKVSLECFHGRSKRVFDVNVLSNEPFSDHDFQRWHHQMMEDK 324

Query: 191 VALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMA 250
           +++P+K+ V+RK  ++++   Y   E++V  I+  K+     P N A +KT+L + R  A
Sbjct: 325 LSMPSKNFVQRKLNDLRDMSKYVLSEKEVSDIINRKKELSRVPSNIAAEKTRLRQRRQAA 384

Query: 251 QSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEE 301
              G+ E    +  +++ LEE +   ++   S +  ++ +N RNRR+N  E
Sbjct: 385 YVAGNAELVKEIDDQLNTLEELSMGSNQNSNSAMDQLAKVNERNRRRNHTE 435

The PAF1 complex is a multifunctional complex. Involved in transcription initiation via genetic interactions with TATA-binding proteins. Involved in elongation. Also has a role in transcription-coupled histone modification. Important for TATA site selection by TBP. Directly or indirectly regulates the DNA-binding properties of the TATA box-binding protein, and the relative activities of different TATA elements.

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	388
307187750	702	RNA polymerase-associated protein Rtf1 [	0.461	0.254	0.715	2e-70
322799130	696	hypothetical protein SINV_08701 [Solenop	0.458	0.255	0.715	4e-70
350427275	695	PREDICTED: RNA polymerase-associated pro	0.461	0.257	0.715	5e-70
332016344	678	RNA polymerase-associated protein Rtf1 [	0.458	0.262	0.715	6e-70
383851969	695	PREDICTED: RNA polymerase-associated pro	0.502	0.280	0.66	6e-70
328789618	695	PREDICTED: RNA polymerase-associated pro	0.461	0.257	0.715	8e-70
380026154	695	PREDICTED: RNA polymerase-associated pro	0.461	0.257	0.715	8e-70
307205224	694	RNA polymerase-associated protein Rtf1 [	0.461	0.257	0.703	2e-69
345493971	657	PREDICTED: RNA polymerase-associated pro	0.461	0.272	0.675	5e-66
193657299	636	PREDICTED: hypothetical protein LOC10016	0.456	0.278	0.659	3e-62

>gi|307187750|gb|EFN72722.1| RNA polymerase-associated protein Rtf1 [Camponotus floridanus]

 Score =  272 bits (696), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 128/179 (71%), Positives = 155/179 (86%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCETGKIY LG TRTNKGLKLRHG  ERVFRLEF+SNQEFT+SEF +WK+ C  
Sbjct: 398 VAEISGVCETGKIYQLGGTRTNKGLKLRHGAQERVFRLEFVSNQEFTDSEFFKWKETCAV 457

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G+++PT DEVE+K K+I   ++Y++KEED+E+IVREKERFK TPYNYAMKK QLM+ERD
Sbjct: 458 QGISVPTFDEVEQKLKDINEALLYEYKEEDIEKIVREKERFKQTPYNYAMKKAQLMRERD 517

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GDDE AS L +++ +LEERA+ELDK RT+TISSISYIN+RNR+KNVEEAEKAIM
Sbjct: 518 AANCRGDDETASRLNQELSELEERASELDKMRTATISSISYINDRNRKKNVEEAEKAIM 576

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322799130|gb|EFZ20577.1| hypothetical protein SINV_08701 [Solenopsis invicta]

 Score =  271 bits (693), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 128/179 (71%), Positives = 155/179 (86%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCETGKIY LG TRTNKGLKLRHG  ERVFRLEF+SNQEFT+SEF +WK+ C  
Sbjct: 393 VAEISGVCETGKIYQLGGTRTNKGLKLRHGAQERVFRLEFVSNQEFTDSEFFKWKETCAL 452

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G++ PT DEVE+K K+I+  M+Y++KEED+E+IVREKERFK TPYNYAMKK QLM++RD
Sbjct: 453 QGISTPTFDEVEQKLKDIKEAMVYEFKEEDIEKIVREKERFKQTPYNYAMKKAQLMRDRD 512

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GDDE AS L +++ +LEERA+ELDK RT+TISSISYIN+RNR+KNVEEAEKAIM
Sbjct: 513 AANCRGDDETASRLNQELSELEERASELDKMRTATISSISYINDRNRKKNVEEAEKAIM 571

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350427275|ref|XP_003494708.1| PREDICTED: RNA polymerase-associated protein Rtf1-like [Bombus impatiens]

 Score =  271 bits (692), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 128/179 (71%), Positives = 156/179 (87%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCETGKIY LG TRTNKGLKLRHG  ERVFRLEF+SNQEFTESEF +WK+ C  
Sbjct: 393 VAEISGVCETGKIYQLGGTRTNKGLKLRHGAQERVFRLEFVSNQEFTESEFFKWKETCAL 452

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G+++PT +EVE+K K+I+  ++Y++KEED+E+IVREKERFK TPYNYAMKK QLM+ERD
Sbjct: 453 QGISMPTFEEVEQKLKDIKEALVYEFKEEDIEKIVREKERFKQTPYNYAMKKAQLMRERD 512

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GDDE AS L +++ +LEERA+ELDK RT+TISSISYIN+RNR+KNVEEAEKAIM
Sbjct: 513 AANCRGDDETASRLNQELSELEERASELDKMRTATISSISYINDRNRKKNVEEAEKAIM 571

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332016344|gb|EGI57257.1| RNA polymerase-associated protein Rtf1 [Acromyrmex echinatior]

 Score =  271 bits (692), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 128/179 (71%), Positives = 155/179 (86%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCETGKIY LG TRTNKGLKLRHG  ERVFRLEF+SNQEFT+SEF +WK+ C  
Sbjct: 376 VAEISGVCETGKIYQLGGTRTNKGLKLRHGAQERVFRLEFVSNQEFTDSEFFKWKETCAL 435

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G++ PT DEVE+K K+I+  ++Y++KEED+E+IVREKERFK TPYNYAMKK QLM+ERD
Sbjct: 436 QGISTPTFDEVEQKLKDIKEALVYEFKEEDIEKIVREKERFKQTPYNYAMKKAQLMRERD 495

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GDDE AS L +++ +LEERA+ELDK RT+TISSISYIN+RNR+KNVEEAEKAIM
Sbjct: 496 AANCRGDDETASRLNQELSELEERASELDKMRTATISSISYINDRNRKKNVEEAEKAIM 554

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383851969|ref|XP_003701503.1| PREDICTED: RNA polymerase-associated protein Rtf1-like [Megachile rotundata]

 Score =  270 bits (691), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 132/200 (66%), Positives = 161/200 (80%), Gaps = 5/200 (2%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCETGKIY LG TRTNKGLKLRHG  ERVFRLEF+SNQEFTESEF +WK+ C  
Sbjct: 393 VAEISGVCETGKIYQLGGTRTNKGLKLRHGAQERVFRLEFVSNQEFTESEFFKWKETCAL 452

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G+++PT +EVE+K K+I+  ++Y++KEED+E+IVREKERFK TPYNYAMKK QLM+ERD
Sbjct: 453 QGISMPTFEEVEQKLKDIKEALVYEFKEEDIEKIVREKERFKQTPYNYAMKKAQLMRERD 512

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMV 308
            A  +GDDE AS L +++ +LEERA+ELDK RT+TISSISYIN+RNR+KNVEEAEKAIM 
Sbjct: 513 AANCRGDDETASRLNQELSELEERASELDKMRTATISSISYINDRNRKKNVEEAEKAIME 572

Query: 309 SCCC-----CCSGFSYRSVK 323
                        F+ RS K
Sbjct: 573 EVKANKGKKVDDPFTRRSTK 592

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328789618|ref|XP_001121513.2| PREDICTED: RNA polymerase-associated protein Rtf1 [Apis mellifera]

 Score =  270 bits (690), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 128/179 (71%), Positives = 156/179 (87%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCETGKIY LG TRTNKGLKLRHG  ERVFRLEF+SNQEFTESEF +WK+ C  
Sbjct: 393 VAEISGVCETGKIYQLGGTRTNKGLKLRHGAQERVFRLEFVSNQEFTESEFFKWKETCAL 452

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G+++PT +EVE+K K+I+  ++Y++KEED+E+IVREKERFK TPYNYAMKK QLM+ERD
Sbjct: 453 QGISMPTFEEVEQKLKDIKEALVYEFKEEDIEKIVREKERFKQTPYNYAMKKAQLMRERD 512

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GDDE AS L +++ +LEERA+ELDK RT+TISSISYIN+RNR+KNVEEAEKAIM
Sbjct: 513 AANCRGDDETASRLNQELSELEERASELDKMRTATISSISYINDRNRKKNVEEAEKAIM 571

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380026154|ref|XP_003696824.1| PREDICTED: RNA polymerase-associated protein Rtf1-like [Apis florea]

 Score =  270 bits (690), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 128/179 (71%), Positives = 156/179 (87%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCETGKIY LG TRTNKGLKLRHG  ERVFRLEF+SNQEFTESEF +WK+ C  
Sbjct: 393 VAEISGVCETGKIYQLGGTRTNKGLKLRHGAQERVFRLEFVSNQEFTESEFFKWKETCAL 452

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G+++PT +EVE+K K+I+  ++Y++KEED+E+IVREKERFK TPYNYAMKK QLM+ERD
Sbjct: 453 QGISMPTFEEVEQKLKDIKEALVYEFKEEDIEKIVREKERFKQTPYNYAMKKAQLMRERD 512

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GDDE AS L +++ +LEERA+ELDK RT+TISSISYIN+RNR+KNVEEAEKAIM
Sbjct: 513 AANCRGDDETASRLNQELSELEERASELDKMRTATISSISYINDRNRKKNVEEAEKAIM 571

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307205224|gb|EFN83614.1| RNA polymerase-associated protein Rtf1 [Harpegnathos saltator]

 Score =  269 bits (688), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 126/179 (70%), Positives = 156/179 (87%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCETGKIY LG TRTNKGLKLRHG  ERVFRLEF+SNQEFT+SEF +WK+ C  
Sbjct: 392 VAEISGVCETGKIYQLGGTRTNKGLKLRHGAQERVFRLEFVSNQEFTDSEFFKWKETCAL 451

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G+++PT DEVE+K K+I+  ++Y++KEED+E+IVREKERFK TPYNYAMKK QLM+ERD
Sbjct: 452 QGISMPTFDEVEQKLKDIKEALVYEFKEEDIEKIVREKERFKQTPYNYAMKKAQLMRERD 511

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GDDE AS L +++ +LEERA+ELDK RT++ISSISYIN+RNR++NVEEAEKAIM
Sbjct: 512 AANCRGDDETASRLNQELSELEERASELDKMRTASISSISYINDRNRKRNVEEAEKAIM 570

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345493971|ref|XP_001601558.2| PREDICTED: RNA polymerase-associated protein Rtf1-like [Nasonia vitripennis]

 Score =  257 bits (657), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 121/179 (67%), Positives = 153/179 (85%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EISGVCET KIY LG T+TNKGLKLRHG  ERVFRLEF+SNQEFTESEF +WK+ C  
Sbjct: 394 VAEISGVCETAKIYQLGNTKTNKGLKLRHGAQERVFRLEFVSNQEFTESEFFKWKETCAL 453

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
           +G+++PT +E+++K K+I+  M+Y++KEED+E+IV+EK RFK TPYNYAMKK QLM+ERD
Sbjct: 454 QGISMPTSEEMDQKLKDIKEAMVYEFKEEDIEKIVQEKGRFKGTPYNYAMKKAQLMRERD 513

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            A  +GDDE AS L  +I +LEERA++LDK R++TISSISYIN+RNR+KNVEEAEKAI+
Sbjct: 514 AANCRGDDETASRLNIEISELEERASDLDKKRSATISSISYINDRNRKKNVEEAEKAIL 572

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193657299|ref|XP_001943293.1| PREDICTED: hypothetical protein LOC100162144 [Acyrthosiphon pisum]

 Score =  245 bits (625), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 118/179 (65%), Positives = 146/179 (81%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI  VCET K+Y LG TRTNKGL+L+HG +E+VFRLEFISNQEFTESEF++WK+ C  
Sbjct: 371 VAEICNVCETAKVYQLGSTRTNKGLRLKHGTNEKVFRLEFISNQEFTESEFVKWKELCHM 430

Query: 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
             + LPT  E+E K ++I+  + YQ+KEEDVEQIVREKERFK  P+NYAMKKT LMK+RD
Sbjct: 431 NRIPLPTLAELEIKVRDIKAALAYQFKEEDVEQIVREKERFKTNPHNYAMKKTSLMKDRD 490

Query: 249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIM 307
            AQ+ G  EE   +++++ DLEERAN LDK RTSTISSISYIN+RNR++NVEEAEKAI+
Sbjct: 491 DAQALGKVEEVLKIEQQLSDLEERANHLDKMRTSTISSISYINDRNRKRNVEEAEKAIL 549

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

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	388
FB|FBgn0034722	775	Rtf1 "Rtf1" [Drosophila melano	0.461	0.230	0.553	3.4e-49
UNIPROTKB|Q92541	710	RTF1 "RNA polymerase-associate	0.476	0.260	0.5	7.7e-48
UNIPROTKB|Q5RAD5	665	RTF1 "RNA polymerase-associate	0.476	0.278	0.5	7.7e-48
UNIPROTKB|E2RPD2	714	RTF1 "Uncharacterized protein"	0.476	0.259	0.5	8.3e-48
MGI|MGI:1309480	715	Rtf1 "Rtf1, Paf1/RNA polymeras	0.476	0.258	0.5	8.5e-48
UNIPROTKB|D4A6Z3	715	Rtf1 "Protein Rtf1" [Rattus no	0.476	0.258	0.5	1.1e-47
UNIPROTKB|F1NY87	701	RTF1 "Uncharacterized protein"	0.476	0.263	0.494	2.6e-47
UNIPROTKB|Q5ZKE3	585	RTF1 "Uncharacterized protein"	0.476	0.316	0.494	2.6e-47
UNIPROTKB|F1SSV6	701	RTF1 "Uncharacterized protein"	0.476	0.263	0.494	2.6e-47
UNIPROTKB|F1N6E9	714	RTF1 "Uncharacterized protein"	0.476	0.259	0.494	3.3e-47

FB|FBgn0034722 Rtf1 "Rtf1" [Drosophila melanogaster (taxid:7227)]

 Score = 497 (180.0 bits), Expect = 3.4e-49, Sum P(2) = 3.4e-49
 Identities = 99/179 (55%), Positives = 126/179 (70%)

Query:   129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
             + EI GV ETGKIYSLG TRTN+GL+L+HG  ERVFRLEFISNQEFTE+EF +W + C  
Sbjct:   477 VAEIVGVVETGKIYSLGTTRTNRGLRLKHGTQERVFRLEFISNQEFTENEFNKWNEVCQQ 536

Query:   189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERD 248
               V +PT D +  K  +I+  + Y++K+EDV++IV EK RF+  P NYAMKKT LMKERD
Sbjct:   537 SHVQMPTIDLIAIKQNDIKKALNYEFKDEDVDKIVEEKNRFRNRPTNYAMKKTCLMKERD 596

Query:   249 MAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEEAEKAIM 307
              A  +GD + A  L ++ID+LE RA+ELDK R+ T             KNVE+AEKAI+
Sbjct:   597 AAMLRGDYDIAQDLGQQIDELENRASELDKRRSHTLNLISYINDRNRKKNVEDAEKAIL 655

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0035327 "transcriptionally active chromatin" evidence=IDA

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

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IMP

GO:0045747 "positive regulation of Notch signaling pathway" evidence=IGI

UNIPROTKB|Q92541 RTF1 "RNA polymerase-associated protein RTF1 homolog" [Homo sapiens (taxid:9606)]

 Score = 500 (181.1 bits), Expect = 7.7e-48, P = 7.7e-48
 Identities = 93/186 (50%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++
Sbjct:   395 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMK 454

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   455 WKEAMFSAGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 514

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   515 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 574

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   575 SEKALV 580

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IEA

GO:0080182 "histone H3-K4 trimethylation" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IDA

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

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:0019827 "stem cell maintenance" evidence=IDA

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

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

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q5RAD5 RTF1 "RNA polymerase-associated protein RTF1 homolog" [Pongo abelii (taxid:9601)]

 Score = 500 (181.1 bits), Expect = 7.7e-48, P = 7.7e-48
 Identities = 93/186 (50%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++
Sbjct:   390 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMK 449

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   450 WKEAMFSAGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 509

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   510 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 569

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   570 SEKALV 575

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

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

GO:0003697 "single-stranded DNA binding" evidence=ISS

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

GO:0019827 "stem cell maintenance" 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

UNIPROTKB|E2RPD2 RTF1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 500 (181.1 bits), Expect = 8.3e-48, P = 8.3e-48
 Identities = 93/186 (50%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++
Sbjct:   399 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMK 458

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   459 WKEAMFSAGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 518

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   519 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 578

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   579 SEKALV 584

GO:0080182 "histone H3-K4 trimethylation" evidence=IEA

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IEA

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

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

GO:0019827 "stem cell maintenance" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

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

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

MGI|MGI:1309480 Rtf1 "Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 500 (181.1 bits), Expect = 8.5e-48, P = 8.5e-48
 Identities = 93/186 (50%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++
Sbjct:   400 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMK 459

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   460 WKEAMFSAGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 519

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   520 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 579

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   580 SEKALV 585

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

GO:0016570 "histone modification" evidence=IEA

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

GO:0019827 "stem cell maintenance" evidence=ISO;IMP

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

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

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IMP

GO:0080182 "histone H3-K4 trimethylation" evidence=IMP

UNIPROTKB|D4A6Z3 Rtf1 "Protein Rtf1" [Rattus norvegicus (taxid:10116)]

 Score = 499 (180.7 bits), Expect = 1.1e-47, P = 1.1e-47
 Identities = 93/186 (50%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++
Sbjct:   400 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMK 459

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   460 WKEAMFSAGMQLPTLDEINKKEFSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 519

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   520 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 579

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   580 SEKALV 585

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

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

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

GO:0019827 "stem cell maintenance" evidence=IEA

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

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

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IEA

GO:0080182 "histone H3-K4 trimethylation" evidence=IEA

UNIPROTKB|F1NY87 RTF1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 495 (179.3 bits), Expect = 2.6e-47, P = 2.6e-47
 Identities = 92/186 (49%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHG+ +RVFRLEF+SNQEFTESEF++
Sbjct:   386 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGSDQRVFRLEFVSNQEFTESEFMK 445

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   446 WKEAMFSAGMQLPTLDEINKKEVSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 505

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   506 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 565

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   566 SEKALV 571

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

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

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0019827 "stem cell maintenance" evidence=IEA

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

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

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IEA

GO:0080182 "histone H3-K4 trimethylation" evidence=IEA

UNIPROTKB|Q5ZKE3 RTF1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 495 (179.3 bits), Expect = 2.6e-47, P = 2.6e-47
 Identities = 92/186 (49%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHG+ +RVFRLEF+SNQEFTESEF++
Sbjct:   355 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGSDQRVFRLEFVSNQEFTESEFMK 414

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   415 WKEAMFSAGMQLPTLDEINKKEVSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 474

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   475 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 534

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   535 SEKALV 540

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

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

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0019827 "stem cell maintenance" evidence=IEA

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

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

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IEA

GO:0080182 "histone H3-K4 trimethylation" evidence=IEA

UNIPROTKB|F1SSV6 RTF1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 495 (179.3 bits), Expect = 2.6e-47, P = 2.6e-47
 Identities = 92/186 (49%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHG+ +RVFRLEF+SNQEFTESEF++
Sbjct:   386 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGSDQRVFRLEFVSNQEFTESEFMK 445

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   446 WKEAMFSAGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 505

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   506 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 565

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   566 SEKALV 571

GO:0016570 "histone modification" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1N6E9 RTF1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 495 (179.3 bits), Expect = 3.3e-47, P = 3.3e-47
 Identities = 92/186 (49%), Positives = 132/186 (70%)

Query:   123 SSHP-QEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIR 181
             +S P   + EI+GV ET K+Y LG TRTNKGL+LRHG+ +RVFRLEF+SNQEFTESEF++
Sbjct:   399 NSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGSDQRVFRLEFVSNQEFTESEFMK 458

Query:   182 WKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKT 241
             WK+   + G+ LPT DE+ +K   I+  + Y++ ++D+E+IV+EKERF+  P NYAMKKT
Sbjct:   459 WKEAMFSAGMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKT 518

Query:   242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTXXXXXXXXXXXXXKNVEE 301
             QL+KE+ MA+  GD ++A  +Q ++++LEERA  LD+ RT                N+ E
Sbjct:   519 QLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAISYINQRNREWNIVE 578

Query:   302 AEKAIM 307
             +EKA++
Sbjct:   579 SEKALV 584

GO:0080182 "histone H3-K4 trimethylation" evidence=IEA

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IEA

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

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

GO:0019827 "stem cell maintenance" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

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

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

---

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)
Q9W261	RTF1_DROME	No assigned EC number	0.5977	0.4613	0.2309	yes	N/A
Q92541	RTF1_HUMAN	No assigned EC number	0.5611	0.4639	0.2535	yes	N/A
A2AQ19	RTF1_MOUSE	No assigned EC number	0.5611	0.4639	0.2517	yes	N/A
Q5RAD5	RTF1_PONAB	No assigned EC number	0.5611	0.4639	0.2706	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	388
COG5296	521	COG5296, COG5296, Transcription factor involved in	3e-22
pfam03126	105	pfam03126, Plus-3, Plus-3 domain	2e-18
smart00719	109	smart00719, Plus3, Short conserved domain in trans	2e-18
pfam03126	105	pfam03126, Plus-3, Plus-3 domain	1e-12
smart00719	109	smart00719, Plus3, Short conserved domain in trans	3e-10

>gnl|CDD|227615 COG5296, COG5296, Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]

 Score = 98.2 bits (244), Expect = 3e-22
 Identities = 41/174 (23%), Positives = 83/174 (47%)

Query: 132 ISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGV 191
           +       K Y   + +TN+ L +  G + +VFR+  ISN  F   E+ R         +
Sbjct: 259 VGKGSTYSKPYGRKEVKTNRYLDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKL 318

Query: 192 ALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQ 251
           ++P+  +V+ K  ++ + M  +  ++++ ++V  K+   P   N   +KT+L ++R  A 
Sbjct: 319 SMPSIAKVKEKYDKLVDTMGRRLSDKEISKMVACKDEVHPKRSNVIHEKTELRQKRQRAI 378

Query: 252 SKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKA 305
              + + A   QR+++++E+          S    ++ +N RNRR+N  E   A
Sbjct: 379 ELKNKKAAMEYQRQLEEIEDNEGARVHNVNSGRPLLAKVNERNRRRNHTEIRLA 432

Length = 521

>gnl|CDD|190531 pfam03126, Plus-3, Plus-3 domain

 Score = 79.6 bits (197), Expect = 2e-18
 Identities = 31/58 (53%), Positives = 38/58 (65%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQC 186
           + +I+GV E  K Y LG   T+K LK+ HG SERVFR+ F+SN  FTE EF RW   C
Sbjct: 48  LAQITGVKEGKKPYQLGGKTTDKYLKVTHGKSERVFRISFVSNSPFTEEEFERWLQSC 105

This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor. Length = 105

>gnl|CDD|197843 smart00719, Plus3, Short conserved domain in transcriptional regulators

 Score = 79.7 bits (197), Expect = 2e-18
 Identities = 28/59 (47%), Positives = 40/59 (67%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCM 187
           + +++GV E  K YSLG   TN  L++ +G+SE+V ++ FISNQ+FTE EF RWK    
Sbjct: 51  LVQVTGVKEADKPYSLGGKTTNVLLEVLNGDSEKVVQINFISNQDFTEEEFQRWKQAIK 109

Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1. Length = 109

>gnl|CDD|190531 pfam03126, Plus-3, Plus-3 domain

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 22/48 (45%), Positives = 31/48 (64%), Gaps = 2/48 (4%)

Query: 338 EELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNN--TGIPLYRV 383
           +++NRIRL R  + KL+  P F   V+GCFVR+ IG +  TG   YR+
Sbjct: 1   DDINRIRLGRSLLAKLLFYPGFESTVVGCFVRVNIGPDKETGQQSYRL 48

This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor. Length = 105

>gnl|CDD|197843 smart00719, Plus3, Short conserved domain in transcriptional regulators

 Score = 56.9 bits (138), Expect = 3e-10
 Identities = 21/47 (44%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 338 EELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNN-TGIPLYRV 383
           + LN +RL R  +E+L+  P F   V+GCFVR+ IG N    P+YR+
Sbjct: 5   DNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKQPIYRL 51

Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1. Length = 109

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	388
KOG2402|consensus	525		100.0
COG5296	521	Transcription factor involved in TATA site selecti	100.0
smart00719	109	Plus3 Short conserved domain in transcriptional re	99.95
PF03126	108	Plus-3: Plus-3 domain; InterPro: IPR004343 The yea	99.94
KOG2402|consensus	525		99.74
smart00719	109	Plus3 Short conserved domain in transcriptional re	99.74
PF03126	108	Plus-3: Plus-3 domain; InterPro: IPR004343 The yea	99.65
COG5296	521	Transcription factor involved in TATA site selecti	99.49
PF08858	37	IDEAL: IDEAL domain; InterPro: IPR014957 This entr	82.71
PRK03057	180	hypothetical protein; Provisional	82.25
PRK03636	179	hypothetical protein; Provisional	82.22

>KOG2402|consensus

Probab=100.00  E-value=1.6e-48  Score=400.80  Aligned_cols=230  Identities=39%  Similarity=0.572  Sum_probs=215.8

Q ss_pred             ccccEEEechHHHHhccc--cCccccccceeec------CCCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCceee
Q psy14634         92 PEIVEVVYKKDLISSAMF--YGSVCDLTSWHIF------SSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERV  163 (388)
Q Consensus        92 ~~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~------g~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~eR~  163 (388)
                      .|++.|+|+|+.|++||+  ||+..|+|||||+      |.++||||+|+||.+++|+|.+++++||+||.|.||.++++
T Consensus       219 ~dln~~rlsR~~vak~~~~P~Fe~~V~gCfvRv~ig~~~~~p~YRv~~I~gV~es~k~Y~l~~~~Tnk~l~~~~G~s~r~  298 (525)
T KOG2402|consen  219 SDLNALRLSRHKVAKWLFSPFFESTVTGCFVRVGIGGEGSKPVYRVAEIVGVLESDKPYKLEGVKTNKYLRVRHGRSERV  298 (525)
T ss_pred             HHHHHHHhhHHHHHHHHhhhHHHHHhhhheEEeeecCcCCCCceeEEEEeeecccCccccccceeecceeeeecCcchhh
Confidence            579999999999999999  8999999999997      47899999999999999999999999999999999999999


Q ss_pred             eeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHH
Q psy14634        164 FRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQL  243 (388)
Q Consensus       164 f~m~~VSNspfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL  243 (388)
                      |+|++|||++||++||++|+.+|...++.+||++.|.+|..+|.++++|+|++++|++||++|.+++..|.|+||+|++|
T Consensus       299 f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~~a~~~~~sd~~v~~~v~~k~~~~~~p~N~ameK~~l  378 (525)
T KOG2402|consen  299 FRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIVKALNYRLSDKEVDQMVAEKFEASPRPRNVAMEKTGL  378 (525)
T ss_pred             cchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHhcCccCcccHHHHHHhhhhcCcCcchHHHHHHhH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHhhHHHHHHHHHhhhhh-----hcCCCc
Q psy14634        244 MKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMVSCCC-----CCSGFS  318 (388)
Q Consensus       244 ~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l~k~~~~~~~~La~IN~RNRk~N~e~irKA~l~E~k~-----~~~gfs  318 (388)
                      ++++++|...||.+.+++|+.||.+||+++.++++.+++.+..+++||+|||++    |++|+....+.     +.++|+
T Consensus       379 ~k~r~~A~~~~d~~~a~~~~~qi~elE~~a~~~~~~~~s~i~~~~~lN~rNR~~----~~~a~~~~~~~~~~~~~~dpfT  454 (525)
T KOG2402|consen  379 RKERDLAQLLGDAKSAEEIQRQINELEARAEELDKARASPILKLAELNRRNRRR----IAKAELSGGAVAKNLSAPDPFT  454 (525)
T ss_pred             HHHHHHHHhcccHhHHHHHHHHHHHHHHHHhhhccccccccccccccchhHHHH----hhhhhhhhhhhhhcCCCCCCcc
Confidence            999999999999999999999999999999889988999999999999999999    44444444332     227799


Q ss_pred             ccccccc
Q psy14634        319 YRSVKSS  325 (388)
Q Consensus       319 ~rs~kss  325 (388)
                      .|++.++
T Consensus       455 Rr~~~~~  461 (525)
T KOG2402|consen  455 RRKTRTS  461 (525)
T ss_pred             ccccccc
Confidence            9998765

>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]

Probab=100.00  E-value=1.4e-41  Score=337.67  Aligned_cols=217  Identities=20%  Similarity=0.269  Sum_probs=202.8

Q ss_pred             ccccEEEechHHHHhccc--cCccccccceeec------CCCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCceee
Q psy14634         92 PEIVEVVYKKDLISSAMF--YGSVCDLTSWHIF------SSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERV  163 (388)
Q Consensus        92 ~~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~------g~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~eR~  163 (388)
                      .||+.|+|.|+++.++|+  -|++.|.|||+|+      |+.+||||+|.++....|||.+++..||+||.|.||++.|+
T Consensus       211 ~Dfn~~rvgR~~VA~~~f~P~Fed~v~Gcf~Rv~Ig~R~g~~vyRiv~V~~~~~~~kpy~~~~v~Tn~yl~v~~Gr~~kv  290 (521)
T COG5296         211 YDFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVGKGSTYSKPYGRKEVKTNRYLDVSTGRTYKV  290 (521)
T ss_pred             hhhhhhhhhHHHHHHHhcccchhhhhcceeeEEEecccCCeeEEEEEEeccceeccccccccceeeeeeEeeecCcceee
Confidence            469999999999999999  4888999999985      68899999999998789999999999999999999999999


Q ss_pred             eeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHH
Q psy14634        164 FRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQL  243 (388)
Q Consensus       164 f~m~~VSNspfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL  243 (388)
                      |+|+++||+||.++||+||...+......+|++..|.+|.+++-.+++++||+++|++||++|..+.+.+.|++++|++|
T Consensus       291 F~in~~Sn~pf~~~eyQr~~r~~~~~kl~~PS~~~v~~k~~~l~d~~~~~LSdkeis~~V~~k~e~~~k~sNvi~eKt~L  370 (521)
T COG5296         291 FRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRRLSDKEISKMVACKDEVHPKRSNVIHEKTEL  370 (521)
T ss_pred             eEeecccCCcccHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHhCCcCchhHHHHHHHHHHhcCccchhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHhhHHHHHHHHHh
Q psy14634        244 MKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMV  308 (388)
Q Consensus       244 ~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l~k~~~~~~~~La~IN~RNRk~N~e~irKA~l~  308 (388)
                      ++.|+.|...||.+.|.+++.||++||..........++.+..|+++|+|||++|+.+||-|+..
T Consensus       371 rqkrq~A~e~~n~k~~~ey~~qL~~~E~~~~~~~hN~ns~~~~L~~v~~rNRr~N~t~IR~AE~~  435 (521)
T COG5296         371 RQKRQRAIELKNKKAAMEYQRQLEEIEDNEGARVHNVNSGRPLLAKVNERNRRRNHTEIRLAEQR  435 (521)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHhhhccccccccchHHHHHhhhhhhhccchhhhhHHHH
Confidence            99999999999999999999999999997522211225678999999999999999999987654

>smart00719 Plus3 Short conserved domain in transcriptional regulators

Probab=99.95  E-value=1.2e-28  Score=209.62  Aligned_cols=98  Identities=29%  Similarity=0.418  Sum_probs=92.0

Q ss_pred             ccccccEEEechHHHHhccc--cCccccccceeecC-------CCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCc
Q psy14634         90 IEPEIVEVVYKKDLISSAMF--YGSVCDLTSWHIFS-------SHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNS  160 (388)
Q Consensus        90 ~~~~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~g-------~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~  160 (388)
                      .-.||++|+|+|+.|++||+  +|++++.|||||++       +++||||+|+||.+++++|+++++.||+||.|+||+.
T Consensus         3 ~l~~l~~i~L~R~~l~~~~~~p~Fe~~v~GcFVRv~ig~~~~~~~~Yrl~qI~gv~~~~k~Y~~~~~~t~~~L~v~~g~~   82 (109)
T smart00719        3 VFDNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKQPIYRLVQVTGVKEADKPYELGGKTTNVLLEVLNGDS   82 (109)
T ss_pred             ChHHhheEEEEHHHHHHHhcCCchhHhceEeEEEEEECCCCCCCCeEEEEEEeeEEecCcceecCCceeeEEEEEecCCc
Confidence            33569999999999999999  89999999999972       3899999999999889999999999999999999999


Q ss_pred             eeeeeeeeccCCcCCHHHHHHHHHHHH
Q psy14634        161 ERVFRLEFISNQEFTESEFIRWKDQCM  187 (388)
Q Consensus       161 eR~f~m~~VSNspfTe~EF~Rw~~~~~  187 (388)
                      ++.|+|+.||||||||+||++|+++|.
T Consensus        83 ~~~~~i~~iSn~~fte~E~~~w~~~~~  109 (109)
T smart00719       83 EKVVQINFISNQDFTEEEFQRWKQAIK  109 (109)
T ss_pred             eEEEEEEEecCCCCCHHHHHHHHHHhC
Confidence            999999999999999999999999884

Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.

>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1

Probab=99.94  E-value=6.4e-28  Score=204.06  Aligned_cols=97  Identities=35%  Similarity=0.567  Sum_probs=82.9

Q ss_pred             cccEEEechHHHHhccc--cCccccccceeec--C------CCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCcee
Q psy14634         93 EIVEVVYKKDLISSAMF--YGSVCDLTSWHIF--S------SHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSER  162 (388)
Q Consensus        93 ~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~--g------~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~eR  162 (388)
                      ||++|+|+|++|++||+  +|+.+++|||||+  |      .++||||+|+||.+..|+|++++..||++|.|+||+..|
T Consensus         2 ~i~~i~l~Rs~l~~~~~~P~Fe~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~v~~~~k~Y~~~~~~t~~~L~l~~g~~~r   81 (108)
T PF03126_consen    2 DIKRIRLSRSQLEKWLFKPFFEDAVVGCFVRVNIGPNDYTQNPVYRLCQIVGVKEGKKPYKLGSKKTNKYLVLRHGNSER   81 (108)
T ss_dssp             HHHHTBE-HHHHHHHTTSTTHHHHHTT-EEEEEEETTSSS-E--EEEEEEEEEEEEEEEEEETTEEEEEEEEEEETTEEE
T ss_pred             chHeEEEEHHHHHHHHcCCChhHheeEEEEEEEecCCCCCCceeEEEEEEEEEecccccEecCCeEEEEEEEEEECCcee
Confidence            68999999999999999  9999999999997  2      236999999999987789999999999999999999999


Q ss_pred             eeeeeeccCCcCCHHHHHHHHHHHHhc
Q psy14634        163 VFRLEFISNQEFTESEFIRWKDQCMTE  189 (388)
Q Consensus       163 ~f~m~~VSNspfTe~EF~Rw~~~~~~~  189 (388)
                      .|+|+.|||||||++||++|+++|+++
T Consensus        82 ~~~i~~vSn~~~te~E~~~w~~~~~~~  108 (108)
T PF03126_consen   82 DFPIDMVSNSPFTEEEFERWKQSCEKD  108 (108)
T ss_dssp             EEEGGGBBSS---HHHHHHHHHHH---
T ss_pred             EEEeEeeECCCCCHHHHHHHHHHhccC
Confidence            999999999999999999999999863

The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.

>KOG2402|consensus

Probab=99.74  E-value=5.6e-19  Score=183.01  Aligned_cols=56  Identities=43%  Similarity=0.774  Sum_probs=54.8

Q ss_pred             ccccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCCCCceEEEEecC
Q psy14634        333 YIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC  388 (388)
Q Consensus       333 ~~~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g~~~YR~~~I~~  388 (388)
                      ++++++||+++|||||+||+|||+|||+++|+||||||+||.++|+|+||||+|+|
T Consensus       214 ~v~~~~dln~~rlsR~~vak~~~~P~Fe~~V~gCfvRv~ig~~~~~p~YRv~~I~g  269 (525)
T KOG2402|consen  214 RVPSISDLNALRLSRHKVAKWLFSPFFESTVTGCFVRVGIGGEGSKPVYRVAEIVG  269 (525)
T ss_pred             CCCCHHHHHHHHhhHHHHHHHHhhhHHHHHhhhheEEeeecCcCCCCceeEEEEee
Confidence            78999999999999999999999999999999999999999999999999999986

>smart00719 Plus3 Short conserved domain in transcriptional regulators

Probab=99.74  E-value=1.3e-18  Score=148.15  Aligned_cols=54  Identities=39%  Similarity=0.663  Sum_probs=50.3

Q ss_pred             ccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCC-CCceEEEEecC
Q psy14634        335 ETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTG-IPLYRVSENFC  388 (388)
Q Consensus       335 ~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g-~~~YR~~~I~~  388 (388)
                      ++++||++|+|+|+.|++||++|+|+++|.||||||+||++.. +|+||||+|+|
T Consensus         2 ~~l~~l~~i~L~R~~l~~~~~~p~Fe~~v~GcFVRv~ig~~~~~~~~Yrl~qI~g   56 (109)
T smart00719        2 IVFDNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKQPIYRLVQVTG   56 (109)
T ss_pred             CChHHhheEEEEHHHHHHHhcCCchhHhceEeEEEEEECCCCCCCCeEEEEEEee
Confidence            6899999999999999999999999999999999999999633 39999999986

Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.

>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1

Probab=99.65  E-value=7.5e-17  Score=136.55  Aligned_cols=51  Identities=47%  Similarity=0.866  Sum_probs=43.2

Q ss_pred             hhhcceeechhhhhhhhcCCchhhhhccceEEEeecCC--CCCCceEEEEecC
Q psy14634        338 EELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNN--TGIPLYRVSENFC  388 (388)
Q Consensus       338 ~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~--~g~~~YR~~~I~~  388 (388)
                      +||++|+|+|+.|++||++|+|+++|.||||||+||+.  ++.++||||+|++
T Consensus         1 e~i~~i~l~Rs~l~~~~~~P~Fe~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~   53 (108)
T PF03126_consen    1 EDIKRIRLSRSQLEKWLFKPFFEDAVVGCFVRVNIGPNDYTQNPVYRLCQIVG   53 (108)
T ss_dssp             HHHHHTBE-HHHHHHHTTSTTHHHHHTT-EEEEEEETTSSS-E--EEEEEEEE
T ss_pred             CchHeEEEEHHHHHHHHcCCChhHheeEEEEEEEecCCCCCCceeEEEEEEEE
Confidence            68999999999999999999999999999999999996  4455799999975

The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.

>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]

Probab=99.49  E-value=1e-14  Score=146.62  Aligned_cols=55  Identities=33%  Similarity=0.535  Sum_probs=51.9

Q ss_pred             ccccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCCCCceEEEEec
Q psy14634        333 YIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENF  387 (388)
Q Consensus       333 ~~~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g~~~YR~~~I~  387 (388)
                      .-+.|-|||+|||||+++|+|||+|+|+++|+|||+||+||.++|+.+||||.|-
T Consensus       206 ~~a~l~Dfn~~rvgR~~VA~~~f~P~Fed~v~Gcf~Rv~Ig~R~g~~vyRiv~V~  260 (521)
T COG5296         206 DFAELYDFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVG  260 (521)
T ss_pred             hhhhhhhhhhhhhhHHHHHHHhcccchhhhhcceeeEEEecccCCeeEEEEEEec
Confidence            3566899999999999999999999999999999999999999999999999974

>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90

Probab=82.71  E-value=3.1  Score=29.28  Aligned_cols=30  Identities=27%  Similarity=0.256  Sum_probs=26.7

Q ss_pred             hHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Q psy14634        237 AMKKTQLMKERDMAQSKGDDEEASILQRKI  266 (388)
Q Consensus       237 a~eK~rL~~ere~A~~~GD~eev~~L~~qL  266 (388)
                      ..+|.+|..+++.|.+.||.+.-.+|.++|
T Consensus         8 ~~~~~~L~~~ID~ALd~~D~e~F~~Ls~eL   37 (37)
T PF08858_consen    8 EFRKEQLLELIDEALDNRDKEWFYELSEEL   37 (37)
T ss_dssp             HHHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHhhC
Confidence            478999999999999999999999998886

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.

>PRK03057 hypothetical protein; Provisional

Probab=82.25  E-value=2.5  Score=39.65  Aligned_cols=34  Identities=29%  Similarity=0.293  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q psy14634        238 MKKTQLMKERDMAQSKGDDEEASILQRKIDDLEE  271 (388)
Q Consensus       238 ~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~  271 (388)
                      .++.+|++++|.|.++||.+.-.+|..+|.+|+.
T Consensus       144 ~~~~~L~~~ID~ALd~~D~e~F~~Lt~~L~~l~~  177 (180)
T PRK03057        144 NEVSRLRMQIDQALDRKDMEEFQRLTEKLKKLEG  177 (180)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            6899999999999999999999999999999965

>PRK03636 hypothetical protein; Provisional

Probab=82.22  E-value=2.4  Score=39.73  Aligned_cols=34  Identities=24%  Similarity=0.419  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q psy14634        238 MKKTQLMKERDMAQSKGDDEEASILQRKIDDLEE  271 (388)
Q Consensus       238 ~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~  271 (388)
                      .+|.+|+.++|.|.++||.+.-.+|..+|++|+.
T Consensus       145 ~r~~~L~~~ID~ALd~~D~e~F~~Ls~~l~~L~~  178 (179)
T PRK03636        145 FRREKLLKQIDEALDRRDKEAFHRLSDELNQLRT  178 (179)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhc
Confidence            6889999999999999999999999999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	388
2bze_A	153	Nmr Structure Of Human Rtf1 Plus3 Domain Length = 1		5e-25
2bze_A	153	Nmr Structure Of Human Rtf1 Plus3 Domain Length = 1		7e-13
2db9_A	149	Solution Structure Of The Plus-3 Domain Of Human Ki		6e-25
2db9_A	149	Solution Structure Of The Plus-3 Domain Of Human Ki		4e-13
3u1u_A	137	Crystal Structure Of Rna Polymerase-Associated Prot		4e-24
3u1u_A	137	Crystal Structure Of Rna Polymerase-Associated Prot		1e-12

>pdb|2BZE|A Chain A, Nmr Structure Of Human Rtf1 Plus3 Domain Length = 153

Iteration: 1
 Score =  112 bits (279), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 49/82 (59%), Positives = 64/82 (78%)
Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++WK+   +
Sbjct: 71  VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 130
Query: 189 EGVALPTKDEVERKSKEIQNGM 210
            G+ LPT DE+ +K   I+  +
Sbjct: 131 AGMQLPTLDEINKKELSIKEAL 152

>pdb|2BZE|A Chain A, Nmr Structure Of Human Rtf1 Plus3 Domain Length = 153

Iteration: 1
 Score = 71.6 bits (174), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 39/52 (75%)
Query: 334 IETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSE 385
           +   EELNR+RLSR K+E+  H+P F + V GCFVRIGIGN+   P+YRV+E
Sbjct: 22  VSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAE 73

>pdb|2DB9|A Chain A, Solution Structure Of The Plus-3 Domain Of Human Kiaa0252 Protein Length = 149

Iteration: 1
 Score =  111 bits (278), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 49/79 (62%), Positives = 63/79 (79%)
Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++WK+   +
Sbjct: 63  VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 122
Query: 189 EGVALPTKDEVERKSKEIQ 207
            G+ LPT DE+ +K   I+
Sbjct: 123 AGMQLPTLDEINKKELSIK 141

>pdb|2DB9|A Chain A, Solution Structure Of The Plus-3 Domain Of Human Kiaa0252 Protein Length = 149

Iteration: 1
 Score = 72.4 bits (176), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 39/52 (75%)
Query: 334 IETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSE 385
           +   EELNR+RLSR K+E+  H+P F + V GCFVRIGIGN+   P+YRV+E
Sbjct: 14  VSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAE 65

>pdb|3U1U|A Chain A, Crystal Structure Of Rna Polymerase-Associated Protein Rtf1 Homolog Plus-3 Domain Length = 137

Iteration: 1
 Score =  108 bits (271), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 49/79 (62%), Positives = 61/79 (77%)
Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF +WK+   +
Sbjct: 57  VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFXKWKEAXFS 116
Query: 189 EGVALPTKDEVERKSKEIQ 207
            G  LPT DE+ +K   I+
Sbjct: 117 AGXQLPTLDEINKKELSIK 135

>pdb|3U1U|A Chain A, Crystal Structure Of Rna Polymerase-Associated Protein Rtf1 Homolog Plus-3 Domain Length = 137

Iteration: 1
 Score = 71.2 bits (173), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 38/52 (73%)
Query: 334 IETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSE 385
           +   EELNR+RLSR K+E+  H P F + V GCFVRIGIGN+   P+YRV+E
Sbjct: 8   VSLPEELNRVRLSRHKLERWCHXPFFAKTVTGCFVRIGIGNHNSKPVYRVAE 59

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	388
3u1u_A	137	RNA polymerase-associated protein RTF1 homolog; pl	1e-27
3u1u_A	137	RNA polymerase-associated protein RTF1 homolog; pl	3e-13
2bze_A	153	KIAA0252 protein; human RTF1 PLUS3 domain, transcr	2e-26
2bze_A	153	KIAA0252 protein; human RTF1 PLUS3 domain, transcr	1e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3, transcription elongation, structural genomics, struc genomics consortium, SGC; 1.80A {Homo sapiens} PDB: 2db9_A Length = 137

 Score =  104 bits (262), Expect = 1e-27
 Identities = 49/80 (61%), Positives = 63/80 (78%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++WK+   +
Sbjct: 57  VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 116

Query: 189 EGVALPTKDEVERKSKEIQN 208
            G+ LPT DE+ +K   I+ 
Sbjct: 117 AGMQLPTLDEINKKELSIKE 136

>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3, transcription elongation, structural genomics, struc genomics consortium, SGC; 1.80A {Homo sapiens} PDB: 2db9_A Length = 137

 Score = 65.7 bits (160), Expect = 3e-13
 Identities = 30/54 (55%), Positives = 40/54 (74%)

Query: 332 EYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSE 385
           + +   EELNR+RLSR K+E+  H+P F + V GCFVRIGIGN+   P+YRV+E
Sbjct: 6   QPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAE 59

>2bze_A KIAA0252 protein; human RTF1 PLUS3 domain, transcription, elongation, PAF1 complex, histone H3 methylation, H2B ubiquitination, CDC73, LEO1, CTR9; NMR {Homo sapiens} SCOP: b.34.21.1 Length = 153

 Score =  102 bits (256), Expect = 2e-26
 Identities = 49/80 (61%), Positives = 63/80 (78%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++WK+   +
Sbjct: 71  VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 130

Query: 189 EGVALPTKDEVERKSKEIQN 208
            G+ LPT DE+ +K   I+ 
Sbjct: 131 AGMQLPTLDEINKKELSIKE 150

>2bze_A KIAA0252 protein; human RTF1 PLUS3 domain, transcription, elongation, PAF1 complex, histone H3 methylation, H2B ubiquitination, CDC73, LEO1, CTR9; NMR {Homo sapiens} SCOP: b.34.21.1 Length = 153

 Score = 66.9 bits (163), Expect = 1e-13
 Identities = 32/71 (45%), Positives = 43/71 (60%)

Query: 315 SGFSYRSVKSSASRKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGN 374
           S   +    S    +    +   EELNR+RLSR K+E+  H+P F + V GCFVRIGIGN
Sbjct: 3   SSHHHHHHSSGLVPRGSHMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGN 62

Query: 375 NTGIPLYRVSE 385
           +   P+YRV+E
Sbjct: 63  HNSKPVYRVAE 73

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 1e-04
 Identities = 35/267 (13%), Positives = 81/267 (30%), Gaps = 69/267 (25%)

Query: 93  EIVEVVYKKDLISSAMFYGSVCDLTSWHIFSSHPQEIGEISGVCETGKIYSLGKTRTNKG 152
           +I+ V ++   + +      V D+    I S   +EI  I             K   +  
Sbjct: 20  DILSV-FEDAFVDNFDCK-DVQDMPK-SILSK--EEIDHIIMS----------KDAVSGT 64

Query: 153 LKL----RHGNSERVFRLEFISNQEFTESEFI--RWKDQCMTEGVALPTKDEVERKSKEI 206
           L+L         E V +  F+        +F+    K +      ++ T+  +E++ +  
Sbjct: 65  LRLFWTLLSKQEEMVQK--FVEEVLRINYKFLMSPIKTEQ--RQPSMMTRMYIEQRDRLY 120

Query: 207 QNGMMYQ----WKEEDVEQIVREK-ERFKPTPYN--YAMK---KTQLMKE--RD------ 248
            +  ++      + +   ++ R+     +P        +    KT +  +          
Sbjct: 121 NDNQVFAKYNVSRLQPYLKL-RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCK 179

Query: 249 ---------MAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRK-- 297
                    +      +    +LQ+ +  ++          ++    I  I    RR   
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Query: 298 ------------NVEEAE--KAIMVSC 310
                       NV+ A+   A  +SC
Sbjct: 240 SKPYENCLLVLLNVQNAKAWNAFNLSC 266

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	388
2bze_A	153	KIAA0252 protein; human RTF1 PLUS3 domain, transcr	100.0
3u1u_A	137	RNA polymerase-associated protein RTF1 homolog; pl	100.0
3u1u_A	137	RNA polymerase-associated protein RTF1 homolog; pl	99.82
2bze_A	153	KIAA0252 protein; human RTF1 PLUS3 domain, transcr	99.81
1gp8_A	40	Protein (scaffolding protein); coat protein-bindin	81.31

>2bze_A KIAA0252 protein; human RTF1 PLUS3 domain, transcription, elongation, PAF1 complex, histone H3 methylation, H2B ubiquitination, CDC73, LEO1, CTR9; NMR {Homo sapiens} SCOP: b.34.21.1

Probab=100.00  E-value=7e-35  Score=260.20  Aligned_cols=123  Identities=42%  Similarity=0.693  Sum_probs=116.8

Q ss_pred             cccccccEEEechHHHHhccc--cCccccccceeec------CCCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCc
Q psy14634         89 GIEPEIVEVVYKKDLISSAMF--YGSVCDLTSWHIF------SSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNS  160 (388)
Q Consensus        89 ~~~~~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~------g~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~  160 (388)
                      ++-.||++|+|+|++|++||+  +|+.++.|||||+      |+++||||||+||.+++|+|+++++.||+||.|+||+.
T Consensus        23 ~~l~di~~irL~Rs~l~~~~~~P~Fe~~V~GcFVRV~ig~~~~~~~YRl~qI~gv~~~~k~Y~l~~~~T~~~L~l~~g~~  102 (153)
T 2bze_A           23 SLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGND  102 (153)
T ss_dssp             CCHHHHHHSEECHHHHHHHSSSSSCHHHHTTCEEEEESSTTSSSCCEEEEEEEEEEEEEEEEEETTEEEEEEEEEESSSC
T ss_pred             CCHHHhhheEEEHHHHHHHhcCCchhHheEEEEEEEEeCCCCCCccEEEEEEEeEEecCcccccCCcccceEEEEEECCc
Confidence            444589999999999999998  9999999999997      45799999999999899999999999999999999999


Q ss_pred             eeeeeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhc
Q psy14634        161 ERVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMM  211 (388)
Q Consensus       161 eR~f~m~~VSNspfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n  211 (388)
                      +|.|+|++|||||||++||++|++.|+++++++||+++|++|.++|++|+|
T Consensus       103 ~r~~~m~~vSN~~fte~Ef~~w~~~~~~~~~~~PT~~~v~~K~~~i~~a~n  153 (153)
T 2bze_A          103 QRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEALN  153 (153)
T ss_dssp             EEEECGGGBCCSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHHHHHC-
T ss_pred             ceEEEeeEeeCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence            999999999999999999999999999999999999999999999999975

>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3, transcription elongation, structural genomics, struc genomics consortium, SGC; 1.80A {Homo sapiens} PDB: 2db9_A

Probab=100.00  E-value=3e-35  Score=258.00  Aligned_cols=120  Identities=43%  Similarity=0.707  Sum_probs=113.5

Q ss_pred             ccccccEEEechHHHHhccc--cCccccccceeec------CCCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCce
Q psy14634         90 IEPEIVEVVYKKDLISSAMF--YGSVCDLTSWHIF------SSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSE  161 (388)
Q Consensus        90 ~~~~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~------g~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~e  161 (388)
                      +-.||++|+|+|++|++||+  +|+..+.|||||+      |+++||||+|+||.+++++|+++++.||+||.|+||+.+
T Consensus        10 ~l~dl~~i~L~R~~l~~~~~~P~Fe~~V~GcFVRv~ig~~~~~~~Yrl~qI~gv~~~~k~Y~l~~~~T~~~L~l~~g~~~   89 (137)
T 3u1u_A           10 LPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQ   89 (137)
T ss_dssp             SHHHHHTTBCCHHHHHHHTTSTTHHHHHTTCEEEEEEEC----CEEEEEEEEEEEEEEEEEEETTEEEEEEEEEEETTEE
T ss_pred             CHHHhcceEEEHHHHHHHhcCCChhHheEEEEEEEEeCCCCCCccEEEEEEEEEEecCcccccCCceeeEEEEEEeCCcc
Confidence            44579999999999999998  8999999999997      467999999999998999999999999999999999999


Q ss_pred             eeeeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHh
Q psy14634        162 RVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNG  209 (388)
Q Consensus       162 R~f~m~~VSNspfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~  209 (388)
                      +.|+|+.|||||||++||++|+++|.++++++||+++|++|.++|++|
T Consensus        90 r~~~~~~vSN~~fte~E~~~w~~~~~~~~~~~Pt~~~l~~K~~~i~~a  137 (137)
T 3u1u_A           90 RVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEA  137 (137)
T ss_dssp             EEEEGGGBCSSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHTCCC
T ss_pred             eEEEeeeecCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhhC
Confidence            999999999999999999999999999999999999999999999865

>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3, transcription elongation, structural genomics, struc genomics consortium, SGC; 1.80A {Homo sapiens} PDB: 2db9_A

Probab=99.82  E-value=4.5e-21  Score=167.96  Aligned_cols=59  Identities=51%  Similarity=0.882  Sum_probs=52.6

Q ss_pred             cccccccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCCCCceEEEEecC
Q psy14634        330 VIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC  388 (388)
Q Consensus       330 ~~~~~~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g~~~YR~~~I~~  388 (388)
                      ...|+++++||++|+|+|+.|++|||+|+|+++|.||||||+||+++|+|+||||+|+|
T Consensus         4 ~~~~v~~l~dl~~i~L~R~~l~~~~~~P~Fe~~V~GcFVRv~ig~~~~~~~Yrl~qI~g   62 (137)
T 3u1u_A            4 KSQPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITG   62 (137)
T ss_dssp             TTSBCCSHHHHHTTBCCHHHHHHHTTSTTHHHHHTTCEEEEEEEC----CEEEEEEEEE
T ss_pred             CcCCCCCHHHhcceEEEHHHHHHHhcCCChhHheEEEEEEEEeCCCCCCccEEEEEEEE
Confidence            35689999999999999999999999999999999999999999999999999999985

>2bze_A KIAA0252 protein; human RTF1 PLUS3 domain, transcription, elongation, PAF1 complex, histone H3 methylation, H2B ubiquitination, CDC73, LEO1, CTR9; NMR {Homo sapiens} SCOP: b.34.21.1

Probab=99.81  E-value=8.5e-21  Score=169.24  Aligned_cols=61  Identities=49%  Similarity=0.863  Sum_probs=57.1

Q ss_pred             cccccccccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCCCCceEEEEecC
Q psy14634        328 RKVIEYIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC  388 (388)
Q Consensus       328 ~~~~~~~~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g~~~YR~~~I~~  388 (388)
                      -+...|+++++||++|||+|++|++||++|+|+++|.||||||+||+++|+|+||||+|+|
T Consensus        16 ~~~~~~v~~l~di~~irL~Rs~l~~~~~~P~Fe~~V~GcFVRV~ig~~~~~~~YRl~qI~g   76 (153)
T 2bze_A           16 PRGSHMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITG   76 (153)
T ss_dssp             CSSCSBCCCHHHHHHSEECHHHHHHHSSSSSCHHHHTTCEEEEESSTTSSSCCEEEEEEEE
T ss_pred             CCCCCCcCCHHHhhheEEEHHHHHHHhcCCchhHheEEEEEEEEeCCCCCCccEEEEEEEe
Confidence            3345689999999999999999999999999999999999999999999999999999985

>1gp8_A Protein (scaffolding protein); coat protein-binding domain, helix- loop-helix motif, viral protein; NMR {Enterobacteria phage P22} SCOP: j.58.1.1 PDB: 2gp8_A

Probab=81.31  E-value=1.9  Score=30.05  Aligned_cols=34  Identities=35%  Similarity=0.405  Sum_probs=29.2

Q ss_pred             hhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy14634        236 YAMKKTQLMKERDMAQSKGDDEEASILQRKIDDL  269 (388)
Q Consensus       236 ~a~eK~rL~~ere~A~~~GD~eev~~L~~qL~eL  269 (388)
                      .+-...-|++++..|-..||.+.|..|+.||+.|
T Consensus         6 ~~d~I~aiEQqiyvA~seGd~etv~~Le~QL~~l   39 (40)
T 1gp8_A            6 SAANKDAIRKQMDAAASKGDVETYRKLKAKLKGI   39 (40)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Confidence            3456678999999999999999999999999653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	388
d2bzea1	132	b.34.21.1 (A:345-476) RNA polymerase-associated pr	1e-28
d2bzea1	132	b.34.21.1 (A:345-476) RNA polymerase-associated pr	2e-16

>d2bzea1 b.34.21.1 (A:345-476) RNA polymerase-associated protein RTF1 homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 132

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

 Score =  106 bits (266), Expect = 1e-28
 Identities = 49/82 (59%), Positives = 64/82 (78%)

Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMT 188
           + EI+GV ET K+Y LG TRTNKGL+LRHGN +RVFRLEF+SNQEFTESEF++WK+   +
Sbjct: 50  VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 109

Query: 189 EGVALPTKDEVERKSKEIQNGM 210
            G+ LPT DE+ +K   I+  +
Sbjct: 110 AGMQLPTLDEINKKELSIKEAL 131

>d2bzea1 b.34.21.1 (A:345-476) RNA polymerase-associated protein RTF1 homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 132

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

 Score = 72.9 bits (179), Expect = 2e-16
 Identities = 30/52 (57%), Positives = 39/52 (75%)

Query: 334 IETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSE 385
           +   EELNR+RLSR K+E+  H+P F + V GCFVRIGIGN+   P+YRV+E
Sbjct: 1   VSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAE 52

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	388
d2bzea1	132	RNA polymerase-associated protein RTF1 homolog {Hu	100.0
d2bzea1	132	RNA polymerase-associated protein RTF1 homolog {Hu	99.8

>d2bzea1 b.34.21.1 (A:345-476) RNA polymerase-associated protein RTF1 homolog {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=100.00  E-value=7.2e-36  Score=258.20  Aligned_cols=119  Identities=44%  Similarity=0.710  Sum_probs=115.1

Q ss_pred             cccEEEechHHHHhccc--cCccccccceeec------CCCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCceeee
Q psy14634         93 EIVEVVYKKDLISSAMF--YGSVCDLTSWHIF------SSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVF  164 (388)
Q Consensus        93 ~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~------g~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~eR~f  164 (388)
                      ||++|+|+|+.|++||+  +|+.++.|||||+      |+++||||+|+||.+++++|+++++.||+||.|+||+.++.|
T Consensus         6 ~l~~irL~R~~l~~~~~~P~Fe~~v~GcFVRv~ig~~~~~~~Yrl~~I~gv~~~~k~Y~~~~~~T~~~L~l~~g~~~~~~   85 (132)
T d2bzea1           6 ELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVF   85 (132)
T ss_dssp             HHHHSEECHHHHHHHSSSSSCHHHHTTCEEEEESSTTSSSCCEEEEEEEEEEEEEEEEEETTEEEEEEEEEESSSCEEEE
T ss_pred             HhhheEEeHHHHHHHHcCCchHHhheeeEEEEEeCCCCCCCceEEEEEEeeeecCcccccCCCcccEEEEEEECCceeEE
Confidence            69999999999999999  9999999999997      478999999999998999999999999999999999999999


Q ss_pred             eeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhc
Q psy14634        165 RLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMM  211 (388)
Q Consensus       165 ~m~~VSNspfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n  211 (388)
                      +|+.|||||||++||++|+++|.++++++||+++|++|.++|++|+|
T Consensus        86 ~l~~vSn~~fte~E~~~w~~~~~~~~~~~Pt~~~l~~K~~~i~~a~n  132 (132)
T d2bzea1          86 RLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEALN  132 (132)
T ss_dssp             CGGGBCCSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHHHHHC-
T ss_pred             EeEEEeCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999986

>d2bzea1 b.34.21.1 (A:345-476) RNA polymerase-associated protein RTF1 homolog {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.80  E-value=8.7e-21  Score=163.04  Aligned_cols=55  Identities=55%  Similarity=0.976  Sum_probs=52.9

Q ss_pred             cccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCCCCceEEEEecC
Q psy14634        334 IETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC  388 (388)
Q Consensus       334 ~~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g~~~YR~~~I~~  388 (388)
                      ++++|||++|||||+.|++|||+|+|+++|.||||||+||+++|+|+||||+|+|
T Consensus         1 ~~~~e~l~~irL~R~~l~~~~~~P~Fe~~v~GcFVRv~ig~~~~~~~Yrl~~I~g   55 (132)
T d2bzea1           1 VSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITG   55 (132)
T ss_dssp             CCCHHHHHHSEECHHHHHHHSSSSSCHHHHTTCEEEEESSTTSSSCCEEEEEEEE
T ss_pred             CCChHHhhheEEeHHHHHHHHcCCchHHhheeeEEEEEeCCCCCCCceEEEEEEe
Confidence            4688999999999999999999999999999999999999999999999999975