Citrus Sinensis ID: 005794

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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-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------
Protein Sequence
MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPPGVKKVNGGSGRVETEEERRIRKKREYEKHRQEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYSNSKGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDMYD
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHccccccccccccEEEEccccccccccccccEEEEEcccccccHHHHHcccHHHHcHHHHHHHHHHHHHccccccccccEEEcccccccccccccccccccccccEEEEccccccccccccccEEEEEEccccEEEEccccccccccccccccccccccccccccccEEEEEcccccHHHHHHHHcccccccccccccccccccHHHHHHHccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHccccccccccccccccccccccEEEEEEEccccccccccccEEccccccccEEEccccHHHHHccccccccccccccEcccccHHcccccccccccHHHHHHHccccccccccccccccccccccccccEEEEEEEEcccccccccccccccHHHHHHHccccccHHHHcccHHHHHHHHHHHHHHHccccccccccccEEEEEccccccHHHccccEEEEEEccccccccccccccccccHHHHHHHHHHHHHHHcccccccccEEEEEEEccHHHHHHcccccccccEEEEEEEEcEcEcccccccccEEEEEEcccEEEEEccccEEEEEEEEcccccccccccccccccEEEEEEccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
masyrpfpqppqssfppppppnqnpsqpppppqqqqqqqrpnpysqnwggysntgggaqqhyhqpysyaqpppppppessypppppppppppptqqqtqpsmyyssnqynqnsmyppmqpplpppppsspppsssippppppgsppppppkdvegrdtgtsdrdkraskevsrhdpghskqhrppvpppgvkkvnggsgrvetEEERRIRKKREYEKHRQEEKHRLQMKESQNVVMQKSqmvasgkgghgsmvgsrmgdrraapllsgertenrlkkpttfLCKLkfrnelpepsaqpkLMALKKDKDRFTRYTFSSLeknykpqlhvepdlgipldlldlsvynppsvrppldpedeellrddevvtpvkkdgikrkerptdkgvsWLVKTqyisplsmESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEacklrpihatnknlqpveilpllpdferyddqfvaatfdgaptadseiYSKMDKSVRDAHESRAIMKSYVatgsdsanpEKFLAYMVPsvnelskdmydenedvsfsWVREyhwdvrgddaddpttylvsfdddearyvplptklnlrkkraiegrsndevehfpipssiAVRRRANVTAIELKeqgaysnskgnsssskmgrvdsqedlershngsrqqdpyqssgaeddmyd
Flexible Loop (DISEMBL)
masyrpfpqppqSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTgtsdrdkraskevsrhdpghskqhrppvpppgvkkvnggsgrveteeerrirkkreyekhrqeekhrlqmkesqnvvMQKSQMVASGKGGHGSMVGSRMGDRRAApllsgertenrlkkpttflcklkfrnelpepsaqpklmalkkdkDRFTRYTFSsleknykpqlhVEPDLGIPLDLLDLSVYNPPSVRppldpedeellrddevvtpvkkdgikrkerptdkgvswlVKTQyisplsmesarQSLTEKQAKelremkggrsilenlndRERQIKEIEASFEACKLRpihatnknlqpvEILPLLPDFERYDDQFVAATfdgaptadseiySKMDKSVRDAHESRAIMKSYvatgsdsanpEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDvrgddaddpTTYLVsfdddearyvplptklnlrkkraiegrsndevehfpipssiavrRRANVTAIelkeqgaysnskgnsssskmgRVDSQEDlershngsrqqdpyqssgaeddmyd
Low Complexity Region (SEG)
MAsyrpfpqppqssfppppppnqnpsqpppppqqqqqqqrpnpysqnWGGYSNTGGGAqqhyhqpysyaqpppppppessypppppppppppptqqqtqpsmyyssNQYNQNSMYppmqpplpppppsspppsssippppppgsppppppKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRppvpppgvkkvnggSGrveteeerrirkkreyekhrQEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEpdlgipldlldlSVYNPPSvrppldpedeellrddevvTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYsnskgnsssskMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDMYD
Disordered region (IsUnstruct)
***************************************************************************************************************************************************************************************************************************************************************************************TFLCKLKF**********************FTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVY*****************************************VSWLVKTQYI******************************************IEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGA****************************************FLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEARYVPLPTKLN****************************************************************************************
Disordered Region (DISOPRED)
****************************************************************************************************************************************************************************************************************************************************************************************FLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRD***********************SWLVKTQYIS***************************************KEIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAP****************************************LAYMV*****************SFSWVREYHWDVRG**ADDPTTYLVSFDDDEARYVPLPTKLN*******************IPSSIAVRR************************************************************
Disordered Region (DISEMBL)
*******************************************YSQNWGGYSNTGGGAQQHYHQPY*********************************PSMYYSSNQYNQNSMYPPMQPPL***************************************************************VPPPGV*****************IRKKRE***********LQMKESQNVVMQKS***************SRMGDRRAAPLLSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQ************************************************
Disordered Region (DISPRO)
****RPFPQPPQSSFPPPPPPNQNPSQPPP*********RPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQ**TQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSS***SSSIPPPPPPGS************************************************************************************************************************************KPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRD*********************GVSWLVKTQYISPL**********************GRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTAD********KSVRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAI**RSNDEVEHFPIPSSIAVRRRAN*********************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPPGVKKVNGGSGRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYSNSKGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDMYD
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	677	2.2.26 [Sep-21-2011]
Q5RAX0	533	RNA polymerase II-associa	yes	no	0.432	0.549	0.304	5e-26
Q8N7H5	531	RNA polymerase II-associa	yes	no	0.432	0.551	0.304	6e-26
Q8K2T8	535	RNA polymerase II-associa	yes	no	0.432	0.547	0.301	9e-26
Q4V886	535	RNA polymerase II-associa	yes	no	0.432	0.547	0.301	1e-25
Q2KJ14	532	RNA polymerase II-associa	yes	no	0.432	0.550	0.301	1e-25
Q4U0S5	503	RNA polymerase II-associa	yes	no	0.426	0.574	0.294	3e-25
Q6P2Y1	520	RNA polymerase II-associa	yes	no	0.451	0.588	0.284	2e-24
A2BD83	524	RNA polymerase II-associa	N/A	no	0.431	0.557	0.282	2e-23
P90783	425	RNA polymerase II-associa	yes	no	0.387	0.616	0.258	1e-13

>sp|Q5RAX0|PAF1_PONAB RNA polymerase II-associated factor 1 homolog OS=Pongo abelii GN=PAF1 PE=2 SV=1

 Score =  120 bits (300), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 102/335 (30%), Positives = 163/335 (48%), Gaps = 42/335 (12%)

Query: 282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDL 341
           +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  EPDLG+ +DL++ 
Sbjct: 30  VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTIDLINP 89

Query: 342 SVYN-PPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSM 400
             Y   P+V   LDP DE+LL ++E+  P      KR ++   K V W+ KT+YIS    
Sbjct: 90  DTYRIDPNV--LLDPADEKLL-EEEIQAPTSS---KRSQQHA-KVVPWMRKTEYIST--- 139

Query: 401 ESARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHAT 453
           E  R  ++     E  E+K G S+ +         DR+ QI  IE +FE A K    H +
Sbjct: 140 EFNRYGIS----NEKPEVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYS 195

Query: 454 NKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYV 513
              + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   +
Sbjct: 196 KPRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAM 245

Query: 514 ATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDAD 565
             G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   + 
Sbjct: 246 IRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASK 305

Query: 566 --DPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEG 598
             +   + +  + D   Y  L T++ L K+RA  G
Sbjct: 306 GYEENYFFIFREGDGVYYNELETRVRLSKRRAKAG 340

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 RNF20/40 E3 ubiquitin-protein ligase complex. Involved in polyadenylation of mRNA precursors.
Pongo abelii (taxid: 9601)

>sp|Q8N7H5|PAF1_HUMAN RNA polymerase II-associated factor 1 homolog OS=Homo sapiens GN=PAF1 PE=1 SV=2

 Score =  119 bits (299), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 102/335 (30%), Positives = 163/335 (48%), Gaps = 42/335 (12%)

Query: 282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDL 341
           +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  EPDLG+ +DL++ 
Sbjct: 30  VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTIDLINP 89

Query: 342 SVYN-PPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSM 400
             Y   P+V   LDP DE+LL ++E+  P      KR ++   K V W+ KT+YIS    
Sbjct: 90  DTYRIDPNV--LLDPADEKLL-EEEIQAPTSS---KRSQQHA-KVVPWMRKTEYIST--- 139

Query: 401 ESARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHAT 453
           E  R  ++     E  E+K G S+ +         DR+ QI  IE +FE A K    H +
Sbjct: 140 EFNRYGIS----NEKPEVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYS 195

Query: 454 NKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYV 513
              + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   +
Sbjct: 196 KPRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAM 245

Query: 514 ATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDAD 565
             G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   + 
Sbjct: 246 IRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASK 305

Query: 566 --DPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEG 598
             +   + +  + D   Y  L T++ L K+RA  G
Sbjct: 306 GYEENYFFIFREGDGVYYNELETRVRLSKRRAKAG 340

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 RNF20/40 E3 ubiquitin-protein ligase complex. Involved in polyadenylation of mRNA precursors. Has oncogenic activity in vivo and in vitro.

Homo sapiens (taxid: 9606)

>sp|Q8K2T8|PAF1_MOUSE RNA polymerase II-associated factor 1 homolog OS=Mus musculus GN=Paf1 PE=2 SV=1

 Score =  119 bits (298), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 101/335 (30%), Positives = 164/335 (48%), Gaps = 42/335 (12%)

Query: 282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDL 341
           +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  EPDLG+ +DL++ 
Sbjct: 30  VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTIDLINP 89

Query: 342 SVYN-PPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSM 400
             Y   P+V   LDP DE+LL ++E+  P      KR ++   K V W+ KT+YIS    
Sbjct: 90  DTYRIDPNV--LLDPADEKLL-EEEIQAPTSS---KRSQQHA-KVVPWMRKTEYIST--- 139

Query: 401 ESARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHAT 453
           E  R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H +
Sbjct: 140 EFNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYS 195

Query: 454 NKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYV 513
              + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   +
Sbjct: 196 KPRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAM 245

Query: 514 ATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDAD 565
             G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   + 
Sbjct: 246 IRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASK 305

Query: 566 --DPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEG 598
             +   + +  + D   Y  L T++ L K+RA  G
Sbjct: 306 GYEENYFFIFREGDGVYYNELETRVRLSKRRAKAG 340

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 RNF20/40 E3 ubiquitin-protein ligase complex. Involved in polyadenylation of mRNA precursors.

Mus musculus (taxid: 10090)

>sp|Q4V886|PAF1_RAT RNA polymerase II-associated factor 1 homolog OS=Rattus norvegicus GN=Paf1 PE=2 SV=1

 Score =  119 bits (297), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 101/335 (30%), Positives = 164/335 (48%), Gaps = 42/335 (12%)

Query: 282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDL 341
           +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  EPDLG+ +DL++ 
Sbjct: 30  VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTIDLINP 89

Query: 342 SVYN-PPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSM 400
             Y   P+V   LDP DE+LL ++E+  P      KR ++   K V W+ KT+YIS    
Sbjct: 90  DTYRIDPNV--LLDPADEKLL-EEEIQAPTSS---KRSQQHA-KVVPWMRKTEYIST--- 139

Query: 401 ESARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHAT 453
           E  R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H +
Sbjct: 140 EFNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYS 195

Query: 454 NKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYV 513
              + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   +
Sbjct: 196 KPRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAM 245

Query: 514 ATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDAD 565
             G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   + 
Sbjct: 246 IRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASK 305

Query: 566 --DPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEG 598
             +   + +  + D   Y  L T++ L K+RA  G
Sbjct: 306 GYEENYFFIFREGDGVYYNELETRVRLSKRRAKAG 340

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 RNF20/40 E3 ubiquitin-protein ligase complex. Involved in polyadenylation of mRNA precursors.

Rattus norvegicus (taxid: 10116)

>sp|Q2KJ14|PAF1_BOVIN RNA polymerase II-associated factor 1 homolog OS=Bos taurus GN=PAF1 PE=2 SV=1

 Score =  119 bits (297), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 101/335 (30%), Positives = 164/335 (48%), Gaps = 42/335 (12%)

Query: 282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDL 341
           +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  EPDLG+ +DL++ 
Sbjct: 30  VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTIDLINP 89

Query: 342 SVYN-PPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSM 400
             Y   P+V   LDP DE+LL ++E+  P      KR ++   K V W+ KT+YIS    
Sbjct: 90  DTYRIDPNV--LLDPADEKLL-EEEIQAPTSS---KRSQQHA-KVVPWMRKTEYIST--- 139

Query: 401 ESARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHAT 453
           E  R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H +
Sbjct: 140 EFNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYS 195

Query: 454 NKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYV 513
              + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   +
Sbjct: 196 KPRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAM 245

Query: 514 ATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDAD 565
             G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   + 
Sbjct: 246 IRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASK 305

Query: 566 --DPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEG 598
             +   + +  + D   Y  L T++ L K+RA  G
Sbjct: 306 GYEENYFFIFREGDGVYYNELETRVRLSKRRAKAG 340

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 RNF20/40 E3 ubiquitin-protein ligase complex. Involved in polyadenylation of mRNA precursors.

Bos taurus (taxid: 9913)

>sp|Q4U0S5|PAF1_DANRE RNA polymerase II-associated factor 1 homolog OS=Danio rerio GN=paf1 PE=1 SV=1

 Score =  117 bits (293), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 100/339 (29%), Positives = 162/339 (47%), Gaps = 50/339 (14%)

Query: 282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDL 341
           +C++K+ N LP+    PK +    D+ RF +Y  +SLEK +K +L  EPDLG+ +DL+  
Sbjct: 30  VCRVKYGNSLPDIPFDPKFITYPFDQHRFVQYKATSLEKQHKHELLTEPDLGVTIDLI-- 87

Query: 342 SVYNPPSVRPP----LDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISP 397
              NP + R      LDP DE+LL ++E+  P      KR ++   K V W+ KT+YIS 
Sbjct: 88  ---NPDTYRIDPNILLDPADEKLL-EEEIQAP---SSSKRSQQHA-KVVPWMRKTEYIST 139

Query: 398 LSMESARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPI 450
              E  R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    
Sbjct: 140 ---EFNRYGVSNEKV----EVKIGVSVKQQFTEEEIYKDRDSQIAAIEKTFEDAQKSISQ 192

Query: 451 HATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPT-ADSEIYSKMDKSVRDAHESRAIM 509
           H +   + PVE+LP+ PDF+ + +      FD  P   D    + +D           +M
Sbjct: 193 HYSKPRVTPVEVLPVFPDFKMWINPCAQVIFDSDPAPKDVSAPAGVD-----------MM 241

Query: 510 KSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDV--------SFSWVREYHWDVRG 561
              +  G       +F+AY +P+ + + K   D  E++         +   REY+W+V+ 
Sbjct: 242 SQAMIRGMMDEEGNQFVAYFLPNEDTMRKRKRDVEEELDYMPEEVYEYKIAREYNWNVKN 301

Query: 562 DDAD--DPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEG 598
             +   +   + +  D D   Y  L T++ L K+RA  G
Sbjct: 302 KASKGYEENYFFIFRDADGVYYNELETRVRLSKRRAKVG 340

Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II. PAF1C associates with RNA polymerase II, is involved in transcriptional elongation and in histone modifications including methylation on histone H3 'Lys-4' (H3K4me3) (By similarity). PAF1C seems to be required for multiple steps in cardiac formation. Involved in the migration of myocardial precursors to the midline and the differentiation of the atrioventricular boundary in the developing heart.

Danio rerio (taxid: 7955)

>sp|Q6P2Y1|PAF1_XENTR RNA polymerase II-associated factor 1 homolog OS=Xenopus tropicalis GN=paf1 PE=2 SV=1

 Score =  114 bits (286), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 104/366 (28%), Positives = 168/366 (45%), Gaps = 60/366 (16%)

Query: 254 GSRMGDRRAAPLLSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRY 313
           G R    R  P  SG             +C++K+ N LP+    PK +    D++RF +Y
Sbjct: 14  GHRSSSHRTVPERSG------------VVCRVKYCNTLPDIPFDPKFITYPFDQNRFVQY 61

Query: 314 TFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYN-PPSVRPPLDPEDEELLRDDEVVTPVKK 372
             +SLEK +K  L  EPDLG+ +DL++   Y   P+V   LD  DE+LL ++E+  P   
Sbjct: 62  KATSLEKQHKHDLLTEPDLGVTIDLINPDTYRIDPNV--TLDIADEKLL-EEEIQAPSSS 118

Query: 373 DGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLN--- 429
              KR ++   K V W+ KT+YIS    E  R  ++ ++     E+K G S+ +      
Sbjct: 119 ---KRSQQHA-KVVPWMRKTEYIST---EFNRYGVSNEKP----EVKIGVSVKQQFTEED 167

Query: 430 ---DRERQIKEIEASFEACKLRPI--HATNKNLQPVEILPLLPDFERYDDQFVAATFDGA 484
              DR+ QI  IE +FE  + +PI  H +   + PVE++P+ PDF+ + +      FD  
Sbjct: 168 IYKDRDSQISAIEKTFEDAQ-KPISQHYSKPRVTPVEVMPVFPDFKMWINPCAQVIFDSD 226

Query: 485 PTADSEIYSKMDKSVRDAHESRAI--MKSYVATGSDSANPEKFLAYMVPSVNELSKDMYD 542
           P              +DA  S A+  M   +  G       +F+AY +P    + K   D
Sbjct: 227 PAP------------KDASGSAALDMMSQAMIRGMMDEEGNQFVAYFLPGEETMRKRKRD 274

Query: 543 ENEDV--------SFSWVREYHWDVRGDDAD--DPTTYLVSFDDDEARYVPLPTKLNLRK 592
           + E +         +   REY+W+V+   +   +   + +  + D   Y  L T++ L K
Sbjct: 275 QEEGLDYMPEDIYDYKIAREYNWNVKNKASKGYEENYFFIFREGDGVYYNELETRVRLSK 334

Query: 593 KRAIEG 598
           +R   G
Sbjct: 335 RRVKAG 340

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).

Xenopus tropicalis (taxid: 8364)

>sp|A2BD83|PAF1_XENLA RNA polymerase II-associated factor 1 homolog OS=Xenopus laevis GN=paf1 PE=2 SV=1

 Score =  111 bits (277), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 95/336 (28%), Positives = 161/336 (47%), Gaps = 44/336 (13%)

Query: 282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDL 341
           +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  EPDLG+ +DL++ 
Sbjct: 30  VCRVKYCNTLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTIDLINP 89

Query: 342 SVYN-PPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSM 400
             Y   P+V   LD  DE+LL ++E+  P      KR ++   K V W+ KT+YIS    
Sbjct: 90  DTYRIDPNV--TLDFADEKLL-EEEIQAPSSS---KRSQQHA-KVVPWMRKTEYIST--- 139

Query: 401 ESARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASF-EACKLRPIHAT 453
           E  R  ++ ++     E+K G S+ +         DR+ QI  IE +F +A K    H +
Sbjct: 140 EFNRYGVSNEKP----EVKIGVSVKQQFTEEDIYKDRDSQISAIEKTFDDAQKDISQHYS 195

Query: 454 NKNLQPVEILPLLPDFERYDDQFVAATFDGAPT-ADSEIYSKMDKSVRDAHESRAIMKSY 512
              + PVE++P+ PDF+ + +      FD  P   D+   + +D           +M   
Sbjct: 196 KPRVTPVEVMPVFPDFKMWINPCAQVIFDSDPAPKDASGTAALD-----------MMSQA 244

Query: 513 VATGSDSANPEKFLAYMVPSVNELSKDMYDENEDV--------SFSWVREYHWDVRGDDA 564
           +  G       +F+AY +P  + + K   D+ E +         +   REY+W+V+   +
Sbjct: 245 MIRGMMDEEGNQFVAYFLPGEDTMRKRKRDQEEGLDYMPEDIYDYKIAREYNWNVKNKAS 304

Query: 565 D--DPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEG 598
              +   + +  + D   Y  L T++ L K+R   G
Sbjct: 305 KGYEENYFFIFREGDGVYYNELETRVRLSKRRVKAG 340

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).

Xenopus laevis (taxid: 8355)

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

 Score = 79.3 bits (194), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 76/294 (25%), Positives = 135/294 (45%), Gaps = 32/294 (10%)

Query: 277 KPTTFLCKLKFRNELPEPSAQPKLMAL-KKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIP 335
           +   F+ K +F N +P+     K M        RF  +  +++ ++YK  +  + D+G+ 
Sbjct: 15  RKVDFMLKPRFTNTVPDVPFDAKFMTCPFVPLGRFVEFQPAAIYRDYKHAVICDDDMGLN 74

Query: 336 LDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYI 395
           +DL+DL  Y+   +   +D +D  LL DD     + K     + +   K V W+ KT+YI
Sbjct: 75  VDLIDLKKYDEDPIETEIDEKDNILLEDDGAAKLIAK-----RSQQHSKLVPWMRKTEYI 129

Query: 396 SPLSMESARQSLT-EKQAKEL-REMKGGRSILENLNDRERQIKEIEASFEACKLRPI--H 451
           S    E  R  +T ++Q  +L   +K  + + +   D++ QI  I  +FE  + +P+  H
Sbjct: 130 ST---EFNRFGVTADRQETKLGYNLKKNQQVEDMYRDKQSQIDAINKTFEDVR-KPVKEH 185

Query: 452 ATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKS 511
            + K ++ VE   + PDF+ +   F    FDG  T  +E   + ++  + A ES  I   
Sbjct: 186 YSKKGVKAVEESFVFPDFDHWKHLFAHVQFDG-DTITTEFEEEDER--QQARESSVI--- 239

Query: 512 YVATGSDSANPEKFLAYMVPSVNELSKDM--------YDENEDVSFSWVREYHW 557
                +     +KF A  VP++  L+  M        +DE+    F   REY +
Sbjct: 240 ----KAMEFEDQKFAAVFVPTIGCLTSFMDDLELERPFDEDMKYEFLLSREYTF 289


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.309    0.130    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 323,326,824
Number of Sequences: 539616
Number of extensions: 18284233
Number of successful extensions: 468551
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 3042
Number of HSP's successfully gapped in prelim test: 3299
Number of HSP's that attempted gapping in prelim test: 132466
Number of HSP's gapped (non-prelim): 100296
length of query: 677
length of database: 191,569,459
effective HSP length: 124
effective length of query: 553
effective length of database: 124,657,075
effective search space: 68935362475
effective search space used: 68935362475
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 65 (29.6 bits)

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.

Caenorhabditis elegans (taxid: 6239)

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	677
356522920	659	PREDICTED: uncharacterized protein LOC10	0.745	0.766	0.737	0.0
449480786	706	PREDICTED: uncharacterized LOC101203806	0.973	0.933	0.616	0.0
449448058	706	PREDICTED: uncharacterized protein LOC10	0.973	0.933	0.607	0.0
356526079	666	PREDICTED: uncharacterized protein LOC10	0.748	0.761	0.723	0.0
359482895	589	PREDICTED: RNA polymerase II-associated	0.846	0.972	0.711	0.0
255549826	672	conserved hypothetical protein [Ricinus	0.760	0.766	0.722	0.0
224070975	569	PAF1 complex component [Populus trichoca	0.754	0.898	0.711	0.0
297839959	576	hypothetical protein ARALYDRAFT_477298 [	0.726	0.854	0.661	0.0
224054406	691	PAF1 complex component [Populus trichoca	0.698	0.684	0.648	0.0
297743192	420	unnamed protein product [Vitis vinifera]	0.620	1.0	0.764	0.0

>gi|356522920|ref|XP_003530090.1| PREDICTED: uncharacterized protein LOC100800148 [Glycine max]

 Score =  765 bits (1975), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/515 (73%), Positives = 436/515 (84%), Gaps = 10/515 (1%)

Query: 166 RASKEVSRHDPGHSKQHR--PPVPPPGVKKVNGGS-GRVETEEERRIRKKREYEKHRQEE 222
           R   E S H   H KQH+  PPVP   VKK+N G  GR ET+EE+R+RKKRE+EK RQEE
Sbjct: 152 RREYEHSNHGIAH-KQHKQQPPVP---VKKMNNGPPGRAETDEEKRLRKKREFEKQRQEE 207

Query: 223 KHRLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTENRLKKPTTFL 282
           KHR Q+KESQN V+QK+ M++SGKG HG + GSRMG+RR+ PLL  ER ENRLKKPTTFL
Sbjct: 208 KHRQQLKESQNTVLQKTHMLSSGKG-HGMIAGSRMGERRSTPLLGAERVENRLKKPTTFL 266

Query: 283 CKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLS 342
           CKLKFRNELP+PSAQPKLMA KKDKD++ +YT +SLEK YKP+L VEPDLGIPLDLLDLS
Sbjct: 267 CKLKFRNELPDPSAQPKLMASKKDKDQYAKYTITSLEKMYKPKLFVEPDLGIPLDLLDLS 326

Query: 343 VYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMES 402
           VYNPPSVRPPL PED+ELLRDDE VTP+KKDGIKRKERPTDKGV+WLVKTQYISPLSMES
Sbjct: 327 VYNPPSVRPPLAPEDKELLRDDEAVTPIKKDGIKRKERPTDKGVAWLVKTQYISPLSMES 386

Query: 403 ARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQPVEI 462
            +QSLTEKQAKELREMKGGR IL+NLN RERQI+EIEASFEA K  P+HATNK+L PVE+
Sbjct: 387 TKQSLTEKQAKELREMKGGRGILDNLNSRERQIREIEASFEAAKSDPVHATNKDLYPVEV 446

Query: 463 LPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVATGSDSANP 522
           +PLLPDF+RYDDQFV A FD APTADSE+++KMDKSVRDA ES+A+MKSYVAT SD ANP
Sbjct: 447 MPLLPDFDRYDDQFVVAAFDNAPTADSEMHAKMDKSVRDAFESKAVMKSYVATSSDPANP 506

Query: 523 EKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEARYV 582
           EKFLAYMVP+  ELSKD+YDENEDVS+SW+REYHWDVRGDDADDP T+LV+FD+ EARY+
Sbjct: 507 EKFLAYMVPAPGELSKDIYDENEDVSYSWIREYHWDVRGDDADDPATFLVAFDESEARYL 566

Query: 583 PLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYSNSKGNSSSS 642
           PLPTKL LRKKRA EGRS DEVE  P+P+ + VRRR++V AIE K+ G Y++SKGN  SS
Sbjct: 567 PLPTKLVLRKKRAKEGRSGDEVEQCPVPARVTVRRRSSVAAIERKDSGVYTSSKGN--SS 624

Query: 643 KMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDMYD 677
           K G ++  + LE  H G+  QD YQSSGAED M D
Sbjct: 625 KRGGLEMDDGLEDQHRGAPHQDNYQSSGAEDYMSD 659

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449480786|ref|XP_004155995.1| PREDICTED: uncharacterized LOC101203806 [Cucumis sativus]

 Score =  764 bits (1973), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/724 (61%), Positives = 518/724 (71%), Gaps = 65/724 (8%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQR-----PNPYSQNWG------ 49
           MASYRP+P  PQSSF   P  N   S PPP  Q      +        Y+QNWG      
Sbjct: 1   MASYRPYP--PQSSFGSAPAQN---SIPPPSAQSASVSSQQRGGATTQYNQNWGTYAGDA 55

Query: 50  ------------GYSNTGGGAQQHYHQPY----SYAQPPPPPPPESSYPPPPPPPPPPPP 93
                        Y+N       ++HQ Y    +   PPPPPPP  SYP    PPPPPPP
Sbjct: 56  SAPSAPSSSYPQNYNNQLHQTSNYHHQQYGPPRTQHPPPPPPPPHQSYPYASQPPPPPPP 115

Query: 94  TQQQTQP----------SMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPG 143
                 P          ++YY S+QY+Q +       P PPP    P  S   PPPP   
Sbjct: 116 DSSYPPPPPPPATSQPPNLYYPSSQYSQGNQNQQSMQPPPPPSSPPPSSSIPPPPPPNSP 175

Query: 144 SPPPPPPKDVEGRDTGTSDRDK---------RASKEVSRHDPGHSKQHRPPVPPPGVKKV 194
            PP    +  EG + G  +RDK         R  +E S HD  H K   PP+PP   KK 
Sbjct: 176 PPPSASQQKAEGTNMGAHERDKGAPKDPSYGRRDRENSNHDK-HQKHSGPPMPP---KKA 231

Query: 195 NGGSGRVETEEERRIRKKREYEKHRQEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVG 254
           NG SGR+ET++E+R+RKKRE+EK RQ+E+HR  +KESQN ++QK+QM+++GK  HGS+VG
Sbjct: 232 NGPSGRMETDDEKRLRKKREFEKQRQDERHRHHLKESQNTILQKTQMLSTGKV-HGSIVG 290

Query: 255 SRMGDRRAAPLLSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYT 314
           SRMG+R+A P LSGER ENRLKKPTTFLCKLKFRNELP+ SAQPKLM+L+K+KD +TRYT
Sbjct: 291 SRMGERKATPFLSGERIENRLKKPTTFLCKLKFRNELPDTSAQPKLMSLRKEKDHYTRYT 350

Query: 315 FSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDG 374
            +SLEK YKPQL+VEPDLGIPLDLLDLSVYNP SVR PL PEDEELLRDD + TPVKKDG
Sbjct: 351 ITSLEKTYKPQLYVEPDLGIPLDLLDLSVYNPSSVRMPLAPEDEELLRDDVLKTPVKKDG 410

Query: 375 -IKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRER 433
            IKRKERPTDKGV+WLVKTQYISPLS+ESA+QSLTEKQAKELREMKGGR+ILENLN+RER
Sbjct: 411 GIKRKERPTDKGVAWLVKTQYISPLSIESAKQSLTEKQAKELREMKGGRNILENLNNRER 470

Query: 434 QIKEIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYS 493
           QIKEIE SFEACK RPIHATNKNL PVE+LPLLPDF+RYDD FV   FD APTADSE ++
Sbjct: 471 QIKEIETSFEACKSRPIHATNKNLYPVEVLPLLPDFDRYDDPFVVVAFDSAPTADSETFN 530

Query: 494 KMDKSVRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVR 553
           K+D+S+RDAHES+AIMKSY+ATGSD + PEKFLAYMVPS +ELSKD+YDE EDVS+SWVR
Sbjct: 531 KLDQSIRDAHESQAIMKSYMATGSDPSKPEKFLAYMVPSPDELSKDIYDEQEDVSYSWVR 590

Query: 554 EYHWDVRGDDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSI 613
           EYHWDVRGD+ DDPTTYLVSFDD EARYVPLPTKL LRKKRA EGRS+DEVEHFP P+ +
Sbjct: 591 EYHWDVRGDNVDDPTTYLVSFDDAEARYVPLPTKLVLRKKRAKEGRSSDEVEHFPAPARV 650

Query: 614 AVRRRANVTAIELKEQGAYSNSKGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAED 673
            VRRR  V  +E+K+ G YSNSK  S        D ++ + RSH   R QD  Q SGAED
Sbjct: 651 TVRRRPTVATLEVKDPGIYSNSKRGS--------DIEDGIGRSHKHDRNQDMDQFSGAED 702

Query: 674 DMYD 677
           +M D
Sbjct: 703 EMSD 706

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448058|ref|XP_004141783.1| PREDICTED: uncharacterized protein LOC101203806 [Cucumis sativus]

 Score =  763 bits (1970), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 440/724 (60%), Positives = 512/724 (70%), Gaps = 65/724 (8%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQR-----PNPYSQNWG------ 49
           MASYRP+P  PQSSF   P  N   S PPP  Q      +        Y+QNWG      
Sbjct: 1   MASYRPYP--PQSSFGSAPAQN---SIPPPSAQSASVSSQQRGGATTQYNQNWGTYAGDA 55

Query: 50  ------------GYSNTGGGAQQHYHQPYS--------------YAQPPPPPPPESSYPP 83
                        Y+N       ++HQ Y               +   P  P P    PP
Sbjct: 56  SAPPAPSSSYPQNYNNQLHQTSNYHHQQYGPPRTQHPPPPPPPPHQSYPYAPQPPPPPPP 115

Query: 84  PPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPG 143
               PPPPPP      P++YY S+QY+Q +       P PPP    P  S   PPPP   
Sbjct: 116 DSSYPPPPPPPATSQPPNLYYPSSQYSQGNQNQQSMQPPPPPSSPPPSSSIPPPPPPNSP 175

Query: 144 SPPPPPPKDVEGRDTGTSDRDK---------RASKEVSRHDPGHSKQHRPPVPPPGVKKV 194
            PP    +  EG + G  +RDK         R  +E S HD  H K   PP+PP   KK 
Sbjct: 176 PPPSASQQKAEGTNMGAHERDKGVPKDPSYGRRDRENSNHDK-HQKHSGPPMPP---KKA 231

Query: 195 NGGSGRVETEEERRIRKKREYEKHRQEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVG 254
           NG SGR+ET++E+R+RKKRE+EK RQ+E+HR  +KESQN ++QK+QM+++GK  HGS+VG
Sbjct: 232 NGPSGRMETDDEKRLRKKREFEKQRQDERHRHHLKESQNTILQKTQMLSTGKV-HGSIVG 290

Query: 255 SRMGDRRAAPLLSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYT 314
           SRMG+R+A P LSGER ENRLKKPTTFLCKLKFRNELP+ SAQPKLM+L+K+KD +TRYT
Sbjct: 291 SRMGERKATPFLSGERIENRLKKPTTFLCKLKFRNELPDTSAQPKLMSLRKEKDHYTRYT 350

Query: 315 FSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDG 374
            +SLEK YKPQL+VEPDLGIPLDLLDLSVYNP SVR PL PEDEELLRDD + TPVKKDG
Sbjct: 351 ITSLEKTYKPQLYVEPDLGIPLDLLDLSVYNPSSVRMPLAPEDEELLRDDVLKTPVKKDG 410

Query: 375 -IKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRER 433
            IKRKERPTDKGV+WLVKTQYISPLS+ESA+QSLTEKQAKELREMKGGR+ILENLN+RER
Sbjct: 411 GIKRKERPTDKGVAWLVKTQYISPLSIESAKQSLTEKQAKELREMKGGRNILENLNNRER 470

Query: 434 QIKEIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYS 493
           QIKEIEASFEACK RPIHATNKNL PVE+LPLLPDF+RYDD FV   FD APTADSE ++
Sbjct: 471 QIKEIEASFEACKSRPIHATNKNLYPVEVLPLLPDFDRYDDPFVVVAFDSAPTADSETFN 530

Query: 494 KMDKSVRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVR 553
           K+D+S+RDAHES+AIMKSY+AT SD + PEKFLAYMVPS +ELSKD+YDE EDVS+SWVR
Sbjct: 531 KLDQSIRDAHESQAIMKSYMATSSDPSKPEKFLAYMVPSPDELSKDIYDEQEDVSYSWVR 590

Query: 554 EYHWDVRGDDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSI 613
           EYHWDVRGD+ DDPTTYLVSFDD EARYVPLPTKL LRKKRA EGRS+DEVEHFP P+ +
Sbjct: 591 EYHWDVRGDNVDDPTTYLVSFDDAEARYVPLPTKLVLRKKRAKEGRSSDEVEHFPAPARV 650

Query: 614 AVRRRANVTAIELKEQGAYSNSKGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAED 673
            VRRR  V  +E+K+ G YSNSK  S        D ++ + RSH   R QD  Q SGAED
Sbjct: 651 TVRRRPTVATLEVKDPGIYSNSKRGS--------DIEDGIGRSHKHDRHQDMDQFSGAED 702

Query: 674 DMYD 677
           +M D
Sbjct: 703 EMSD 706

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526079|ref|XP_003531647.1| PREDICTED: uncharacterized protein LOC100797526 [Glycine max]

 Score =  749 bits (1935), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/513 (72%), Positives = 431/513 (84%), Gaps = 6/513 (1%)

Query: 166 RASKEVSRHDPGHSKQHRPPVPPPGVKKVNGGS-GRVETEEERRIRKKREYEKHRQEEKH 224
           R   E S H   H KQH+   PP  VKK+N G  GR ET+EE+R+RKKRE+EK RQEEKH
Sbjct: 159 RREYEHSNHGIAH-KQHKQQQPPLPVKKMNNGPPGRAETDEEKRLRKKREFEKQRQEEKH 217

Query: 225 RLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTENRLKKPTTFLCK 284
           R Q+KESQN V+QK+ +++SGKG HG + GSRMG+RR+ PLL  ER ENRLKKPTTFLCK
Sbjct: 218 RQQLKESQNTVLQKTHLLSSGKG-HGMIAGSRMGERRSTPLLGAERVENRLKKPTTFLCK 276

Query: 285 LKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVY 344
           LKFRNELP+PSAQPKLM+ KKDKD++ +YT +SLEK YKP+L VEPDLGIPLDLLDLSVY
Sbjct: 277 LKFRNELPDPSAQPKLMSFKKDKDQYAKYTITSLEKMYKPKLFVEPDLGIPLDLLDLSVY 336

Query: 345 NPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESAR 404
           NPP VRPPL PEDEELLRDDE  TP+KKDGIKRKERPTDKGV+WLVKTQYISPLSMES +
Sbjct: 337 NPPRVRPPLAPEDEELLRDDEAATPIKKDGIKRKERPTDKGVAWLVKTQYISPLSMESTK 396

Query: 405 QSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQPVEILP 464
           QSLTEKQAKELREMKG R IL+NLN RERQI+EI+ASFEA K  P+HATNK+L PVE++P
Sbjct: 397 QSLTEKQAKELREMKG-RGILDNLNSRERQIREIQASFEAAKSDPVHATNKDLYPVEVMP 455

Query: 465 LLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVATGSDSANPEK 524
           LLPDF+RYDDQFV A FD APTADSE+Y+KM+KSVRDA ES+A+MKSYVATG D ANPEK
Sbjct: 456 LLPDFDRYDDQFVVAAFDNAPTADSEMYAKMNKSVRDAFESKAVMKSYVATGLDPANPEK 515

Query: 525 FLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEARYVPL 584
           FLAYM P+  ELSKD+YDENEDVS+SW+REYHWDVRGDDADDPTT+LV+FD+ EARY+PL
Sbjct: 516 FLAYMAPAPGELSKDIYDENEDVSYSWIREYHWDVRGDDADDPTTFLVAFDESEARYLPL 575

Query: 585 PTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYSNSKGNSSSSKM 644
           PTKL LRKKRA EGRS DEVE  P+P+ + VRRR++V AIE K+ G Y++SKGN S  ++
Sbjct: 576 PTKLVLRKKRAKEGRSGDEVEQCPVPARVTVRRRSSVAAIERKDSGVYTSSKGN-SFKRV 634

Query: 645 GRVDSQEDLERSHNGSRQQDPYQSSGAEDDMYD 677
           G ++  + LE  H G+  QD YQSSGAED M D
Sbjct: 635 G-LEMDDGLEDQHRGAPHQDNYQSSGAEDYMSD 666

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482895|ref|XP_002278075.2| PREDICTED: RNA polymerase II-associated factor 1 homolog [Vitis vinifera]

 Score =  749 bits (1933), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 421/592 (71%), Positives = 486/592 (82%), Gaps = 19/592 (3%)

Query: 102 MYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGR----- 156
           MYY S+QY+Q S + PMQPP PPPP S PP S   PPPPP   PPPP     +G+     
Sbjct: 1   MYYPSSQYSQFS-HQPMQPPPPPPPSSPPPSSLIPPPPPPASPPPPPSSVPPQGQNKEPA 59

Query: 157 -DTGTSDRDKRASKEV---SRHDPGHS------KQHRPPVPPPGVKKVNGGSGRVETEEE 206
            D G+  RDK A K++    R +PGHS      KQ +PPVPP  VKK NG  GRVETEEE
Sbjct: 60  PDGGSHGRDKGAPKDLRGAGRREPGHSNQGPSGKQQKPPVPPAPVKKSNGPPGRVETEEE 119

Query: 207 RRIRKKREYEKHRQEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVG-SRMGDRRAAPL 265
           RR+RKKRE+EK RQEEK + Q+KESQN V+QK+QM++SGKG HGS+VG SRMG+RR  P 
Sbjct: 120 RRLRKKREFEKQRQEEKQKHQLKESQNTVLQKTQMLSSGKG-HGSVVGGSRMGERRTTPF 178

Query: 266 LSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQ 325
           LSG+R ENRL+KPTTFLCKLKFRNELP+P+AQPKLMALK DKDRFT+YT +SLEK +KPQ
Sbjct: 179 LSGDRIENRLRKPTTFLCKLKFRNELPDPTAQPKLMALKTDKDRFTKYTITSLEKMHKPQ 238

Query: 326 LHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKG 385
           L VEPDLGIPLDLLDLSVYNPPSVR PLDPEDEELLRDDE VTPVKK+GIK+KERPTDKG
Sbjct: 239 LFVEPDLGIPLDLLDLSVYNPPSVRRPLDPEDEELLRDDESVTPVKKEGIKKKERPTDKG 298

Query: 386 VSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEAC 445
           VSWLVKTQYISPLS ES +QSLTEKQAKELRE KGGR+ILEN N RER+I+ IEA+F A 
Sbjct: 299 VSWLVKTQYISPLSTESTKQSLTEKQAKELRETKGGRNILENFNSRERKIQNIEAAFAAS 358

Query: 446 KLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHES 505
           K+ P+H+TNK+L+PVEILPLLPDF RYDD FV A+FD APTADSEIYSK+DK+VRD+HES
Sbjct: 359 KITPVHSTNKSLKPVEILPLLPDFARYDDSFVVASFDSAPTADSEIYSKLDKTVRDSHES 418

Query: 506 RAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDAD 565
           +AI+KSY+ATGSD + PEKFLAYM PS +ELSKD+YDENED S+SWVREYHWDVRGDDAD
Sbjct: 419 QAILKSYMATGSDPSKPEKFLAYMAPSPDELSKDIYDENEDTSYSWVREYHWDVRGDDAD 478

Query: 566 DPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIE 625
           DPTTYLVSF+  +ARY+PLPTKL LRKKRA EGRS+DEVEHFP+PS + VR+R NV AIE
Sbjct: 479 DPTTYLVSFNKTDARYLPLPTKLLLRKKRAKEGRSSDEVEHFPVPSKVTVRQRPNVAAIE 538

Query: 626 LKEQGAYSNSKGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDMYD 677
           LK++  YS+SK   SSSK G VD ++ L RS+ G + Q   QSSGAED+M D
Sbjct: 539 LKDEEVYSSSKRGVSSSKRG-VDMEDGLGRSYKGVQDQHMDQSSGAEDEMSD 589

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549826|ref|XP_002515964.1| conserved hypothetical protein [Ricinus communis] gi|223544869|gb|EEF46384.1| conserved hypothetical protein [Ricinus communis]

 Score =  745 bits (1924), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/527 (72%), Positives = 438/527 (83%), Gaps = 12/527 (2%)

Query: 156 RDTGTSDRDKRASKEVSRHDPG----HSKQHRPPVPPPGVKKVNGG-SGRVETEEERRIR 210
           RD G S    R  +E+   + G    H +QHRPP PPPG KKV+G  SGRVETEEERR+R
Sbjct: 149 RDKGMS----RERRELGNSNHGDVSRHEQQHRPPAPPPGGKKVSGPPSGRVETEEERRLR 204

Query: 211 KKREYEKHRQEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGER 270
           KKRE+EKHRQEEKHR Q+KESQN ++QK+QM+++ KG HGS+VGSRMGDRRA PLL GER
Sbjct: 205 KKREFEKHRQEEKHRQQVKESQNSILQKTQMLSAQKG-HGSIVGSRMGDRRAPPLLGGER 263

Query: 271 TENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEP 330
            ENRLKKPTTFLCKLKFRNELP+PSAQPKLM +K+DKDRFT+YT +SLEK YKPQL VEP
Sbjct: 264 IENRLKKPTTFLCKLKFRNELPDPSAQPKLMTMKRDKDRFTKYTITSLEKMYKPQLFVEP 323

Query: 331 DLGIPLDLLDLSVYN--PPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSW 388
           DLGIPLDLLDLSVYN  P S RPPLDPEDEELLRDDE VTPVK++G+K KERPTDKGVSW
Sbjct: 324 DLGIPLDLLDLSVYNRPPASERPPLDPEDEELLRDDEAVTPVKREGLKIKERPTDKGVSW 383

Query: 389 LVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLR 448
           LVKTQYIS LS +S +QS+TEKQAKELRE KGG ++L+NLN+RE QIKEIEASFEACKL 
Sbjct: 384 LVKTQYISSLSTDSTKQSMTEKQAKELRERKGGHNLLKNLNNRESQIKEIEASFEACKLT 443

Query: 449 PIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAI 508
           P+HATNKNL+PVEILPL+PDF+RY+D+FV   FD APTADSEIYSK+D SVR+A ESRA+
Sbjct: 444 PVHATNKNLKPVEILPLIPDFDRYEDKFVTVAFDNAPTADSEIYSKLDSSVREACESRAV 503

Query: 509 MKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPT 568
           MK+ VATGSD ANPEKFLAYM PS NELSKDMYDENED+S++WVREYHWDV+GD  +DPT
Sbjct: 504 MKACVATGSDPANPEKFLAYMAPSPNELSKDMYDENEDISYNWVREYHWDVQGDGGNDPT 563

Query: 569 TYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKE 628
           T+LVSFD+D ARYVPLPTK+NLRKKRA EGRS DEVEHFP PSS+ VRRR    A EL++
Sbjct: 564 TFLVSFDEDAARYVPLPTKINLRKKRAREGRSGDEVEHFPAPSSVTVRRRPTAAARELRD 623

Query: 629 QGAYSNSKGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDM 675
               S+S+GN   S+MG  D  + L R H  +R  D   SS AEDD+
Sbjct: 624 SAGASSSRGNILDSRMGTGDDDDGLGRVHRVARDDDLDHSSEAEDDL 670

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224070975|ref|XP_002303312.1| PAF1 complex component [Populus trichocarpa] gi|222840744|gb|EEE78291.1| PAF1 complex component [Populus trichocarpa]

 Score =  731 bits (1886), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/516 (71%), Positives = 426/516 (82%), Gaps = 5/516 (0%)

Query: 162 DRDKRASKEVSRHD-PGHSK-QHRPPVPPPGVKKVNGGSGRVETEEERRIRKKREYEKHR 219
           +RDK  S+E   HD P H K Q +    P  VKK NG  GRVETEEERR+RKKRE+EK R
Sbjct: 55  ERDKGVSQEKREHDHPNHGKHQQQQSQLPLVVKKANGHPGRVETEEERRLRKKREFEKQR 114

Query: 220 QEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTENRLKKPT 279
           QEE  R Q+KESQN  + K+ +++S KG HGS+VGSR+GDR A PLL GER ENRLKKPT
Sbjct: 115 QEENRRQQLKESQNSALLKNHVISSQKG-HGSIVGSRLGDRVATPLLGGERAENRLKKPT 173

Query: 280 TFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLL 339
           TF+CKLKFRNELP+PSAQPKLM LK++KDRFT+YT +SLEK YKPQL+VEPDLGIPLDLL
Sbjct: 174 TFMCKLKFRNELPDPSAQPKLMPLKREKDRFTKYTITSLEKMYKPQLYVEPDLGIPLDLL 233

Query: 340 DLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLS 399
           DLSVYNPPSVRP L PEDEELL DDE VTPVK+DGIKRKERPTDKGVSWLVKTQYISPLS
Sbjct: 234 DLSVYNPPSVRPLLAPEDEELLHDDESVTPVKRDGIKRKERPTDKGVSWLVKTQYISPLS 293

Query: 400 MESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQP 459
           MESA+ SLTEKQAKELREMKGG  +L+NLN RERQIKEI+ASF + KL P+HATNKNL+P
Sbjct: 294 MESAKLSLTEKQAKELREMKGGCKLLDNLNKRERQIKEIQASFASNKLPPVHATNKNLKP 353

Query: 460 VEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVATGSDS 519
           VEILPLLPDF+RY D+FV   FDGAPTAD+E Y K D S RDA+ES AIMK+ VA+GSD 
Sbjct: 354 VEILPLLPDFDRYGDKFVTVAFDGAPTADAENYRKFDPSDRDAYESWAIMKACVASGSDP 413

Query: 520 ANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEA 579
           ANPEKFLAY VPS +ELSKDMYDENED+ +SW+REYHWDVRGDD DDP+T+LVSFD+ EA
Sbjct: 414 ANPEKFLAYTVPSPDELSKDMYDENEDILYSWIREYHWDVRGDDVDDPSTFLVSFDEAEA 473

Query: 580 RYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYSNSKGNS 639
           RY+PLPTK++LRKKRA EGRS DE+EHFPIPS + VR+RA    IE ++ GA SNS+GN 
Sbjct: 474 RYLPLPTKISLRKKRAREGRSGDEIEHFPIPSRVTVRKRAVAATIEQRDSGAISNSRGN- 532

Query: 640 SSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDM 675
            +S+M R + ++ L R    +  +D + SSGAED+M
Sbjct: 533 -NSRMERFEDEDGLGRLQRVALDEDLHHSSGAEDEM 567

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839959|ref|XP_002887861.1| hypothetical protein ARALYDRAFT_477298 [Arabidopsis lyrata subsp. lyrata] gi|297333702|gb|EFH64120.1| hypothetical protein ARALYDRAFT_477298 [Arabidopsis lyrata subsp. lyrata]

 Score =  671 bits (1732), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 344/520 (66%), Positives = 410/520 (78%), Gaps = 28/520 (5%)

Query: 156 RDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPPGVKKVNGGSGRVETEEERRIRKKREY 215
           R+ G +DRDK AS+   R  P  SK HR  +P          + ++ETEEERR+RKK+E 
Sbjct: 81  RNQGPNDRDKGASRR-ERAKPDPSKHHRSHLP---------HTKKIETEEERRLRKKKEL 130

Query: 216 EKHRQEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTENRL 275
           EK RQEEK R QMK S      KSQM      GH         +++  PLL+ +R ENRL
Sbjct: 131 EKQRQEEKLRQQMKNSH-----KSQM----PKGHTE-------EKKPTPLLTTDRVENRL 174

Query: 276 KKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIP 335
           KKPTTF+CKLKFRNELP+PSAQ KLM +K+DKD+FT+YT +SLEK +KP++ VEPDLGIP
Sbjct: 175 KKPTTFICKLKFRNELPDPSAQLKLMTIKRDKDQFTKYTITSLEKLWKPKIFVEPDLGIP 234

Query: 336 LDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYI 395
           LDLLDLSVYNPP  + PL PEDEELLRDD+ +TP+KKDGI+RKERPTDKGVSWLVKTQYI
Sbjct: 235 LDLLDLSVYNPPKFKAPLAPEDEELLRDDDAITPIKKDGIRRKERPTDKGVSWLVKTQYI 294

Query: 396 SPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNK 455
           S ++ ESARQSLTEKQAKELREMKGG +IL NLN+RERQIK+IEASFEACK RP+HATNK
Sbjct: 295 SSINNESARQSLTEKQAKELREMKGGINILHNLNNRERQIKDIEASFEACKSRPVHATNK 354

Query: 456 NLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVAT 515
           +LQPVE+LPLLP F+RYD+QFV A FD APTADSE + K+D S+RD HESRAI+KSYV  
Sbjct: 355 SLQPVEVLPLLPYFDRYDEQFVVANFDSAPTADSEFFGKLDPSIRDEHESRAILKSYVVA 414

Query: 516 GSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFD 575
           GSD+ANPEKFLAYMVPS++ELSKDM+DE+ED+S++WVREYHWDVRGDDA+D  TYLVSFD
Sbjct: 415 GSDTANPEKFLAYMVPSLDELSKDMHDEDEDISYTWVREYHWDVRGDDANDIGTYLVSFD 474

Query: 576 DDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYSNS 635
           D  A Y+PLPTKLNLRKKR  EGRS+DE+EHFP+PS + VRRR+ V+ IE K+ G YS+ 
Sbjct: 475 DGAASYLPLPTKLNLRKKRPREGRSSDEIEHFPVPSRVTVRRRSTVSVIEHKDSGVYSSR 534

Query: 636 KGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQ-SSGAEDD 674
            G +SSSKM R++ +E L RS     +QD  Q S G EDD
Sbjct: 535 VG-ASSSKMRRLEDEEGLGRSWKHEPEQDANQYSDGNEDD 573

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224054406|ref|XP_002298244.1| PAF1 complex component [Populus trichocarpa] gi|222845502|gb|EEE83049.1| PAF1 complex component [Populus trichocarpa]

 Score =  667 bits (1721), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/520 (64%), Positives = 403/520 (77%), Gaps = 47/520 (9%)

Query: 184 PPVPPPGVKKVNGGSGRVETEEERRIRKKREYEKHRQEEKHRLQMKESQNVVMQKSQMVA 243
           P +PP G KK NG SGR ET++ERR+RKKRE++K RQEEKHR  +KESQN  + K+QM++
Sbjct: 189 PQLPPVG-KKANGHSGRAETDQERRLRKKREFDKQRQEEKHRQLLKESQNPALPKNQMMS 247

Query: 244 SGKGGHGSMVGSRMGDRRAAPLLSGERTENRLKKPTTFLCKLKF---------------- 287
           S KG HGS+ GSR+GDRRA PLL  ERTENRLKKPTTFLCKLKF                
Sbjct: 248 SQKG-HGSIAGSRLGDRRATPLLGAERTENRLKKPTTFLCKLKFSVMHVVISCACCMSKI 306

Query: 288 ------------RNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIP 335
                       RNELP+PSAQPKLM LK+DKDR+T+YT +SLEK YKPQL+VEPDLGIP
Sbjct: 307 FMYCMDVPVCRFRNELPDPSAQPKLMPLKRDKDRYTKYTITSLEKMYKPQLYVEPDLGIP 366

Query: 336 LDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYI 395
           LDLLDLSVYNPPS+RPPL PEDEELLRDDE V PVK+DGI+RKERPTDKGVSWL      
Sbjct: 367 LDLLDLSVYNPPSIRPPLAPEDEELLRDDETVAPVKRDGIRRKERPTDKGVSWL------ 420

Query: 396 SPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNK 455
                     SL + QAKELREMKGGR++L+NLN+RERQIKEI+ASFEA KL P+HATNK
Sbjct: 421 ----------SLNKNQAKELREMKGGRNLLDNLNNRERQIKEIQASFEANKLPPVHATNK 470

Query: 456 NLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVAT 515
           NL P+E+LPLLPDF+RY+D+FV ATFDGAPT D+E Y+K D S R+A+ESRAIMK+ VAT
Sbjct: 471 NLHPIEVLPLLPDFDRYEDKFVTATFDGAPTVDAENYNKFDSSDREAYESRAIMKACVAT 530

Query: 516 GSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFD 575
           GSD  NPEKFLAYMVPS +E+SKDM+DE+ED+S+SW+R YHWD+RGDDA+DPTT+LVSFD
Sbjct: 531 GSDPTNPEKFLAYMVPSPDEMSKDMHDESEDISYSWIRGYHWDIRGDDANDPTTFLVSFD 590

Query: 576 DDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYSNS 635
           + EARY+PLPTK+NL K+RA EGRS DE+EHF +PS + VR+RA    IE +  GA S+S
Sbjct: 591 EAEARYLPLPTKINLTKRRAREGRSGDEIEHFSVPSRVTVRKRAIAATIEQRNLGAASSS 650

Query: 636 KGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDM 675
           +GN S    GR +  + L R    ++ +D  QSS AED+M
Sbjct: 651 RGNDSRMG-GRFEDDDGLGRLQRVAQDEDLEQSSEAEDEM 689

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743192|emb|CBI36059.3| unnamed protein product [Vitis vinifera]

 Score =  652 bits (1681), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/421 (76%), Positives = 368/421 (87%), Gaps = 1/421 (0%)

Query: 257 MGDRRAAPLLSGERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFS 316
           MG+RR  P LSG+R ENRL+KPTTFLCKLKFRNELP+P+AQPKLMALK DKDRFT+YT +
Sbjct: 1   MGERRTTPFLSGDRIENRLRKPTTFLCKLKFRNELPDPTAQPKLMALKTDKDRFTKYTIT 60

Query: 317 SLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIK 376
           SLEK +KPQL VEPDLGIPLDLLDLSVYNPPSVR PLDPEDEELLRDDE VTPVKK+GIK
Sbjct: 61  SLEKMHKPQLFVEPDLGIPLDLLDLSVYNPPSVRRPLDPEDEELLRDDESVTPVKKEGIK 120

Query: 377 RKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIK 436
           +KERPTDKGVSWLVKTQYISPLS ES +QSLTEKQAKELRE KGGR+ILEN N RER+I+
Sbjct: 121 KKERPTDKGVSWLVKTQYISPLSTESTKQSLTEKQAKELRETKGGRNILENFNSRERKIQ 180

Query: 437 EIEASFEACKLRPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMD 496
            IEA+F A K+ P+H+TNK+L+PVEILPLLPDF RYDD FV A+FD APTADSEIYSK+D
Sbjct: 181 NIEAAFAASKITPVHSTNKSLKPVEILPLLPDFARYDDSFVVASFDSAPTADSEIYSKLD 240

Query: 497 KSVRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYH 556
           K+VRD+HES+AI+KSY+ATGSD + PEKFLAYM PS +ELSKD+YDENED S+SWVREYH
Sbjct: 241 KTVRDSHESQAILKSYMATGSDPSKPEKFLAYMAPSPDELSKDIYDENEDTSYSWVREYH 300

Query: 557 WDVRGDDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVR 616
           WDVRGDDADDPTTYLVSF+  +ARY+PLPTKL LRKKRA EGRS+DEVEHFP+PS + VR
Sbjct: 301 WDVRGDDADDPTTYLVSFNKTDARYLPLPTKLLLRKKRAKEGRSSDEVEHFPVPSKVTVR 360

Query: 617 RRANVTAIELKEQGAYSNSKGNSSSSKMGRVDSQEDLERSHNGSRQQDPYQSSGAEDDMY 676
           +R NV AIELK++  YS+SK   SSSK G VD ++ L RS+ G + Q   QSSGAED+M 
Sbjct: 361 QRPNVAAIELKDEEVYSSSKRGVSSSKRG-VDMEDGLGRSYKGVQDQHMDQSSGAEDEMS 419

Query: 677 D 677
           D
Sbjct: 420 D 420

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	677
TAIR|locus:2017879	589	ELF7 "AT1G79730" [Arabidopsis	0.645	0.741	0.609	1.3e-145
FB|FBgn0010750	538	atms "antimeros" [Drosophila m	0.478	0.602	0.258	2e-21
ZFIN|ZDB-GENE-050506-101	503	paf1 "paf1, RNA polymerase II	0.534	0.719	0.236	2.2e-16
UNIPROTKB|G1K1Z2	355	PAF1 "RNA polymerase II-associ	0.434	0.828	0.260	6.1e-16
MGI|MGI:1923988	535	Paf1 "Paf1, RNA polymerase II	0.543	0.687	0.243	7.3e-16
RGD|1306219	535	Paf1 "Paf1, RNA polymerase II	0.543	0.687	0.243	9.4e-16
UNIPROTKB|Q8N7H5	531	PAF1 "RNA polymerase II-associ	0.543	0.693	0.240	2e-15
UNIPROTKB|Q2KJ14	532	PAF1 "RNA polymerase II-associ	0.543	0.691	0.240	3.4e-15
UNIPROTKB|F1SEH0	532	PAF1 "Uncharacterized protein"	0.543	0.691	0.240	3.4e-15
UNIPROTKB|Q5RAX0	533	PAF1 "RNA polymerase II-associ	0.543	0.690	0.240	3.5e-15

TAIR|locus:2017879 ELF7 "AT1G79730" [Arabidopsis thaliana (taxid:3702)]

 Score = 1384 (492.3 bits), Expect = 1.3e-145, Sum P(2) = 1.3e-145
 Identities = 278/456 (60%), Positives = 336/456 (73%)

Query:   220 QEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTENRLKKPT 279
             Q+EKHR QMK S      KSQM      GH         +++  PLL+ +R ENRLKKPT
Sbjct:   149 QDEKHRQQMKNSH-----KSQMPK----GHTE-------EKKPTPLLTTDRVENRLKKPT 192

Query:   280 TFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXX 339
             TF+CKLKFRNELP+PSAQ KLM +K+DKD+FT+YT +SLEK +KP++ VE          
Sbjct:   193 TFICKLKFRNELPDPSAQLKLMTIKRDKDQFTKYTITSLEKLWKPKIFVEPDLGIPLDLL 252

Query:   340 XXSVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLS 399
               SVYNPP                    TP+KKDGI+RKERPTDKG+SWLVKTQYIS ++
Sbjct:   253 DLSVYNPPKVKAPLAPEDEELLRDDDAVTPIKKDGIRRKERPTDKGMSWLVKTQYISSIN 312

Query:   400 MESARQSLTEKQAKELREMKGGRSILENLNDRERQIKEIEASFEACKLRPIHATNKNLQP 459
              ESARQSLTEKQAKELREMKGG +IL NLN+RERQIK+IEASFEACK RP+HATNKNLQP
Sbjct:   313 NESARQSLTEKQAKELREMKGGINILHNLNNRERQIKDIEASFEACKSRPVHATNKNLQP 372

Query:   460 VEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVATGSDS 519
             VE+LPLLP F+RYD+QFV A FDGAP ADSE + K+D S+RDAHESRAI+KSYV  GSD+
Sbjct:   373 VEVLPLLPYFDRYDEQFVVANFDGAPIADSEFFGKLDPSIRDAHESRAILKSYVVAGSDT 432

Query:   520 ANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVREYHWDVRGDDADDPTTYLVSFDDDEA 579
             ANPEKFLAYMVPS++ELSKD++DENE++S++WVREY WDV+  +A+DP TYLVSFD+  A
Sbjct:   433 ANPEKFLAYMVPSLDELSKDIHDENEEISYTWVREYLWDVQ-PNANDPGTYLVSFDNGTA 491

Query:   580 RYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAIELKEQGAYXXXXXXX 639
              Y+PLP +LNLRKKRA EGRS+DE+EHFP+PS + VRRR+ V+ IE K+ G Y       
Sbjct:   492 SYLPLPMRLNLRKKRAREGRSSDEIEHFPVPSRVTVRRRSTVSVIEHKDSGVYSSRVGAS 551

Query:   640 XXXXMGRVDSQEDLERSHNGSRQQDPYQ-SSGAEDD 674
                 M R++ +  L RS     +QD  Q S G EDD
Sbjct:   552 SSK-MRRLEDEGGLGRSWKHEPEQDANQYSDGNEDD 586

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

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

GO:0016571 "histone methylation" evidence=RCA;IMP

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

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

FB|FBgn0010750 atms "antimeros" [Drosophila melanogaster (taxid:7227)]

 Score = 276 (102.2 bits), Expect = 2.0e-21, P = 2.0e-21
 Identities = 93/360 (25%), Positives = 161/360 (44%)

Query:   269 ERTENRLKKPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHV 328
             +R + + ++ +  +C++K+ N LP+     K +    D  RF +Y  +SLE+N+K  +  
Sbjct:    16 KRPQRQTERKSEIICRVKYGNNLPDIPFDLKFLQYPFDSHRFVQYNPTSLERNFKYDVLT 75

Query:   329 EXXXXXXXXXXXXSVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSW 388
             E             +Y   S                   TP   D ++ ++    + VSW
Sbjct:    76 EHDLGVTVDLINRELYQADSMTLLDPADEKLLEEETL--TPT--DSVRSRQH--SRTVSW 129

Query:   389 LVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLN--DRERQIKEIEASFEACK 446
             L K++YIS        Q+L   +AK    +K  +S+ E     DRE QIK IE +F   K
Sbjct:   130 LRKSEYISTEQTRFQPQNLENIEAKVGYNVK--KSLREETLYLDREAQIKAIEKTFSDTK 187

Query:   447 LRPI-HATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPT-ADSEIYSKMDKSVRDAHE 504
                  H +  N+ PVE+LP+ PDF  +        FD  P  A   + +++++       
Sbjct:   188 SEITKHYSKPNVVPVEVLPIFPDFTNWKFPCAQVIFDSDPAPAGKNVPAQLEEM------ 241

Query:   505 SRAIMKSYVATGSDSANPEKFLAYMVPSVNELSK--------DMYDENEDVSFSWVREYH 556
             S+A+++  +    D +  E+F+AY +P+   L K        ++Y E E+  +   REY+
Sbjct:   242 SQAMIRGVM----DESG-EQFVAYFLPTEQTLEKRRTDFINGELYKEEEEYEYKIAREYN 296

Query:   557 WDVRGDDADD-PTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGR--SNDE--VEHFPIPS 611
             W+V+   +      Y      D   Y  L T++ L K+R   G+  +N +  V+H P+ S
Sbjct:   297 WNVKTKASKGYEENYFFVMRQDGIYYNELETRVRLNKRRVKVGQQPNNTKLVVKHRPLDS 356

GO:0019894 "kinesin binding" evidence=IDA

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

GO:0035327 "transcriptionally active chromatin" evidence=IDA

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

GO:0022008 "neurogenesis" evidence=IMP

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

 Score = 231 (86.4 bits), Expect = 2.2e-16, P = 2.2e-16
 Identities = 97/411 (23%), Positives = 174/411 (42%)

Query:   282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXXXX 341
             +C++K+ N LP+    PK +    D+ RF +Y  +SLEK +K +L  E            
Sbjct:    30 VCRVKYGNSLPDIPFDPKFITYPFDQHRFVQYKATSLEKQHKHELLTEPDLGVTI----- 84

Query:   342 SVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSME 401
              + NP +                           KR ++   K V W+ KT+YIS    E
Sbjct:    85 DLINPDTYRIDPNILLDPADEKLLEEEIQAPSSSKRSQQHA-KVVPWMRKTEYIST---E 140

Query:   402 SARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHATN 454
               R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H + 
Sbjct:   141 FNRYGVSNEKV----EVKIGVSVKQQFTEEEIYKDRDSQIAAIEKTFEDAQKSISQHYSK 196

Query:   455 KNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVA 514
               + PVE+LP+ PDF+ + +      FD  P A  ++ +     +     S+A+++  + 
Sbjct:   197 PRVTPVEVLPVFPDFKMWINPCAQVIFDSDP-APKDVSAPAGVDMM----SQAMIRGMM- 250

Query:   515 TGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSF--------SWVREYHWDVRGDDADD 566
                +  N  +F+AY +P+ + + K   D  E++ +           REY+W+V+   +  
Sbjct:   251 --DEEGN--QFVAYFLPNEDTMRKRKRDVEEELDYMPEEVYEYKIAREYNWNVKNKASKG 306

Query:   567 -PTTYLVSFDD-DEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRANVTAI 624
                 Y   F D D   Y  L T++ L K+RA  G  +         +++ V +  ++   
Sbjct:   307 YEENYFFIFRDADGVYYNELETRVRLSKRRAKVGAQSST-------NAVLVCKHRDMNEK 359

Query:   625 ELKEQGAYXXXXXXXX-XXXMGRVDSQEDLERSHNGSRQQDPYQSSGAEDD 674
             EL+ Q A                +D ++D++   +G  ++ P  S  +E +
Sbjct:   360 ELEAQEARKAQLENHEPEDEEEELDLEKDMQED-SGEEREKPSDSENSESE 409

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

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

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

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

GO:0005634 "nucleus" evidence=IEA;IDA

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

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

GO:0007507 "heart development" evidence=IMP

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

UNIPROTKB|G1K1Z2 PAF1 "RNA polymerase II-associated factor 1 homolog" [Bos taurus (taxid:9913)]

 Score = 222 (83.2 bits), Expect = 6.1e-16, P = 6.1e-16
 Identities = 87/334 (26%), Positives = 140/334 (41%)

Query:   282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXXXX 341
             +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  E            
Sbjct:    30 VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTI----- 84

Query:   342 SVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSME 401
              + NP +                           KR ++   K V W+ KT+YIS    E
Sbjct:    85 DLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKRSQQHA-KVVPWMRKTEYIST---E 140

Query:   402 SARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHATN 454
               R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H + 
Sbjct:   141 FNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYSK 196

Query:   455 KNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVA 514
               + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   + 
Sbjct:   197 PRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAMI 246

Query:   515 TGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDADD 566
              G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   +  
Sbjct:   247 RGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASKG 306

Query:   567 -PTTYLVSF-DDDEARYVPLPTKLNLRKKRAIEG 598
                 Y   F + D   Y  L T++ L K+RA  G
Sbjct:   307 YEENYFFIFREGDGVYYNELETRVRLSKRRAKAG 340

GO:0071222 "cellular response to lipopolysaccharide" 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:0031442 "positive regulation of mRNA 3'-end processing" 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:0005739 "mitochondrion" evidence=IEA

GO:0003682 "chromatin binding" 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

MGI|MGI:1923988 Paf1 "Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 227 (85.0 bits), Expect = 7.3e-16, P = 7.3e-16
 Identities = 101/415 (24%), Positives = 166/415 (40%)

Query:   282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXXXX 341
             +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  E            
Sbjct:    30 VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTI----- 84

Query:   342 SVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSME 401
              + NP +                           KR ++   K V W+ KT+YIS    E
Sbjct:    85 DLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKRSQQHA-KVVPWMRKTEYIST---E 140

Query:   402 SARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHATN 454
               R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H + 
Sbjct:   141 FNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYSK 196

Query:   455 KNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVA 514
               + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   + 
Sbjct:   197 PRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAMI 246

Query:   515 TGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDADD 566
              G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   +  
Sbjct:   247 RGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASKG 306

Query:   567 -PTTYLVSF-DDDEARYVPLPTKLNLRKKRAIEG-RSNDE----VEHFPIPSSIAVRRRA 619
                 Y   F + D   Y  L T++ L K+RA  G +S       V+H  +       + A
Sbjct:   307 YEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEA 366

Query:   620 NVTAIELKEQGAYXXXXXXXXXXXMGRVDSQEDLERSHNGSRQQDPYQSSGAEDD 674
                 +E  E                G   S E+ E+  +  ++    + SG+E D
Sbjct:   367 RKAQLENHEPEEEEEEEMEAEEKEAG--GSDEEQEKGSSSEKEGSEDEHSGSESD 419

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

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

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

GO:0003682 "chromatin binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0006378 "mRNA polyadenylation" 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:0031442 "positive regulation of mRNA 3'-end processing" 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:0071222 "cellular response to lipopolysaccharide" evidence=IDA

RGD|1306219 Paf1 "Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 226 (84.6 bits), Expect = 9.4e-16, P = 9.4e-16
 Identities = 101/415 (24%), Positives = 166/415 (40%)

Query:   282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXXXX 341
             +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  E            
Sbjct:    30 VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTI----- 84

Query:   342 SVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSME 401
              + NP +                           KR ++   K V W+ KT+YIS    E
Sbjct:    85 DLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKRSQQHA-KVVPWMRKTEYIST---E 140

Query:   402 SARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHATN 454
               R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H + 
Sbjct:   141 FNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYSK 196

Query:   455 KNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVA 514
               + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   + 
Sbjct:   197 PRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAMI 246

Query:   515 TGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDADD 566
              G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   +  
Sbjct:   247 RGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASKG 306

Query:   567 -PTTYLVSF-DDDEARYVPLPTKLNLRKKRAIEG-RSNDE----VEHFPIPSSIAVRRRA 619
                 Y   F + D   Y  L T++ L K+RA  G +S       V+H  +       + A
Sbjct:   307 YEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEA 366

Query:   620 NVTAIELKEQGAYXXXXXXXXXXXMGRVDSQEDLERSHNGSRQQDPYQSSGAEDD 674
                 +E  E                G   S E+ E+  +  ++    + SG+E D
Sbjct:   367 RKAQLENHEPEEEEEEEMEAEEKEAG--GSDEEHEKGSSSEKEGSEDERSGSESD 419

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

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

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

GO:0003682 "chromatin binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

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

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

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

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

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

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

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

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

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

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

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

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

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

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q8N7H5 PAF1 "RNA polymerase II-associated factor 1 homolog" [Homo sapiens (taxid:9606)]

 Score = 223 (83.6 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 100/415 (24%), Positives = 166/415 (40%)

Query:   282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXXXX 341
             +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  E            
Sbjct:    30 VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTI----- 84

Query:   342 SVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSME 401
              + NP +                           KR ++   K V W+ KT+YIS    E
Sbjct:    85 DLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKRSQQHA-KVVPWMRKTEYIST---E 140

Query:   402 SARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHATN 454
               R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H + 
Sbjct:   141 FNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYSK 196

Query:   455 KNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVA 514
               + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   + 
Sbjct:   197 PRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAMI 246

Query:   515 TGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDADD 566
              G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   +  
Sbjct:   247 RGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASKG 306

Query:   567 -PTTYLVSF-DDDEARYVPLPTKLNLRKKRAIEG-RSNDE----VEHFPIPSSIAVRRRA 619
                 Y   F + D   Y  L T++ L K+RA  G +S       V+H  +       + A
Sbjct:   307 YEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEA 366

Query:   620 NVTAIELKEQGAYXXXXXXXXXXXMGRVDSQEDLERSHNGSRQQDPYQSSGAEDD 674
                 +E  E                G   S E+ E+  +  ++    + SG+E +
Sbjct:   367 RKAQLENHEPEEEEEEEMETEEKEAG--GSDEEQEKGSSSEKEGSEDEHSGSESE 419

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

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0010390 "histone monoubiquitination" evidence=IDA

GO:0033523 "histone H2B ubiquitination" evidence=IDA

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

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

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

GO:0006378 "mRNA polyadenylation" evidence=IMP

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB|Q2KJ14 PAF1 "RNA polymerase II-associated factor 1 homolog" [Bos taurus (taxid:9913)]

 Score = 223 (83.6 bits), Expect = 3.4e-15, Sum P(2) = 3.4e-15
 Identities = 100/415 (24%), Positives = 166/415 (40%)

Query:   282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXXXX 341
             +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  E            
Sbjct:    30 VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTI----- 84

Query:   342 SVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSME 401
              + NP +                           KR ++   K V W+ KT+YIS    E
Sbjct:    85 DLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKRSQQHA-KVVPWMRKTEYIST---E 140

Query:   402 SARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHATN 454
               R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H + 
Sbjct:   141 FNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYSK 196

Query:   455 KNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVA 514
               + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   + 
Sbjct:   197 PRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAMI 246

Query:   515 TGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDADD 566
              G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   +  
Sbjct:   247 RGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASKG 306

Query:   567 -PTTYLVSF-DDDEARYVPLPTKLNLRKKRAIEG-RSNDE----VEHFPIPSSIAVRRRA 619
                 Y   F + D   Y  L T++ L K+RA  G +S       V+H  +       + A
Sbjct:   307 YEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEA 366

Query:   620 NVTAIELKEQGAYXXXXXXXXXXXMGRVDSQEDLERSHNGSRQQDPYQSSGAEDD 674
                 +E  E                G  D  E+ E+  +  ++    + SG+E +
Sbjct:   367 RKAQLENHEPEEEEEEEMETEEKEAGASD--EEREKGSSSEKEGSEDERSGSESE 419

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

GO:0006378 "mRNA polyadenylation" evidence=ISS

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

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

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

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

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

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

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

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

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

GO:0033523 "histone H2B ubiquitination" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0010390 "histone monoubiquitination" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

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

UNIPROTKB|F1SEH0 PAF1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 223 (83.6 bits), Expect = 3.4e-15, Sum P(2) = 3.4e-15
 Identities = 100/415 (24%), Positives = 166/415 (40%)

Query:   282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXXXX 341
             +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  E            
Sbjct:    30 VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTI----- 84

Query:   342 SVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSME 401
              + NP +                           KR ++   K V W+ KT+YIS    E
Sbjct:    85 DLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKRSQQHA-KVVPWMRKTEYIST---E 140

Query:   402 SARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHATN 454
               R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H + 
Sbjct:   141 FNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYSK 196

Query:   455 KNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVA 514
               + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   + 
Sbjct:   197 PRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAMI 246

Query:   515 TGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDADD 566
              G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   +  
Sbjct:   247 RGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASKG 306

Query:   567 -PTTYLVSF-DDDEARYVPLPTKLNLRKKRAIEG-RSNDE----VEHFPIPSSIAVRRRA 619
                 Y   F + D   Y  L T++ L K+RA  G +S       V+H  +       + A
Sbjct:   307 YEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEA 366

Query:   620 NVTAIELKEQGAYXXXXXXXXXXXMGRVDSQEDLERSHNGSRQQDPYQSSGAEDD 674
                 +E  E                G   S E+ E+  +  ++    + SG+E +
Sbjct:   367 RKAQLENHEPEEEEEEEMETEEKEAG--GSDEEREKGSSSEKEGSEDERSGSESE 419

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

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

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

UNIPROTKB|Q5RAX0 PAF1 "RNA polymerase II-associated factor 1 homolog" [Pongo abelii (taxid:9601)]

 Score = 223 (83.6 bits), Expect = 3.5e-15, Sum P(2) = 3.5e-15
 Identities = 100/415 (24%), Positives = 166/415 (40%)

Query:   282 LCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEXXXXXXXXXXXX 341
             +C++K+ N LP+    PK +    D++RF +Y  +SLEK +K  L  E            
Sbjct:    30 VCRVKYCNSLPDIPFDPKFITYPFDQNRFVQYKATSLEKQHKHDLLTEPDLGVTI----- 84

Query:   342 SVYNPPSXXXXXXXXXXXXXXXXXXXTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSME 401
              + NP +                           KR ++   K V W+ KT+YIS    E
Sbjct:    85 DLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKRSQQHA-KVVPWMRKTEYIST---E 140

Query:   402 SARQSLTEKQAKELREMKGGRSILENLN------DRERQIKEIEASFE-ACKLRPIHATN 454
               R  ++ ++     E+K G S+ +         DR+ QI  IE +FE A K    H + 
Sbjct:   141 FNRYGISNEKP----EVKIGVSVKQQFTEEEIYKDRDSQITAIEKTFEDAQKSISQHYSK 196

Query:   455 KNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVA 514
               + PVE++P+ PDF+ + +      FD  P       +  D S   A E   +M   + 
Sbjct:   197 PRVTPVEVMPVFPDFKMWINPCAQVIFDSDP-------APKDTSGAAALE---MMSQAMI 246

Query:   515 TGSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFS--------WVREYHWDVRGDDADD 566
              G       +F+AY +P    L K   D+ E++ ++          REY+W+V+   +  
Sbjct:   247 RGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVKNKASKG 306

Query:   567 -PTTYLVSF-DDDEARYVPLPTKLNLRKKRAIEG-RSNDE----VEHFPIPSSIAVRRRA 619
                 Y   F + D   Y  L T++ L K+RA  G +S       V+H  +       + A
Sbjct:   307 YEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEA 366

Query:   620 NVTAIELKEQGAYXXXXXXXXXXXMGRVDSQEDLERSHNGSRQQDPYQSSGAEDD 674
                 +E  E                G   S E+ E+  +  ++    + SG+E +
Sbjct:   367 RKAQLENHEPEEEEEEEMETEEKEAG--GSDEEQEKGSSSEKEGSEDERSGSESE 419

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

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

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

GO:0006378 "mRNA polyadenylation" evidence=ISS

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

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

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

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

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

---

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

Fail to connect to STRING server

---

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	677
pfam03985	431	pfam03985, Paf1, Paf1	4e-78
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	4e-15
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-11
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-11
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-11
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-11
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	7e-11
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-10
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	7e-10
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	9e-10
pfam04652	315	pfam04652, DUF605, Vta1 like	2e-09
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	4e-09
pfam04652	315	pfam04652, DUF605, Vta1 like	5e-09
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	8e-09
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	8e-09
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-08
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	1e-08
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	2e-08
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	7e-08
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-07
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	1e-07
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	1e-07
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	1e-07
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	2e-07
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	2e-07
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-07
pfam03276	582	pfam03276, Gag_spuma, Spumavirus gag protein	2e-07
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-07
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	3e-07
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	4e-07
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	4e-07
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	6e-07
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-06
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-06
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-06
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	2e-06
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	2e-06
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	2e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-06
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	3e-06
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	4e-06
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	4e-06
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	5e-06
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	7e-06
pfam06682	317	pfam06682, DUF1183, Protein of unknown function (D	7e-06
pfam04652	315	pfam04652, DUF605, Vta1 like	8e-06
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	8e-06
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	9e-06
pfam03276	582	pfam03276, Gag_spuma, Spumavirus gag protein	9e-06
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	9e-06
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	1e-05
COG5178	2365	COG5178, PRP8, U5 snRNP spliceosome subunit [RNA p	1e-05
pfam04487	206	pfam04487, CITED, CITED	1e-05
pfam05518	753	pfam05518, Totivirus_coat, Totivirus coat protein	1e-05
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	2e-05
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	2e-05
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-05
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	2e-05
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	2e-05
pfam12526	115	pfam12526, DUF3729, Protein of unknown function (D	2e-05
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	2e-05
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	2e-05
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	2e-05
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-05
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	3e-05
pfam14179	110	pfam14179, YppG, YppG-like protein	3e-05
pfam03276	582	pfam03276, Gag_spuma, Spumavirus gag protein	4e-05
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	5e-05
pfam05518	753	pfam05518, Totivirus_coat, Totivirus coat protein	5e-05
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	5e-05
PHA03378	991	PHA03378, PHA03378, EBNA-3B; Provisional	6e-05
pfam05044	908	pfam05044, Prox1, Homeobox prospero-like protein (	6e-05
pfam10349	111	pfam10349, WWbp, WW-domain ligand protein	6e-05
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	7e-05
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	8e-05
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	8e-05
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	8e-05
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	8e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	9e-05
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	9e-05
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	1e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	1e-04
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	1e-04
COG5178	2365	COG5178, PRP8, U5 snRNP spliceosome subunit [RNA p	1e-04
COG5178	2365	COG5178, PRP8, U5 snRNP spliceosome subunit [RNA p	1e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	1e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	1e-04
pfam12273	124	pfam12273, RCR, Chitin synthesis regulation, resis	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-04
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	2e-04
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	2e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	2e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	2e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	2e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	2e-04
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	2e-04
PLN02983	274	PLN02983, PLN02983, biotin carboxyl carrier protei	2e-04
pfam11029	136	pfam11029, DAZAP2, DAZ associated protein 2 (DAZAP	2e-04
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	2e-04
PRK14954	620	PRK14954, PRK14954, DNA polymerase III subunits ga	2e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	4e-04
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	4e-04
PHA03369	663	PHA03369, PHA03369, capsid maturational protease;	4e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	5e-04
pfam07415	489	pfam07415, Herpes_LMP2, Gammaherpesvirus latent me	5e-04
pfam02993	238	pfam02993, MCPVI, Minor capsid protein VI	5e-04
pfam06003	264	pfam06003, SMN, Survival motor neuron protein (SMN	5e-04
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	6e-04
pfam12273	124	pfam12273, RCR, Chitin synthesis regulation, resis	7e-04
pfam04652	315	pfam04652, DUF605, Vta1 like	8e-04
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	9e-04
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	0.001
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	0.001
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.001
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	0.001
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
pfam07415	489	pfam07415, Herpes_LMP2, Gammaherpesvirus latent me	0.001
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	0.001
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.002
pfam06682	317	pfam06682, DUF1183, Protein of unknown function (D	0.002
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.002
PLN02983	274	PLN02983, PLN02983, biotin carboxyl carrier protei	0.002
pfam11029	136	pfam11029, DAZAP2, DAZ associated protein 2 (DAZAP	0.002
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	0.002
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	0.002
TIGR02031	589	TIGR02031, BchD-ChlD, magnesium chelatase ATPase s	0.002
TIGR03354	396	TIGR03354, VI_FHA, type VI secretion system FHA do	0.002
pfam03276	582	pfam03276, Gag_spuma, Spumavirus gag protein	0.003
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	0.003
TIGR02031	589	TIGR02031, BchD-ChlD, magnesium chelatase ATPase s	0.003
PRK00404	141	PRK00404, tatB, sec-independent translocase; Provi	0.003
PRK11633	226	PRK11633, PRK11633, cell division protein DedD; Pr	0.003
pfam03251	458	pfam03251, Tymo_45kd_70kd, Tymovirus 45/70Kd prote	0.003
PRK09111	598	PRK09111, PRK09111, DNA polymerase III subunits ga	0.003
PRK01741	332	PRK01741, PRK01741, cell division protein ZipA; Pr	0.003
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	0.003
pfam12868	135	pfam12868, DUF3824, Domain of unknwon function (DU	0.003
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	0.004
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	0.004
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.004
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	0.004
PHA03294	835	PHA03294, PHA03294, envelope glycoprotein H; Provi	0.004
PTZ00449	943	PTZ00449, PTZ00449, 104 kDa microneme/rhoptry anti	0.004

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score =  255 bits (653), Expect = 4e-78
 Identities = 122/430 (28%), Positives = 189/430 (43%), Gaps = 62/430 (14%)

Query: 279 TTFLCKLKFRNELPEPSAQPKLMALK-KDKDRFTRYTFSSLEKNYKPQ--LHVEPDLGIP 335
             ++ K+K+ N LP+P   PKL+     D++RF+    +SL +  K    + ++ DLG+P
Sbjct: 1   QDYIAKVKYTNNLPDPPFPPKLITYPFPDENRFSPQLITSLYRKTKVTVLIQLDHDLGMP 60

Query: 336 LDLL--------DLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVS 387
           LDLL        D  VY    V   LDPED  LLRD          G  ++ +   K VS
Sbjct: 61  LDLLKIPGLLQGDTKVYYGDDVNVKLDPEDRILLRDP---------GADKRTKTDSKKVS 111

Query: 388 WLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENL------NDRERQIKEIEAS 441
           +L +T+YIS    ESAR +    QA EL E K GR++ +NL       DRE QI+ IE +
Sbjct: 112 FLRRTEYIST---ESARFA---VQALELTESKVGRNVKQNLREEDEYLDREAQIEAIEKT 165

Query: 442 FEACKLR-PIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVR 500
           FE  K     H + KN++ VE+ PLLPD    D QF    FDG                +
Sbjct: 166 FEDVKKEILKHPSKKNVKAVEVWPLLPDTASMDQQFFQVRFDGDA----------APDGK 215

Query: 501 DAHESRAIMKSYVATGSDSANPEKFLAYMVPS----------VNELSKDM--YDENEDVS 548
           + H       S    G      E+F++Y +P           + + S D+  YDE+E+  
Sbjct: 216 EKHAQLTQASSTAIFGPVELEEEEFVSYYLPDEKDSEILEDTLEKRSDDLHDYDEDEEYK 275

Query: 549 FSWVREYHWDVRG--DDADDPTTYLVSFDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEH 606
           F  VREY   V+      ++   + VS ++    Y PL +++ LR++R         +  
Sbjct: 276 FKRVREYDMKVKSKATKLNELALFFVSDENGVVYYKPLRSRVELRRRR--VNDVIRPLVR 333

Query: 607 FPIPSSIAVRRRANVTAIELKEQGAYSNSKGNSSSSKMGRVDSQEDLERS--HNGSRQQD 664
                 + V+ R N +  E K +             ++   + +E+ +RS  H     +D
Sbjct: 334 EHNNDQLNVKLR-NPSTKESKMRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGED 392

Query: 665 PYQSSGAEDD 674
             +      +
Sbjct: 393 SEEEGSQSRE 402

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

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 78.7 bits (194), Expect = 4e-15
 Identities = 47/184 (25%), Positives = 61/184 (33%), Gaps = 17/184 (9%)

Query: 7   FPQPPQSSFPPPPPPNQNPSQ-PPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
             Q  Q+   P PP    P   PP      QQ     P      GY        Q + + 
Sbjct: 163 LQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQP-----PGY----PQPPQGHPEQ 213

Query: 66  YSYAQPPPPPPPE-SSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
               Q  P P    +  P PP  P  PPP QQ   P     S Q       PP Q   PP
Sbjct: 214 VQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPG---LSQQMPPPPPQPPQQQQQPP 270

Query: 125 PPPSSPPPSSSIPPPPPP---GSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQ 181
            P + PPP +   P P      + P PPP+  +        + ++   +        S+Q
Sbjct: 271 QPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQLSQQ 330

Query: 182 HRPP 185
            R  
Sbjct: 331 QREA 334

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 68.0 bits (166), Expect = 1e-11
 Identities = 48/211 (22%), Positives = 62/211 (29%), Gaps = 48/211 (22%)

Query: 8    PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
             +PP      P       S   PP Q ++  Q   P                     P  
Sbjct: 2879 ARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAP-------------------PPPQP 2919

Query: 68   YAQPPPPPPPESSYPPPPPPPPPPPPTQQ-----QTQPSMYYSSNQYNQNSMYPPMQPPL 122
              QPPPPP P+   PPPP P PP  PT       +   ++                +  +
Sbjct: 2920 QPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRV 2979

Query: 123  PPPPPSSPPPSSSIPPPPPPGSP----------------PPP--------PPKDVEGRDT 158
            P P PS   P+SS PP                       PPP        PP D E  D 
Sbjct: 2980 PQPAPSREAPASSTPPLTGHSLSRVSSWASSLALHEETDPPPVSLKQTLWPPDDTEDSDA 3039

Query: 159  GTSDRDKRASKEVSRHDPGHSKQHRPPVPPP 189
             +         ++   DP   + H P    P
Sbjct: 3040 DSLFDSDSERSDLEALDPLPPEPHDPFAHEP 3070

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 68.0 bits (166), Expect = 1e-11
 Identities = 47/193 (24%), Positives = 68/193 (35%), Gaps = 13/193 (6%)

Query: 10   PPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTG----GGAQQHYHQP 65
            PP    P P P     + P PP     +Q  P   +         G    GG  +    P
Sbjct: 2702 PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPP 2761

Query: 66   YSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP- 124
             +   P P PP   +  PP     P   +  +++ S+    +  +  +        LPP 
Sbjct: 2762 TTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPA 2821

Query: 125  --PPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKR------ASKEVSRHDP 176
              P    PPP+S+ P  PPP   PPPP   + G      D  +R      A+K  +   P
Sbjct: 2822 ASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARP 2881

Query: 177  GHSKQHRPPVPPP 189
               +  RP V   
Sbjct: 2882 PVRRLARPAVSRS 2894

Length = 3151

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 67.3 bits (165), Expect = 1e-11
 Identities = 38/183 (20%), Positives = 55/183 (30%), Gaps = 14/183 (7%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
              P P  ++  P             P    +    P+      G  +  GG A      
Sbjct: 624 PAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPP 683

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
             + A P  P     + P P P   PP             ++   +  S       PLPP
Sbjct: 684 APAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPP 743

Query: 125 PPPSSPPPSSSIPPPPPPG--------------SPPPPPPKDVEGRDTGTSDRDKRASKE 170
            P   P P+ +   PPPP               SPP    +  E       D D+R ++E
Sbjct: 744 EPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRRDAEE 803

Query: 171 VSR 173
           V+ 
Sbjct: 804 VAM 806

Length = 824

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 66.5 bits (162), Expect = 3e-11
 Identities = 42/197 (21%), Positives = 59/197 (29%), Gaps = 13/197 (6%)

Query: 2    ASYRPFPQPPQSSFPPPPPPNQNPSQPPPP----PQQQQQQQRPNPYSQNWGGYSNTGGG 57
                   +PP ++ PP P P   P+  PP     P      +        W         
Sbjct: 2752 GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAV 2811

Query: 58   AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPP 117
                   P + +   P PPP S+ P  PPPPP PPP       S+    +        PP
Sbjct: 2812 LAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDV----RRRPP 2867

Query: 118  MQPPLPPPPPSSPPPSSSIPPPPPPGSP-----PPPPPKDVEGRDTGTSDRDKRASKEVS 172
             + P   P   + PP   +  P    S      PP  P+           + +       
Sbjct: 2868 SRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPP 2927

Query: 173  RHDPGHSKQHRPPVPPP 189
            +  P      RP  P  
Sbjct: 2928 QPQPPPPPPPRPQPPLA 2944

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 65.7 bits (160), Expect = 7e-11
 Identities = 43/156 (27%), Positives = 50/156 (32%), Gaps = 29/156 (18%)

Query: 2    ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQH 61
            A+  P    P    PPP         PPP P        P   S   GG       ++  
Sbjct: 2815 AAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSL---PLGGSVAPGGDVRRRPPSRSP 2871

Query: 62   YHQPYSYAQPP-----PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYP 116
              +P + A+PP      P    S+     PP  P  P Q                     
Sbjct: 2872 AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQ--------------------- 2910

Query: 117  PMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKD 152
            P  PP P P P  PPP    PPPPPP  P PP    
Sbjct: 2911 PQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPT 2946

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 64.2 bits (156), Expect = 2e-10
 Identities = 51/212 (24%), Positives = 69/212 (32%), Gaps = 30/212 (14%)

Query: 8    PQPPQSSFPPPPPPNQN--PSQP---PPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHY 62
            P PP     PP  P+++  P +P   P  P    + +RP+   Q     S          
Sbjct: 2551 PPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQ-----SARPRAPVDDR 2605

Query: 63   HQPYSYAQPPPPPPPESSYPPPPPPPPP-------------PPPTQQQTQPSMYYSSNQY 109
              P   A P P PP   +  PPPP P P             PPP + +  P+    S   
Sbjct: 2606 GDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR 2665

Query: 110  NQNSMYPPMQ---PPLPPPPPSSPPPSSSIP----PPPPPGSPPPPPPKDVEGRDTGTSD 162
                +    Q   PP  P   ++ P   S+     PPPPP +P P P   V         
Sbjct: 2666 RARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGP 2725

Query: 163  RDKRASKEVSRHDPGHSKQHRPPVPPPGVKKV 194
               R +       P        P  P G  + 
Sbjct: 2726 AAARQASPALPAAPAPPAVPAGPATPGGPARP 2757

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 62.3 bits (151), Expect = 7e-10
 Identities = 52/201 (25%), Positives = 65/201 (32%), Gaps = 17/201 (8%)

Query: 6    PFPQPPQSSFPPPPPPNQNPS-------QPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGA 58
            P P PP +  P PPPP+ +P+        PP  P  ++ +  P P   +    +   G A
Sbjct: 2614 PSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRA 2673

Query: 59   QQHYHQPYSYAQPPPPPP----PESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSM 114
             Q    P    +    P        + PPPPPP P P P    +   +        Q S 
Sbjct: 2674 AQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASP 2733

Query: 115  YPPMQPPLPPPPPSSPPPSSSIPPPPPP---GSPPPPPPKDVEGRDTGTSDRDKRASKEV 171
              P  P  P  P     P     P  PP   G P P PP            R   AS   
Sbjct: 2734 ALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSE 2793

Query: 172  SRHD---PGHSKQHRPPVPPP 189
            SR     P         V  P
Sbjct: 2794 SRESLPSPWDPADPPAAVLAP 2814

Length = 3151

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 61.7 bits (150), Expect = 9e-10
 Identities = 27/129 (20%), Positives = 31/129 (24%), Gaps = 18/129 (13%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
            F   P  +   PP P Q P QPPP  Q Q                        Q   Q 
Sbjct: 218 QFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPP-----------PQPPQQ- 265

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPP 125
                    PP   + PPP   P P P   Q     +           +  P      P 
Sbjct: 266 ------QQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQ 319

Query: 126 PPSSPPPSS 134
                   S
Sbjct: 320 FREQLVQLS 328

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 58.9 bits (143), Expect = 2e-09
 Identities = 20/81 (24%), Positives = 24/81 (29%), Gaps = 3/81 (3%)

Query: 71  PPPPPPPESSYPP-PPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSS 129
                         P    P  PP+     PS  + S   + +S      PP P    S 
Sbjct: 165 TTNSDNSFPGEDADPASASPSDPPSSSPGVPS--FPSPPEDPSSPSDSSLPPAPSSFQSD 222

Query: 130 PPPSSSIPPPPPPGSPPPPPP 150
            PP S   P  P   P P  P
Sbjct: 223 TPPPSPESPTNPSPPPGPAAP 243

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 59.7 bits (144), Expect = 4e-09
 Identities = 39/143 (27%), Positives = 49/143 (34%), Gaps = 16/143 (11%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
           P         P    Q P QP  P  Q QQ Q+P      +          QQ       
Sbjct: 751 PVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQY-------QQPQQPVAPQPQ 803

Query: 68  YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPM----QPPLP 123
           Y QP  P  P+  Y  P  P  P P  QQ  QP          Q+++  P+        P
Sbjct: 804 YQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVA-----PQPQDTLLHPLLMRNGDSRP 858

Query: 124 PPPPSSPPPSSSIPPPPPPGSPP 146
              P++P PS  +  PPP    P
Sbjct: 859 LHKPTTPLPSLDLLTPPPSEVEP 881

Length = 1355

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 58.2 bits (141), Expect = 5e-09
 Identities = 31/97 (31%), Positives = 33/97 (34%), Gaps = 7/97 (7%)

Query: 63  HQPYSYAQPPPPPPPESSYPPPPP-PPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPP 121
               S   P  P PPE    P     PP P   Q  T P    S       +  PP  P 
Sbjct: 187 PPSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESP-----TNPSPPPGPA 241

Query: 122 LPPPPPSSPPPSSSIPPP-PPPGSPPPPPPKDVEGRD 157
            PPPPP    P  S   P PP  S  P P   +   D
Sbjct: 242 APPPPPVQQVPPLSTAKPTPPSASATPAPIGGITLDD 278

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 57.4 bits (139), Expect = 8e-09
 Identities = 31/145 (21%), Positives = 39/145 (26%), Gaps = 21/145 (14%)

Query: 5   RPFPQPPQSSFPPPPPP-NQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYH 63
           R    P  +       P  Q+  QPP    Q +Q  +  P +Q             QH  
Sbjct: 70  RVNHAPANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQV----------PPQHAP 119

Query: 64  QPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLP 123
           +P   A  P   P     P  P   P  P      QP                P Q    
Sbjct: 120 RPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAP----------QPAQQAFQ 169

Query: 124 PPPPSSPPPSSSIPPPPPPGSPPPP 148
           P  P + P    +  P P    P  
Sbjct: 170 PAEPVAAPQPEPVAEPAPVMDKPKR 194

Length = 333

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 57.4 bits (139), Expect = 8e-09
 Identities = 32/183 (17%), Positives = 42/183 (22%), Gaps = 27/183 (14%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNT--------GGG 57
           P+   PQ+  P    P   P  PP    Q         ++   G  +           G 
Sbjct: 48  PWDPSPQAPPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALPAGP 107

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPP--PPTQQQTQPSMYYSSNQYNQNSMY 115
           A            P   P   +  P   P   P      QQ  Q     +S Q       
Sbjct: 108 AGPTIQTEPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQL------ 161

Query: 116 PPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDT---GTSDRDKRASKEVS 172
                   P    S   +        P    PP   D  G D        R+   + E  
Sbjct: 162 --------PSQQQSAQKNDESQLQQQPNGETPPQQTDGAGDDESEALVRLREADGTLEQR 213

Query: 173 RHD 175
              
Sbjct: 214 IKG 216

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 57.7 bits (140), Expect = 1e-08
 Identities = 25/154 (16%), Positives = 33/154 (21%), Gaps = 27/154 (17%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQH 61
                    P ++ P         +  P                            A   
Sbjct: 385 LGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAP-----------------APAA 427

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPP 121
             QP     P P PP  +   P    P PPP      QP            +     +P 
Sbjct: 428 APQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQP----------APAPAAAPEPT 477

Query: 122 LPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEG 155
             P P     P+ +  P  P     P    D   
Sbjct: 478 AAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAAT 511

Length = 824

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 56.9 bits (137), Expect = 1e-08
 Identities = 45/150 (30%), Positives = 50/150 (33%), Gaps = 19/150 (12%)

Query: 9   QPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSY 68
            PP  +   P P  Q  SQ PP    Q   Q P    Q+           QQ   Q   Y
Sbjct: 73  LPPAPAPQSPQPDQQQQSQAPP--SHQYPSQLPPQQVQS---------VPQQPTPQQEPY 121

Query: 69  AQPP--PPPPPESSYPPPPPPPPPPPPTQQQTQP---SMYYSSNQYNQNSMYPP---MQP 120
             PP  P PPP        P PPP  P QQQ Q       Y  N   Q    P    + P
Sbjct: 122 YPPPSQPQPPPAQQPQAQQPQPPPQVPQQQQYQSPPQQPQYQQNPPPQAQSAPQVSGLYP 181

Query: 121 PLPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
              P  P S PP+  +P       P    P
Sbjct: 182 EESPYQPQSYPPNEPLPSSMAMQPPYSGAP 211

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 57.4 bits (138), Expect = 2e-08
 Identities = 47/165 (28%), Positives = 56/165 (33%), Gaps = 36/165 (21%)

Query: 10  PPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYA 69
           P +  F P   P Q P QP  P QQ QQ Q+P                          Y 
Sbjct: 740 PHEPLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQP--------------------QYQ 779

Query: 70  QPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSS 129
           QP  P  P+  Y  P  P  P P  QQ  QP       Q  Q  + P  Q   P  P + 
Sbjct: 780 QPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAP 839

Query: 130 PPPSSSI----------PPPPPPGSPPP------PPPKDVEGRDT 158
            P  + +           P   P +P P      PPP +VE  DT
Sbjct: 840 QPQDTLLHPLLMRNGDSRPLHKPTTPLPSLDLLTPPPSEVEPVDT 884

Length = 1355

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 55.4 bits (134), Expect = 7e-08
 Identities = 27/185 (14%), Positives = 36/185 (19%), Gaps = 3/185 (1%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
            P P           P        P  P        P   S              +H   
Sbjct: 600 PPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAV 659

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
           P +       P       P  PPP P P        +   +  Q        P       
Sbjct: 660 PDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGA---APAQPAPAPAATPPAGQADD 716

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRP 184
           P    P  +     P P    P P P + +          +             +    P
Sbjct: 717 PAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPP 776

Query: 185 PVPPP 189
             P  
Sbjct: 777 SPPSE 781

Length = 824

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 54.9 bits (132), Expect = 1e-07
 Identities = 42/183 (22%), Positives = 48/183 (26%), Gaps = 19/183 (10%)

Query: 10   PPQSSFPPPPPPNQNP--SQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
            PPQ        P      S   PPP     +  P+             G A      P  
Sbjct: 2679 PPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVS---ATPLPPGPAAARQASPAL 2735

Query: 68   YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPP 127
             A P PP  P     P  P  P  PPT                     PP  P    PP 
Sbjct: 2736 PAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPA-------------PPAAPA-AGPPR 2781

Query: 128  SSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVP 187
                P+ +         P P  P D        +     A+       P  S Q   P P
Sbjct: 2782 RLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPP 2841

Query: 188  PPG 190
            PPG
Sbjct: 2842 PPG 2844

Length = 3151

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 55.1 bits (132), Expect = 1e-07
 Identities = 39/189 (20%), Positives = 54/189 (28%), Gaps = 14/189 (7%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHY-- 62
           +P         P    P Q P   P P Q  QQ        Q   G +      Q  +  
Sbjct: 399 QPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAP 458

Query: 63  ---HQPYSYAQPPPPPPPESSYPPPPPPPP--PPPPTQQQTQPS---MYY----SSNQYN 110
              +Q     Q P    P    P P    P   P P  ++T+P+   +YY       +  
Sbjct: 459 QSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPVVEETKPARPPLYYFEEVEEKRAR 518

Query: 111 QNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKE 170
           +         P+P P     P  SS+  P     PP      V    +G           
Sbjct: 519 EREQLAAWYQPIPEPVKEPEPIKSSLKAPSVAAVPPVEAAAAVSPLASGVKKATLATGAA 578

Query: 171 VSRHDPGHS 179
            +   P  S
Sbjct: 579 ATVAAPVFS 587

Length = 1355

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 54.8 bits (132), Expect = 1e-07
 Identities = 35/182 (19%), Positives = 51/182 (28%), Gaps = 25/182 (13%)

Query: 25  PSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPP 84
           P+ PPP  ++  + + P P  + + GY   G  A           Q P   P   +Y   
Sbjct: 95  PAPPPPHARRTSEPELPRPGRRPYEGY--GGPRADDRPPGLPRQDQLPTARPAYPAYQQR 152

Query: 85  PPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGS 144
           P P   P                       Y   Q  L  PP +     +S  P      
Sbjct: 153 PEPGAWPRAADD------------------YGWQQQRLGFPPRAPYASPASYAPEQERDR 194

Query: 145 PPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPPGVKKVNGGSGRVETE 204
            P    +    +     D  +          P   +  RP  PP       GG G  E +
Sbjct: 195 EPYDAGRPEYDQRRRDYDHPRPDWDR-----PRRDRTDRPEPPPGAGHVHRGGPGPPERD 249

Query: 205 EE 206
           + 
Sbjct: 250 DA 251

Length = 617

>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 53.7 bits (129), Expect = 1e-07
 Identities = 31/88 (35%), Positives = 36/88 (40%), Gaps = 17/88 (19%)

Query: 67  SYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPP 126
           + A P PPPPP S+    P P  PPPP      P+              P    P   PP
Sbjct: 37  ANADPAPPPPPPSTAAAAPAPAAPPPPPPPAAPPA--------------PQPDDPNAAPP 82

Query: 127 PSSPPPSSSIPPPPPPGSPPPPPPKDVE 154
           P    P++   PPPPP  P  PPP   E
Sbjct: 83  PPPADPNA---PPPPPVDPNAPPPPAPE 107

This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. Length = 297

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 53.4 bits (128), Expect = 2e-07
 Identities = 40/141 (28%), Positives = 46/141 (32%), Gaps = 8/141 (5%)

Query: 10  PPQSSFPPPPPPNQNPSQ---PPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPY 66
            PQS  P     +Q P     P   P QQ Q     P  Q    Y            QP 
Sbjct: 78  APQSPQPDQQQQSQAPPSHQYPSQLPPQQVQSVPQQPTPQQEPYYPPPSQPQPPPAQQPQ 137

Query: 67  SYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPP 126
           +    PPP  P+         PP  P  QQ   P    +           P QP     P
Sbjct: 138 AQQPQPPPQVPQ---QQQYQSPPQQPQYQQNPPPQAQSAPQVSGLYPEESPYQP--QSYP 192

Query: 127 PSSPPPSSSIPPPPPPGSPPP 147
           P+ P PSS    PP  G+PP 
Sbjct: 193 PNEPLPSSMAMQPPYSGAPPS 213

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 53.0 bits (127), Expect = 2e-07
 Identities = 43/144 (29%), Positives = 46/144 (31%), Gaps = 20/144 (13%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
                PQ   P   P    PSQP PPP QQ Q Q+P P  Q            QQ Y  P
Sbjct: 106 QVQSVPQQPTPQQEPYYPPPSQPQPPPAQQPQAQQPQPPPQV---------PQQQQYQSP 156

Query: 66  YSYAQPPP-PPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
               Q    PPP   S P      P   P Q Q+ P           N   P      PP
Sbjct: 157 PQQPQYQQNPPPQAQSAPQVSGLYPEESPYQPQSYPP----------NEPLPSSMAMQPP 206

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPP 148
              + P      PP P P     P
Sbjct: 207 YSGAPPSQQFYGPPQPSPYMYGGP 230

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 54.0 bits (130), Expect = 2e-07
 Identities = 22/144 (15%), Positives = 37/144 (25%), Gaps = 17/144 (11%)

Query: 11  PQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQ 70
           P ++     P      + P  P+       P   +      +     A      P + A 
Sbjct: 366 PAAAAEAAAPA---EKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAP 422

Query: 71  PPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSP 130
           P P   P ++ P   P   P         P+                    +  P   +P
Sbjct: 423 PAPVAAPAAAAPAAAPAAAPAAVALAPAPPA--------------QAAPETVAIPVRVAP 468

Query: 131 PPSSSIPPPPPPGSPPPPPPKDVE 154
            P+ +   P P  +P        E
Sbjct: 469 EPAVASAAPAPAAAPAAARLTPTE 492

Length = 618

>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein

 Score = 53.8 bits (129), Expect = 2e-07
 Identities = 25/78 (32%), Positives = 29/78 (37%)

Query: 73  PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPP 132
               P +  PPPP   P  PP      PS   +         + P  P   P  PS+PP 
Sbjct: 179 GGNIPGAIQPPPPSSLPGLPPGSSSLAPSASSTPGNRLPRVSFNPFLPGPSPAQPSAPPA 238

Query: 133 SSSIPPPPPPGSPPPPPP 150
           S   PP PP      PPP
Sbjct: 239 SIPAPPIPPVIQYVAPPP 256

Length = 582

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 53.7 bits (129), Expect = 2e-07
 Identities = 32/188 (17%), Positives = 51/188 (27%), Gaps = 10/188 (5%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQR-PNPYSQNWGGYSNTGGGAQQ 60
           A+  P    P  + PP  P     +            +R P P +      ++  G    
Sbjct: 388 AAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPG-- 445

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
                     P P   P ++  P    P P              ++     +   PP + 
Sbjct: 446 ----GAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEE 501

Query: 121 PLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSK 180
              PP  +SP P+     P    +   P P   +  D   +     A+    R       
Sbjct: 502 L--PPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEP 559

Query: 181 QHRPPVPP 188
               P PP
Sbjct: 560 V-VAPRPP 566

Length = 700

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 53.3 bits (128), Expect = 3e-07
 Identities = 33/142 (23%), Positives = 42/142 (29%), Gaps = 52/142 (36%)

Query: 16  PPPPPPNQNPSQPPPPPQQQQ--QQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPP 73
           P P P    P+   P P +       RP                         + A   P
Sbjct: 362 PVPAPQPAKPTAAAPSPVRPTPAPSTRPKA-----------------------AAAANIP 398

Query: 74  PPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPP-P 132
           P  P      PPP PP                           P+ PP+P  P S+P   
Sbjct: 399 PKEPVRETATPPPVPP--------------------------RPVAPPVPHTPESAPKLT 432

Query: 133 SSSIPPPPPPGSPPPPPPKDVE 154
            ++IP    P   PP PPK+ E
Sbjct: 433 RAAIPVDEKPKYTPPAPPKEEE 454

Length = 585

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 53.6 bits (128), Expect = 4e-07
 Identities = 36/147 (24%), Positives = 43/147 (29%), Gaps = 7/147 (4%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
           P PQ  +    P P        P      Q   Q   P  Q           A +   Q 
Sbjct: 364 PGPQTGEPVIAPAPE-----GYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQ 418

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMY--YSSNQYNQNSMYPPMQPPLP 123
             YA  P  P  +  Y P P  P      Q + Q S +   S+ Q  Q    P  Q PL 
Sbjct: 419 PYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLY 478

Query: 124 PPPPSSPPPSSSIPPPPPPGSPPPPPP 150
             P          P P    + P  PP
Sbjct: 479 QQPQPVEQQPVVEPEPVVEETKPARPP 505

Length = 1355

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 52.3 bits (126), Expect = 4e-07
 Identities = 32/117 (27%), Positives = 38/117 (32%), Gaps = 13/117 (11%)

Query: 39  QRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPP--PPPESSYPPPPPPPPPPPPTQQ 96
            R N    N   +       Q  Y  PY+ AQP  P   PPE+  PP   P P  P  Q 
Sbjct: 69  HRVNHAPANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQP 128

Query: 97  QTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDV 153
             QP+               P QP   P  P   P    +   P P      P + V
Sbjct: 129 VQQPA-----------YQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPV 174

Length = 333

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 52.6 bits (126), Expect = 6e-07
 Identities = 23/149 (15%), Positives = 38/149 (25%), Gaps = 33/149 (22%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQH 61
           A   P    P ++ P P  P   P+  P      +                      +  
Sbjct: 383 AQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAA--------------APARRSP 428

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPP 121
             +  + A+      P  +  P P P   P    +                   P    P
Sbjct: 429 APEALAAARQASARGPGGAPAPAPAPAAAPAAAAR-------------------PAAAGP 469

Query: 122 LPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
            P    ++  P+ + P   P  +   PPP
Sbjct: 470 RPVAAAAAAAPARAAPAAAPAPADDDPPP 498

Length = 700

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 52.2 bits (125), Expect = 1e-06
 Identities = 44/195 (22%), Positives = 53/195 (27%), Gaps = 35/195 (17%)

Query: 3    SYRPFPQPPQSSFPPPPPPNQNPSQP-------------PPPPQQQQQQQRPNPYSQNWG 49
            S   F  PP     PP P    P QP             PPPP + Q    P       G
Sbjct: 2894 STESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAG 2953

Query: 50   GYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQY 109
              S            P   A P    P  +     P    PP      ++ S + SS   
Sbjct: 2954 EPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRVSSWASSLAL 3013

Query: 110  NQNSMYPP---MQPPLPPPPPSSPPPSSSI-------------PPPPPPGSPPPPPPKDV 153
            ++ +  PP    Q   PP         S               P PP P  P    P   
Sbjct: 3014 HEETDPPPVSLKQTLWPPDDTEDSDADSLFDSDSERSDLEALDPLPPEPHDPFAHEP--- 3070

Query: 154  EGRDTGTSDRDKRAS 168
               D  T +   R S
Sbjct: 3071 ---DPATPEAGARES 3082

Length = 3151

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 51.9 bits (125), Expect = 1e-06
 Identities = 31/173 (17%), Positives = 42/173 (24%), Gaps = 11/173 (6%)

Query: 18  PPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPP 77
           P P       PP P      ++   P        +     A          A     P  
Sbjct: 590 PAPGAAGGEGPPAPASSGPPEEAARP-----AAPAAPAAPAAPA------PAGAAAAPAE 638

Query: 78  ESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIP 137
            S+ P P    P   P       +         +     P  PP  P P +   P+ + P
Sbjct: 639 ASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAP 698

Query: 138 PPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPPG 190
             P P     PP    +          + AS      D        P  PP  
Sbjct: 699 AQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDP 751

Length = 824

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 51.3 bits (123), Expect = 1e-06
 Identities = 21/126 (16%), Positives = 33/126 (26%), Gaps = 9/126 (7%)

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
           P + A+   P   ++   P    P   P  Q    P+   +                   
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAP---------AAAASAPAA 416

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRP 184
           PP ++PP   + P    P + P   P  V       +           R  P  +     
Sbjct: 417 PPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAA 476

Query: 185 PVPPPG 190
           P P   
Sbjct: 477 PAPAAA 482

Length = 618

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 51.3 bits (123), Expect = 2e-06
 Identities = 36/187 (19%), Positives = 43/187 (22%), Gaps = 45/187 (24%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQN------------WGGYSNTG 55
            +  Q++   P                   Q      +              WG      
Sbjct: 75  VRYNQNAPGAPSVGPD-SDLSQKTSTFSPCQSGYEASTDPEYIPDLQPDPSLWGTAPKPE 133

Query: 56  -GGAQQHYHQP---------------------YSYAQPPPPPPPESSYPPPPPPPPPPPP 93
               Q    QP                        A   P PP +      PP     P 
Sbjct: 134 PQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQ 193

Query: 94  TQQQTQPSMYYSSNQYNQNSMYPP----------MQPPLPPPPPSSPPPSSSIPPPPPPG 143
                QP  Y    Q +   + P            QPPLPP  P  PPP      P    
Sbjct: 194 QGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQ 253

Query: 144 SPPPPPP 150
             PPPPP
Sbjct: 254 QMPPPPP 260

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 50.6 bits (121), Expect = 2e-06
 Identities = 35/192 (18%), Positives = 46/192 (23%), Gaps = 20/192 (10%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQ--QQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
           P PP    PP       P  P P  +  +     R +               A+  Y   
Sbjct: 95  PAPP----PPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQD-QLPTARPAYPAY 149

Query: 66  YSYAQPPPPPPPESSYPP------PPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQ 119
               +P   P     Y         PP  P   P     +           +       +
Sbjct: 150 QQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRR 209

Query: 120 PPLPPPPPSSPPPSSSIPPP-PPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGH 178
               P P    P       P PPPG+              G  +RD      +    PG 
Sbjct: 210 DYDHPRPDWDRPRRDRTDRPEPPPGAGHVHRGGP------GPPERDDAPVVPIRPSAPGP 263

Query: 179 SKQHRPPVPPPG 190
                 P P PG
Sbjct: 264 LAAQPAPAPGPG 275

Length = 617

>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 49.9 bits (119), Expect = 2e-06
 Identities = 26/89 (29%), Positives = 30/89 (33%), Gaps = 20/89 (22%)

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPP 121
              P     PP       +   PPPPPPP  P                      P    P
Sbjct: 38  NADPAPPPPPPSTAAAAPAPAAPPPPPPPAAPPA--------------------PQPDDP 77

Query: 122 LPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
              PPP    P++  PPP  P +PPPP P
Sbjct: 78  NAAPPPPPADPNAPPPPPVDPNAPPPPAP 106

This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. Length = 297

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 50.9 bits (122), Expect = 2e-06
 Identities = 32/166 (19%), Positives = 44/166 (26%), Gaps = 11/166 (6%)

Query: 18  PPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPP 77
                + P+ PPP P  +                      A++    P   + P PPPP 
Sbjct: 61  ACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPT 120

Query: 78  ESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSS--- 134
               PPP  PPP P P   +    +         +       P       +S   ++   
Sbjct: 121 ----PPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPL 176

Query: 135 SIPP----PPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDP 176
           S P      P      PPP             R    S   S   P
Sbjct: 177 SSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAP 222

Length = 1352

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 50.4 bits (121), Expect = 3e-06
 Identities = 24/97 (24%), Positives = 30/97 (30%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
           A   P P       P P P P PP            S       S  P   P   P P +
Sbjct: 419 AAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTA 478

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDK 165
           +P P+    P P      P  P    G D   + R++
Sbjct: 479 APAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRER 515

Length = 824

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 50.5 bits (120), Expect = 3e-06
 Identities = 50/161 (31%), Positives = 60/161 (37%), Gaps = 15/161 (9%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYS---------QNWGGY 51
             + +  PQPP  S   P   +  P  P P   QQ      +P S         Q+    
Sbjct: 247 QTASQQSPQPPAPSSRHPQSSHHGPGPPMPHALQQGPVFLQHPSSNPPQPFGLAQSQVPP 306

Query: 52  SNTGGGAQQHYHQPYS-YAQPPPPPPPESSYPPPPPPP---PPPPPTQQQTQPSMYYSSN 107
                 AQ H H P S  A  P  PP E   PP P  P   PPP     Q     +    
Sbjct: 307 LPLPSQAQPHSHTPPSQSALQPQQPPREQPLPPAPSMPHIKPPPTTPIPQLPNQSHKHPP 366

Query: 108 QYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPP 148
                S +P M   LPPPP  +  P SS+P   PP + PPP
Sbjct: 367 HLQGPSPFPQMPSNLPPPP--ALKPLSSLPTHHPPSAHPPP 405

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 50.1 bits (119), Expect = 4e-06
 Identities = 58/248 (23%), Positives = 90/248 (36%), Gaps = 22/248 (8%)

Query: 6   PFPQPPQSSFPPPP--------PPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGG 57
           PFPQ P S+ PPPP        P +  PS  PPP Q   Q Q            + +   
Sbjct: 373 PFPQMP-SNLPPPPALKPLSSLPTHHPPSAHPPPLQLMPQSQPLQSVPAQPPVLTQSQSL 431

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYP----------PPPPPPPPPPPTQQQTQPSMYYSSN 107
             +    P+S     PP  P + +P          PPP  P   P    +         +
Sbjct: 432 PPKASTHPHSGLHSGPPQSPFAQHPFTSGGLPAIGPPPSLPTSTPAAPPRASSGSQPPGS 491

Query: 108 QYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRA 167
               +       PPLPP      P   +  P  PP  P  P P+         + +  R 
Sbjct: 492 ALPSSGGCAGPGPPLPPIQIKEEPLDEAEEPESPPPPPRSPSPEPTVVNTPSHASQSARF 551

Query: 168 SKEVSRHDPGHSKQHRPPVPPPG---VKKVNGGSGRVETEEERRIRKKREYEKHRQEEKH 224
            K + R     ++      P       KK      + + E E++ R++RE EK +++E+ 
Sbjct: 552 YKHLDRGYNSCARTDLYFTPLASSKLAKKREEAVEKAKREAEQKAREEREREKEKEKERE 611

Query: 225 RLQMKESQ 232
           R + +E++
Sbjct: 612 REREREAE 619

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 49.7 bits (119), Expect = 4e-06
 Identities = 25/104 (24%), Positives = 31/104 (29%), Gaps = 23/104 (22%)

Query: 73  PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPP 132
           P PP  +   P P  P  PPP                      PP+ P  P  P ++ P 
Sbjct: 382 PAPPSAAWGAPTPAAPAAPPPAAA-------------------PPVPPAAPARPAAARP- 421

Query: 133 SSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDP 176
               P P PP +  PP             DR +     V    P
Sbjct: 422 ---APAPAPPAAAAPPARSADPAAAASAGDRWRAFVAFVKGKKP 462

Length = 576

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.5 bits (119), Expect = 5e-06
 Identities = 25/154 (16%), Positives = 33/154 (21%), Gaps = 32/154 (20%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
           M ++ P    P+   PP        +Q    P                            
Sbjct: 356 MLAFHPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAP---------------------- 393

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
                    Q P  PPP +S P   P  P P  T Q           Q    +     +P
Sbjct: 394 --------PQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQ--GATKAKKSEP 443

Query: 121 PLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVE 154
                          +    P  S     P   E
Sbjct: 444 AAASRARPVNSALERLASVRPAPSALEKAPAKKE 477

Length = 647

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 48.7 bits (117), Expect = 7e-06
 Identities = 23/156 (14%), Positives = 32/156 (20%), Gaps = 17/156 (10%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
            AS +    P  +    PP     P  P   PQQ      P   SQ              
Sbjct: 378 AASAQATAAPTAA--VAPPQAPAVPPPPASAPQQAPAVPLPETTSQ-----------LLA 424

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYP--PM 118
              Q             E +      P           +P+         +   Y     
Sbjct: 425 ARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAPAKKEAYRWKAT 484

Query: 119 QPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVE 154
            P      P + P   ++         P    K   
Sbjct: 485 NPVEVKKEPVATP--KALKKALEHEKTPELAAKLAA 518

Length = 647

>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183)

 Score = 48.2 bits (115), Expect = 7e-06
 Identities = 30/136 (22%), Positives = 35/136 (25%), Gaps = 33/136 (24%)

Query: 32  PQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPP 91
               +   RP       GG    GGG              P PPPP      PPP  P  
Sbjct: 180 CGGVRGGPRPERAGYGGGGGGGGGGGG--------GGGSGPGPPPPGFKSSFPPPYGPGA 231

Query: 92  PPT-------QQQTQPSM---------------YYSSNQYNQNSMYPPMQPPLPPPPPSS 129
            P+        +  Q                  Y   ++ N NS Y           PS 
Sbjct: 232 GPSSGYGSGGTRSGQGGWGPGFWTGLGAGGALGYLFGSRRNNNSSYG---RSYGSGSPSY 288

Query: 130 PPPSSSIPPPPPPGSP 145
            P SSS        S 
Sbjct: 289 SPSSSSNSSSSSSSSS 304

This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown. Length = 317

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 48.1 bits (115), Expect = 8e-06
 Identities = 25/138 (18%), Positives = 29/138 (21%), Gaps = 33/138 (23%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
                  P     S PP   P       PP                             +
Sbjct: 172 FPGEDADPASASPSDPPSSSPGVPSFPSPP-----------------------------E 202

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
               P   + PP P           PPP P  PT     P          Q         
Sbjct: 203 DPSSPSDSSLPPAPSSF----QSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAK 258

Query: 121 PLPPPPPSSPPPSSSIPP 138
           P PP   ++P P   I  
Sbjct: 259 PTPPSASATPAPIGGITL 276

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 49.1 bits (118), Expect = 8e-06
 Identities = 12/93 (12%), Positives = 20/93 (21%), Gaps = 14/93 (15%)

Query: 70  QPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSS 129
            P     P ++          P        P+               P   P     P++
Sbjct: 37  GPGSTAAPTAAAAAAAAAASAPAAAPAAKAPA--------------APAPAPPAAAAPAA 82

Query: 130 PPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSD 162
           PP  ++        + PP              D
Sbjct: 83  PPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVED 115

Length = 1228

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 48.0 bits (114), Expect = 9e-06
 Identities = 43/147 (29%), Positives = 46/147 (31%), Gaps = 17/147 (11%)

Query: 6   PFPQPPQSSFPPP---PPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHY 62
           P+  PP    PPP   P   Q    P  P QQQ Q     P  Q            Q   
Sbjct: 120 PYYPPPSQPQPPPAQQPQAQQPQPPPQVPQQQQYQSPPQQPQYQ------------QNPP 167

Query: 63  HQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPL 122
            Q  S  Q     P ES Y P   PP  P P+    QP   YS    +Q    PP   P 
Sbjct: 168 PQAQSAPQVSGLYPEESPYQPQSYPPNEPLPSSMAMQPP--YSGAPPSQQFYGPPQPSPY 225

Query: 123 PPPPPSSPPPSSSIPPPPPPGSPPPPP 149
               P   P S       PP S     
Sbjct: 226 MYGGPGGRPNSGFPSGQQPPPSQGQEG 252

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein

 Score = 48.4 bits (115), Expect = 9e-06
 Identities = 23/81 (28%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 72  PPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLP--PPPPSS 129
               P     PPP   P  PP +      +     N+  + S  P +  P P  P  P +
Sbjct: 179 GGNIPGAIQPPPPSSLPGLPPGSSSLAPSASSTPGNRLPRVSFNPFLPGPSPAQPSAPPA 238

Query: 130 PPPSSSIPPPPPPGSPPPPPP 150
             P+  IPP     +PPP PP
Sbjct: 239 SIPAPPIPPVIQYVAPPPVPP 259

Length = 582

>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated

 Score = 48.4 bits (116), Expect = 9e-06
 Identities = 16/95 (16%), Positives = 21/95 (22%), Gaps = 13/95 (13%)

Query: 64  QPYSYAQPPPPPPPESSYPPPPPPPPPPP---PTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
            P +   PP   P   S P  P   P P      ++ T         Q    +  P    
Sbjct: 58  APAAAQPPPAAAPAAVSRPAAPAAEPAPWLVEHAKRLTAQRE-----QLVARAAAPAAPE 112

Query: 121 PLPPPPPSS-----PPPSSSIPPPPPPGSPPPPPP 150
              P  P+                     P  P  
Sbjct: 113 AQAPAAPAERAAAENAARRLARAAAAAPRPRVPAD 147

Length = 484

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 48.1 bits (114), Expect = 1e-05
 Identities = 36/151 (23%), Positives = 47/151 (31%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
           +P P  P      PPP    P  P    +     Q P+P+ Q                  
Sbjct: 335 QPLPPAPSMPHIKPPPTTPIPQLPNQSHKHPPHLQGPSPFPQMPSNLPPPPALKPLSSLP 394

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
            +      PPP        P    P  PP   Q+Q     +S   +      P Q P   
Sbjct: 395 THHPPSAHPPPLQLMPQSQPLQSVPAQPPVLTQSQSLPPKASTHPHSGLHSGPPQSPFAQ 454

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPPPPKDVEG 155
            P +S    +  PPP  P S P  PP+   G
Sbjct: 455 HPFTSGGLPAIGPPPSLPTSTPAAPPRASSG 485

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and modification]

 Score = 48.8 bits (116), Expect = 1e-05
 Identities = 25/88 (28%), Positives = 36/88 (40%), Gaps = 9/88 (10%)

Query: 116 PPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVE---------GRDTGTSDRDKR 166
           PP  PP PPPPP   PPS   PPPPP  +      K +          G    +     +
Sbjct: 5   PPGNPPPPPPPPGFEPPSQPPPPPPPGVNVKKRSRKQLSIVGDILGHSGNPIYSLRVSDK 64

Query: 167 ASKEVSRHDPGHSKQHRPPVPPPGVKKV 194
             K  ++    H    + P+PP  ++K+
Sbjct: 65  PVKLGNKAKTLHVLTLKAPIPPEHLRKI 92

Length = 2365

>gnl|CDD|218108 pfam04487, CITED, CITED

 Score = 46.4 bits (110), Expect = 1e-05
 Identities = 23/138 (16%), Positives = 32/138 (23%), Gaps = 11/138 (7%)

Query: 19  PPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPP--- 75
                  +    P       +       ++ G      G  +      S       P   
Sbjct: 19  KGARMGMNSLAAPNHGPHDLRALMGTLLHYPGGGMDASGRPRS---AMSGPMGGGHPHQS 75

Query: 76  -PPESSYPPPPPPPPPPPPTQQQTQPSMYYSS--NQYNQNSMYPPMQPPLPPPPPSSPPP 132
            P    + P   P P       Q   SM       QY  ++  P   P      P    P
Sbjct: 76  MPAYMMFNPSSKPQPFMLVPGPQLMASMQLQKLNTQYQGHAGAPAGHPG--GGGPQQFRP 133

Query: 133 SSSIPPPPPPGSPPPPPP 150
            +  PP       P  PP
Sbjct: 134 GAGQPPGMQHMPAPALPP 151

CITED, CBP/p300-interacting transactivator with ED-rich tail, are characterized by a conserved 32-amino acid sequence at the C-terminus. CITED proteins do not bind DNA directly and are thought to function as transcriptional co-activators. Length = 206

>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein

 Score = 47.9 bits (114), Expect = 1e-05
 Identities = 26/152 (17%), Positives = 31/152 (20%), Gaps = 35/152 (23%)

Query: 9   QPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSY 68
            PP      P P      +   P         P P                     P   
Sbjct: 635 FPPVFKTALPRPDYNRGGEAGGPGVPG-----PVPVGMPAHTAR------------PSRV 677

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
           A+  P  P         P  P P                            PP P  P +
Sbjct: 678 ARGDPVRPTAHHAALRAPQAPRPGG------------------PPGGGGGLPPPPDLPAA 719

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGT 160
           + P          P +PP P P   E  D   
Sbjct: 720 AGPAPCGSSLIASPTAPPEPEPPGAEQADGAE 751

Length = 753

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 47.3 bits (113), Expect = 2e-05
 Identities = 31/129 (24%), Positives = 39/129 (30%), Gaps = 27/129 (20%)

Query: 4   YRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYH 63
           Y+P     Q   P   PP +    P   P+  Q   +P                 QQ  +
Sbjct: 92  YQPPYASAQPRQPVQQPP-EAQVPPQHAPRPAQPAPQP----------------VQQPAY 134

Query: 64  QPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLP 123
           QP    QP   P      P P P    P P QQ  QP+         +    P  +P   
Sbjct: 135 QPQP-EQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPA---------EPVAAPQPEPVAE 184

Query: 124 PPPPSSPPP 132
           P P    P 
Sbjct: 185 PAPVMDKPK 193

Length = 333

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 22/101 (21%), Positives = 29/101 (28%)

Query: 54  TGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS 113
                     Q +  A+P P    +  Y    P  P   P + Q  P       Q     
Sbjct: 69  HRVNHAPANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQP 128

Query: 114 MYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVE 154
           +  P   P P  P   P      P P P  S P P  +  +
Sbjct: 129 VQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQ 169

Length = 333

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 24/181 (13%), Positives = 41/181 (22%), Gaps = 18/181 (9%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQH 61
           A+    P    ++          P++  P P+     ++ +               A   
Sbjct: 400 AAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPA 459

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQP-----------SMYYSSNQYN 110
                + A P P     ++ P    P   P P      P           +         
Sbjct: 460 AAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPA 519

Query: 111 QNSMYPPMQPPLPPPPPSSP-----PPSSSIPPPPPPGSP--PPPPPKDVEGRDTGTSDR 163
                    P    P  +       P ++  P       P   P PP+          D 
Sbjct: 520 GWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDMFDG 579

Query: 164 D 164
           D
Sbjct: 580 D 580

Length = 700

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 41/187 (21%), Positives = 59/187 (31%), Gaps = 7/187 (3%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
           P   P +++  P  PP + P   PP     +  +R +P S +    +   G +       
Sbjct: 175 PLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGA 234

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPP 125
            S              P    P P P P    T P+  + ++ +N  S  P        P
Sbjct: 235 SSSDSSSSESSGCGWGPENECPLPRPAP---ITLPTRIWEASGWNGPSSRPGPASSSSSP 291

Query: 126 PPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQ--HR 183
              SP PS S P   P  +P  P           +S     +S E SR           R
Sbjct: 292 RERSPSPSPSSPGSGP--APSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSR 349

Query: 184 PPVPPPG 190
            P P   
Sbjct: 350 SPSPSRP 356

Length = 1352

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 47.8 bits (113), Expect = 2e-05
 Identities = 49/165 (29%), Positives = 58/165 (35%), Gaps = 20/165 (12%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYS--QNWGGYSNTGGGAQQHYH 63
           P  + PQSS   P PP  +  Q  P   Q      P P+   Q+          AQ H H
Sbjct: 259 PSSRHPQSSHHGPGPPMPHALQQGPVFLQHPSSNPPQPFGLAQSQVPPLPLPSQAQPHSH 318

Query: 64  QPYSYA----------QPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS 113
            P S +          QP PP P      PPP  P P  P Q    P      + + Q  
Sbjct: 319 TPPSQSALQPQQPPREQPLPPAPSMPHIKPPPTTPIPQLPNQSHKHPPHLQGPSPFPQMP 378

Query: 114 MYPPMQPPLPP--------PPPSSPPPSSSIPPPPPPGSPPPPPP 150
              P  P L P        PP + PPP   +P   P  S P  PP
Sbjct: 379 SNLPPPPALKPLSSLPTHHPPSAHPPPLQLMPQSQPLQSVPAQPP 423

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|152960 pfam12526, DUF3729, Protein of unknown function (DUF3729)

 Score = 44.3 bits (105), Expect = 2e-05
 Identities = 30/79 (37%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 74  PPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPP-- 131
             PPES++P  PPP   P P    T P     S  +       P  PP  P PP   P  
Sbjct: 29  FSPPESAHPDDPPPVGDPRPPVVDTPPP---VSAVWVLPPPSEPAAPPPDPEPPVPGPAG 85

Query: 132 PSSSIPPPPPPGSPPPPPP 150
           P S + PP P   PP PPP
Sbjct: 86  PPSPLAPPAPARKPPLPPP 104

This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with pfam01443, pfam01661, pfam05417, pfam01660, pfam00978. There is a single completely conserved residue L that may be functionally important. Length = 115

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.3 bits (113), Expect = 2e-05
 Identities = 23/84 (27%), Positives = 28/84 (33%), Gaps = 16/84 (19%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
           + P  P P  +  PPP P  P  P T+Q                    P  PP    PP 
Sbjct: 372 SAPANPTPAPNPSPPPAPIQPSAPKTKQAATT----------------PSPPPAKASPPI 415

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKD 152
             P   + P P PP +    PP  
Sbjct: 416 PVPAEPTEPSPTPPANAANAPPSL 439

Length = 620

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.3 bits (113), Expect = 2e-05
 Identities = 24/99 (24%), Positives = 26/99 (26%), Gaps = 12/99 (12%)

Query: 59  QQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPM 118
            Q      +   PPPP        P PP P P       T P               P  
Sbjct: 512 SQSGSASNTAKTPPPPQKSPPPPAPTPPLPQPTATAPPPTPP------------PPPPTA 559

Query: 119 QPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRD 157
                  P   P  SS  PP P   +P P      E  D
Sbjct: 560 TQASSNAPAQIPADSSPPPPIPEEPTPSPTKDSSPEEID 598

Length = 620

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.3 bits (113), Expect = 2e-05
 Identities = 18/90 (20%), Positives = 23/90 (25%), Gaps = 9/90 (10%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
           +       P      PPPP P PP  Q                 +  PP          +
Sbjct: 516 SASNTAKTPPPPQKSPPPPAPTPPLPQPTATA---------PPPTPPPPPPTATQASSNA 566

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKDVEGRDT 158
                +   PPPP    P P P      + 
Sbjct: 567 PAQIPADSSPPPPIPEEPTPSPTKDSSPEE 596

Length = 620

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 47.2 bits (112), Expect = 3e-05
 Identities = 38/218 (17%), Positives = 57/218 (26%), Gaps = 34/218 (15%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPP----------PPQQQQQQQRPNPYSQNWGGYSNTG 55
                     P    PN   + PP           P         P P         +  
Sbjct: 272 ARGATGPPPPPEAAAPN-GAAAPPDGVWGAALAGAPLALPAPPDPPPPAPAGDAEEEDDE 330

Query: 56  GGA----------QQHYHQPYSYAQPPPPPPPES----SYPPPPPPPPPPPPTQQQTQPS 101
            GA          +QHY   +   + P   PP S    S     P     P  ++++   
Sbjct: 331 DGAMEVVSPLPRPRQHYPLGFPKRRRPTWTPPSSLEDLSAGRHHPKRASLPTRKRRSARH 390

Query: 102 MYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPP---------PPPKD 152
                 +            P+P   P+  P       PPPP +P P         P P  
Sbjct: 391 AATPFARGPGGDDQTRPAAPVPASVPTPAPTPVPASAPPPPATPLPSAEPGSDDGPAPPP 450

Query: 153 VEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPPG 190
                   ++       + +R      ++ RPP PP  
Sbjct: 451 ERQPPAPATEPAPDDPDDATRKALDALRERRPPEPPGA 488

Length = 3151

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 46.9 bits (112), Expect = 3e-05
 Identities = 23/83 (27%), Positives = 30/83 (36%)

Query: 53  NTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQN 112
            +  G+  +  +     Q  PPPP  +   P P    PPP        +   SSN   Q 
Sbjct: 511 ESQSGSASNTAKTPPPPQKSPPPPAPTPPLPQPTATAPPPTPPPPPPTATQASSNAPAQI 570

Query: 113 SMYPPMQPPLPPPPPSSPPPSSS 135
                  PP+P  P  SP   SS
Sbjct: 571 PADSSPPPPIPEEPTPSPTKDSS 593

Length = 620

>gnl|CDD|222579 pfam14179, YppG, YppG-like protein

 Score = 43.2 bits (102), Expect = 3e-05
 Identities = 24/64 (37%), Positives = 28/64 (43%), Gaps = 3/64 (4%)

Query: 42  NPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPP---ESSYPPPPPPPPPPPPTQQQT 98
           NPY QN   Y       Q +  QPY    PPPP  P   +  +  PP P P P  + QQ 
Sbjct: 1   NPYQQNTNQYPPQNQQQQPYQQQPYHQQMPPPPYSPPQQQQGHFMPPQPQPYPKQSPQQQ 60

Query: 99  QPSM 102
           QP  
Sbjct: 61  QPPQ 64

The YppG-like protein family includes the B. subtilis YppG protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 181 amino acids in length. There are two completely conserved residues (F and G) that may be functionally important. Length = 110

>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein

 Score = 46.4 bits (110), Expect = 4e-05
 Identities = 20/86 (23%), Positives = 27/86 (31%), Gaps = 2/86 (2%)

Query: 70  QPPPPPPPESSYPPPPPPPPPP--PPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPP 127
           +    P      PP   P  PP           +      + + N   P   P  P  PP
Sbjct: 178 RGGNIPGAIQPPPPSSLPGLPPGSSSLAPSASSTPGNRLPRVSFNPFLPGPSPAQPSAPP 237

Query: 128 SSPPPSSSIPPPPPPGSPPPPPPKDV 153
           +S P     P       PP PPP+ +
Sbjct: 238 ASIPAPPIPPVIQYVAPPPVPPPQPI 263

Length = 582

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 46.3 bits (110), Expect = 5e-05
 Identities = 31/150 (20%), Positives = 37/150 (24%), Gaps = 5/150 (3%)

Query: 64  QPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQT-QPSMYYSSNQYNQNSMYPPMQPPL 122
                 +PP  PPP      P       P     T  P+               P  PP 
Sbjct: 60  AACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPP 119

Query: 123 PPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHD----PGH 178
            PPP S PP  +            P PP        G S     +    SR         
Sbjct: 120 TPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSP 179

Query: 179 SKQHRPPVPPPGVKKVNGGSGRVETEEERR 208
            +  R P  PP     +           RR
Sbjct: 180 EETARAPSSPPAEPPPSTPPAAASPRPPRR 209

Length = 1352

>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein

 Score = 46.3 bits (110), Expect = 5e-05
 Identities = 22/94 (23%), Positives = 27/94 (28%), Gaps = 17/94 (18%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
           P       P  P  +    + P  P+               GG    GGG       P  
Sbjct: 674 PSRVARGDPVRPTAHHAALRAPQAPRP--------------GGPPGGGGGLPPP---PDL 716

Query: 68  YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPS 101
            A   P P   S    P  PP P PP  +Q   +
Sbjct: 717 PAAAGPAPCGSSLIASPTAPPEPEPPGAEQADGA 750

Length = 753

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 45.8 bits (108), Expect = 5e-05
 Identities = 23/98 (23%), Positives = 29/98 (29%), Gaps = 24/98 (24%)

Query: 17  PPPPPNQNPSQPPP-------------PPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYH 63
           PP PP + P+   P              P+  QQ    NP  Q                 
Sbjct: 173 PPNPPREAPAPGLPKTFTSSHGHRHRHAPKPTQQPTVQNPAQQ-----------PTVQNP 221

Query: 64  QPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPS 101
                 QP   P   +  P P  P   PP T+Q  + S
Sbjct: 222 AQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRS 259

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional

 Score = 46.2 bits (109), Expect = 6e-05
 Identities = 34/142 (23%), Positives = 43/142 (30%), Gaps = 22/142 (15%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
           P P  P ++ P         +    PP     + RP        G +     A      P
Sbjct: 701 PTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARP---PAAAPGRARPPAAAPGRARPP 757

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPP 125
            +      PP      P P PPP  PP  QQ+                   P   P P P
Sbjct: 758 AAAPGRARPPAAAPGAPTPQPPPQAPPAPQQR-------------------PRGAPTPQP 798

Query: 126 PPSSPPPSSSIPPPPPPGSPPP 147
           PP + P S  + P   PG   P
Sbjct: 799 PPQAGPTSMQLMPRAAPGQQGP 820

Length = 991

>gnl|CDD|218397 pfam05044, Prox1, Homeobox prospero-like protein (PROX1)

 Score = 46.2 bits (109), Expect = 6e-05
 Identities = 30/144 (20%), Positives = 39/144 (27%), Gaps = 12/144 (8%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQP----PPPPQQQQQQQRPNPYSQNWGGYSNTGGG 57
           A Y      PQ+   P   P Q  +      P   + +    R  P + +         G
Sbjct: 551 ALYNSPFCMPQT-PQPQDAPEQTEALSLVVTPKKKRHKVTDTRITPRTVSRILALRDAVG 609

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPP 117
                H        P        + PPP   P P P          + S    +  M  P
Sbjct: 610 PAAGTHHQ---PLHPSSLSASMGFHPPPFRHPFPLPLTVAIPNPSLHQS----EVFMGYP 662

Query: 118 MQPPLPPPPPSSPPPSSSIPPPPP 141
            Q P    P  SPP      P  P
Sbjct: 663 FQSPHLGAPSGSPPGKDRDSPDLP 686

The homeobox gene Prox1 is expressed in a subpopulation of endothelial cells that, after budding from veins, gives rise to the mammalian lymphatic system. Prox1 has been found to be an early specific marker for the developing liver and pancreas in the mammalian foregut endoderm. This family contains an atypical homeobox domain. Length = 908

>gnl|CDD|220708 pfam10349, WWbp, WW-domain ligand protein

 Score = 42.4 bits (100), Expect = 6e-05
 Identities = 21/66 (31%), Positives = 25/66 (37%), Gaps = 2/66 (3%)

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPP 121
           Y+ P        P P    Y  PPP    PPP      P +Y +    N   M  P +PP
Sbjct: 46  YYPPPGAYVHLEPLPAYGQYAAPPP--YGPPPPYYPAPPGVYPTPPPPNSGYMADPQEPP 103

Query: 122 LPPPPP 127
            P P P
Sbjct: 104 PPYPGP 109

The WWbp domain is characterized by several short PY and PT-like motifs of the PPPPY form. These appear to bind directly to the WW domains of WWP1 and WWP2 and other such diverse proteins as dystrophin and YAP (Yes-associated protein). This is the WW-domain binding protein WWbp via PY and PY_like motifs. The presence of a phosphotyrosine residue in the pWBP-1 peptide abolishes WW domain binding which suggests a potential regulatory role for tyrosine phosphorylation in modulating WW domain-ligand interactions. Given the likelihood that WWP1 and WWP2 function as E3 ubiquitin-protein ligases, it is possible that initial substrate-specific recognition occurs via WW domain-substrate protein interaction followed by ubiquitin transfer and subsequent proteolysis. This domain lies just downstream of the GRAM (pfam02893) in many members. Length = 111

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.5 bits (108), Expect = 7e-05
 Identities = 17/78 (21%), Positives = 21/78 (26%), Gaps = 21/78 (26%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
             P  P  P  +  PP PP  P  P   +                   P   P PP    
Sbjct: 392 PTPAAPAAPPPAAAPPVPPAAPARPAAAR-------------------PAPAPAPPAAA- 431

Query: 129 SPPPSSSIPPPPPPGSPP 146
             PP+ S  P     +  
Sbjct: 432 -APPARSADPAAAASAGD 448

Length = 576

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 45.6 bits (108), Expect = 8e-05
 Identities = 27/144 (18%), Positives = 44/144 (30%), Gaps = 33/144 (22%)

Query: 6   PFPQPP-------QSSFPPPPPPNQNPSQPPPPPQQQQQ---QQRPNPYSQNWGGYSNTG 55
            +P+         Q    PP  P  +P+   P  ++ ++     RP  Y Q    Y +  
Sbjct: 157 AWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERDREPYDAGRPE-YDQRRRDYDHPR 215

Query: 56  GGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMY 115
                 + +P       P PPP + +     P PP                         
Sbjct: 216 P----DWDRPRRDRTDRPEPPPGAGHVHRGGPGPPERDDAPV------------------ 253

Query: 116 PPMQPPLPPPPPSSPPPSSSIPPP 139
            P++P  P P  + P P+     P
Sbjct: 254 VPIRPSAPGPLAAQPAPAPGPGEP 277

Length = 617

>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 44.9 bits (106), Expect = 8e-05
 Identities = 26/78 (33%), Positives = 32/78 (41%), Gaps = 14/78 (17%)

Query: 75  PPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSS 134
           P   ++ P PPPPPP                          PP  PP  PP P    P++
Sbjct: 34  PATANADPAPPPPPPSTAAAAPAPAAP--------------PPPPPPAAPPAPQPDDPNA 79

Query: 135 SIPPPPPPGSPPPPPPKD 152
           + PPPP   + PPPPP D
Sbjct: 80  APPPPPADPNAPPPPPVD 97

This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. Length = 297

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 45.8 bits (108), Expect = 8e-05
 Identities = 40/150 (26%), Positives = 50/150 (33%), Gaps = 7/150 (4%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
              QP   S    P  +      P PP Q Q   + +P                     P
Sbjct: 217 QPQQPSPLSLISAPSLHPQRLPSPHPPLQPQTASQQSPQPPAPSSRHPQSSHHGPGPPMP 276

Query: 66  YSYAQPPPPPPPESSYPPPP----PPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPP 121
           ++  Q P      SS PP P        PP P   Q QP  +   +Q       PP + P
Sbjct: 277 HALQQGPVFLQHPSSNPPQPFGLAQSQVPPLPLPSQAQPHSHTPPSQSALQPQQPPREQP 336

Query: 122 LPPPPPSS---PPPSSSIPPPPPPGSPPPP 148
           LPP P      PPP++ IP  P      PP
Sbjct: 337 LPPAPSMPHIKPPPTTPIPQLPNQSHKHPP 366

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.3 bits (108), Expect = 8e-05
 Identities = 35/211 (16%), Positives = 47/211 (22%), Gaps = 73/211 (34%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
              P +  P P P        P  P+ +Q    P+P                     P  
Sbjct: 371 ASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAK---------------ASPPI 415

Query: 68  YAQPPPPPPPESSYPPPPPPPP---------------PPPPTQ----QQTQ--------- 99
                P  P  +        PP                 P T+    QQ +         
Sbjct: 416 PVPAEPTEPSPTPPANAANAPPSLNLEELWQQILAKLELPSTRMLLSQQAELVSLDSNRA 475

Query: 100 --------PSMYYS----------------------SNQYNQNSMYPPMQPPLPPPPPSS 129
                     M  S                      S   + ++      PP   PPP +
Sbjct: 476 VIAVSPNWLGMVQSRKPLLEQAFAKVLGRSIKLNLESQSGSASNTAKTPPPPQKSPPPPA 535

Query: 130 PPPSSSIPPPPPPGSPPPPPPKDVEGRDTGT 160
           P P    P    P   PPPPP       +  
Sbjct: 536 PTPPLPQPTATAPPPTPPPPPPTATQASSNA 566

Length = 620

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.4 bits (108), Expect = 9e-05
 Identities = 18/122 (14%), Positives = 26/122 (21%), Gaps = 15/122 (12%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
                P    ++    P P    P       P                    P P P P+
Sbjct: 394 PAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAP---------------AAAPQPAPAPAPA 438

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPP 188
             PPS +   P      PPP            +   +  +          +    P  P 
Sbjct: 439 PAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPA 498

Query: 189 PG 190
             
Sbjct: 499 AP 500

Length = 824

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 45.0 bits (106), Expect = 9e-05
 Identities = 26/100 (26%), Positives = 32/100 (32%), Gaps = 15/100 (15%)

Query: 72  PPPPPPESSYPPPPPP---------PPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPL 122
           PP PP E+  P  P              P PTQQ T        N   Q ++  P Q P 
Sbjct: 173 PPNPPREAPAPGLPKTFTSSHGHRHRHAPKPTQQPTVQ------NPAQQPTVQNPAQQPQ 226

Query: 123 PPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSD 162
             P      P+    P  P   PP         R+ G  +
Sbjct: 227 QQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRSREQGNQE 266

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 20/112 (17%), Positives = 27/112 (24%), Gaps = 26/112 (23%)

Query: 1   MASYRPFPQPPQSSFPP-PPPPNQNPSQP-----PPPPQQQQQQQRPNPYSQNWGGYSNT 54
            AS +P     Q      PP     P+QP       P  Q Q +Q               
Sbjct: 96  YASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPEQPLQQP---------- 145

Query: 55  GGGAQQHYHQPYSYAQPPPPPPPESSYPPPP-------PPPPPPPPTQQQTQ 99
                             P P  ++  P  P       P   P P   +  +
Sbjct: 146 ---VSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPEPVAEPAPVMDKPKR 194

Length = 333

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 45.2 bits (107), Expect = 1e-04
 Identities = 44/213 (20%), Positives = 57/213 (26%), Gaps = 39/213 (18%)

Query: 3   SYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHY 62
           S  P         PP PPP    S PP P     +  RP                     
Sbjct: 105 SPTPPGPSSPDPPPPTPPP---ASPPPSPAPDLSEMLRP--------------------- 140

Query: 63  HQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPL 122
                    P PPP  S       P           Q ++  SS +            P 
Sbjct: 141 ------VGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSPE----ETARAPSSPP 190

Query: 123 PPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRH----DPGH 178
             PPPS+PP ++S P PP   SP              ++  D  AS   S        G 
Sbjct: 191 AEPPPSTPPAAAS-PRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGW 249

Query: 179 SKQHRPPVPPPGVKKVNGGSGRVETEEERRIRK 211
             ++  P+P P    +               R 
Sbjct: 250 GPENECPLPRPAPITLPTRIWEASGWNGPSSRP 282

Length = 1352

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 44.9 bits (107), Expect = 1e-04
 Identities = 22/127 (17%), Positives = 33/127 (25%), Gaps = 35/127 (27%)

Query: 35  QQQQQRPN-------PYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPP 87
           QQ    PN        +  ++G  S     A        + A    P     + P P PP
Sbjct: 16  QQYLADPNSVDPSWREFFADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPP 75

Query: 88  PPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPP 147
               P                              PP P ++   +++   PP   +   
Sbjct: 76  AAAAPAA----------------------------PPKPAAAAAAAAAPAAPPAAAAAAA 107

Query: 148 PPPKDVE 154
           P    VE
Sbjct: 108 PAAAAVE 114

Length = 1228

>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and modification]

 Score = 45.4 bits (107), Expect = 1e-04
 Identities = 15/22 (68%), Positives = 16/22 (72%)

Query: 72 PPPPPPESSYPPPPPPPPPPPP 93
          PPPPPP   + PP  PPPPPPP
Sbjct: 9  PPPPPPPPGFEPPSQPPPPPPP 30

Length = 2365

>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and modification]

 Score = 45.4 bits (107), Expect = 1e-04
 Identities = 16/22 (72%), Positives = 16/22 (72%)

Query: 71 PPPPPPPESSYPPPPPPPPPPP 92
          PPPPPPP    PP  PPPPPPP
Sbjct: 9  PPPPPPPPGFEPPSQPPPPPPP 30

Length = 2365

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 19/78 (24%), Positives = 22/78 (28%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
                     +S P  P P P P P     QPS   +       S  P    P  P P  
Sbjct: 361 PSAFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAE 420

Query: 129 SPPPSSSIPPPPPPGSPP 146
              PS + P       P 
Sbjct: 421 PTEPSPTPPANAANAPPS 438

Length = 620

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.2 bits (107), Expect = 1e-04
 Identities = 20/86 (23%), Positives = 26/86 (30%), Gaps = 17/86 (19%)

Query: 64  QPYSYAQPP----PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQ 119
           QP +  QP       P P  S     P  P        T P++          S+ PP  
Sbjct: 385 QPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTV----------SVDPPAA 434

Query: 120 PPLPPP---PPSSPPPSSSIPPPPPP 142
            P+ PP   P +  P         P 
Sbjct: 435 VPVNPPSTAPQAVRPAQFKEEKKIPV 460

Length = 614

>gnl|CDD|221501 pfam12273, RCR, Chitin synthesis regulation, resistance to Congo red

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 3/87 (3%)

Query: 67  SYAQPPPPPPPE---SSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLP 123
           ++  PP     +   ++ P   PP   PP T+   +  + Y   Q   +         L 
Sbjct: 38  AWLAPPSYRQSQQQYNNTPQGRPPQYVPPYTETANENDLGYYDGQGEFHPNPKAPAIELQ 97

Query: 124 PPPPSSPPPSSSIPPPPPPGSPPPPPP 150
           PPP +    + S         P  PPP
Sbjct: 98  PPPNAYERGTRSPTTDDEYQPPAGPPP 124

RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5. Length = 124

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 22/113 (19%), Positives = 27/113 (23%), Gaps = 11/113 (9%)

Query: 31  PPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPP-P 89
           P  +Q     P   +     Y   G   Q           P     P    P  P  P  
Sbjct: 380 PRMRQLPMGSPMGGAMGQPPYYGQGPQQQ---FNGQPLGWPRMSMMPTPMGPGGPLRPNG 436

Query: 90  PPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPP 142
             P    +             QN+   P   P+  PP     P S   P P  
Sbjct: 437 LAPMNAVRAPSRNA-------QNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQS 482

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 20/96 (20%), Positives = 27/96 (28%), Gaps = 8/96 (8%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
            A+  P   P  +  P P P   +P+   P            P        S     A  
Sbjct: 420 AAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAP--------SAQPAPAPA 471

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQ 96
              +P +   P PP  P  +  P  P  P  P    
Sbjct: 472 AAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGAD 507

Length = 824

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 44.7 bits (105), Expect = 2e-04
 Identities = 27/151 (17%), Positives = 34/151 (22%), Gaps = 6/151 (3%)

Query: 8   PQPPQSSFPPPPPPNQNPS---QPPPPPQQQQQQQRPNPYS-QNWGGYSNTGGGAQQHYH 63
           P            P   P+   QP P PQ  +    P P        Y+       +   
Sbjct: 339 PVTQTPPVASVDVPPAQPTVAWQPVPGPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQ 398

Query: 64  QPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLP 123
           QP    Q P   P        P   P P    QQ   +                 Q    
Sbjct: 399 QPVQ-PQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFA 457

Query: 124 PPPPSSPPPSSSIP-PPPPPGSPPPPPPKDV 153
           P        +   P    P    P P  +  
Sbjct: 458 PQSTYQTEQTYQQPAAQEPLYQQPQPVEQQP 488

Length = 1355

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 31/166 (18%), Positives = 43/166 (25%), Gaps = 28/166 (16%)

Query: 3   SYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHY 62
            Y  +  P     PP  P         P     QQ+  P  + +    Y     G QQ  
Sbjct: 117 PYEGYGGPRADDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPRAADDY-----GWQQ-- 169

Query: 63  HQPYSYAQPPPPPPPESSYPPPPPPPPPP--------PPTQQQTQPSMYYSSNQYNQNSM 114
            Q   +    P   P S  P       P            +    P      ++  ++  
Sbjct: 170 -QRLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRRDYDHPR--PDWDRPRRDRT 226

Query: 115 YPPMQPP----------LPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
             P  PP           PP    +P        P P  + P P P
Sbjct: 227 DRPEPPPGAGHVHRGGPGPPERDDAPVVPIRPSAPGPLAAQPAPAP 272

Length = 617

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 44.8 bits (106), Expect = 2e-04
 Identities = 43/213 (20%), Positives = 53/213 (24%), Gaps = 31/213 (14%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
           P    P S+    P P    S                     WG  +            P
Sbjct: 207 PRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLP 266

Query: 66  YSYAQ------PPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS------ 113
               +      P   P P SS   P    P P P+   + P+        + +S      
Sbjct: 267 TRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSS 326

Query: 114 -------------MYPPMQPPLPPPPPSSPPPSSSIPPPPPP----GSPPPPPPKDVEGR 156
                           P   P   P PS PPP +   P  P      S  P  P    GR
Sbjct: 327 SSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPA--DPSSPRKRPRPSRAPSSPAASAGR 384

Query: 157 DTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPP 189
            T    R   A +   R   G     RP   P 
Sbjct: 385 PTRRRARAAVAGRARRRDATGRFPAGRPRPSPL 417

Length = 1352

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 44.8 bits (106), Expect = 2e-04
 Identities = 26/143 (18%), Positives = 39/143 (27%), Gaps = 6/143 (4%)

Query: 16  PPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTG--GGAQQHYHQPYSYAQPPP 73
           P  P      S P       ++  R           S T     ++ H     S +  P 
Sbjct: 777 PAEPQRGAGSSPPVRAEAAFRRPGRLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPA 836

Query: 74  PPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPS 133
            PP  ++ PPP                     + +       P  +P    PP ++    
Sbjct: 837 RPPGAAARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAA- 895

Query: 134 SSIPPPPPPGSPPPPPPKDVEGR 156
              PP   P   P P P+   G 
Sbjct: 896 ---PPAGAPAPRPRPAPRVKLGP 915

Length = 1352

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 17/75 (22%), Positives = 22/75 (29%)

Query: 78  ESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIP 137
           ES           PPP Q+   P            +  PP  PP PP    +   + +  
Sbjct: 511 ESQSGSASNTAKTPPPPQKSPPPPAPTPPLPQPTATAPPPTPPPPPPTATQASSNAPAQI 570

Query: 138 PPPPPGSPPPPPPKD 152
           P      PP P    
Sbjct: 571 PADSSPPPPIPEEPT 585

Length = 620

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 32/154 (20%), Positives = 50/154 (32%), Gaps = 8/154 (5%)

Query: 72  PPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYN-QNSMYPPMQPPLPPPPPSSP 130
                P+    P    P   P        S   S +    Q S       P   PP  S 
Sbjct: 370 SGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSV 429

Query: 131 PPSSSIPPPPPPGSPPP-PPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPP 189
            P +++P  PP  +P    P +  E +    S   K +S   S   P   K  +      
Sbjct: 430 DPPAAVPVNPPSTAPQAVRPAQFKEEKKIPVS---KVSSLGPSTLRPIQEKAEQATG--- 483

Query: 190 GVKKVNGGSGRVETEEERRIRKKREYEKHRQEEK 223
            +K+   G+ +    EE      +E+   R +E+
Sbjct: 484 NIKEAPTGTQKEIFTEEDLQYYWQEFAGTRPQEE 517

Length = 614

>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 33/102 (32%), Positives = 34/102 (33%), Gaps = 15/102 (14%)

Query: 59  QQHYHQPYSYAQPP--------PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYN 110
           Q H+H P   AQ P        P P   S  P     P  P P QQ  QP       Q  
Sbjct: 53  QPHHHIPVLPAQQPVVPQQPLMPVPGQHSMTPTQHHQPNLPQPAQQPFQP-------QPL 105

Query: 111 QNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKD 152
           Q         P PP  P  P P     PP  P  P PP   D
Sbjct: 106 QPPQPQQPMQPQPPVHPIPPLPPQPPLPPMFPMQPLPPLLPD 147

They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide. Length = 165

>gnl|CDD|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA carboxylase

 Score = 43.7 bits (103), Expect = 2e-04
 Identities = 29/84 (34%), Positives = 31/84 (36%), Gaps = 27/84 (32%)

Query: 70  QPPPPPPPESSYPPPPP--PPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPP 127
           QPPPP P     PPPP   PP  PP  Q                         P P  P 
Sbjct: 143 QPPPPAPVVMMQPPPPHAMPPASPPAAQ-------------------------PAPSAPA 177

Query: 128 SSPPPSSSIPPPPPPGSPPPPPPK 151
           SSPPP+ + PPP        PP K
Sbjct: 178 SSPPPTPASPPPAKAPKSSHPPLK 201

Length = 274

>gnl|CDD|220950 pfam11029, DAZAP2, DAZ associated protein 2 (DAZAP2)

 Score = 41.8 bits (98), Expect = 2e-04
 Identities = 28/97 (28%), Positives = 34/97 (35%), Gaps = 9/97 (9%)

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPP 117
           A    +QP SY  PP    P++S P P P    P        P   +    Y      PP
Sbjct: 7   AYSELYQP-SYVVPPQAQMPQASAPYPGPSMYLPMAQVMAVGPQSSHPPMAYYPIGAPPP 65

Query: 118 MQPPLPPPPPSSP--------PPSSSIPPPPPPGSPP 146
           + PP                 P + S  PPPPPG  P
Sbjct: 66  VYPPGSTVLVQGGFDAGARFGPGTGSSIPPPPPGCAP 102

DAZ associated protein 2 has a highly conserved sequence throughout evolution including a conserved polyproline region and several SH2/SH3 binding sites. It occurs as a single copy gene with a four-exon organisation and is located on chromosome 12. It encodes a ubiquitously expressed protein and binds to DAZ and DAZL1 through DAZ repeats. Length = 136

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 31/180 (17%), Positives = 45/180 (25%), Gaps = 4/180 (2%)

Query: 9   QPPQSSFPPPPPPNQN----PSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
           QPPQ   P  P             P   QQQ  Q +    +Q         G A      
Sbjct: 192 QPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQGPADAQAQM 251

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
                      P +        P    PP QQ  Q  +    NQ  Q        P  P 
Sbjct: 252 GQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLGMLPNQMQQMPGGGQGGPGQPM 311

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRP 184
            PP   P +                 + ++          ++  ++  +    H   H+ 
Sbjct: 312 GPPPQRPGAVPQGGQAVQQGVMSAGQQQLKQMKLRNMRGQQQTQQQQQQQGGNHPAAHQQ 371

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau; Provisional

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 19/78 (24%), Positives = 26/78 (33%), Gaps = 1/78 (1%)

Query: 69  AQPPPPPPPESSYPPPPPPPPP-PPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPP 127
             P   P  +   P P  P P   P   +   P    +      ++  P  QPP+    P
Sbjct: 382 PSPAGSPDVKKKAPEPDLPQPDRHPGPAKPEAPGARPAELPSPASAPTPEQQPPVARSAP 441

Query: 128 SSPPPSSSIPPPPPPGSP 145
             P P +S P     G P
Sbjct: 442 LPPSPQASAPRNVASGKP 459

Length = 620

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.4 bits (103), Expect = 4e-04
 Identities = 19/81 (23%), Positives = 24/81 (29%)

Query: 9   QPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSY 68
               S+    PPP Q    PP P     Q     P              +     Q  + 
Sbjct: 514 SGSASNTAKTPPPPQKSPPPPAPTPPLPQPTATAPPPTPPPPPPTATQASSNAPAQIPAD 573

Query: 69  AQPPPPPPPESSYPPPPPPPP 89
           + PPPP P E +  P     P
Sbjct: 574 SSPPPPIPEEPTPSPTKDSSP 594

Length = 620

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 42.7 bits (100), Expect = 4e-04
 Identities = 23/105 (21%), Positives = 30/105 (28%), Gaps = 25/105 (23%)

Query: 28  PPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPP 87
           PP PP++      P  ++ + G          +H H P    QP    P +      P  
Sbjct: 173 PPNPPREAPAPGLPKTFTSSHG---------HRHRHAPKPTQQPTVQNPAQQPTVQNPAQ 223

Query: 88  PPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPP 132
            P   P QQ  Q                P  QP    P    P  
Sbjct: 224 QPQQQPQQQPVQ----------------PAQQPTPQNPAQQPPQT 252

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|223061 PHA03369, PHA03369, capsid maturational protease; Provisional

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 30/175 (17%), Positives = 47/175 (26%), Gaps = 9/175 (5%)

Query: 57  GAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYP 116
           G + H     + +   P     ++        P         Q         Y+  +  P
Sbjct: 340 GLKAHNEILKTASLTAPSRVLAAAAKVAVIAAPQTHTGPADRQRPQRPDGIPYSVPARSP 399

Query: 117 PMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDP 176
               P  P     P   S   P  P  S  P P   V  + T         +  V    P
Sbjct: 400 MTAYPPVPQFCGDPGLVSPYNPQSPGTSYGPEPVGPVPPQPTNPYVMPISMANMVYPGHP 459

Query: 177 GHSKQHRPPVPPPGVKKVNGGSGRVETEEER-RIRKKREYEKHRQEEKHRLQMKE 230
                 R        K+  GG  + E  E    ++K +E ++   +E      K 
Sbjct: 460 QEHGHER--------KRKRGGELKEELIETLKLVKKLKEEQESLAKELEATAHKS 506

Length = 663

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 21/127 (16%), Positives = 37/127 (29%), Gaps = 1/127 (0%)

Query: 63  HQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPL 122
            +P   A   PP   E+++  P       P     ++ +    S  +  +       P  
Sbjct: 778 AEPQRGAGSSPPVRAEAAFRRPGRLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPAR 837

Query: 123 PPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQH 182
           PP   + PPP+ S        +      +   GR       + RA    +      +   
Sbjct: 838 PPGAAARPPPARSSESSKSKPAAAGGRARGKNGRR-RPRPPEPRARPGAAAPPKAAAAAP 896

Query: 183 RPPVPPP 189
               P P
Sbjct: 897 PAGAPAP 903

Length = 1352

>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein (LMP2) protein

 Score = 42.9 bits (101), Expect = 5e-04
 Identities = 29/123 (23%), Positives = 35/123 (28%), Gaps = 37/123 (30%)

Query: 25  PSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPP--PPPPPESSYP 82
           P     P        R +      GG     G +  +Y  P S+      P PP    Y 
Sbjct: 8   PLGAGGP--------RSH------GGPDGDEGDSNPYY--PSSFGSSWDRPGPPVPEDYD 51

Query: 83  PPPPPPPP----------PPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPP 132
            P   PPP                Q  PS+Y    Q     +         PPPP SP  
Sbjct: 52  APSHRPPPYGGSNGDRHGGYQPLGQQDPSLYAGLGQNGGGGL---------PPPPYSPRD 102

Query: 133 SSS 135
             S
Sbjct: 103 QGS 105

This family consists of several Gammaherpesvirus latent membrane protein (LMP2) proteins. Epstein-Barr virus is a human Gammaherpesvirus that infects and establishes latency in B lymphocytes in vivo. The latent membrane protein 2 (LMP2) gene is expressed in latently infected B cells and encodes two protein isoforms, LMP2A and LMP2B, that are identical except for an additional N-terminal 119 aa cytoplasmic domain which is present in the LMP2A isoform. LMP2A is thought to play a key role in either the establishment or the maintenance of latency and/or the reactivation of productive infection from the latent state. The significance of LMP2B and its role in pathogenesis remain unclear. Length = 489

>gnl|CDD|217310 pfam02993, MCPVI, Minor capsid protein VI

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 21/110 (19%), Positives = 30/110 (27%), Gaps = 19/110 (17%)

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
             +    P P   E   P  P PP      +                     P++ P+  
Sbjct: 126 IQALQPRPRPDVEEVLVPAAPEPPSYEETIKP-----------------GPAPVEEPVDS 168

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRH 174
              + P   + +    PP   PPPP   V    T    R  R  +  S  
Sbjct: 169 MAIAVPAIDTPVTLELPPAPQPPPPV--VPQPSTMVVHRRSRIKRTRSSG 216

This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. The C-terminal 11 residues may function as a protease cofactor leading to enzyme activation. Length = 238

>gnl|CDD|114709 pfam06003, SMN, Survival motor neuron protein (SMN)

 Score = 41.9 bits (98), Expect = 5e-04
 Identities = 36/121 (29%), Positives = 46/121 (38%), Gaps = 18/121 (14%)

Query: 28  PPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPP 87
            PPP   +   +  N    N    S        H H+  S +  P  PP   +   PP P
Sbjct: 120 TPPPDVDEDALKEAN---VNETESSTDESDRSSHSHEVRSKSNFPMGPPSPWNPRFPPGP 176

Query: 88  PPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPP 147
           PPPPP   +  +           + S +PP     PPP P  PP    + PPPPP SP  
Sbjct: 177 PPPPPGFGRHGE-----------KPSGWPPFLSGWPPPFPLGPP----MIPPPPPMSPDF 221

Query: 148 P 148
            
Sbjct: 222 G 222

This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs. Length = 264

>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth

 Score = 40.9 bits (96), Expect = 6e-04
 Identities = 35/132 (26%), Positives = 39/132 (29%), Gaps = 30/132 (22%)

Query: 19  PPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPE 78
            P +  P  P   P   QQ   P P                QH   P  + QP  P P +
Sbjct: 53  QPHHHIPVLPAQQPVVPQQPLMPVP---------------GQHSMTPTQHHQPNLPQPAQ 97

Query: 79  SSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPP 138
             + P P  PP P    Q   P                   PPLPP PP  P       P
Sbjct: 98  QPFQPQPLQPPQPQQPMQPQPP---------------VHPIPPLPPQPPLPPMFPMQPLP 142

Query: 139 PPPPGSPPPPPP 150
           P  P  P    P
Sbjct: 143 PLLPDLPLEAWP 154

They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide. Length = 165

>gnl|CDD|221501 pfam12273, RCR, Chitin synthesis regulation, resistance to Congo red

 Score = 39.8 bits (93), Expect = 7e-04
 Identities = 20/84 (23%), Positives = 26/84 (30%), Gaps = 10/84 (11%)

Query: 16  PPPPPPNQNP--SQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPP 73
            PP         +  P     Q         ++N  GY +  G    +   P    QPPP
Sbjct: 41  APPSYRQSQQQYNNTPQGRPPQYVPPYTETANENDLGYYDGQGEFHPNPKAPAIELQPPP 100

Query: 74  --------PPPPESSYPPPPPPPP 89
                    P  +  Y PP  PPP
Sbjct: 101 NAYERGTRSPTTDDEYQPPAGPPP 124

RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5. Length = 124

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 41.6 bits (98), Expect = 8e-04
 Identities = 20/119 (16%), Positives = 27/119 (22%), Gaps = 9/119 (7%)

Query: 82  PPPPPPPPP------PPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSS 135
            P P PP           T           ++  + +   PP   P  P  PS P   SS
Sbjct: 147 DPNPGPPLDEEDEDADVATTNSDNSFPGEDADPASASPSDPPSSSPGVPSFPSPPEDPSS 206

Query: 136 IPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSK---QHRPPVPPPGV 191
                 P +P               ++             P           P PP   
Sbjct: 207 PSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTPPSAS 265

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.0 bits (99), Expect = 9e-04
 Identities = 18/87 (20%), Positives = 23/87 (26%), Gaps = 24/87 (27%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
           A    P P   + PPP   PP PP    +                  P    P P P P 
Sbjct: 387 AAWGAPTPAAPAAPPPAAAPPVPPAAPAR------------------PAAARPAPAPAPP 428

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKDVEG 155
           +         PP   + P       + 
Sbjct: 429 AA------AAPPARSADPAAAASAGDR 449

Length = 576

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 25/101 (24%), Positives = 33/101 (32%), Gaps = 19/101 (18%)

Query: 3   SYRPFPQPPQSSFPPPPPPNQNPSQPPPP-----PQQQQQQQRPNPYSQNWGGYSNTGGG 57
           +  P    P+ + P P P  Q   QP P      P   Q    P P              
Sbjct: 111 AQVPPQHAPRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHS----------- 159

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQT 98
           A Q   Q +  A+P   P PE   P   P P    P +++ 
Sbjct: 160 APQPAQQAFQPAEPVAAPQPE---PVAEPAPVMDKPKRKEA 197

Length = 333

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 34/151 (22%), Positives = 37/151 (24%), Gaps = 17/151 (11%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
           +P PQ PQ      PP      Q PPP  Q   Q                          
Sbjct: 142 QPPPQVPQQQQYQSPPQQPQYQQNPPPQAQSAPQVSG-----------------LYPEES 184

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
           PY     PP  P  SS    PP    PP  Q    P                       P
Sbjct: 185 PYQPQSYPPNEPLPSSMAMQPPYSGAPPSQQFYGPPQPSPYMYGGPGGRPNSGFPSGQQP 244

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPPPPKDVEG 155
           PP           PPP  G+         +G
Sbjct: 245 PPSQGQEGYGYSGPPPSKGNHGSVASYAPQG 275

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 16/93 (17%), Positives = 21/93 (22%), Gaps = 9/93 (9%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQH 61
           A+    P  P ++ PP P      + P   P          P              A   
Sbjct: 408 AAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPP---------AQAAPE 458

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPT 94
                    P P     +  P   P      PT
Sbjct: 459 TVAIPVRVAPEPAVASAAPAPAAAPAAARLTPT 491

Length = 618

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.8 bits (98), Expect = 0.001
 Identities = 24/140 (17%), Positives = 35/140 (25%), Gaps = 1/140 (0%)

Query: 49  GGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQ 108
           GG +     A     QP   A  P    P  +  PP  P   P         +   +   
Sbjct: 369 GGGAGPATAAAAPVAQPAPAAAAPAAAAPAPA-APPAAPAAAPAAAAAARAVAAAPARRS 427

Query: 109 YNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRAS 168
               ++    Q     P  +  P  +    P     P    P+ V         R   A+
Sbjct: 428 PAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAA 487

Query: 169 KEVSRHDPGHSKQHRPPVPP 188
                 D     +  PP   
Sbjct: 488 APAPADDDPPPWEELPPEFA 507

Length = 700

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 21/113 (18%), Positives = 32/113 (28%), Gaps = 19/113 (16%)

Query: 52  SNTGGGAQQHYHQPYSYAQPPPPPPPESSYPP---PPPPPPPPPPTQQQTQPSMYYSSNQ 108
             +GGGA      P + A  P   P  ++  P    P P  PP         +    +  
Sbjct: 366 GQSGGGAG-----PATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVA 420

Query: 109 YNQNSMYPPMQP-----------PLPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
                  P  +            P   P P+  P ++      P  + P P  
Sbjct: 421 AAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVA 473

Length = 700

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 26/122 (21%), Positives = 29/122 (23%), Gaps = 13/122 (10%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPN---PYSQNWGGYSNTGGG 57
                P+            P         P P       RPN   P +       N    
Sbjct: 394 AMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNA 453

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPP 117
           AQ+   QP  Y      PP   S P     P P     Q  Q             S  P 
Sbjct: 454 AQKPPMQPVMY------PPNYQSLPLSQDLPQPQSTASQGGQNKKLAQVLA----SATPQ 503

Query: 118 MQ 119
           MQ
Sbjct: 504 MQ 505

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein (LMP2) protein

 Score = 41.8 bits (98), Expect = 0.001
 Identities = 29/125 (23%), Positives = 33/125 (26%), Gaps = 27/125 (21%)

Query: 3   SYRP--FPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
            Y P  F        PP P     PS  PPP                 GGY   G     
Sbjct: 29  PYYPSSFGSSWDRPGPPVPEDYDAPSHRPPPYG--------GSNGDRHGGYQPLGQQDPS 80

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
            Y           PPPP   Y P           + Q    +Y    +     M PP  P
Sbjct: 81  LYAGLGQNGGGGLPPPP---YSP-----------RDQGSEHVY---EEPRDARMVPPWLP 123

Query: 121 PLPPP 125
            +  P
Sbjct: 124 VICAP 128

This family consists of several Gammaherpesvirus latent membrane protein (LMP2) proteins. Epstein-Barr virus is a human Gammaherpesvirus that infects and establishes latency in B lymphocytes in vivo. The latent membrane protein 2 (LMP2) gene is expressed in latently infected B cells and encodes two protein isoforms, LMP2A and LMP2B, that are identical except for an additional N-terminal 119 aa cytoplasmic domain which is present in the LMP2A isoform. LMP2A is thought to play a key role in either the establishment or the maintenance of latency and/or the reactivation of productive infection from the latent state. The significance of LMP2B and its role in pathogenesis remain unclear. Length = 489

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 41.5 bits (98), Expect = 0.001
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQ 38
           PQPP+   PPPPPP ++   PP   ++Q   
Sbjct: 262 PQPPEEEPPPPPPPPEDDDDPPEDEEEQDDA 292

Length = 584

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 35/176 (19%), Positives = 46/176 (26%), Gaps = 39/176 (22%)

Query: 5   RPFPQPPQSSFPP--PPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHY 62
           RP P    SS     P P   +P   P P             S +      +   +    
Sbjct: 281 RPGPASSSSSPRERSPSPSPSSPGSGPAPS--------SPRASSSSSSSRESSSSSTSSS 332

Query: 63  HQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQ-------------Y 109
            +    A   P P P  S  P  PPPP  P + ++        S+               
Sbjct: 333 SESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARA 392

Query: 110 NQNSMYPPMQPP-------LPPPPPSSPPPSSSIPPPPP---------PGSPPPPP 149
                                P P  +   S +     P         PGSPPPPP
Sbjct: 393 AVAGRARRRDATGRFPAGRPRPSPLDAGAASGAFYARYPLLTPSGEPWPGSPPPPP 448

Length = 1352

>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183)

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 21/99 (21%), Positives = 23/99 (23%), Gaps = 16/99 (16%)

Query: 3   SYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTG---GGA- 58
                P PP   F    PP   P   P         +        WG    TG   GGA 
Sbjct: 207 GGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGSGGTRSG---QGGWGPGFWTGLGAGGAL 263

Query: 59  --------QQHYHQPYSYAQP-PPPPPPESSYPPPPPPP 88
                     +     SY    P   P  SS        
Sbjct: 264 GYLFGSRRNNNSSYGRSYGSGSPSYSPSSSSNSSSSSSS 302

This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown. Length = 317

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 41.4 bits (98), Expect = 0.002
 Identities = 11/99 (11%), Positives = 17/99 (17%), Gaps = 13/99 (13%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQH 61
           A Y P       +           +    P  +      P                A   
Sbjct: 34  ADYGP-GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAP------------APPAAAAP 80

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQP 100
              P   A       P +         P     + +  P
Sbjct: 81  AAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEVTP 119

Length = 1228

>gnl|CDD|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA carboxylase

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 27/97 (27%), Positives = 29/97 (29%), Gaps = 41/97 (42%)

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
               P  +A PP  PP     P P  P   PPPT                         P
Sbjct: 152 MMQPPPPHAMPPASPPAAQ--PAPSAPASSPPPT-------------------------P 184

Query: 121 PLPPPPPSSPPPSSSIPP-----------PPPPGSPP 146
             PPP  +   P SS PP            P PG PP
Sbjct: 185 ASPPPAKA---PKSSHPPLKSPMAGTFYRSPAPGEPP 218

Length = 274

>gnl|CDD|220950 pfam11029, DAZAP2, DAZ associated protein 2 (DAZAP2)

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 27/84 (32%), Positives = 31/84 (36%), Gaps = 8/84 (9%)

Query: 72  PPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPP 131
           P  PP  S    P    PP     Q + P        Y   SMY PM   +   P SS P
Sbjct: 2   PDAPPAYSELYQPSYVVPPQAQMPQASAP--------YPGPSMYLPMAQVMAVGPQSSHP 53

Query: 132 PSSSIPPPPPPGSPPPPPPKDVEG 155
           P +  P   PP   PP     V+G
Sbjct: 54  PMAYYPIGAPPPVYPPGSTVLVQG 77

DAZ associated protein 2 has a highly conserved sequence throughout evolution including a conserved polyproline region and several SH2/SH3 binding sites. It occurs as a single copy gene with a four-exon organisation and is located on chromosome 12. It encodes a ubiquitously expressed protein and binds to DAZ and DAZL1 through DAZ repeats. Length = 136

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 12/30 (40%), Positives = 14/30 (46%)

Query: 72  PPPPPPESSYPPPPPPPPPPPPTQQQTQPS 101
           P PP P    PPPPPPPP       + +  
Sbjct: 259 PAPPQPPEEEPPPPPPPPEDDDDPPEDEEE 288

Length = 584

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 16/75 (21%), Positives = 24/75 (32%), Gaps = 3/75 (4%)

Query: 71  PPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSP 130
            P    P +S  P     P P    QQ       + +Q N ++   P       P  ++P
Sbjct: 180 APVDTTPTNSQTPAVATAPAPAVDPQQNAVV---APSQANVDTAATPAPAAPATPDGAAP 236

Query: 131 PPSSSIPPPPPPGSP 145
            P+       P   P
Sbjct: 237 LPTDQAGVSTPAADP 251

Length = 331

>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 14/40 (35%), Positives = 15/40 (37%), Gaps = 2/40 (5%)

Query: 115 YPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVE 154
             P    LP P P  PPP    PP PP     P  P   +
Sbjct: 259 LLPRATRLPEPEPQPPPPPP--PPEPPEPEEEPDEPDQTD 296

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll]. Length = 589

>gnl|CDD|234178 TIGR03354, VI_FHA, type VI secretion system FHA domain protein

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 18/92 (19%), Positives = 26/92 (28%), Gaps = 10/92 (10%)

Query: 74  PPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLP--PPPPSSPP 131
           P       P P P     P      +P         + + +  P+ PPL    P  ++P 
Sbjct: 122 PTAGGPPTPDPAPLAQLDPLKALDQEPLSAA-----DLDDLSAPLFPPLDARLPAFAAPI 176

Query: 132 PSSSI---PPPPPPGSPPPPPPKDVEGRDTGT 160
            +      P  P P   P P P          
Sbjct: 177 DAEPTMVPPFVPLPAPEPAPAPASQAPSSDAV 208

Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis]. Length = 396

>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 22/82 (26%), Positives = 26/82 (31%), Gaps = 2/82 (2%)

Query: 11  PQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQ 70
           P +  PPPP     P  PP                     ++    G           + 
Sbjct: 183 PGAIQPPPPSS--LPGLPPGSSSLAPSASSTPGNRLPRVSFNPFLPGPSPAQPSAPPASI 240

Query: 71  PPPPPPPESSYPPPPPPPPPPP 92
           P PP PP   Y  PPP PPP P
Sbjct: 241 PAPPIPPVIQYVAPPPVPPPQP 262

Length = 582

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.2 bits (95), Expect = 0.003
 Identities = 18/80 (22%), Positives = 24/80 (30%), Gaps = 14/80 (17%)

Query: 77  PESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSI 136
           P +  P P  PP    P       +               P     PP  P+ PPP +S 
Sbjct: 361 PAAPLPEPEVPPQSAAPAASAQATA--------------APTAAVAPPQAPAVPPPPASA 406

Query: 137 PPPPPPGSPPPPPPKDVEGR 156
           P   P    P    + +  R
Sbjct: 407 PQQAPAVPLPETTSQLLAAR 426

Length = 647

>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D

 Score = 40.2 bits (94), Expect = 0.003
 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 7/61 (11%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYP-----PMQPPLP 123
           A   P P P+   PPPPPPP PP P ++  +P      +    + +        ++  LP
Sbjct: 263 ATRLPEPEPQP--PPPPPPPEPPEPEEEPDEPDQTDPDDGEETDQIPEELMFDAVEADLP 320

Query: 124 P 124
            
Sbjct: 321 D 321

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll]. Length = 589

>gnl|CDD|166942 PRK00404, tatB, sec-independent translocase; Provisional

 Score = 38.3 bits (89), Expect = 0.003
 Identities = 24/84 (28%), Positives = 27/84 (32%), Gaps = 23/84 (27%)

Query: 68  YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPP 127
            A   PP PPE   PP    P P  PT                         P   P  P
Sbjct: 79  LAPLTPPAPPEPVTPPTAQSPAPAVPTPP-----------------------PTSTPAVP 115

Query: 128 SSPPPSSSIPPPPPPGSPPPPPPK 151
            +P  +   P   PP S PP PP+
Sbjct: 116 PAPAAAVPAPAAAPPPSDPPQPPR 139

Length = 141

>gnl|CDD|236940 PRK11633, PRK11633, cell division protein DedD; Provisional

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 17/81 (20%), Positives = 21/81 (25%), Gaps = 15/81 (18%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
           A  P   P   + P  P  P P P    + +P                    P P P   
Sbjct: 80  AAAPSLDPATVAPPNTPVEPEPAPVEPPKPKPV---------------EKPKPKPKPQQK 124

Query: 129 SPPPSSSIPPPPPPGSPPPPP 149
              P +  P P P       P
Sbjct: 125 VEAPPAPKPEPKPVVEEKAAP 145

Length = 226

>gnl|CDD|217453 pfam03251, Tymo_45kd_70kd, Tymovirus 45/70Kd protein

 Score = 40.1 bits (94), Expect = 0.003
 Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 2/89 (2%)

Query: 63  HQPYSYAQPPPPPPPESSYPPPPPPPPP--PPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
                  +  P PPP+    P     P     P+     P     S+    +S +  + P
Sbjct: 361 PPTKRRLRLLPVPPPKVQALPLTALAPLVRHSPSIPLPHPPSALPSHVGASSSKHHRLPP 420

Query: 121 PLPPPPPSSPPPSSSIPPPPPPGSPPPPP 149
            + P P  S P  S   P   PG+PPPP 
Sbjct: 421 SVLPGPRLSSPSPSPSLPTRRPGTPPPPA 449

Tymoviruses are single stranded RNA viruses. This family includes a protein of unknown function that has been named based on its molecular weight. Tymoviruses such as the ononis yellow mosaic tymovirus encode only three proteins. Of these two are overlapping this protein overlaps a larger ORF that is thought to be the polymerase. Length = 458

>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.3 bits (95), Expect = 0.003
 Identities = 9/70 (12%), Positives = 15/70 (21%)

Query: 73  PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPP 132
           PP P      PP     P  P       +   +       +    +            P 
Sbjct: 391 PPSPGGGGGGPPGGGGAPGAPAAAAAPGAAAAAPAAGGPAAALAAVPDAAAAAAAPPAPA 450

Query: 133 SSSIPPPPPP 142
           ++  P     
Sbjct: 451 AAPQPAVRLN 460

Length = 598

>gnl|CDD|234977 PRK01741, PRK01741, cell division protein ZipA; Provisional

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 20/146 (13%), Positives = 38/146 (26%), Gaps = 27/146 (18%)

Query: 11  PQSSFP-------PPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYH 63
           P +  P       PPP       +     + Q QQ+      +      N         H
Sbjct: 58  PNTLNPQSYVETTPPPFQQPQTEESESENEVQIQQEVEQSVDEIKITLPNQEPAYYMQNH 117

Query: 64  Q--PYSYAQPPPPPPPESSYPPPPPPPPPPP-------------PTQQQTQPSMYYSSN- 107
           +  P    QP    P +++           P                +  + +    S+ 
Sbjct: 118 RSEPIQPTQPQYQSPTQTNVASMTIEETQSPNVPIEGINSSSEQLRVELAELAAEIYSDA 177

Query: 108 ----QYNQNSMYPPMQPPLPPPPPSS 129
               +  +N M P  +    P   ++
Sbjct: 178 SHRVELAKNFMEPQAETEAQPEATTN 203

Length = 332

>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 40.1 bits (94), Expect = 0.003
 Identities = 20/76 (26%), Positives = 24/76 (31%), Gaps = 13/76 (17%)

Query: 82  PPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPP 141
           PP   P        ++T P               P    P P PP +S P   +   PP 
Sbjct: 124 PPAAAPAAAAAAKAEKTTPEK-------------PKAAAPTPEPPAASKPTPPAAAKPPE 170

Query: 142 PGSPPPPPPKDVEGRD 157
           P     PPP  V   D
Sbjct: 171 PAPAAKPPPTPVARAD 186

Length = 418

>gnl|CDD|221818 pfam12868, DUF3824, Domain of unknwon function (DUF3824)

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 24/78 (30%), Positives = 29/78 (37%), Gaps = 11/78 (14%)

Query: 73  PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPP 132
                E  Y P P PP PP                 Y  ++ +PP     P PPP   P 
Sbjct: 46  YSDSYEEPYDPTPYPPSPPVS-----------DPRYYPNSNYFPPPPGSTPVPPPGPQPG 94

Query: 133 SSSIPPPPPPGSPPPPPP 150
            +    PPPPG+ PPP  
Sbjct: 95  YNPADYPPPPGAVPPPQN 112

This is a repeating domain found in fungal proteins. It is proline-rich, and the function is not known. Length = 135

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 33/141 (23%), Positives = 40/141 (28%), Gaps = 13/141 (9%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQ--------QQRPNPYSQNWGGYSN 53
           A   P          P  P +  P++P P     Q         QQ   P   +   Y  
Sbjct: 170 AQSAPQVSGLYPEESPYQPQSYPPNEPLPSSMAMQPPYSGAPPSQQFYGPPQPSPYMYGG 229

Query: 54  TGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS 113
            GG     +       QPPP    E      PPP      +     P    SS  Y+   
Sbjct: 230 PGGRPNSGFPSGQ---QPPPSQGQEGYGYSGPPPSKGNHGSVASYAPQ--GSSQSYSTAY 284

Query: 114 MYPPMQPPLPPPPPSSPPPSS 134
              P    LP   P S  P S
Sbjct: 285 PSLPAATVLPQALPMSSAPMS 305

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 39.5 bits (92), Expect = 0.004
 Identities = 27/86 (31%), Positives = 29/86 (33%), Gaps = 25/86 (29%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
           P PP S+    P P   P  PPP      Q   PN                         
Sbjct: 44  PPPPPSTAAAAPAPAAPPPPPPPAAPPAPQPDDPNA------------------------ 79

Query: 68  YAQPPPPPPPESSYPPPPPPPPPPPP 93
            A PPPP  P +  PPP  P  PPPP
Sbjct: 80  -APPPPPADPNAPPPPPVDPNAPPPP 104

This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. Length = 297

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 21/125 (16%), Positives = 29/125 (23%), Gaps = 14/125 (11%)

Query: 11  PQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQ-QHYHQPYSYA 69
           P+    P   P    +   PP   Q  QQ+ N     W   S            +P   A
Sbjct: 380 PRMRQLPMGSPMG-GAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLA 438

Query: 70  QPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSS 129
                  P  +       PP  P                Y    +   +  P P    S 
Sbjct: 439 PMNAVRAPSRNAQNAAQKPPMQP----------VMYPPNYQSLPLSQDL--PQPQSTASQ 486

Query: 130 PPPSS 134
              + 
Sbjct: 487 GGQNK 491

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 12/32 (37%), Positives = 12/32 (37%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQP 100
           A   P PP      PPPPPPPP          
Sbjct: 255 ATRLPAPPQPPEEEPPPPPPPPEDDDDPPEDE 286

Length = 584

>gnl|CDD|223035 PHA03294, PHA03294, envelope glycoprotein H; Provisional

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 14/103 (13%), Positives = 22/103 (21%), Gaps = 14/103 (13%)

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSN--------QYNQNS 113
           +  P +    P           P   P    P        +  + N             S
Sbjct: 95  FVLPTALLGQPTF------AKLPARAPTGRLPPPVAPLSGLLGNPNLAPYLRTRHLVDFS 148

Query: 114 MYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGR 156
           + P  +         S   ++   P      PP  PP      
Sbjct: 149 VVPDPRSLTRWVFDRSDTAATKAHPSGVALPPPRAPPPRNTTD 191

Length = 835

>gnl|CDD|185628 PTZ00449, PTZ00449, 104 kDa microneme/rhoptry antigen; Provisional

 Score = 40.1 bits (93), Expect = 0.004
 Identities = 34/158 (21%), Positives = 52/158 (32%), Gaps = 18/158 (11%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPP---PPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
           P+ P++S  PP  P     +        +  + ++   P     G      G A++H   
Sbjct: 511 PEGPEASGLPPKAPGDKEGEEGEHEDSKESDEPKEGGKPGETKEGEVGKKPGPAKEHKPS 570

Query: 65  -----------PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS 113
                      P     P  P  P+    P     P  P + +  +      S +  ++ 
Sbjct: 571 KIPTLSKKPEFPKDPKHPKDPEEPKKPKRPRSAQRPTRPKSPKLPELLDIPKSPKRPESP 630

Query: 114 MYPPMQPPLPPPPPSSP--PPSSSIPPPPPPGSPPPPP 149
             P  + P PP  PSSP  P    I   P P   P PP
Sbjct: 631 KSP--KRPPPPQRPSSPERPEGPKIIKSPKPPKSPKPP 666

Length = 943

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	677
PF03985	436	Paf1: Paf1 ; InterPro: IPR007133 Members of this f	100.0
KOG2478	452	consensus Putative RNA polymerase II regulator [Tr	100.0
KOG2478	452	consensus Putative RNA polymerase II regulator [Tr	99.46
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	98.7
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	98.48
KOG1923	830	consensus Rac1 GTPase effector FRL [Signal transdu	97.71
PHA03247	3151	large tegument protein UL36; Provisional	96.82
KOG3671	569	consensus Actin regulatory protein (Wiskott-Aldric	96.68
KOG1830	518	consensus Wiskott Aldrich syndrome proteins [Cytos	95.01
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	87.24
KOG1923	830	consensus Rac1 GTPase effector FRL [Signal transdu	86.13
KOG2236	483	consensus Uncharacterized conserved protein [Funct	80.73
KOG2236	483	consensus Uncharacterized conserved protein [Funct	80.3

>PF03985 Paf1: Paf1 ; InterPro: IPR007133 Members of this family are components of the RNA polymerase II associated Paf1 complex

Probab=100.00  E-value=1.4e-73  Score=624.41  Aligned_cols=357  Identities=34%  Similarity=0.610  Sum_probs=265.6

Q ss_pred             cccccccccccCCCCCCCCCceeeccC-CccccccCcCcchhhccCCCCcc--CCCCCcccccC--------CccCCCCC
Q 005794          279 TTFLCKLKFRNELPEPSAQPKLMALKK-DKDRFTRYTFSSLEKNYKPQLHV--EPDLGIPLDLL--------DLSVYNPP  347 (677)
Q Consensus       279 ~~fi~~iry~N~LP~pP~~PKLL~~p~-d~~r~t~y~~tSLe~~~k~~i~~--D~DLGmPLDLi--------~~~~Y~~p  347 (677)
                      ++|||+|||+|+||+|||+||||.|++ +..+++.|.++||++++++.|++  |+|||||||||        |.++|+.+
T Consensus         1 qd~i~~iry~N~LP~pp~~pK~L~~p~~~~~~~~~~~~tsL~~~~~~~~l~~~d~dlGmplDLi~~~g~~~~d~~~~~~~   80 (436)
T PF03985_consen    1 QDFICRIRYRNNLPPPPFPPKFLDIPFTDEQRFSPYFATSLEREYKFNILVEVDADLGMPLDLIGIPGVFEGDPSAYNAP   80 (436)
T ss_pred             CceeeeeeecCCCcccCCCCeeecCCCCchhccccchhhhHHHhcCcceecccccccCcccccccccCcccCChhhcCCC
Confidence            689999999999999999999999999 78999999999999999999966  99999999999        77888887


Q ss_pred             CCCCCCChhhhhccCCCCccCcccccCCcccCCCCCCCccCccccccccccchhhhhchhhHHHHHHHHhhhcCCchh--
Q 005794          348 SVRPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSIL--  425 (677)
Q Consensus       348 d~~~~LdPeD~aLLrD~e~~~p~~s~Gi~kksR~~~~~VSWLRRTEYISs~~~~~~~~~~t~kqake~~E~k~G~~~~--  425 (677)
                      ...++|||+|++||+|+.++         ++++.++++|||||||||||++.++.+ .+.      ...+.+.|+.+.  
T Consensus        81 ~~~~~L~p~D~~LL~d~~~~---------~~~~~~~~~VswLRrTeYiS~~~~~~~-~~~------~~~~~~~~~~~~~~  144 (436)
T PF03985_consen   81 PNNPPLDPEDRALLRDPGAL---------KRSKPDAKNVSWLRRTEYISSEFTRKG-QSK------EKSEAKRGRNVKKK  144 (436)
T ss_pred             CCCCCCCHHHHHHhcCcccc---------ccccCCcCCCcccccceeecccccccc-ccc------cchhhccccccccc
Confidence            77889999999999998653         246667789999999999999876543 111      112233443332  


Q ss_pred             ----ccccCHHHHHHHHHhhHHHHhc---CCCCCCCCCCceeEeecCCCCcccccCceEEEEEcCCCCCCchhhcccChh
Q 005794          426 ----ENLNDRERQIKEIEASFEACKL---RPIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKS  498 (677)
Q Consensus       426 ----~~~~dresQI~aIEkTFeaAkk---~lkHPtKpnLkaVev~PLLPD~d~w~n~Yv~VkFD~dPs~~~e~~~kl~~s  498 (677)
                          +.+.++++||++||+||++|++   .++||||||||||++|||||||++|++.|++|+||++|+.+.....    .
T Consensus       145 ~~~~~~~~d~~~qi~~Ie~tF~~a~~~~~~~~HPtK~~lk~Ve~~PllPD~~~~~~~y~~v~Fd~~P~~~~~~~~----~  220 (436)
T PF03985_consen  145 FKEEELYNDRESQIRAIEKTFEAAKKDLPRLKHPTKPNLKAVEVWPLLPDFDAWPNPYVQVKFDGDPAPDDKEKE----E  220 (436)
T ss_pred             ccccccccCHHHHHHHHHHHHHHHhhccccccCCCCCCCeEEEEecCCCCchhcCCceEEEEECCCCcccccccc----c
Confidence                2368999999999999999987   7999999999999999999999999999999999999986542211    1


Q ss_pred             hhhHHHHHHHHhhhhccCCCCCCcceeEEeecCCcc-------ccccc---c----cCCCCCeecceeeeeeceeccCCC
Q 005794          499 VRDAHESRAIMKSYVATGSDSANPEKFLAYMVPSVN-------ELSKD---M----YDENEDVSFSWVREYHWDVRGDDA  564 (677)
Q Consensus       499 ~r~~~es~Ailk~~~~~~~D~~~~e~flaY~lP~~~-------el~k~---l----~dede~~~Yk~vReYd~~v~~~~~  564 (677)
                      ........+|++++.      .++++||+||||+..       .+.+.   .    +++++.|.|+|||+|+|++++...
T Consensus       221 ~~~~~~~~~i~~p~~------~~~~~fvsy~lP~~~~~~~~~~~l~~~~~d~~~~~~~~~~~~~y~~vReY~~~~~~~~~  294 (436)
T PF03985_consen  221 QEEQALQAAIFRPMD------SEGDQFVSYYLPDKEDAKELKEKLEKNSPDRDEEDDDDDEEYEYKRVREYEWSVQNEAS  294 (436)
T ss_pred             hhHHHHhhhccCCCC------CCCcceeeEEecChhhhhHhHHhhhcccccccccccCCCceeeccceecccceeeccCC
Confidence            112222346777764      356789999999322       12211   1    245577999999999999986442


Q ss_pred             -CCCceEEEE-EcCCceEEecCCCcceecccccccCCCCcccccCCCCceEEEeeccc-hHHHHHhhhcccccCCCCCCC
Q 005794          565 -DDPTTYLVS-FDDDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRAN-VTAIELKEQGAYSNSKGNSSS  641 (677)
Q Consensus       565 -~~~~e~~l~-Fddg~AyY~PL~tRi~LRKrRaK~~~~~dei~~f~~ps~Itv~~r~~-~~e~e~~e~~~~~~~~~~~~~  641 (677)
                       .+..+|+|+ +++++||||||.+||+|||||....  ........+.+.|+|++|++ ..|+..++.... ..++..+ 
T Consensus       295 ~~~e~~i~f~~~~~k~ayY~pI~~Rv~LrkrR~~~~--~~~~~~~~~~d~i~V~~R~p~e~E~~~~~~~r~-~~dp~~~-  370 (436)
T PF03985_consen  295 KGYEENIFFVDFKQKAAYYYPIETRVRLRKRRTNSK--IRPKVREQRPDQITVKHRDPTEEEEAERDKRRA-QLDPIEY-  370 (436)
T ss_pred             CCccceEEEEecCCCceEEeeccccceeeeeccccc--cccccccCCCceEEEEeCCCCHHHHHHHHHHHh-hccCCCc-
Confidence             445567777 6689999999999999999993322  22345567789999999975 566655554322 3344432 


Q ss_pred             CcCCCCCccchhhhccCCCCCCCC
Q 005794          642 SKMGRVDSQEDLERSHNGSRQQDP  665 (677)
Q Consensus       642 ~~~~~~~~~~~~~~~~~~~~~~~~  665 (677)
                      ..+.+.+++++.++...+...++.
T Consensus       371 ~~~ee~eeeee~~~e~~~~~~e~~  394 (436)
T PF03985_consen  371 EEEEEEEEEEEEEEEEEEEEEEED  394 (436)
T ss_pred             cccCcccccccccccccccccccc
Confidence            222333333333344444433333

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

>KOG2478 consensus Putative RNA polymerase II regulator [Transcription]

Probab=100.00  E-value=6.9e-56  Score=475.44  Aligned_cols=319  Identities=30%  Similarity=0.552  Sum_probs=254.5

Q ss_pred             CCcccccccccccCCCCCCCCCceeeccCCccccccCcCcchhhccCCCCccCCCCCcccccCCccCCCC-C------CC
Q 005794          277 KPTTFLCKLKFRNELPEPSAQPKLMALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNP-P------SV  349 (677)
Q Consensus       277 r~~~fi~~iry~N~LP~pP~~PKLL~~p~d~~r~t~y~~tSLe~~~k~~i~~D~DLGmPLDLi~~~~Y~~-p------d~  349 (677)
                      +.++|||+|+|.|.||+|||+||||.||++..+|+.|..++++.++++.+++|.||||++|||+...|.. +      ..
T Consensus        14 rk~~~i~pvky~N~LP~pPfd~Kfl~yP~~p~~~~~y~~~~~~~q~k~~~i~d~dlg~pvdLi~~~~~~q~~~~~~~~~d   93 (452)
T KOG2478|consen   14 RKNDFICPVKYTNPLPDPPFDPKFLTYPFPPPRFVQYQPTSLYKQFKHDLITDPDLGMPVDLINDPGYDQDPNSLLDPAD   93 (452)
T ss_pred             cccccccCcccCCCCCCCCCCcccccCCCCcchhhhcCccccccccccccccCCCCCCCccccCCccccCCchhhccccc
Confidence            5799999999999999999999999999999999999999999999999988999999999999976654 2      23


Q ss_pred             CCCCChhhhhccCCCCccCcccccCCcccCCCCCCCccCccccccccccchhhhhchhhHHHHHHHHhhhcCCc------
Q 005794          350 RPPLDPEDEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRS------  423 (677)
Q Consensus       350 ~~~LdPeD~aLLrD~e~~~p~~s~Gi~kksR~~~~~VSWLRRTEYISs~~~~~~~~~~t~kqake~~E~k~G~~------  423 (677)
                      ...|+++|++||.+.             ++..+++.|+|||+|||||.+.++......      ...+.+.|++      
T Consensus        94 ~~~L~~~~rall~~~-------------R~~~h~~~vp~lrkteyiste~~r~~~~~~------~~~~~k~~~~~~k~~~  154 (452)
T KOG2478|consen   94 SKLLEPRERALLKDK-------------RSQQHSKTVPWLRKTEYISTEFNRAKIEAH------DNLELKKGRSLKKNSQ  154 (452)
T ss_pred             ccccChhhhcccccc-------------ccccccccccchhhhHHHHHHHHhhhhhcc------Cccchhhhhhcccccc
Confidence            456777777777653             234578899999999999998765432110      1112223332      


Q ss_pred             hhccccCHHHHHHHHHhhHHHHhcC-CCCCCCCCCceeEeecCCCCcccccCceEEEEEcCCCCCCchhhcccChhhhhH
Q 005794          424 ILENLNDRERQIKEIEASFEACKLR-PIHATNKNLQPVEILPLLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDA  502 (677)
Q Consensus       424 ~~~~~~dresQI~aIEkTFeaAkk~-lkHPtKpnLkaVev~PLLPD~d~w~n~Yv~VkFD~dPs~~~e~~~kl~~s~r~~  502 (677)
                      ..+.+.++++||++||+||+++.++ .+||+|++|++|++|+|||||++|.+.|++|+||.+|.... .      .....
T Consensus       155 ~~~~~~d~~~Qi~aI~~tF~d~~kpl~~Hpskpgv~pV~~~~vfPDts~~k~~~~qV~fD~dp~~~~-~------~~~~~  227 (452)
T KOG2478|consen  155 KEEMYKDVESQIKAIEKTFEDVQKPLRQHPSKPGVKPVEVWPVFPDTSMWKHLFAQVIFDLDPAPST-K------STIAE  227 (452)
T ss_pred             hhhcccchHHHHhhhhhhhhhhcchhhhCCCCCCceeeeecccCCChhhhhCcceEEEecCCCCccc-c------cchHH
Confidence            2345689999999999999999987 68999999999999999999999999999999999998543 1      11223


Q ss_pred             HH--HHHHHhhhhccCCCCCCcceeEEeecCCccccccc--------ccCCCCCeecceeeeeeceeccCCC-CCCceEE
Q 005794          503 HE--SRAIMKSYVATGSDSANPEKFLAYMVPSVNELSKD--------MYDENEDVSFSWVREYHWDVRGDDA-DDPTTYL  571 (677)
Q Consensus       503 ~e--s~Ailk~~~~~~~D~~~~e~flaY~lP~~~el~k~--------l~dede~~~Yk~vReYd~~v~~~~~-~~~~e~~  571 (677)
                      |+  ..+||+++     +++.+++||+||||+..++.+.        ++++++.+.|+.+|+|+|++++.+. .+..+++
T Consensus       228 le~~~~~~~~~~-----~~~e~e~fvs~~~p~ee~~~~~~~~~e~~~l~~eddv~ey~~~R~y~~~mk~~a~~~~~~~~f  302 (452)
T KOG2478|consen  228 LESMNESIFRGP-----MDEEGEQFVSYFLPTEETLKKRLADLEEEMLRDEDDVYEYKIAREYDWNMKGKASKGYTENYF  302 (452)
T ss_pred             Hhhhchhheecc-----ccccchhhhheecCChhhhhhhhhhhhhcccccccchhhhhhhhcccchhccCCCccccceEE
Confidence            32  34666655     4567899999999998876643        3455677889999999999998885 5566777


Q ss_pred             EEEc-CCceEEecCCCcceecccccccCCCCcccccCCCCceEEEeecc-chHHHHHhhhccc
Q 005794          572 VSFD-DDEARYVPLPTKLNLRKKRAIEGRSNDEVEHFPIPSSIAVRRRA-NVTAIELKEQGAY  632 (677)
Q Consensus       572 l~Fd-dg~AyY~PL~tRi~LRKrRaK~~~~~dei~~f~~ps~Itv~~r~-~~~e~e~~e~~~~  632 (677)
                      |.++ +++|||++|.+||+|+|||+|.+.+...      -+.|+|++|. +..|++++++..+
T Consensus       303 ~i~~~~~~v~yn~~~~rvrl~kr~vk~~~~~~~------i~~l~vs~r~~n~~e~~~~~~~~~  359 (452)
T KOG2478|consen  303 FINDEDNQVYYNELETRVRLMKRRVKAGVSLNN------IDKLEVSLRDLNSKELEAQDKNRR  359 (452)
T ss_pred             EEEecCCceeechHhhHHHHhhcccccccCccc------ccceeEeecCCCchHHHHHHHhhc
Confidence            7777 4789999999999999999998876543      3678999997 4777777777655

>KOG2478 consensus Putative RNA polymerase II regulator [Transcription]

Probab=99.46  E-value=3.1e-14  Score=154.92  Aligned_cols=325  Identities=24%  Similarity=0.210  Sum_probs=237.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccchhccCCCCCCCcccccCCccccCCCCCcccccc-ccCCCc
Q 005794          201 VETEEERRIRKKREYEKHRQEEKHRLQMKESQNVVMQKSQMVASGKGGHGSMVGSRMGDRRAAPLLSGERTEN-RLKKPT  279 (677)
Q Consensus       201 ~e~~ee~~~r~~r~~~k~~~~ek~~q~~k~~q~~~~~~~q~~~~~~~~~~~~~~~r~~~~~~~~~~~~er~~~-~~~r~~  279 (677)
                      .|..+|+..|.++......+-+++++++|.+|...|-+...         ++.       .++...-.++-.+ +.....
T Consensus       123 teyiste~~r~~~~~~~~~~~k~~~~~~k~~~~~~~~~d~~---------~Qi-------~aI~~tF~d~~kpl~~Hpsk  186 (452)
T KOG2478|consen  123 TEYISTEFNRAKIEAHDNLELKKGRSLKKNSQKEEMYKDVE---------SQI-------KAIEKTFEDVQKPLRQHPSK  186 (452)
T ss_pred             hHHHHHHHHhhhhhccCccchhhhhhcccccchhhcccchH---------HHH-------hhhhhhhhhhcchhhhCCCC
Confidence            48899999998887777777788888776666644433221         110       0001111111121 333466


Q ss_pred             ccccccccccCCCCCCCC-CceeeccCC--ccccccCcCcchhhccCCCCccCCCCCcccccCCccCCCCCCCCCCCChh
Q 005794          280 TFLCKLKFRNELPEPSAQ-PKLMALKKD--KDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPE  356 (677)
Q Consensus       280 ~fi~~iry~N~LP~pP~~-PKLL~~p~d--~~r~t~y~~tSLe~~~k~~i~~D~DLGmPLDLi~~~~Y~~pd~~~~LdPe  356 (677)
                      .++|.|++.|-||+.-.- -+|+.+-+|  ...++.+.+++|+. ....|.++.+++...+++.+.+|+.......|.+.
T Consensus       187 pgv~pV~~~~vfPDts~~k~~~~qV~fD~dp~~~~~~~~~~le~-~~~~~~~~~~~~e~e~fvs~~~p~ee~~~~~~~~~  265 (452)
T KOG2478|consen  187 PGVKPVEVWPVFPDTSMWKHLFAQVIFDLDPAPSTKSTIAELES-MNESIFRGPMDEEGEQFVSYFLPTEETLKKRLADL  265 (452)
T ss_pred             CCceeeeecccCCChhhhhCcceEEEecCCCCcccccchHHHhh-hchhheeccccccchhhhheecCChhhhhhhhhhh
Confidence            789999999999997764 567777776  46778888889987 66688889999999999999999987777889999


Q ss_pred             hhhccCCCCccCcccccCCcccCCCCCCCccCccccccccccchhhhhchhhHHHHHHHHhhhcCCchhccccCHHHHHH
Q 005794          357 DEELLRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKELREMKGGRSILENLNDRERQIK  436 (677)
Q Consensus       357 D~aLLrD~e~~~p~~s~Gi~kksR~~~~~VSWLRRTEYISs~~~~~~~~~~t~kqake~~E~k~G~~~~~~~~dresQI~  436 (677)
                      +..+|++.+.+..   -+|.++-+.+.+.++|+-.|+|+....... .+..........+.+|.+.++....++    |.
T Consensus       266 e~~~l~~eddv~e---y~~~R~y~~~mk~~a~~~~~~~~f~i~~~~-~~v~yn~~~~rvrl~kr~vk~~~~~~~----i~  337 (452)
T KOG2478|consen  266 EEEMLRDEDDVYE---YKIAREYDWNMKGKASKGYTENYFFINDED-NQVYYNELETRVRLMKRRVKAGVSLNN----ID  337 (452)
T ss_pred             hhcccccccchhh---hhhhhcccchhccCCCccccceEEEEEecC-CceeechHhhHHHHhhcccccccCccc----cc
Confidence            9999999877554   355554556778999999999999876543 222333344445666665544333333    88


Q ss_pred             HHHhhHHHHhcCCCCCCCCCCceeEeec-CCCCcccccCceEEEEEcCCCCCCchhhcccChhhhhHHHHHHHHhhhhcc
Q 005794          437 EIEASFEACKLRPIHATNKNLQPVEILP-LLPDFERYDDQFVAATFDGAPTADSEIYSKMDKSVRDAHESRAIMKSYVAT  515 (677)
Q Consensus       437 aIEkTFeaAkk~lkHPtKpnLkaVev~P-LLPD~d~w~n~Yv~VkFD~dPs~~~e~~~kl~~s~r~~~es~Ailk~~~~~  515 (677)
                      .||-||++++..-.|-++++...+++++ ++++++-+...++ .-|++.+..+.+.....++..+.+-++.++.+-....
T Consensus       338 ~l~vs~r~~n~~e~~~~~~~~~~~e~~~~~~~~~Ee~e~e~~-~~~~~e~~~~se~~~~~~e~~~~ade~~~~~~e~~~~  416 (452)
T KOG2478|consen  338 KLEVSLRDLNSKELEAQDKNRRQLEVLGFELELEEEYEEEEQ-EEILGEPEEDSEFFGSEDEGIEDADESSASEKEYQQR  416 (452)
T ss_pred             ceeEeecCCCchHHHHHHHhhccccccccchhhhhhhHHHHH-hhhccCchhccccccccccccccccccccccchhhhc
Confidence            9999999999889999999999999999 8999999998888 8999999888876666666666666777888877765


Q ss_pred             CCCCCCcceeEEeecCCcccccccccCCCCCeecceeee
Q 005794          516 GSDSANPEKFLAYMVPSVNELSKDMYDENEDVSFSWVRE  554 (677)
Q Consensus       516 ~~D~~~~e~flaY~lP~~~el~k~l~dede~~~Yk~vRe  554 (677)
                      +++.  .+.+.++++|+.++....+.+.+ +..+.|+|+
T Consensus       417 ~~s~--~~s~~as~~ps~de~~~~~~~~~-e~~~s~~d~  452 (452)
T KOG2478|consen  417 GEST--AESGSASDVPSLDEARADIRDKE-EISGSDSDE  452 (452)
T ss_pred             ccch--hhhcccCCCCCccccccccCCcc-ccccccccC
Confidence            5432  37799999999998866655543 677888764

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=98.70  E-value=3.3e-08  Score=113.26  Aligned_cols=11  Identities=18%  Similarity=0.413  Sum_probs=5.8

Q ss_pred             HHHHhhHHHHh
Q 005794          436 KEIEASFEACK  446 (677)
Q Consensus       436 ~aIEkTFeaAk  446 (677)
                      ..|.++|....
T Consensus       897 d~ikK~~~~m~  907 (1102)
T KOG1924|consen  897 DEIKKNLQQME  907 (1102)
T ss_pred             HHHHHHHHHHH
Confidence            45555555443

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=98.48  E-value=6.7e-07  Score=102.90  Aligned_cols=9  Identities=11%  Similarity=-0.119  Sum_probs=4.1

Q ss_pred             HHHHHHHHH
Q 005794          217 KHRQEEKHR  225 (677)
Q Consensus       217 k~~~~ek~~  225 (677)
                      |.+..-|++
T Consensus       659 fakL~~~Fa  667 (1102)
T KOG1924|consen  659 FAKLALKFA  667 (1102)
T ss_pred             HHHHHHHhh
Confidence            444444444

>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]

Probab=97.71  E-value=0.00031  Score=81.72  Aligned_cols=34  Identities=18%  Similarity=-0.017  Sum_probs=31.3

Q ss_pred             CCcccCCCCCCc--ccHHHHHHHHHHHHHHHHHHHH
Q 005794          190 GVKKVNGGSGRV--ETEEERRIRKKREYEKHRQEEK  223 (677)
Q Consensus       190 ~~~~~~~~~g~~--e~~ee~~~r~~r~~~k~~~~ek  223 (677)
                      ..-|-+|++|||  +++||+++++++..+|+++|+.
T Consensus       377 ~alKP~qv~~tvf~~~~De~Il~~lD~~~~ee~Fk~  412 (830)
T KOG1923|consen  377 LALKPIQVKGTVFHELNDEKILEALDFSRFEEQFKI  412 (830)
T ss_pred             cccCccccccchhhhhhHHHHHHhhhHHHHHHHHHh
Confidence            346788999999  9999999999999999999999

>PHA03247 large tegument protein UL36; Provisional

Probab=96.82  E-value=0.037  Score=71.86  Aligned_cols=10  Identities=10%  Similarity=-0.047  Sum_probs=3.8

Q ss_pred             chHHHHHhhh
Q 005794          620 NVTAIELKEQ  629 (677)
Q Consensus       620 ~~~e~e~~e~  629 (677)
                      ++..|.++-.
T Consensus      3128 TR~~L~~~~~ 3137 (3151)
T PHA03247       3128 TRHALLDRSG 3137 (3151)
T ss_pred             HHHHHHhhHH
Confidence            3333333333

>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]

Probab=96.68  E-value=0.023  Score=64.04  Aligned_cols=8  Identities=13%  Similarity=-0.135  Sum_probs=3.6

Q ss_pred             CCCCCCCC
Q 005794           46 QNWGGYSN   53 (677)
Q Consensus        46 ~~~~~~~~   53 (677)
                      ++|++.+|
T Consensus       331 ~~gnq~p~  338 (569)
T KOG3671|consen  331 PGGNQPPN  338 (569)
T ss_pred             CCCCCCCc
Confidence            44544443

>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]

Probab=95.01  E-value=1.5  Score=49.19  Aligned_cols=30  Identities=17%  Similarity=0.343  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhcccch
Q 005794          212 KREYEKHRQEEKHRLQMKESQNVVMQKSQM  241 (677)
Q Consensus       212 ~r~~~k~~~~ek~~q~~k~~q~~~~~~~q~  241 (677)
                      ||+-+++|+.|.++..+-+-=.+||.+-=+
T Consensus       469 LrKVeeqreqeakr~~v~ndvatiLsRRia  498 (518)
T KOG1830|consen  469 LRKVEEQREQEAKREAVENDVATILSRRIA  498 (518)
T ss_pred             hHHHHHHHHHHHhhccccchHHHHHHHHHH
Confidence            444445555555554433334445544333

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=87.24  E-value=6.2  Score=43.63  Aligned_cols=8  Identities=50%  Similarity=0.463  Sum_probs=3.5

Q ss_pred             CcCcchhh
Q 005794          313 YTFSSLEK  320 (677)
Q Consensus       313 y~~tSLe~  320 (677)
                      ..++||+.
T Consensus       416 vLissL~d  423 (498)
T KOG4849|consen  416 VLISSLED  423 (498)
T ss_pred             HHHHHHHH
Confidence            33444443

>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]

Probab=86.13  E-value=2  Score=51.30  Aligned_cols=12  Identities=17%  Similarity=-0.180  Sum_probs=6.8

Q ss_pred             ccHHHHHHHHHH
Q 005794          202 ETEEERRIRKKR  213 (677)
Q Consensus       202 e~~ee~~~r~~r  213 (677)
                      .++=++...++.
T Consensus       386 ~tvf~~~~De~I  397 (830)
T KOG1923|consen  386 GTVFHELNDEKI  397 (830)
T ss_pred             cchhhhhhHHHH
Confidence            555556555554

>KOG2236 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.73  E-value=8.8  Score=43.76  Aligned_cols=10  Identities=20%  Similarity=-0.061  Sum_probs=4.2

Q ss_pred             CCCCCCCccc
Q 005794           95 QQQTQPSMYY  104 (677)
Q Consensus        95 ~~~~~~~~~~  104 (677)
                      +.+++.+|++
T Consensus       444 ~~~P~~~mpp  453 (483)
T KOG2236|consen  444 QANPFNQMPP  453 (483)
T ss_pred             ccCccccCCC
Confidence            3333344444

>KOG2236 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.30  E-value=4.6  Score=45.93  Aligned_cols=7  Identities=14%  Similarity=0.126  Sum_probs=4.0

Q ss_pred             ccCCCcc
Q 005794          103 YYSSNQY  109 (677)
Q Consensus       103 ~~~~~~~  109 (677)
                      |.-+..|
T Consensus       449 ~~mpp~~  455 (483)
T KOG2236|consen  449 NQMPPAY  455 (483)
T ss_pred             ccCCCCC
Confidence            4466665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	677
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-21
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-19
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	9e-18
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-13
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-13
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	4e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	4e-13
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	7e-11
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-09
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-08
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	4e-08
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	3e-04
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-04
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-11
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-09
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-07
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-06
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-05
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-04
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	8e-10
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	4e-08
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-08
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	3e-07
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	3e-06
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	3e-05
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-04
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-08
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	1e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	3e-08
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	5e-08
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	4e-05
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	1e-07
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	5e-05
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	5e-07
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	8e-07
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	2e-06
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	2e-04
3gdb_A	937	Endo-D, putative uncharacterized protein SPR0440;	2e-06
3gdb_A	937	Endo-D, putative uncharacterized protein SPR0440;	8e-06
3gdb_A	937	Endo-D, putative uncharacterized protein SPR0440;	2e-05
2yew_A	253	Capsid protein, coat protein; alphavirus, molecula	6e-06
2yew_A	253	Capsid protein, coat protein; alphavirus, molecula	3e-05
2yew_A	253	Capsid protein, coat protein; alphavirus, molecula	1e-04
2yew_A	253	Capsid protein, coat protein; alphavirus, molecula	2e-04
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	7e-06
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	1e-05
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	2e-04
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	5e-04
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	6e-04
1kxf_A	264	Sindbis virus capsid protein; chymotrypsin-like se	2e-05
1kxf_A	264	Sindbis virus capsid protein; chymotrypsin-like se	4e-05
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	3e-05
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	4e-05
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	6e-05
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	1e-04
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	6e-04
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-05
1dx0_A	219	Prion protein; brain, repeat; NMR {Bos taurus} SCO	8e-05
1dx0_A	219	Prion protein; brain, repeat; NMR {Bos taurus} SCO	9e-05
3dva_I	428	Dihydrolipoyllysine-residue acetyltransferase comp	9e-05
4af8_A	367	Metacaspase MCA2; hydrolase, cysteine peptidase, c	1e-04
2grx_C	229	Protein TONB; beta barrel, outer membrane, heteroc	1e-04
2grx_C	229	Protein TONB; beta barrel, outer membrane, heteroc	2e-04
2grx_C	229	Protein TONB; beta barrel, outer membrane, heteroc	2e-04
3a58_A	320	Exocyst complex component SEC3; protein complex, P	2e-04
1pcx_A	810	Protein transport protein SEC24; 2.50A {Saccharomy	3e-04
1pcx_A	810	Protein transport protein SEC24; 2.50A {Saccharomy	6e-04
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	4e-04
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	6e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-04
3sv0_A	483	Casein kinase I-like; typical kinase domain fold,	6e-04
3oun_A	157	Putative uncharacterized protein TB39.8; peptidogl	9e-04

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 97.2 bits (241), Expect = 5e-21
 Identities = 24/144 (16%), Positives = 32/144 (22%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
           R +PQ          P  Q     PP                  G   + G        Q
Sbjct: 7   RVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQ 66

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
              + Q        +       P   P    Q   P    +  Q  Q  M  P       
Sbjct: 67  EQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSA 126

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPP 148
               +  P + + P       PPP
Sbjct: 127 AMGQNMRPMNQLYPIDLLTELPPP 150

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 91.4 bits (226), Expect = 3e-19
 Identities = 16/145 (11%), Positives = 28/145 (19%)

Query: 9   QPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSY 68
              +  +P         + P   P Q    Q P     ++G       GA     Q    
Sbjct: 3   HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
                    +                      +           +     Q P+  P   
Sbjct: 63  TPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYG 122

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKDV 153
            P  +      P     P     ++
Sbjct: 123 QPSAAMGQNMRPMNQLYPIDLLTEL 147

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 86.8 bits (214), Expect = 9e-18
 Identities = 28/153 (18%), Positives = 37/153 (24%), Gaps = 3/153 (1%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPP---PPPQQQQQQQRPNPYSQNWGGYSNTGGG 57
                   Q P    PP  P     S      PP        +    +            
Sbjct: 16  YGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQ 75

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPP 117
           A    +  + +  P   P        P     P    QQ      Y   +     +M P 
Sbjct: 76  ATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPM 135

Query: 118 MQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
            Q          PPP + +  PPPP   PP   
Sbjct: 136 NQLYPIDLLTELPPPITDLTLPPPPLVIPPERM 168

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 72.9 bits (178), Expect = 2e-13
 Identities = 13/96 (13%), Positives = 22/96 (22%)

Query: 55  GGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSM 114
               ++ Y Q          P  + +   PP  P     +  Q       +     Q   
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 115 YPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
             P Q  L      +    + +     P   P    
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYM 97

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 72.9 bits (178), Expect = 2e-13
 Identities = 24/140 (17%), Positives = 28/140 (20%), Gaps = 12/140 (8%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
           M      P   Q  F  P     +                  P                 
Sbjct: 47  MPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVD------------PN 94

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
            Y QP    Q   P   +      P    P     Q  +P               P    
Sbjct: 95  AYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDL 154

Query: 121 PLPPPPPSSPPPSSSIPPPP 140
            LPPPP   PP    +P   
Sbjct: 155 TLPPPPLVIPPERMLVPSEL 174

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 61.8 bits (149), Expect = 6e-10
 Identities = 25/157 (15%), Positives = 31/157 (19%), Gaps = 14/157 (8%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
              Q  Q         N       P        Q   P              A   Y QP
Sbjct: 65  AQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQP 124

Query: 66  YSYAQPPPPPPPESSYPP-----PPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
            +       P  +          PPP      P      P           N+    ++ 
Sbjct: 125 SAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRS 184

Query: 121 PLPPPPPSSPPPSSSIPP---------PPPPGSPPPP 148
            L   P +S     S  P                PPP
Sbjct: 185 TLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPP 221

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 42.9 bits (100), Expect = 4e-04
 Identities = 20/141 (14%), Positives = 33/141 (23%), Gaps = 5/141 (3%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQ-QQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
           P   P     P  P     P Q    P       Q      QN    +            
Sbjct: 89  PLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELP 148

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYY---SSNQYNQNSM-YPPMQP 120
           P       PPPP          P      +    + ++     +S+   ++ + +  +  
Sbjct: 149 PPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIR 208

Query: 121 PLPPPPPSSPPPSSSIPPPPP 141
           P         PP  +      
Sbjct: 209 PYQHLYDDIDPPPLNEDGLIV 229

>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 = 78.4 bits (192), Expect = 4e-15
 Identities = 73/539 (13%), Positives = 156/539 (28%), Gaps = 173/539 (32%)

Query: 202 ETEEERRIRKKREYEKH---RQEEKHRL-----QMKESQNVVMQKSQMVASGKGGHG--S 251
             + +R     + + K+   R +   +L     +++ ++NV++        G  G G   
Sbjct: 113 IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLID-------GVLGSGKTW 165

Query: 252 MVGSRMGDRRAAPLLSGE----------RTENRLKKPTTFLCKL-KFRNELPEPSAQPKL 300
           +        +    +  +            E  L+     L ++        + S+  KL
Sbjct: 166 VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225

Query: 301 MALKKDKDRFTRYTFSSLEKNYKPQLHVEPDLGIPLDLLDLSVYNPPSVRPPLDPEDEEL 360
             +   +    R       K Y+  L         L LL+  V N  +     +   + L
Sbjct: 226 -RIHSIQAELRRLLK---SKPYENCL---------LVLLN--VQNAKAWNA-FNLSCKIL 269

Query: 361 LRDDEVVTPVKKDGIKRKERPTDKGVSWLVKTQYISPLSMESARQSLTEKQAKEL----- 415
                + T           R   K V+  +     + +S++    +LT  + K L     
Sbjct: 270 -----LTT-----------R--FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL 311

Query: 416 --------REMKG---------GRSILENLN--------DRERQIKEIEASFEACKLRP- 449
                   RE+             SI + L         + ++    IE+S     L P 
Sbjct: 312 DCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNV--LEPA 369

Query: 450 ----------IHATNKNLQPVEILPLL-PDFERYDDQFVAATF--------DGAPTADS- 489
                     +   + ++ P  +L L+  D  + D   V                +  S 
Sbjct: 370 EYRKMFDRLSVFPPSAHI-PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428

Query: 490 -EIYSKMDKSVRDA---HESRAIMKSY-VATGSDSANPEK---------FLAYMVPSVNE 535
             IY ++   + +    H  R+I+  Y +    DS +             + +       
Sbjct: 429 PSIYLELKVKLENEYALH--RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH------H 480

Query: 536 LSKDMYDENED------VSFSWVRE------YHWDVRGDDAD---DPTTYLVSFDDDEAR 580
           L    + E         + F ++ +        W+  G   +       Y     D++ +
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540

Query: 581 YVPLPTKLNLRKKRAIEGRSNDEVEHF-PIPSSIAVR-RRANVTAIEL--KEQGAYSNS 635
           Y               E   N  +  F P      +  +  ++  I L  +++  +  +
Sbjct: 541 Y---------------ERLVNA-ILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEA 583

>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 = 53.7 bits (128), Expect = 2e-07
 Identities = 73/494 (14%), Positives = 134/494 (27%), Gaps = 158/494 (31%)

Query: 278 PTTFLCKLKFRNELPEPSAQPKLMAL-----KKDKDRFTRYTFSSLEKNYK---PQLHVE 329
           P + L K +  + +    A    + L      K ++   ++    L  NYK     +  E
Sbjct: 42  PKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE 101

Query: 330 PDLGIPLDLLDLSVYNPPSVRPPLDPEDEELLRDDEVVTPVKKDGIKR---KERPTDK-- 384
                P   +   +Y     R  L   D ++     V        +++   + RP     
Sbjct: 102 QR--QP--SMMTRMYI--EQRDRLY-NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL 154

Query: 385 -------GVSWLVKTQYISPLSMESARQSLTEKQAK------ELREMKGGRSILENLNDR 431
                  G +W+          ++       + +         L+      ++LE L   
Sbjct: 155 IDGVLGSGKTWVA---------LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL 205

Query: 432 ERQIKEIEASFEACKLRPIHATNKNLQPVEILPLLPDF---ERY-------DD---QFVA 478
             QI     S      R  H++N  L+   I   L      + Y        +       
Sbjct: 206 LYQIDPNWTS------RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW 259

Query: 479 ATFDGAPTADSEIYSKM-----DKSVRDA----HESRAIMKSYVATGSDSANPEKFLAYM 529
             F+        +  K+      K V D       +   +  +  T +        L Y+
Sbjct: 260 NAFN--------LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL 311

Query: 530 VPSVNELSKDMYDEN-EDVSFSW--VREY--HWD----VRGD----------DADDPTTY 570
                +L +++   N   +S     +R+    WD    V  D          +  +P  Y
Sbjct: 312 DCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEY 371

Query: 571 ------LVSFDDDEARYVPLPTKL------------------NLRKKRAIEGRSNDEVEH 606
                 L  F         +PT L                   L K   +E +  +    
Sbjct: 372 RKMFDRLSVFPPS----AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST-- 425

Query: 607 FPIPSSIAVRRRANVTAIELKEQGAYSNSKGNSSSSKMGRVDSQEDLER----SHNGSRQ 662
             IPS            +ELK +                 ++++  L R     +N  + 
Sbjct: 426 ISIPS----------IYLELKVK-----------------LENEYALHRSIVDHYNIPKT 458

Query: 663 QDPYQSSGAEDDMY 676
            D         D Y
Sbjct: 459 FDSDDLIPPYLDQY 472

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 72.0 bits (176), Expect = 4e-13
 Identities = 50/217 (23%), Positives = 67/217 (30%), Gaps = 23/217 (10%)

Query: 1    MASYRPFPQPPQSSFPPPPPPNQNPSQP---PPPPQQQQQQQRPNPYSQNWGGYSNTGGG 57
             + +  + + P S       P  +P+ P   P  P         +P S ++   S +   
Sbjct: 1520 TSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSP 1579

Query: 58   AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS---- 113
                Y  P S    P   P   SY P  P   P  P+   T PS   +S  Y+  S    
Sbjct: 1580 TSPSY-SPTS----PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1634

Query: 114  -----------MYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSD 162
                        Y P  P   P  P+  P S S  P  P  SP  P         + TS 
Sbjct: 1635 PTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1694

Query: 163  RDKRASKEVSRHDPGHSKQHRPPVPPPGVKKVNGGSG 199
                 S   S   PG+S       P    +K N    
Sbjct: 1695 NYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENEN 1731

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 64.7 bits (157), Expect = 7e-11
 Identities = 43/189 (22%), Positives = 55/189 (29%), Gaps = 7/189 (3%)

Query: 6    PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
             F     + +     P     + P  P         +P S  +   S         Y   
Sbjct: 1507 GFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPT 1566

Query: 66   YSYAQP--PPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLP 123
                 P  P   P   SY P  P   P  P+   T PS   +S  Y+  S  P   P  P
Sbjct: 1567 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPTSP 1624

Query: 124  PPPPSSPPPSSSIP---PPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSK 180
               P+SP  S + P   P  P  SP  P         + TS      S   S   P +S 
Sbjct: 1625 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSP 1684

Query: 181  QHRPPVPPP 189
                  P  
Sbjct: 1685 TSPSYSPTS 1693

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 59.0 bits (142), Expect = 5e-09
 Identities = 39/157 (24%), Positives = 48/157 (30%), Gaps = 13/157 (8%)

Query: 11   PQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQ 70
            P S    P  P+ +P+ P   P           YS     YS T          P     
Sbjct: 1579 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPT 1636

Query: 71   PPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS-MYPPMQPPLPPPP--- 126
             P   P   SY P  P   P  P    T PS   +S  Y+  S  Y P  P   P     
Sbjct: 1637 SPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNY 1696

Query: 127  -PSSPPPSSSIP------PPPPPGSPPPPPPKDVEGR 156
             P+SP  S + P      P   P        ++   R
Sbjct: 1697 SPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR 1733

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 57.0 bits (137), Expect = 2e-08
 Identities = 42/191 (21%), Positives = 52/191 (27%), Gaps = 21/191 (10%)

Query: 6    PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNT--GGGAQQHYH 63
                  +  F P      N +                       G + T  G G      
Sbjct: 1483 DLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGF 1542

Query: 64   QPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS-----MYPPM 118
             P S    P  P    +Y P  P   P  P+   T PS   +S  Y+  S       P  
Sbjct: 1543 SPTSPTYSPTSP----AYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1598

Query: 119  QPPLPPPPPSSP----------PPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRAS 168
             P  P   P+SP          P S S  P  P  SP  P         + TS      S
Sbjct: 1599 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1658

Query: 169  KEVSRHDPGHS 179
               S   P +S
Sbjct: 1659 PAYSPTSPSYS 1669

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 55.9 bits (134), Expect = 4e-08
 Identities = 30/138 (21%), Positives = 42/138 (30%), Gaps = 7/138 (5%)

Query: 8    PQPPQSSFPPPPPPNQNPSQP---PPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
               P S    P  P+ +P+ P   P  P         +P S ++   S +       Y  
Sbjct: 1597 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1656

Query: 65   PYSYAQPPPPP--PPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPL 122
                  P  P   P   SY P  P   P  P+   T P+   +S  Y+  S  P   P  
Sbjct: 1657 TSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTS--PGYSPGS 1714

Query: 123  PPPPPSSPPPSSSIPPPP 140
            P   P       +     
Sbjct: 1715 PAYSPKQDEQKHNENENS 1732

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 43.2 bits (101), Expect = 3e-04
 Identities = 24/138 (17%), Positives = 29/138 (21%), Gaps = 6/138 (4%)

Query: 56   GGAQQHYHQPYSYAQPPPPPPPESSYPP---PPPPPPPPPPTQQQTQPSMYYSSNQYNQN 112
               Q     PYS          +        P                       +    
Sbjct: 1463 EDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSP 1522

Query: 113  SMYPPMQPPLPPPPPSSPPPSSSIP---PPPPPGSPPPPPPKDVEGRDTGTSDRDKRASK 169
                   P  P    SSP  S + P   P  P  SP  P         + TS      S 
Sbjct: 1523 FGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSP 1582

Query: 170  EVSRHDPGHSKQHRPPVP 187
              S   P +S       P
Sbjct: 1583 SYSPTSPSYSPTSPSYSP 1600

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 42.4 bits (99), Expect = 5e-04
 Identities = 28/172 (16%), Positives = 37/172 (21%), Gaps = 6/172 (3%)

Query: 8    PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
            P+   +           P              +          +S               
Sbjct: 1455 PEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDEL------MFSPLVDSGSNDAMAGGF 1508

Query: 68   YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPP 127
             A         +S        P  P     +      S      +  Y P  P   P  P
Sbjct: 1509 TAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSP 1568

Query: 128  SSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHS 179
            S  P S S  P  P  SP  P         + TS      S   S   P +S
Sbjct: 1569 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1620

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 62.0 bits (150), Expect = 7e-11
 Identities = 28/148 (18%), Positives = 37/148 (25%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQH 61
            S      PP+ +     P       P       +      P  Q   G +    G    
Sbjct: 78  VSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGP 137

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPP 121
             Q  +           ++        P   P  +   P               PP   P
Sbjct: 138 SQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRP 197

Query: 122 LPPPPPSSPPPSSSIPPPPPPGSPPPPP 149
              PP   PP   +    PPPG  PPPP
Sbjct: 198 PMGPPMGIPPGRGTPMGMPPPGMRPPPP 225

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 58.5 bits (141), Expect = 1e-09
 Identities = 27/146 (18%), Positives = 33/146 (22%), Gaps = 4/146 (2%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
            P P+    +  P       P       +                G     GG  Q    
Sbjct: 84  GPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMT 143

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPP 124
           P    Q        ++         P      +  P             M PP     P 
Sbjct: 144 P----QGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPM 199

Query: 125 PPPSSPPPSSSIPPPPPPGSPPPPPP 150
            PP   PP    P   PP    PPPP
Sbjct: 200 GPPMGIPPGRGTPMGMPPPGMRPPPP 225

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 50.8 bits (121), Expect = 3e-07
 Identities = 23/113 (20%), Positives = 30/113 (26%)

Query: 38  QQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQ 97
            + P P           G        +      P   P P++      P      P+QQ 
Sbjct: 82  VEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQV 141

Query: 98  TQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
             P    +       +       P   PP    PP       PPPG   PPP 
Sbjct: 142 MTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPG 194

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 48.1 bits (114), Expect = 3e-06
 Identities = 25/134 (18%), Positives = 30/134 (22%), Gaps = 15/134 (11%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
            A+ R  P        P            P  Q    Q R    +      ++  G   Q
Sbjct: 108 RAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQ 167

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
           +         P     P      PPP   PP        P                   P
Sbjct: 168 YPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPP---------------GRGTP 212

Query: 121 PLPPPPPSSPPPSS 134
              PPP   PPP  
Sbjct: 213 MGMPPPGMRPPPPG 226

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 45.0 bits (106), Expect = 3e-05
 Identities = 17/90 (18%), Positives = 20/90 (22%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
                PQ             +     P Q    +   P     G       G       P
Sbjct: 139 QQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPP 198

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPPTQ 95
                  PP        PPP   PPPP  +
Sbjct: 199 MGPPMGIPPGRGTPMGMPPPGMRPPPPGMR 228

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 42.7 bits (100), Expect = 1e-04
 Identities = 19/95 (20%), Positives = 21/95 (22%), Gaps = 3/95 (3%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
               Q   P         +            Q P       G     G GA         
Sbjct: 136 GPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPG---RGGPPPPMGRGAPPPGMMGPP 192

Query: 68  YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSM 102
               PP  PP    P    P   PPP  +   P M
Sbjct: 193 PGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGM 227

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 61.6 bits (149), Expect = 8e-10
 Identities = 46/181 (25%), Positives = 53/181 (29%), Gaps = 9/181 (4%)

Query: 6    PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
                   S F     P    + P   P        P  Y  +   YS T           
Sbjct: 1534 VQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSP-AYMPSSPSYSPTSPSYSPTSPS- 1591

Query: 66   YSYAQPPPPP------PPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS-MYPPM 118
            YS   P   P          SY P  P   P  P+   T PS   +S  Y+  S  Y P 
Sbjct: 1592 YSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1651

Query: 119  QPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGH 178
             P   P  PS  P S S  P  P  SP  P         + TS      S   S   P +
Sbjct: 1652 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1711

Query: 179  S 179
            S
Sbjct: 1712 S 1712

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 56.2 bits (135), Expect = 4e-08
 Identities = 45/166 (27%), Positives = 53/166 (31%), Gaps = 14/166 (8%)

Query: 1    MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWG----GYSNTGG 56
              S    P  P  S   P     +PS  P  P         +P S ++      YS T  
Sbjct: 1594 PTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS- 1652

Query: 57   GAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS-MY 115
                    P      P   P   SY P  P   P  P+   T PS   +S  Y+  S  Y
Sbjct: 1653 --------PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1704

Query: 116  PPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTS 161
             P  P   P  PS  P S S  P  P  SP  P         + TS
Sbjct: 1705 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1750

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 55.5 bits (133), Expect = 5e-08
 Identities = 47/178 (26%), Positives = 57/178 (32%), Gaps = 6/178 (3%)

Query: 8    PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQ--QHYHQP 65
            P    S    P  P+ +P+ P   P           YS     YS T          + P
Sbjct: 1563 PGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSP 1622

Query: 66   YSYAQPPPPPPPESSYPPPPPPPPPPPPT---QQQTQPSMYYSSNQYNQNS-MYPPMQPP 121
             S +  P  P    + P   P  P   PT      T PS   +S  Y+  S  Y P  P 
Sbjct: 1623 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1682

Query: 122  LPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHS 179
              P  PS  P S S  P  P  SP  P         + TS      S   S   P +S
Sbjct: 1683 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1740

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 53.2 bits (127), Expect = 3e-07
 Identities = 43/150 (28%), Positives = 50/150 (33%), Gaps = 9/150 (6%)

Query: 6    PFPQPPQSSFPP------PPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQ 59
            P       S+ P      P  P+ +P+ P   P           YS     YS T     
Sbjct: 1604 PSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1663

Query: 60   QHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS-MYPPM 118
                  YS   P   P    SY P  P   P  P+   T PS   +S  Y+  S  Y P 
Sbjct: 1664 PTSPS-YSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1721

Query: 119  QPPLPPPPPSSPPPSSSIPPPPPPGSPPPP 148
             P   P  PS  P S S  P  P  SP  P
Sbjct: 1722 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1751

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 49.7 bits (118), Expect = 3e-06
 Identities = 42/187 (22%), Positives = 56/187 (29%), Gaps = 17/187 (9%)

Query: 8    PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
            P     S       +        P +  Q     +P+S         G  +  +      
Sbjct: 1507 PLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSS--AMSPGYGLTSPSYSPSSPG 1564

Query: 68   YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSM-YPPMQPPLPPPP 126
            Y+  P   P   SY P  P   P  P+   T PS   +S  Y+  S  Y P  P   P  
Sbjct: 1565 YSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTS 1624

Query: 127  ----PSSPPPSSSIP------PPPPPGSP----PPPPPKDVEGRDTGTSDRDKRASKEVS 172
                P+SP  S + P      P   P SP      P         + TS      S   S
Sbjct: 1625 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1684

Query: 173  RHDPGHS 179
               P +S
Sbjct: 1685 PTSPSYS 1691

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 46.6 bits (110), Expect = 3e-05
 Identities = 29/133 (21%), Positives = 32/133 (24%), Gaps = 6/133 (4%)

Query: 16   PPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPP 75
            P    P  +      P                 G       GA   Y    S     P  
Sbjct: 1485 PYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFS 1544

Query: 76   PPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSS 135
               S       P   P      T P+   SS  Y+      P  P   P  PS  P S S
Sbjct: 1545 SAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYS------PTSPSYSPTSPSYSPTSPS 1598

Query: 136  IPPPPPPGSPPPP 148
              P  P  S   P
Sbjct: 1599 YSPTSPSYSATSP 1611

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 43.9 bits (103), Expect = 2e-04
 Identities = 23/115 (20%), Positives = 30/115 (26%), Gaps = 7/115 (6%)

Query: 43   PYSQ---NWGGYSNTGGGAQ----QHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQ 95
            PY +      G+  +   A                        +S       P    P  
Sbjct: 1485 PYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFS 1544

Query: 96   QQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
                P    +S  Y+ +S      P   P  PS  P S S  P  P  SP  P  
Sbjct: 1545 SAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSY 1599

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 56.3 bits (135), Expect = 2e-08
 Identities = 21/142 (14%), Positives = 31/142 (21%), Gaps = 6/142 (4%)

Query: 61  HYHQPYSYAQPP-PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPP-- 117
           H+H  +             SS   P        P+   +      S  Q +         
Sbjct: 3   HHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSP 62

Query: 118 ---MQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRH 174
              M PP         P S S+P  P  G     P          +S+  K         
Sbjct: 63  INGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVL 122

Query: 175 DPGHSKQHRPPVPPPGVKKVNG 196
                           +  + G
Sbjct: 123 KVPAHPSGNMASFTKHICAICG 144

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 47.4 bits (112), Expect = 1e-05
 Identities = 15/136 (11%), Positives = 26/136 (19%), Gaps = 9/136 (6%)

Query: 26  SQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPP---------PPP 76
           +           +      + +    +  G  A    H         P            
Sbjct: 2   AHHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSS 61

Query: 77  PESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSI 136
           P +   PP      P      + P+            +  PM P         P   + +
Sbjct: 62  PINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGV 121

Query: 137 PPPPPPGSPPPPPPKD 152
              P   S        
Sbjct: 122 LKVPAHPSGNMASFTK 137

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 55.5 bits (133), Expect = 3e-08
 Identities = 20/117 (17%), Positives = 32/117 (27%), Gaps = 7/117 (5%)

Query: 73  PPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPP 132
                 SS   P       P     +  S + ++         PP+  P P PPP   P 
Sbjct: 5   HHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALH-------PPVTVPDPAPPPPPAPA 57

Query: 133 SSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPPP 189
           + + P      S      +   G  T +     R  ++     P  +        P 
Sbjct: 58  AGNPPDTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVPG 114

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 54.8 bits (131), Expect = 5e-08
 Identities = 18/125 (14%), Positives = 24/125 (19%), Gaps = 14/125 (11%)

Query: 25  PSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPP 84
                       +       S +               H P +   P PPPPP       
Sbjct: 5   HHHHHHSSGLVPRGSHMVIPSASVTS---AASDFLAALHPPVTVPDPAPPPPPAP--AAG 59

Query: 85  PPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGS 144
            PP      +  Q               +                P P +    PP  G 
Sbjct: 60  NPPDTVTGDSVLQRILR---------GPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGR 110

Query: 145 PPPPP 149
             P  
Sbjct: 111 AVPGL 115

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 45.5 bits (107), Expect = 4e-05
 Identities = 15/122 (12%), Positives = 25/122 (20%), Gaps = 2/122 (1%)

Query: 67  SYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPP 126
           S+                  P             +++      +     PP   P    P
Sbjct: 4   SHHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAP--PPPPAPAAGNP 61

Query: 127 PSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPV 186
           P +    S +       + P         R       +  AS   +         H P  
Sbjct: 62  PDTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVPGLYHHPVP 121

Query: 187 PP 188
            P
Sbjct: 122 EP 123

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 53.4 bits (128), Expect = 1e-07
 Identities = 22/91 (24%), Positives = 28/91 (30%), Gaps = 14/91 (15%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
           +          +            P Q    P              YPP   P    PP 
Sbjct: 365 SADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPP-----------QGYPPQGYPPQGYPPQ 413

Query: 129 SPPPSSSIPPP---PPPGSPPPPPPKDVEGR 156
             PP    PPP   PP G+PP  PP+ V+ +
Sbjct: 414 GYPPQGYPPPPQGAPPQGAPPAAPPQGVDNQ 444

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 45.3 bits (107), Expect = 5e-05
 Identities = 28/119 (23%), Positives = 32/119 (26%), Gaps = 36/119 (30%)

Query: 25  PSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPP 84
            S    P     Q +      Q            QQ  + P  YA PP   PP+   P  
Sbjct: 358 ESSDAAPSADAAQMKEMMAMMQ--------KMQQQQAAYPPQGYAPPPQGYPPQGYPPQG 409

Query: 85  PPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPG 143
            PP   PP                               PPPP   PP  + P  PP G
Sbjct: 410 YPPQGYPPQGY----------------------------PPPPQGAPPQGAPPAAPPQG 440

>3gdb_A Endo-D, putative uncharacterized protein SPR0440; alpha-beta-barrels, cell WALL, peptidoglycan-anchor, secreted, hydrolase; HET: PGE; 1.87A {Streptococcus pneumoniae} PDB: 2xqx_A Length = 937

 Score = 50.3 bits (119), Expect = 2e-06
 Identities = 9/183 (4%), Positives = 33/183 (18%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
            +       E +               +   P+   ++      +              +
Sbjct: 46  NEADKQNEGEHARENKLEKAEGVATASETASPASNEAATTETAEAASAAKPEEKASEVVA 105

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPP 188
             P + + P         P      +               +               +  
Sbjct: 106 ETPSAEAKPKSDKETEAKPEATNQGDESKPAAEANKTEKEVQPDVPKNTEKTLKPKEIKF 165

Query: 189 PGVKKVNGGSGRVETEEERRIRKKREYEKHRQEEKHRLQMKESQNVVMQKSQMVASGKGG 248
              +++         ++           +      +    KE++   +  +   A     
Sbjct: 166 NSWEELLKWEPGAREDDAINRGSVVLASRRTGHLVNEKASKEAKVQALSNTNSKAKDHAS 225

Query: 249 HGS 251
            G 
Sbjct: 226 VGG 228

>3gdb_A Endo-D, putative uncharacterized protein SPR0440; alpha-beta-barrels, cell WALL, peptidoglycan-anchor, secreted, hydrolase; HET: PGE; 1.87A {Streptococcus pneumoniae} PDB: 2xqx_A Length = 937

 Score = 48.0 bits (113), Expect = 8e-06
 Identities = 18/166 (10%), Positives = 41/166 (24%), Gaps = 2/166 (1%)

Query: 59  QQHYHQPYS-YAQPPPPPPPESSYPPPPPP-PPPPPPTQQQTQPSMYYSSNQYNQNSMYP 116
             H+HQ  + Y Q      PE+S              T +  + +    + +        
Sbjct: 8   HGHHHQLENLYFQGEETAVPENSGANTELVSGESEHSTNEADKQNEGEHARENKLEKAEG 67

Query: 117 PMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDP 176
                    P S+   ++          P     + V    +  +        E      
Sbjct: 68  VATASETASPASNEAATTETAEAASAAKPEEKASEVVAETPSAEAKPKSDKETEAKPEAT 127

Query: 177 GHSKQHRPPVPPPGVKKVNGGSGRVETEEERRIRKKREYEKHRQEE 222
               + +P       +K         TE+  + ++ +        +
Sbjct: 128 NQGDESKPAAEANKTEKEVQPDVPKNTEKTLKPKEIKFNSWEELLK 173

>3gdb_A Endo-D, putative uncharacterized protein SPR0440; alpha-beta-barrels, cell WALL, peptidoglycan-anchor, secreted, hydrolase; HET: PGE; 1.87A {Streptococcus pneumoniae} PDB: 2xqx_A Length = 937

 Score = 47.3 bits (111), Expect = 2e-05
 Identities = 19/223 (8%), Positives = 48/223 (21%), Gaps = 32/223 (14%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
             P+   ++       +++ +       + +  +                          
Sbjct: 25  AVPENSGANTELVSGESEHSTNEADKQNEGEHARENKL---------------------- 62

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPP 125
              A+        +S                  +P    S             + P    
Sbjct: 63  -EKAEGVATASETASPASNEAATTETAEAASAAKPEEKASE---------VVAETPSAEA 112

Query: 126 PPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPP 185
            P S   + + P     G    P  +  +       D  K   K +   +   +      
Sbjct: 113 KPKSDKETEAKPEATNQGDESKPAAEANKTEKEVQPDVPKNTEKTLKPKEIKFNSWEELL 172

Query: 186 VPPPGVKKVNGGSGRVETEEERRIRKKREYEKHRQEEKHRLQM 228
              PG ++ +  +        RR       +  ++ +   L  
Sbjct: 173 KWEPGAREDDAINRGSVVLASRRTGHLVNEKASKEAKVQALSN 215

>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics; 5.00A {Barmah forest virus} Length = 253

 Score = 47.3 bits (112), Expect = 6e-06
 Identities = 17/92 (18%), Positives = 21/92 (22%), Gaps = 4/92 (4%)

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPP 117
            Q  Y + +    P     P    P PP PP       Q  Q      +           
Sbjct: 6   TQTFYGRRW-RPAPVQRYIP---QPQPPAPPRRRRGPSQLQQLVAALGALALQPKQKQKR 61

Query: 118 MQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPP 149
            Q      PP  P  +     P       P  
Sbjct: 62  AQKKPKKTPPPKPKKTQKPKKPTQKKKSKPGK 93

>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics; 5.00A {Barmah forest virus} Length = 253

 Score = 45.4 bits (107), Expect = 3e-05
 Identities = 11/96 (11%), Positives = 23/96 (23%), Gaps = 12/96 (12%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
             + +  + +      P   P  PP   +   Q Q+                        
Sbjct: 8   TFYGRRWRPAPVQRYIPQPQPPAPPRRRRGPSQLQQLVA------------ALGALALQP 55

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQP 100
                +    P       P     P  P  +++++P
Sbjct: 56  KQKQKRAQKKPKKTPPPKPKKTQKPKKPTQKKKSKP 91

>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics; 5.00A {Barmah forest virus} Length = 253

 Score = 43.5 bits (102), Expect = 1e-04
 Identities = 14/96 (14%), Positives = 18/96 (18%), Gaps = 12/96 (12%)

Query: 5   RPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQ 64
           R  P P Q      P P             Q QQ      +              +   +
Sbjct: 13  RWRPAPVQ---RYIPQPQPPAPPRRRRGPSQLQQLVAALGALALQ---------PKQKQK 60

Query: 65  PYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQP 100
                    PPP       P  P         +   
Sbjct: 61  RAQKKPKKTPPPKPKKTQKPKKPTQKKKSKPGKRMR 96

>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics; 5.00A {Barmah forest virus} Length = 253

 Score = 43.1 bits (101), Expect = 2e-04
 Identities = 14/81 (17%), Positives = 20/81 (24%)

Query: 71  PPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSP 130
           P          P P     P P      +     S  Q    ++      P      +  
Sbjct: 5   PTQTFYGRRWRPAPVQRYIPQPQPPAPPRRRRGPSQLQQLVAALGALALQPKQKQKRAQK 64

Query: 131 PPSSSIPPPPPPGSPPPPPPK 151
            P  + PP P     P  P +
Sbjct: 65  KPKKTPPPKPKKTQKPKKPTQ 85

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score = 47.7 bits (113), Expect = 7e-06
 Identities = 15/102 (14%), Positives = 20/102 (19%), Gaps = 14/102 (13%)

Query: 53  NTGGGAQQHYHQPYSYAQPPPPPPPE----SSYPPPPPPPPPPPPTQQQTQPSMYYSSNQ 108
                 Q  +             PP     S +   P     PP            S   
Sbjct: 19  TISSAIQNIHSASKGLPLNHAALPPTDYDRSPFVTSPISMTMPPHG----------SLQG 68

Query: 109 YNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPP 150
           Y     +P        P P +  P S +            P 
Sbjct: 69  YQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPA 110

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score = 46.9 bits (111), Expect = 1e-05
 Identities = 18/101 (17%), Positives = 23/101 (22%), Gaps = 9/101 (8%)

Query: 54  TGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNS 113
           T   A Q+ H             P + Y   P    P   T              Y    
Sbjct: 19  TISSAIQNIHSASKGLPLNHAALPPTDYDRSPFVTSPISMTMPPHGSL-----QGYQTYG 73

Query: 114 MYPPMQPPLPPPPPSSPPPSSSIPPPP----PPGSPPPPPP 150
            +P        P P +  P S +           SP   P 
Sbjct: 74  HFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPASIPH 114

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score = 43.1 bits (101), Expect = 2e-04
 Identities = 14/126 (11%), Positives = 24/126 (19%), Gaps = 3/126 (2%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
               P   +  PP   +++P    P             Y              +  Y  P
Sbjct: 31  SKGLPLNHAALPPTDYDRSPFVTSPISMTMPPHGSLQGYQTYG---HFPSRAIKSEYPDP 87

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPP 125
           Y+ +                 P   P    +  +        Q    +     Q      
Sbjct: 88  YTSSPESIMGYSYMDSYQTSSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKH 147

Query: 126 PPSSPP 131
              S  
Sbjct: 148 EKLSTF 153

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score = 41.9 bits (98), Expect = 5e-04
 Identities = 14/144 (9%), Positives = 28/144 (19%), Gaps = 12/144 (8%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
                 Q+          N +  PP    +     P   S         G       +  
Sbjct: 19  TISSAIQNIHSASKGLPLNHAALPPTDYDRS----PFVTSPISMTMPPHGSLQGYQTYGH 74

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPP 125
           +         P   +  P          + Q + P+        +   +   +    P  
Sbjct: 75  FPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPA--------SIPHLILELLKCEPDE 126

Query: 126 PPSSPPPSSSIPPPPPPGSPPPPP 149
           P       + +       S     
Sbjct: 127 PQVQAKIMAYLQQEQANRSKHEKL 150

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score = 41.5 bits (97), Expect = 6e-04
 Identities = 18/151 (11%), Positives = 27/151 (17%), Gaps = 17/151 (11%)

Query: 16  PPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPP 75
                    PS        Q           N     +       +   P+  +      
Sbjct: 6   AMSQVIQAMPSDLTISSAIQNIHSASKGLPLN-----HAALPPTDYDRSPFVTSPISMTM 60

Query: 76  PPESSYPPPPPPP--PPPPPTQQQTQPSMYY--SSNQYNQNSMYPPMQPPLPPPP----- 126
           PP  S          P      +   P      S   Y+    Y    P   P       
Sbjct: 61  PPHGSLQGYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPASIPHLILELL 120

Query: 127 ---PSSPPPSSSIPPPPPPGSPPPPPPKDVE 154
              P  P   + I              + + 
Sbjct: 121 KCEPDEPQVQAKIMAYLQQEQANRSKHEKLS 151

>1kxf_A Sindbis virus capsid protein; chymotrypsin-like serine proteinase, wild type, viral protein; 2.38A {Sindbis virus} SCOP: b.47.1.3 PDB: 1ld4_A 3j0f_A Length = 264

 Score = 45.6 bits (107), Expect = 2e-05
 Identities = 22/159 (13%), Positives = 28/159 (17%), Gaps = 39/159 (24%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
           M   RPFP P     P                 Q QQ                       
Sbjct: 8   MLGRRPFPAPTAMWRPRRRRQAAPMPARNGLASQIQQLTTAV------------------ 49

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQP 120
                    Q   P  P    PP      P  P + +                       
Sbjct: 50  ---SALVIGQATRPQNPRPRPPPRQKKQAPKQPPKPKKPK------------------PQ 88

Query: 121 PLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTG 159
                 P+   P           +      K+ +G   G
Sbjct: 89  EKKKKQPAKTKPGKRQRMALKLEADRLFDVKNEDGDVIG 127

>1kxf_A Sindbis virus capsid protein; chymotrypsin-like serine proteinase, wild type, viral protein; 2.38A {Sindbis virus} SCOP: b.47.1.3 PDB: 1ld4_A 3j0f_A Length = 264

 Score = 44.8 bits (105), Expect = 4e-05
 Identities = 19/96 (19%), Positives = 24/96 (25%)

Query: 68  YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPP 127
             +P P P             P P      +Q     ++            Q P P PPP
Sbjct: 10  GRRPFPAPTAMWRPRRRRQAAPMPARNGLASQIQQLTTAVSALVIGQATRPQNPRPRPPP 69

Query: 128 SSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDR 163
                +   PP P    P     K       G   R
Sbjct: 70  RQKKQAPKQPPKPKKPKPQEKKKKQPAKTKPGKRQR 105

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 46.0 bits (108), Expect = 3e-05
 Identities = 8/82 (9%), Positives = 15/82 (18%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
             PPP      + P           T          S         +  +   +     +
Sbjct: 32  PPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGGGFFSSLSNAVKQTTAA 91

Query: 129 SPPPSSSIPPPPPPGSPPPPPP 150
           +    S        G+      
Sbjct: 92  AAATFSEQVGGGSGGAGRGGAA 113

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 45.6 bits (107), Expect = 4e-05
 Identities = 14/122 (11%), Positives = 21/122 (17%), Gaps = 7/122 (5%)

Query: 49  GGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQ 108
            GY       Q     P + +    P    +S        P   P       S       
Sbjct: 20  NGYMTDLQRPQPPPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGGGFFS 79

Query: 109 YNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPP-------GSPPPPPPKDVEGRDTGTS 161
              N++                  S                  P     K  +G+     
Sbjct: 80  SLSNAVKQTTAAAAATFSEQVGGGSGGAGRGGAAARVLLVIDEPHTDWAKYFKGKKIHGE 139

Query: 162 DR 163
             
Sbjct: 140 ID 141

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 45.2 bits (106), Expect = 6e-05
 Identities = 11/114 (9%), Positives = 23/114 (20%)

Query: 52  SNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQ 111
           +N   G      +P     PP    P ++                   P+     +    
Sbjct: 16  ANLPNGYMTDLQRPQPPPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGG 75

Query: 112 NSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDK 165
                           ++   S  +              + +   D   +D  K
Sbjct: 76  GFFSSLSNAVKQTTAAAAATFSEQVGGGSGGAGRGGAAARVLLVIDEPHTDWAK 129

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 44.1 bits (103), Expect = 1e-04
 Identities = 15/94 (15%), Positives = 23/94 (24%)

Query: 100 PSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTG 159
           P+ Y +  Q  Q    PP        P S+   +       P  SP  P P    G    
Sbjct: 19  PNGYMTDLQRPQPPPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGGGFF 78

Query: 160 TSDRDKRASKEVSRHDPGHSKQHRPPVPPPGVKK 193
           +S  +       +       +             
Sbjct: 79  SSLSNAVKQTTAAAAATFSEQVGGGSGGAGRGGA 112

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 41.8 bits (97), Expect = 6e-04
 Identities = 12/88 (13%), Positives = 16/88 (18%), Gaps = 1/88 (1%)

Query: 6   PFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQP 65
             PQPP    P    P   P       ++          +    G S  GG      +  
Sbjct: 27  QRPQPPPPP-PSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGGGFFSSLSNAV 85

Query: 66  YSYAQPPPPPPPESSYPPPPPPPPPPPP 93
                       E               
Sbjct: 86  KQTTAAAAATFSEQVGGGSGGAGRGGAA 113

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 44.3 bits (104), Expect = 4e-05
 Identities = 15/89 (16%), Positives = 20/89 (22%)

Query: 9   QPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSY 68
           Q P  +       +Q   Q     Q  Q               +    G +     P + 
Sbjct: 140 QNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAV 199

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQ 97
                 P P     PPPP P         
Sbjct: 200 PGGDRFPGPAGPGGPPPPFPAGQTHHHHH 228

>1dx0_A Prion protein; brain, repeat; NMR {Bos taurus} SCOP: d.6.1.1 PDB: 1dx1_A 1qlx_A 1qlz_A Length = 219

 Score = 43.7 bits (102), Expect = 8e-05
 Identities = 11/126 (8%), Positives = 21/126 (16%)

Query: 24  NPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPP 83
           +  +P P         R        G      GG          + QP      +     
Sbjct: 2   SKKRPKPGGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGG 61

Query: 84  PPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPG 143
              P                  ++        P           ++      +       
Sbjct: 62  WGQPHGGGWGQPHGGGGWGQGGTHGQWNKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLGS 121

Query: 144 SPPPPP 149
           +   P 
Sbjct: 122 AMSRPL 127

>1dx0_A Prion protein; brain, repeat; NMR {Bos taurus} SCOP: d.6.1.1 PDB: 1dx1_A 1qlx_A 1qlz_A Length = 219

 Score = 43.3 bits (101), Expect = 9e-05
 Identities = 12/92 (13%), Positives = 16/92 (17%)

Query: 9   QPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYSY 68
                S  P          PP       Q         + GG+    GG     H     
Sbjct: 12  WNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWG 71

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQP 100
                    +         P  P    +    
Sbjct: 72  QPHGGGGWGQGGTHGQWNKPSKPKTNMKHVAG 103

>3dva_I Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase...; oxidoreductase, multienzyme complex; HET: TPW; 2.35A {Bacillus stearothermophilus} PDB: 3dv0_I* 3duf_I* 1b5s_A 1lab_A 1lac_A 1w3d_A Length = 428

 Score = 44.5 bits (106), Expect = 9e-05
 Identities = 15/158 (9%), Positives = 27/158 (17%), Gaps = 42/158 (26%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
                    +                                                 +
Sbjct: 80  GYENMTFKGQEQEEAKKEEKTETVSK----------------------------EEKVDA 111

Query: 129 SPPPSSSIPPPPPPGSPPPPPP--------KDVEGRDTGTSDRDKRASKE-VSRHDPGHS 179
             P + +      P       P        K V+ R    + ++ R  KE +     G +
Sbjct: 112 VAPNAPAAEAEAGPNRRVIAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDAFLAGGA 171

Query: 180 KQHRPPVPPPG-----VKKVNGGSGRVETEEERRIRKK 212
           K                     G      E+   IR+ 
Sbjct: 172 KPAPAAAEEKAAPAAAKPATTEGEFPETREKMSGIRRA 209

>4af8_A Metacaspase MCA2; hydrolase, cysteine peptidase, caspase/hemoglobin fold; 1.40A {Trypanosoma brucei} PDB: 4afp_A 4afv_A 4afr_A Length = 367

 Score = 44.2 bits (103), Expect = 1e-04
 Identities = 12/96 (12%), Positives = 21/96 (21%), Gaps = 5/96 (5%)

Query: 56  GGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMY 115
           G +  H+H          P                              SS  Y   ++ 
Sbjct: 2   GSSHHHHHHSS----GLVPGGSHMCSLITQLCDAGQLADYVGLGWLNAVSSQPYLVQAL- 56

Query: 116 PPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPK 151
               PP      ++   +  +    P  + P P   
Sbjct: 57  GLQPPPRRVDVDAAFRDAKGLHGHQPWVATPLPGQT 92

>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229

 Score = 43.2 bits (101), Expect = 1e-04
 Identities = 29/133 (21%), Positives = 36/133 (27%), Gaps = 14/133 (10%)

Query: 69  AQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPS 128
            Q   PPP     P P P P P PP +                     P   P P P P 
Sbjct: 48  PQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIE--------------KPKPKPKPKPKPV 93

Query: 129 SPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVSRHDPGHSKQHRPPVPP 188
                       P  S P  P ++       +S      SK V+    G     R     
Sbjct: 94  KKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQY 153

Query: 189 PGVKKVNGGSGRV 201
           P   +     G+V
Sbjct: 154 PARAQALRIEGQV 166

>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 21/142 (14%), Positives = 35/142 (24%), Gaps = 21/142 (14%)

Query: 8   PQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQHYHQPYS 67
            QP   +   P       +  PPP    + +  P P                        
Sbjct: 32  AQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEP---------------------IPE 70

Query: 68  YAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPP 127
             +  P    +    P P P P     +Q  +      S   +      P +        
Sbjct: 71  PPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATA 130

Query: 128 SSPPPSSSIPPPPPPGSPPPPP 149
           ++  P +S+   P   S   P 
Sbjct: 131 ATSKPVTSVASGPRALSRNQPQ 152

>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 24/158 (15%), Positives = 36/158 (22%), Gaps = 35/158 (22%)

Query: 2   ASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQH 61
            S     + P  + P            PP   Q   +    P                  
Sbjct: 20  MSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEP------------------ 61

Query: 62  YHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPP 121
             +P     P PP         P P P P P   ++ Q                 P +  
Sbjct: 62  --EPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQE---------------QPKRDV 104

Query: 122 LPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTG 159
            P     + P  ++ P      +      K V    +G
Sbjct: 105 KPVESRPASPFENTAPARLTSSTATAATSKPVTSVASG 142

>3a58_A Exocyst complex component SEC3; protein complex, PH domain, GTPase, membrane traffic, coiled coil, exocytosis, phosphoprotein; HET: GNP; 2.60A {Saccharomyces cerevisiae} Length = 320

 Score = 43.4 bits (101), Expect = 2e-04
 Identities = 8/102 (7%), Positives = 17/102 (16%)

Query: 51  YSNTGGGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYN 110
                G   +  +   S           +     P    P          +   S     
Sbjct: 218 IQTFEGHVPELVNWDLSLFYLDERSYQRAVITNRPGSVSPIKSPTSNFTTNTTQSVGSVP 277

Query: 111 QNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKD 152
            ++     +            P+S             P   +
Sbjct: 278 FSAPTERTRRSETESVNPVSTPASVEYHAGMKSLNKAPYSSN 319

>1pcx_A Protein transport protein SEC24; 2.50A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 PDB: 1pd0_A 1pd1_A Length = 810

 Score = 43.1 bits (100), Expect = 3e-04
 Identities = 15/63 (23%), Positives = 17/63 (26%)

Query: 84  PPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPPG 143
            P    P     Q  +P               P     LPPPP   PP    +P      
Sbjct: 2   APAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNA 61

Query: 144 SPP 146
           SP 
Sbjct: 62  SPD 64

>1pcx_A Protein transport protein SEC24; 2.50A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 PDB: 1pd0_A 1pd1_A Length = 810

 Score = 42.3 bits (98), Expect = 6e-04
 Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 2/65 (3%)

Query: 83  PPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSIPPPPPP 142
            P    P     Q     +  Y  +   +  + PP+     PPPP   PP   + P    
Sbjct: 2   APAYGQPSAAMGQNMRPMNQLYPIDLLTE--LPPPITDLTLPPPPLVIPPERMLVPSELS 59

Query: 143 GSPPP 147
            + P 
Sbjct: 60  NASPD 64

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae} Length = 371

 Score = 42.2 bits (98), Expect = 4e-04
 Identities = 15/92 (16%), Positives = 22/92 (23%), Gaps = 5/92 (5%)

Query: 72  PPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPP 131
           P       S   PP      P   +Q+      +S   + +   PP  P       S   
Sbjct: 4   PLSAITVRSMEGPPTVQQQSPSVIRQSPTQRRKTSTTSSTSRAPPPTNPDASSSSSSFAV 63

Query: 132 PSSSIPPPP-----PPGSPPPPPPKDVEGRDT 158
           P+      P               +   GR  
Sbjct: 64  PTIHFKESPFYKIQRLIPELVMNVEVTGGRGM 95

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae} Length = 371

 Score = 41.5 bits (96), Expect = 6e-04
 Identities = 16/71 (22%), Positives = 20/71 (28%)

Query: 77  PESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPPMQPPLPPPPPSSPPPSSSI 136
                         PP  QQQ+   +  S  Q  + S         PP  P +   SSS 
Sbjct: 2   LTPLSAITVRSMEGPPTVQQQSPSVIRQSPTQRRKTSTTSSTSRAPPPTNPDASSSSSSF 61

Query: 137 PPPPPPGSPPP 147
             P       P
Sbjct: 62  AVPTIHFKESP 72

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 42.2 bits (98), Expect = 4e-04
 Identities = 18/94 (19%), Positives = 24/94 (25%)

Query: 58  AQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMYPP 117
                       + P      ++          P     Q          Q  +   + P
Sbjct: 99  GTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMP 158

Query: 118 MQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPK 151
            QPP  PPP   PPP  +    PP   PP     
Sbjct: 159 GQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMP 192

>3sv0_A Casein kinase I-like; typical kinase domain fold, cytosol, transferase; 2.00A {Oryza sativa japonica group} Length = 483

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 25/186 (13%), Positives = 50/186 (26%), Gaps = 10/186 (5%)

Query: 1   MASYRPFPQPPQSSFPPPPPPNQNPSQPPPPPQQQQQQQRPNPYSQNWGGYSNTGGGAQQ 60
           +AS  P      +      PP     +     + +          +     ++ G  A+Q
Sbjct: 300 IASAPPRAVGHGAGPSGLAPPALQNDRQSGVDEGRTSGWSSMDRRRAPPPIASVGTLAKQ 359

Query: 61  HYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQ--------TQPSMYYSSNQYNQN 112
                   +    P    S++          P             ++PS   +++  +  
Sbjct: 360 KAPVGNDASFSKEPVISASNFLGRSSGSSRRPAVSSSRDVMPIDTSEPSRTRATDA-SPG 418

Query: 113 SMYPPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTSDRDKRASKEVS 172
           +      P    P  S+ P  SS               K +EG +    D   + +  + 
Sbjct: 419 AFRRTSGPQKSSPVNSAEPKHSSSARHSSNVKNYESALKGIEGLNFD-GDERVQYAAALE 477

Query: 173 RHDPGH 178
            H   H
Sbjct: 478 HHHHHH 483

>3oun_A Putative uncharacterized protein TB39.8; peptidoglycan, Ser/Thr kinase, pseudokinase, FHA domain, REG phosphorylation; HET: TPO; 2.71A {Mycobacterium tuberculosis} Length = 157

 Score = 39.5 bits (92), Expect = 9e-04
 Identities = 11/106 (10%), Positives = 16/106 (15%), Gaps = 28/106 (26%)

Query: 56  GGAQQHYHQPYSYAQPPPPPPPESSYPPPPPPPPPPPPTQQQTQPSMYYSSNQYNQNSMY 115
           G +Q H+H            P    Y  P         +                     
Sbjct: 2   GSSQHHHHHSSGLVPRGSHMPQGGGYAEPAGRDYDYGQS--------------------- 40

Query: 116 PPMQPPLPPPPPSSPPPSSSIPPPPPPGSPPPPPPKDVEGRDTGTS 161
                    P    P P                         +G +
Sbjct: 41  -------GAPDYGQPAPGGYSGYGQGGYGSAGTSVTLQLDDGSGRT 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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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	677
d1jvra_	137	a.61.1.2 (A:) HTLV-II matrix protein {Human T-cell	0.002
d2gqba1	130	a.282.1.1 (A:1-130) Hypothetical protein RPA2825 {	0.002

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00