Conserved Protein Domain Family
Paf1

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pfam03985: Paf1 
Paf1
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.
Statistics
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PSSM-Id: 309201
View PSSM: pfam03985
Aligned: 38 rows
Threshold Bit Score: 249.948
Threshold Setting Gi: 588253410
Created: 25-Jul-2016
Updated: 4-Aug-2016
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122095530  27 ELISRVKYCNTLPDIPFDLKFITYPFE---NDRFIQYK-PTSLERNYRYEVL-------TEHDLGVTIDLINRDLYQI-D 94
gi 391358161   7 DYILRVRYHNPLPPPPFPPKLINIPNP---VKQYALPNfVSTLVQEKKIPIE-------NDIELGMPLDLAGITGFFEgD 76
gi 969886150  16 DFIARIRFSNALPPPPNPPKLLDIPNTglsSGQYTTPGfASRLAREQPLNIE-------ADAELGMPLDLVGMPGVFDgD 88
gi 927400705  16 DFIARIRFSNALPPPPNPPKLLDIPNTglaSGQYTTPGfASRLAREQPLNIE-------ADAELGMPLDLVGMPGVFDgD 88
gi 399171314  16 DFIARIRFSNALPPPPNPPKLLDIPNTglaSGQYTTPGfASRLAREQPLNIE-------ADAELGMPLDLVGMPGVFDgD 88
gi 891581987   7 DYILRVRYHNPLPPPPFPPRLINISNP---VKQYALPNfVSNLIQEKKIAIE-------NDAELGMPMDLAAVDGFFEgD 76
gi 154323151  12 EYIARIRYSNALPPPPNPPKLLDIPNTglaSGQYTTPGfATRLARDQPLNIE-------ADAELGMPLDLVGMPGIFDgD 84
gi 149239993   9 DYIAKIRYTNNLPPPPLNPKYIEYNTT---NPISPKVE-AEQLLSSLFRKENfqnllgrIDDFSGLELNLLNNAGFFAgD 84
gi 448101449  11 EYISKVRYINDLPPPPLNPKFLEYNTT---ERSSTKTE-SEQVISSLFRKENfhsliecIDEDMGMNLNLLNNKGFLDeN 86
gi 762073128   6 EYIAPIKYQNSLPVPQLPPKLLVYPES---PETNAD---SSQLINSLYIKTNvtn-liqQDEDLGMPVDLMKFPGLLNkL 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122095530  95 ------H-------------L---------AQLDPADEKLLEEDihtpQDSLRSSrHAKSVSWLRKSEYISTE-QT-RFQ 144
gi 391358161  77 t----sW-------------Mhsd---lssVNLDPIDRSLLKVAggs-------gsTHLEVPFLRRTEYISSE------- 122
gi 969886150  89 e----rS-------------Iqap---sqpLALHPHDRALLRPI----AALGKPKvAEANVSFLRRTEYISSL-VP-KRF 142
gi 927400705  89 e----rS-------------Iqap---sqpLAVHPHDRALLRPI----AALGKPKvAEANVSFLRRTEYISSL-IP-KRF 142
gi 399171314  89 ersiqaP-------------Vq-------tPAVHPHDRPLLRPI----AALGKPKvAEANVSFLRRTEYISST-TP-KRL 142
gi 891581987  77 t----sW-------------Nqsd---msgMNLEPVDRSLLKVAg-------gSGsSHVEVPFLRRTEYISAE-VG-R-- 125
gi 154323151  85 e----sS-------------Iqap---lhpPQLHPHDRALLRPl----ATLGKPKfSDTGVSFLRRTEYISSG-FTsKAR 139
gi 149239993  85 s----tV-------------VgqlskngqpVHLHPKDRALLRDAgigkINK-----SEPGVSFLRRTEYISERsLP-KAA 141
gi 448101449  87 d----eSvigmflneknkkdNk-------pVTLHERDRELLRDA----GIERIAR-SELGVSFLRRTEYISEKqFM-KPS 149
gi 762073128  79 d----sK-------------Llyg---fdnVKLDKDDRILLRDP----RIDRLTKtDISKVTFLRRTEYVSNT------- 127
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122095530 145 PQTM-EKVE-AKVGFNVKQsl----rEETLYMDREAQIKA-IEKTFDDNTKEIT-----AHYSKPGVTPVEILPVFPDFA 212
gi 391358161 123 -VARaASNR-GNLRLTASTskalaeqRGRSLREVPKQLEA-INESFDVVQQPLEq---lKHPTKPDLKPVSAWNLLPNTS 196
gi 969886150 143 --EA-NHPR-ALLAKSRRPa-----kRPEPAADSPQVIKRkIDKGFEIAEQDLKdpkriKHPSKKHLKLVDALPLVPDLD 213
gi 927400705 143 --EA-NHPR-ALLAKSRRPv-----kRPEPAADSPQAIKRkIDKGFEVAEQDLKdpkriKHPSKKHLKLVDALPLVPDLD 213
gi 399171314 143 --DA-SHPR-ALLPKARRPlr----tAPDAAADSPLAIKRkIDRSFETAEQDIKdvkrvKHPTKKHLKVVEAIPMLPDLE 214
gi 891581987 126 ---N-SSTR-GNLRLTASTskaiaeqRGRSLREIPNQIQA-IEQTFSAVQQPLEn---lKHPTKPELKPVGAWNFLPNDS 196
gi 154323151 140 MEGT-TSAK-GLVDTRKPKpv----qNLPADRESPAYIKAqVEKGFETAAANLKdrtrvRHPTKRNVQLVNAVPLIPDLD 213
gi 149239993 142 HSVT-AHTEeVKVNEKLKNn-------ESHSLDADAQLNA-VEETFTAANSTLLdvsslKHPRKRHLKAVDAWPLLPDTQ 212
gi 448101449 150 ANGV-ENG-----AHKLTKgk----eDNQEKLDADAQLQA-VEKTFADAQKTLQdfqniKHPRRKNLKAVAAWPILPDTS 218
gi 762073128 128 ---IaAHDN-TSLKRKRRLdd---gdSDDENLDVNHIISR-VEGTFN----KTDk---wQHPVKKGVKMVKKWDLLPDTA 192
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122095530 213 NWKYP--CAQVIFDFDPAP----AGKNVPA--------Q-----MEEMSQAMIR----------------------Gv-- 249
gi 391358161 197 MAGIQ--HLMLRVADDLSErshsYSSLVNL--------QeghnlTKRHEVALFM----------------------P--- 241
gi 969886150 214 AFPDSgaYVTIKFLTNPVSssneYD--------------------NRLRSGLFRpidrtaaeeaaleaameaynqdPv-- 271
gi 927400705 214 AFPDSgaYVTIKFLTNPVSssneYD--------------------NRLRSGLFRpidrtaaeeaaleaameaynqdPv-- 271
gi 399171314 215 AFPDSgaYVTIKFLTNPVSsaneYD--------------------TRLLSGLFR----------------------Pier 252
gi 891581987 197 MAGIQ--HLMLRVSDNLTDrtptSSTPGEE--------Dv----SNRHKVALFM----------------------P--- 237
gi 154323151 214 AFPDAggYVLLKFLTNPVPpsstYD--------------------ARVESSVLR----------------------Padp 251
gi 149239993 213 MMDNV--LMNLRFLGSASIdrelKDLKRKRgtafnekfE-----RQKQESSIFK----------------------Pi-- 261
gi 448101449 219 MLDSK--FLNVKFFGSASFsremQLLKRQEkekydeqfQ-----KNSLETSIFR----------------------Pi-- 267
gi 762073128 193 SMDQV--YFILKFMGSASLdtkeKK---------------------SLNTGIFR----------------------Pv-- 225
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122095530 250 -------------MDESG--------------EQ-------FVAY--FLPSEETLEKRR-------------R------- 273
gi 391358161 242 -------------SSAEG--------------EE-------FLSY--YLPSEETAEEI---------------------- 263
gi 969886150 272 -------------SNPKP--------------AN-------LMNYdfYLGQSRADADRF-------------Rrkfdvdd 304
gi 927400705 272 -------------SNPKP--------------AN-------LMNYdfYLGQSRADADRF-------------Rrkfdvdd 304
gi 399171314 253 teaeeaayeaaleAHEQD--------------PEnnpsphnLMNYdfYLGQSSTVARNF-------------Rrkfdied 305
gi 891581987 238 -------------SSAEG--------------EQ-------YLSY--YLPSEESAEKIQ--------------------- 260
gi 154323151 252 te-------aeleMKEAArqayeldphnnpppDE-------KIQYemFMPDTVTDAKNIkrkfdvldpehddR------- 310
gi 149239993 262 -------------NSEDG--------------E--------WMSM--FEVNDISQAEQV-------------H------- 284
gi 448101449 268 --------------TSDD--------------GE-------WISL--YQSKDPQRTQIL-------------K------- 290
gi 762073128 226 ------------eLEED----------------E-------WISM--YATDHKDSAILE-------------N------- 248
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122095530 274 ------D------LVN-----------ET----LYEd-eE----EYEYKMAREYNWNV----KS--KASkgy----eenY 311
gi 391358161 264 ------Q------AKV-----------ND----ASAdvhE----PFVYNHFRNFDASM----------HvnstgledlcL 302
gi 969886150 305 adrdddD------LYT-----------HR----GDTg--G----YFQFNRIRAYETAQ----ET--ELDhptk--yedeI 349
gi 927400705 305 adrdeeD------LYT-----------HR----GDTg--G----YFQFNRIRAYETAQ----ET--ELDhptk--yedeI 349
gi 399171314 306 adrdntD------LYT-----------HQ----GETg--P----YFQFNRVRAYETAD----ER--ELDhptky-sdeiI 351
gi 891581987 261 ------Q------ASN-----------NS----SSTe--G----PFLYNLFRNFDASM----LV--NPSgle----dlcL 297
gi 154323151 311 ------D------LYS-----------QF----DEEtgkG----AFRLKRLRGYETVQ----TSggTDDkyd----eyvV 351
gi 149239993 285 ------Q------KLNstapeqpinllDL----DDEs-aS----NYNFKFVHNYDMQY----QE--YPEvnq----elaI 333
gi 448101449 291 ------DklnsseKEK-----------QVyvldEEEd-aE----EYKFEHIKEYDMSF----QR--Y-Nkpy-----eeL 336
gi 762073128 249 ------E------LEK-----------GM----DEMdddShegkIYKFKRIRDYDMKQvaekPM--TE-----------L 288
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122095530 312 FLVLRQD------------GMYYNELETRVRLSKRRQKvgq-----------qpNNTKLVVKHRPLNASEHRMQRYRERQ 368
gi 391358161 303 TFHTDKdhp-------eanQVLYTPIYARSTLKRRHVRapv----------sldAVDGIELSLRDLNDEESLQLKRARYD 365
gi 969886150 350 ILSTNEKdtds-----sqkAVFYYPIMQRSTIRPQRTRniartnyglaeddepqVVDQLDLTVDDPTEEMRAAMKMYARH 424
gi 927400705 350 ILSINEKdtda-----sqkAVFYYPIMQRSTIRPQRTRniartnyglaeddepqVVDQLDLTVDEPTEEMRAAMKMYARH 424
gi 399171314 352 VAYNDVDayp------rqkAMYYYPIMQKSTIRPQRTKniartig--inadeeqMVDQLDITVEDPTEEMLDAMKKYKNH 423
gi 891581987 298 SICTDQEnpk-------nnKALYTPIYARSTLKRRHVRapv----------npdTIDGIELTLREPNREESVQLKRARYD 360
gi 154323151 352 IAMHDGTdgl------hqkAAHYYPVVQRSSIRPQRTKniqkmrhn-isgeeeeVLDMVDLSIVDPGAETKQVMEGFKTW 424
gi 149239993 334 KFIPDDEhkdtkaptkkrkVAYYLPVTGKIELRKHRLStnsein----kfvkerTYDEVAFKLREPSTNELKEMDRARSE 409
gi 448101449 337 AIKFASEgepnskgdrkrkAAYYYPVTGKIDLKKHRAStnaein----rfirdsAYDIVNYKLREPNTNEMRRMDTIRSE 412
gi 762073128 289 AIRLNDkd----------gIAYYKPLRSKIELRRRRVNdiikp------lvkehDIDQLNVTLRNPSTKEANIRDKLRMK 352
                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 122095530 369 ---LEP-----PGE-EDDEDIEEEEEEeEDMEEEIQET----QEEEGAEKDEEGEEDKDEdarRSRSRSGSRSRS-VS 432
gi 391358161 366 tfgLGN-----IKD-LEEEEEKLRSVE---GSLNEELSeeekPAESREQLESAEQTNGVK---PETQAQNMSASEsQA 431
gi 969886150 425 ------------------PMGWEQDEE-EELQHGVERSieegDVDADGDAEGEDADRNGA---SSPAEKYHERSPsAd 480
gi 927400705 425 p--MGW-----EQD-EEDE-----------LHQGVERSieegDVDADGDAEGEDADRNGA---SSPAEKYHERSPsAD 480
gi 399171314 424 plgWEQ-----EPD-EEDIAAGATQEQ-Gpdadgdadadvevdgeadadaeagadadpepdadveangvgdkhsqade 494
gi 891581987 361 ---SFA-----MGDvEALEKEEQEIAE-EQAGEENELNeieeQHQDENPLPNPSENPQPL---PTEESGQLSTKNeQk 426
gi 154323151 425 ---PYG-----ENH-EDDAERDAAEVE-DALSEADAEGedddlnspvrpslggktiasrvqsdeedddeneslhsed- 491
gi 149239993 410 ---FDPmeyegDDD-DEEEEDDDDEEE-LEDGEDYEEReeqeELESRQGRSNGNAESGAD---QESVDGKVKHDReDA 479
gi 448101449 413 ---FDP----------MEYEGEEEVAE-TNETQPNEEEqekkDQDNGSSINNDQENNGET---KPEDDSSLKNQEeTN 473
gi 762073128 353 fdpINF-----ATV-DEEDDEDEEQPE------DVKKEsegdSKTEGSEQEGENEKDEEI---KQEKENEQDEENkQD 415
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