BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 006477
(643 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|A2AQ19|RTF1_MOUSE RNA polymerase-associated protein RTF1 homolog OS=Mus musculus
GN=Rtf1 PE=2 SV=1
Length = 715
Score = 109 bits (272), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 104/391 (26%), Positives = 180/391 (46%), Gaps = 45/391 (11%)
Query: 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRS 320
+++ + + R KL +W PFF + + GCFVR+GIG + P+YR+ + V E +
Sbjct: 362 EELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGV--VETAKV 419
Query: 321 YKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDV 380
Y+L T K L + GN+ R + VS+ E EF +W + ++P+ ++
Sbjct: 420 YQLGGTRTNKGLQLRHGNDQRVFR--LEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEI 477
Query: 381 LEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDM 440
+K+ SI++ + ++ ++++++EK+ P N A +K +L +E +A+ D+
Sbjct: 478 NKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKTQLLKEKAMAEDLGDQDKA 537
Query: 441 ERIKKRLQELEASRDS----KVKDAKAIRLAEMNRKNRVENFKNASELKRVNTSLKAGEA 496
++I+ +L ELE ++ + K+ AI + +N++NR N SE V S
Sbjct: 538 KQIQDQLNELEERAEALDRQRTKNISAI--SYINQRNREWNIVE-SEKALVAESHNMRNQ 594
Query: 497 GYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVGMAATEAALEA 556
DPF+RR KP T +N V + A G+ +A E
Sbjct: 595 QMDPFTRRQC--------KP----TIVSNSRDPAVQAAILAQLNAKYGSGVLP-DAPKEM 641
Query: 557 AAGAGKLVDTNAPL--DLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIEAT 614
+ G GK D N+ DL + +HDF++ I L + + + A
Sbjct: 642 SKGQGKDKDLNSKTASDLSEDLFKVHDFDVKIDLQV--------------PSSESKALAI 687
Query: 615 VGCQVPENDG--RRHALTLTVGDYKRRRGLL 643
P DG RR +L + DYK+RRGL+
Sbjct: 688 TSKAPPAKDGAPRR---SLNLEDYKKRRGLI 715
>sp|Q92541|RTF1_HUMAN RNA polymerase-associated protein RTF1 homolog OS=Homo sapiens
GN=RTF1 PE=1 SV=4
Length = 710
Score = 108 bits (271), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 106/401 (26%), Positives = 183/401 (45%), Gaps = 47/401 (11%)
Query: 253 PGSGRPTY--DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVR 310
P +P +++ + + R KL +W PFF + + GCFVR+GIG + P+YR+ +
Sbjct: 347 PPKSQPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEIT 406
Query: 311 NVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERN 370
V E + Y+L T K L + GN+ R + VS+ E EF +W +
Sbjct: 407 GV--VETAKVYQLGGTRTNKGLQLRHGNDQRVFR--LEFVSNQEFTESEFMKWKEAMFSA 462
Query: 371 SGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEV 430
++P+ ++ +K+ SI++ + ++ ++++++EK+ P N A +K +L +E +
Sbjct: 463 GMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKTQLLKEKAM 522
Query: 431 AQSRHDEVDMERIKKRLQELEASRDS----KVKDAKAIRLAEMNRKNRVENFKNASELKR 486
A+ D+ ++I+ +L ELE ++ + K+ AI + +N++NR N SE
Sbjct: 523 AEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAI--SYINQRNREWNIVE-SEKAL 579
Query: 487 VNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVG 546
V S DPF+RR KP T +N V + A G
Sbjct: 580 VAESHNMKNQQMDPFTRRQC--------KP----TIVSNSRDPAVQAAILAQLNAKYGSG 627
Query: 547 MAATEAALEAAAGAGKLVDTN--APLDLGTESNMLHDFELDISLNALKKFGGPQGVLAGF 604
+ +A E + G GK D N + DL + +HDF++ I L
Sbjct: 628 VLP-DAPKEMSKGQGKDKDLNSKSASDLSEDLFKVHDFDVKIDLQV-------------- 672
Query: 605 MARKQRIEATVGCQVPENDG--RRHALTLTVGDYKRRRGLL 643
+ + + A P DG RR +L + DYK+RRGL+
Sbjct: 673 PSSESKALAITSKAPPAKDGAPRR---SLNLEDYKKRRGLI 710
>sp|Q5RAD5|RTF1_PONAB RNA polymerase-associated protein RTF1 homolog (Fragment) OS=Pongo
abelii GN=RTF1 PE=2 SV=2
Length = 665
Score = 102 bits (255), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 92/344 (26%), Positives = 162/344 (47%), Gaps = 28/344 (8%)
Query: 253 PGSGRPTY--DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVR 310
P +P +++ + + R KL +W PFF + + GCFVR+GIG + P+YR+ +
Sbjct: 342 PPKSQPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEIT 401
Query: 311 NVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERN 370
V E + Y+L T K L + GN+ R + VS+ E EF +W +
Sbjct: 402 GV--VETAKVYQLGGTRTNKGLQLRHGNDQRVFR--LEFVSNQEFTESEFMKWKEAMFSA 457
Query: 371 SGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEV 430
++P+ ++ +K+ SI++ + ++ ++++++EK+ P N A +K +L +E +
Sbjct: 458 GMQLPTLDEINKKELSIKEALNYKFNDQDIEEIVKEKERFRKAPPNYAMKKTQLLKEKAM 517
Query: 431 AQSRHDEVDMERIKKRLQELEASRDS----KVKDAKAIRLAEMNRKNRVENFKNASELKR 486
A+ D+ ++I+ +L ELE ++ + K+ AI + +N++NR N SE
Sbjct: 518 AEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAI--SYINQRNREWNIVE-SEKAL 574
Query: 487 VNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVG 546
V S DPF+RR KP T +N V + A G
Sbjct: 575 VAESHNMKNQQMDPFTRRQC--------KP----TIVSNSRDPAVQAAILAQLNAKYGSG 622
Query: 547 MAATEAALEAAAGAGKLVDTN--APLDLGTESNMLHDFELDISL 588
+ +A E + G GK D N + DL + +HDF++ I L
Sbjct: 623 VLP-DAPKEMSKGQGKDKDLNSKSASDLSEDLFKVHDFDVKIDL 665
>sp|P53064|RTF1_YEAST RNA polymerase-associated protein RTF1 OS=Saccharomyces cerevisiae
(strain ATCC 204508 / S288c) GN=RTF1 PE=1 SV=2
Length = 558
Score = 100 bits (249), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 127/490 (25%), Positives = 206/490 (42%), Gaps = 89/490 (18%)
Query: 76 DQGSQEEGDYDGGASEHEGDSSNESDDDNHGQMTELEREMMIFERDDKKVDKNLRDKFRS 135
D GS+EE + EG +ESD ++ + E+ERE ++FER R FR+
Sbjct: 68 DYGSEEEEE--ANPFPLEGKYKDESDREHLESLPEMERETLLFERSQIMQKYQERKLFRA 125
Query: 136 R---REERSTRSTKETPPLPSSRSARLAARSADRAAAKDDALNELRAKRLKQQDPEAHRR 192
R +E+ R+ + SR R + RS D ++A +L Q + R+
Sbjct: 126 RGRDMKEQQQRAKND----EDSRKTRASTRSTHATGHSD-----IKASKLSQLKKQRARK 176
Query: 193 LRDASRGGSGSRVLSPVKRKAFTPAGLSSSSQSESESRSHSDDEGS-TGDGGMADSDDDG 251
R S + + + DDEGS GD D++
Sbjct: 177 NRHYS-------------------DNEDEDDEEDYREEDYKDDEGSEYGD------DEEY 211
Query: 252 APGSGRPTYD---------------------DIKEITIRRSKLAKWFMEPFFEELIVGCF 290
P R TYD D ++ I RS +AK+ P FE+ + GC+
Sbjct: 212 NPFDRRDTYDKREEVEWAEEEDEQDREPEISDFNKLRIGRSFVAKFCFYPGFEDAVKGCY 271
Query: 291 VRVGIGRSKNG--PIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMA 348
RV +G K YR+ + V +P Y + T +Y VT G + +QM
Sbjct: 272 GRVNVGTDKRTGKTSYRMVRIERVFLQKP---YNMGKFYTNQYFGVTQGKDRKV--FQMN 326
Query: 349 MVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEK-KESIQKINTFVYSAAT---VKQML 404
SD E+E++++LR ++ + PS + K KE + +NT + T V+ +
Sbjct: 327 YFSDGLFAEDEYQRYLRALDNSQMIKPSLHSLSNKTKEVMDFVNTPLTDKTTDEVVRHRM 386
Query: 405 QEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMER-------IKKRLQELEASRDSK 457
Q K S N EK LR +L+ A+ ++E D+ + +KR+ E ++
Sbjct: 387 QFNKKLSG--TNAVLEKTVLREKLQYAKETNNEKDIAKYSAQLRNFEKRMSVYEKHHEND 444
Query: 458 VKDAKAI-RLAEMNRKNRVENFKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKP 516
D K + L NRK + N +NA +K+ +++ ++ DPFSR TR++ YY
Sbjct: 445 QSDIKKLGELTSKNRKLNMSNIRNAEHVKKEDSN--NFDSKSDPFSRLKTRTKVYY---- 498
Query: 517 GEEVTAEANG 526
+E+ E N
Sbjct: 499 -QEIQKEENA 507
>sp|O94667|RTF1_SCHPO RNA polymerase-associated protein C651.09c OS=Schizosaccharomyces
pombe (strain 972 / ATCC 24843) GN=SPBC651.09c PE=1 SV=1
Length = 560
Score = 98.2 bits (243), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 129/497 (25%), Positives = 209/497 (42%), Gaps = 85/497 (17%)
Query: 1 MADLENLLLEAAGRTNSAGRNRHSASSSKRRREGSYSGSDSRDDDSDDNRGYGSRKPSGS 60
MAD ++ LL AG +S +S+++R S D D+N G
Sbjct: 1 MADFQDELLALAGIDDS------DVASNRKRAHDDLDDVLSSSSDEDNNENVGQ------ 48
Query: 61 QVPLKKRLDPAERDDDQGSQE-EGDYD---GGASEHEGDSSNESDDDNHGQMTELEREMM 116
D AE +G+++ E +++ EG +E+D MTE+ERE +
Sbjct: 49 --------DYAEESGGEGNEKSEDEFEEKFKNPYRLEGKFKDEADRAKIMAMTEIERESI 100
Query: 117 IFERDDKKVDKNLRDKFRSRRE-------------ERSTRSTKETPPLPSSRSARLAARS 163
+FER+++ K RRE +STR + PL S+
Sbjct: 101 LFEREEEI------SKLMERRELAIRLHQQNAQYMAQSTRRSTRDKPLTSA--------- 145
Query: 164 ADRAAAKDDALNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVK-RKAFTPAGLSSS 222
AA K D L EL+ +R + R A +R SPV + + S
Sbjct: 146 ---AAGKRDKLTELKKRRQE----------RSARSVSERTRKRSPVSDYEEQNESEKSEE 192
Query: 223 SQSESESRSHSDDEGSTGDGGMADSDDDGAPGSGRPTYDDIKEITIRRSKLAKWFMEPFF 282
+ S S + E + D A+ YD + I + R +A++ P F
Sbjct: 193 EEGYSPSYAEEKVEQVSKDNASAN------------LYD-LNAIRLGRKHVAEYMYHPIF 239
Query: 283 EELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSA 342
E + GCFVRV IG +YRLC V+ + E + Y+++ T L G S
Sbjct: 240 ESTVTGCFVRVKIGERDGQGVYRLCQVKGI--LESRKPYRVDGVLTKVSLECFHGR--SK 295
Query: 343 ARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATVKQ 402
+ + ++S+ P + +F++W ++ + MPSK V K ++ ++ +V S V
Sbjct: 296 RVFDVNVLSNEPFSDHDFQRWHHQMMEDKLSMPSKNFVQRKLNDLRDMSKYVLSEKEVSD 355
Query: 403 MLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQEL-EASRDSKVKDA 461
++ KK S P N+AAEK RLR+ + A + ++ I +L L E S S
Sbjct: 356 IINRKKELSRVPSNIAAEKTRLRQRRQAAYVAGNAELVKEIDDQLNTLEELSMGSNQNSN 415
Query: 462 KAI-RLAEMNRKNRVEN 477
A+ +LA++N +NR N
Sbjct: 416 SAMDQLAKVNERNRRRN 432
>sp|Q9W261|RTF1_DROME RNA polymerase-associated protein Rtf1 OS=Drosophila melanogaster
GN=Rtf1 PE=1 SV=1
Length = 775
Score = 94.7 bits (234), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 94/391 (24%), Positives = 170/391 (43%), Gaps = 51/391 (13%)
Query: 259 TYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPD 318
T +D+ ++ + R K+ ++ P FE ++ CFVR+ IG + P+YR+ + V E
Sbjct: 430 TREDLNKLRLSRYKMERFVNLPIFESTVLNCFVRISIGNNGQKPVYRVAEI--VGVVETG 487
Query: 319 RSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQ 378
+ Y L T + L + G + R + +S+ E EF +W +++ +MP+
Sbjct: 488 KIYSLGTTRTNRGLRLKHGTQERVFR--LEFISNQEFTENEFNKWNEVCQQSHVQMPTID 545
Query: 379 DVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEV 438
+ K+ I+K + + V ++++EK +RP N A +K L +E + A R D
Sbjct: 546 LIAIKQNDIKKALNYEFKDEDVDKIVEEKNRFRNRPTNYAMKKTCLMKERDAAMLRGDYD 605
Query: 439 DMERIKKRLQELE--ASRDSKVKDAKAIRLAEMNRKNRVENFKNAS----ELKRVNTSLK 492
+ + +++ ELE AS K + ++ +N +NR +N ++A E R N LK
Sbjct: 606 IAQDLGQQIDELENRASELDKRRSHTLNLISYINDRNRKKNVEDAEKAILEEARANKGLK 665
Query: 493 AGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVGMAATEA 552
DPF+RR T+ R + +E + PG E T + +T++
Sbjct: 666 IS----DPFTRRITQPRMGFKGAKKDEDDMQLAPLPPPPPGKKRPNEAGTSSASVRSTDS 721
Query: 553 ALEAAAGAGKLVDTNAPLDLGTESNMLHDFELDISLNALKKFGGPQGVLAGFMARKQRIE 612
D S LHDF++D+ + P V + +
Sbjct: 722 K-----------------DYSLYS--LHDFDIDLDV--------PLPVNTNSVPKP---- 750
Query: 613 ATVGCQVPENDGRRHALTLTVGDYKRRRGLL 643
+ E +R +L + DYK++RGL+
Sbjct: 751 ---ASKPAETVSKR---SLNLEDYKKKRGLI 775
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
0.310 0.127 0.355
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 246,619,698
Number of Sequences: 539616
Number of extensions: 11377668
Number of successful extensions: 61147
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 169
Number of HSP's successfully gapped in prelim test: 1529
Number of HSP's that attempted gapping in prelim test: 48757
Number of HSP's gapped (non-prelim): 8286
length of query: 643
length of database: 191,569,459
effective HSP length: 124
effective length of query: 519
effective length of database: 124,657,075
effective search space: 64697021925
effective search space used: 64697021925
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)