5IY6


Conserved Protein Domain Family
TFIIF_alpha

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pfam05793: TFIIF_alpha 
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Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II.
Statistics
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PSSM-Id: 310411
View PSSM: pfam05793
Aligned: 9 rows
Threshold Bit Score: 397.783
Threshold Setting Gi: 122199171
Created: 21-Jul-2016
Updated: 4-Aug-2016
Structure
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Program:
Drawing:
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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY6_S         2 AAL---GPSS--QNVTEYVVRVPKNTTK-KYNIMA-------FNAADKVNFATWN---QARLERDLSNKKIYQ-EEEMPE 64
gi 46397744    2 AAL---GPSS--QNVTEYVVRVPKNTTK-KYNIMA-------FNAADKVNFATWN---QARLERDLSNKKIYQ-EEEMPE 64
gi 464522      2 ASL---GTSG--QSVTEYVVRVPRNPSK-RYSLMA-------FNAADKVDFSTWN---QARMERDLSAKKMYQ-EEEMPE 64
gi 74962259    2 SGL---KPVKpeGVQSEFSVRVAKRSDDiRYSVMM-------FNGMDKVDTSKWTidsGVTMEREDNQRVILS-TQTVQE 70
gi 75207777   42 KSKcheCGTVvtRLIREYNVRAAAPTDK-NYFIGRfvtglpnF--KKGSE-NKWS---------------------LRKD 96
gi 122199171  40 RSKcstCGTTltRLIREYNVHASSATDK-KYFLGRfmnglpdFSKKKSAK-NKWS---------------------LKKD 96
gi 122232395  40 RSKcstCGALltRLIREYNVRASSANDK-NYFIGRfmtglpdFSKKKSAE-NKWS---------------------LQKD 96
gi 347968538  15 GAS---GSSAp-TTVQEFVIRVPKNLKK-KYHVMR-------FNATLNVDFTQWR---TVKMERENNQKEYKGiEEVMPK 79
gi 122096252  12 SGA---GSAGppVSVQEFTIRVPXNLKK-KYHVMR-------YNATLNVDFTQWR---TVKMERENNLKEFKGmDEDMPK 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY6_S        65 SGAGSEFNRKLREEARRKKYGIVLKEFRPEDQPWLLRVNG-KSG--RKFKGIKKGGVTENTSYYIFTQCPDGA-FEAFPV 140
gi 46397744   65 SGAGSEFNRKLREEARRKKYGIVLKEFRPEDQPWLLRVNG-KSG--RKFKGIKKGGVTENTSYYIFTQCPDGA-FEAFPV 140
gi 464522     65 SGAGSEYNRKQREESRRKKYGIILREFKVDDQPWILRVNG-KAG--RKYKGVKKGGVTENASYFIFTQCADGA-FEAFPV 140
gi 74962259   71 YGEGSEYGKAAREEARRKKYGRQSKKYRLDNQPWKMAFTE-PEGrqRQMRGIREGGANEHADYWVFLKPNQSSeFKAYKV 149
gi 75207777   97 IPQGRQFTDAQREKLKNK--------------PWILE----DETgqFQYQGHLEGSQS--ATYYLLVM--QNKeFVAIPA 154
gi 122199171  97 GLKGRQVTDSTREKYKNR--------------PWFLE----DETgqSQFQGHLEGSQS--ATYYLLMK--GKK------- 147
gi 122232395  97 GLKGRQVTDATREKYKNR--------------PWLLE----DETgqSQFQGHLEGSQS--ATYYLLMK--EKKeFVAIPA 154
gi 347968538  80 FGAGSEFNRDLREEARRKRFGIISKKYKPEAQPWILRAGG-KSG--KMFRGIREGGVGENAAFYVFTHAPDGA-IEAYPL 155
gi 122096252  78 FGAGSEFNRDLREEARRKRYGIIAKKHRPDAQPWILKAGGkKDG--KKFRGIREGGVGENASFYVFTHAPDGA-IEAYPL 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY6_S       141 HNWYNFTPLARHRTLTAEEAEEEWERRNKVLNHFSIMQQRRLKDQdq----dEDEEEk----EKRGRRKAS----ELRIH 208
gi 46397744  141 HNWYNFTPLARHRTLTAEEAEEEWERRNKVLNHFSIMQQRRLKDQd-----qDEDEE-----EKEKRGRRKa--sELRIH 208
gi 464522    141 SNWYNFTPVAKHRTLTAEEAEQEWERRNKVLNHFTIMQQRRLKDQvg---deDEDEEgggklEKGGKGKKKkkksDLKIH 217
gi 74962259  150 DEWHKFLPAITHKTLDIDQAEEQFSQRYKVMNQFAL---KAAIQNqlsatdeSEMTEq----QKR----------LLKIK 212
gi 75207777  155 GSWYNFNKVAQYKQLTLEEAEEKMKNRRKTADGYQRWMMKAANNGpalfgevDNEKEsg--gTSGGGGRGR--------K 224
gi 122199171 148 ---YNFNKVAQYKQLTLEEAEEKMNNRKKTADGYQRWMMKAANNGpaafgehWKLDDk---eSNAGGGRS---------R 212
gi 122232395 155 GSWYNFNKVAQYKQLTLEEAEEKMKNRKKTADGYQRWMMKAANNGpaafgehGKLDDk---eSNAGGGRG---------R 222
gi 347968538 156 NEWYNFQPINRYKALSAEEAEQEYGRRKKTMNYFSLMFRKRLKKGedneaddQEETKg----KKGEGGKSK----DLKIS 227
gi 122096252 155 NEWYNFQPIQRYKALSAEEAELEFGRRKRTINYFSLMLKKRMKKDddi-pedLEETKg----KKGGVGKAK----DLKIS 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY6_S       209 DLedDLEMSSDASDASGEEGGRVPKAKKK------APL----AKgg-rkKKKKKGSDD---EAFE-DSDDGDFEGQEVDY 273
gi 46397744  209 DLedDLEMSSDASDASGEEGGRVPKAKKK------APLakggRK-----KKKKKGSDD---EAFE-DSDDGDFEGQEVDY 273
gi 464522    218 DLedDLELSSTESENSDEEGESRKKPQKK------VPak-ggKK-----KKRK--SDD---EALE-DSDDGDFEGQEVDY 279
gi 74962259  213 DEasSDDSDGDDEGEGGDDGKKAKNKKKK------KKNakpaKE-----KRQRVEDKD---DVAKyESSDGEDEGREYDY 278
gi 75207777  225 KSsgGDEEEGNVSDRGDEDEEEEAS-RK-------SRLglnrKSnddddEEGPRGGDL---DMDDdDIEKGDDWEHEEIF 293
gi 122199171 213 KKtgDDDDEGPSSDKGEEDEDEEVD-KK-------NRHglnkKSgydddE-GPRGGDLdddDDDDyDVEKGDDWEHEEIF 283
gi 122232395 223 KKtgDDEDEGPSSDKGEEDEDEEVD-RK-------KRPn--kKNtfdddEEGPRGGDH---DEDDyDVEKGDDWEHEEIF 289
gi 347968538 228 DM--DEWIDSDEVSSSGDDDDEGKSKQKDsdddakDKKaknkKKaladsKKKKRDVDE---EAFE-ESDDGDEEGRELDY 301
gi 122096252 226 DM--DEWIDSDEMSSDDDDDGEGKPKEKDsdd-eaDKKaknkKAla-dkKKKKRDVDE---EAFE-ESDDGDEEGRELDY 297
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY6_S       274 MSDGSSSSQEEP--------------------------EsKAKAPQQEEGPKGVDEQSDSSEESEEEKPPEEDKEEEEEK 327
gi 46397744  274 MSDGSSSSQEEPe-------------------------S-KAKAPQQEEGPKGVDEQSDSSEESEEEKPPEEDKEEEEEK 327
gi 464522    280 MSDESSSDEELP--------------------------G-KIKPAKEEEGPKGLDEQSESSEESEEEKAEEE--EGEEEK 330
gi 74962259  279 ISDSGTDS------------------------------D-REQVPSDEKIEKQLVGVAEEEGARESDSSESEDDLTKKLM 327
gi 75207777  294 TDDDEAVGNDPE--------------------------E-REDLLAPEIPAPPEIKQDEDDEENEEEE----GGLSKSGK 342
gi 122199171 284 TDDDEAPGNDPE--------------------------E-RED-LDPEIPAPLEIKQDDDDDEEEDEDNDEGGGLSKPGK 335
gi 122232395 290 TDDDEAVGNDPE--------------------------E-RED-LAPEVPAPPEIKQ-DDEEEEEDEDNEEGGGLSKSGK 340
gi 347968538 302 ISDSSDSESDHDakvvkemksvaeedalrklltsdedsE-EEEKKSEEDEEKED-EKNGKSKEKDKDGKEKEGKESKKKK 379
gi 122096252 298 ISDSSESESEPEakvnkelqsvaeedalrklltsdedsE-DEEKKSDEDENKKDEEKNGKTKDKEEKTKEKDSKESKKKK 376
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY6_S       328 KAPTpQEKKRRKdsSEESDSSEESDI--DSEASSAlfMAKKKTPPKRERKP-SGGSSRGNSRPGTPSAEGGStSSTLRAA 404
gi 46397744  328 KAPTpQEKKRRK--DSSEESDSSEESdiDSEASSAlfMAKKKTPPKRERKP-SGGSSRGNSRPGTPSAEGGStSSTLRAA 404
gi 464522    331 KAPTpQDNKKKKkgDSSDESETSEDSdiDG-ASSSlfMQKKKTPPKKDKKGgSNSSSRGNSRPGTPSPDTGNtSSTLRAA 409
gi 74962259  328 KPYGdKKKGNDIeeRDS-SGTDSDVSdtEKLDSVVfmKANK-----------DGEGGSGGTGKKRPPTEDSD-------- 387
gi 75207777  343 ELKKlLGKANGL--DES-DEDDDDDSddEEETNYGtvTNSKQKEAAKEEPVdNAPAKPAPSGPPRGTPPAKPsKGKRKLN 419
gi 122199171 336 ELKKlLGRTGGP--SES-DEEDADDDdvDDEDGVPaiTATKQKE-PKEEPIdSSPSKPTATGPARGTPTs---KGKRKEn 408
gi 122232395 341 ELKKlLGRTGGL--SESDDDDDDDDDdiDDEDGVPavTATKQKE-PKEEPVdNSPSKPTATGPARGTPTSKSsKAKRKAn 417
gi 347968538 380 KAKKnKSKKSESdkKDSSSDFSSDSSdsDTASA-----KKKPKDKKSKEGVgSNLSSANNSRSASPSVSQFD-SNKRKMT 453
gi 122096252 377 KDKK-KKKKAENdkKDSSSGSSSDSSdsDGDNSNS--KQQKKKHKKDKEGVgSNLSSANNSRSASPSMSQLE-GNKRKMA 452
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY6_S       405 Askle----qgkrVSEMPA---AKRLRLDTGPqslsgkSTPQPPSG----------------KTTPNSGDVQVTEDAVRR 461
gi 46397744  405 Askle----qgkrVSEMPA---AKRLRLDTGPqslsgkSTPQPPSG----------------KTTPNSGDVQVTEDAVRR 461
gi 464522    410 Askleq--skrgtVSNTPA---AKRLKMEAGPqntsgkSTPQPQSG----------------KSTPSSGDIQLTEEAVRR 468
gi 74962259  388 -------------------------LKMDNLGpsdakkAKPAV------------------------KFEEGLNEETVRR 418
gi 75207777  420 d-----------gDSKKPSssvQKKVKTENDPksslkeERANTVSKsntptkavkaepasapASSSSAATGPVTEDEIRA 488
gi 122199171 409 ------------eEAKSSIsvpTKKLKTENAPkss-gkDVNGSTSKsngpp-------rgtpPQSSNAASGPVTEEEIRA 468
gi 122232395 418 ------------eEAKPSIsvpPKKVKTENEPkss-akDVNGSSSKsnapprg--tpppssnSGSSNAASGPVTEEEIKA 482
gi 347968538 454 GsnmpttdltgsdNSNSPVstpAKKVKTEITP------SLPPTFAGi---------------VNATSKDDYGITEEAVRR 512
gi 122096252 453 GsnmpmadftgsdNSNSPVstpAKKAKMDSAP------ALPPTFTGl---------------VSSNNRDDYGITEEAVRR 511
                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
5IY6_S       462 YLT-RKPMTTKDLLKKFQTKKTGLSSEQTV-----NVLAQILK-RLNPERKMINDKMHFSLKE 517
gi 46397744  462 YLT-RKPMTTKDLLKKFQTKKTGLSSEQTV-----NVLAQILK-RLNPERKMINDKMHFSLKE 517
gi 464522    469 YLT-RKPMTTKDLLKKFQTKKTGLSSEQTV-----NVLAQILK-RLNPDRKVVHDKMHFYLKE 524
gi 74962259  419 YLR-RKPHTTKELLHKMNGKCGNMSKSEMV-----TQLASILK-AIEPNQSRQLKGKKEVLFF 474
gi 75207777  489 VLMeKKQVTTQDLVSRFKAR---LKTKEDK-----NAFANILR-KISKIQKNAGSQNFVVLRE 542
gi 122199171 469 VLMqSTPLTIKELAAKFKAR---LKCEEPIlktrlDRFNYRLElDIDTVQKKEKH-----IPC 523
gi 122232395 483 VLLqRTPLTTQELVAKFRAR---LRCKEDK-----EAFANILK-RISKIQKTNGS-SYVILRE 535
gi 347968538 513 YLM-RKPMTTTELLTKFKNKKTGVSSEKLV-----ETMTQILK-RINPVKQTIQGKMYLSIKV 568
gi 122096252 512 YLM-RKPMTTTELLTKFKNKKTGVSSEKLV-----ETMTAILK-KINPVKQTIQGKMYLSIKV 567
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