Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= Dr_sW_005_J14
(885 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II largest... 46 1e-04
sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II largest... 46 1e-04
sp|P11414|RPB1_CRIGR DNA-directed RNA polymerase II largest... 46 1e-04
sp|Q01443|SSP2_PLAYO Sporozoite surface protein 2 precursor 46 2e-04
sp|Q6BQ20|ATG13_DEBHA Autophagy-related protein 13 44 5e-04
sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II largest... 44 5e-04
sp|P24152|EXTN_SORBI Extensin precursor (Proline-rich glyco... 43 0.001
sp|P23253|TCNA_TRYCR Sialidase (Neuraminidase) (NA) (Major ... 43 0.001
sp|P04050|RPB1_YEAST DNA-directed RNA polymerase II largest... 42 0.003
sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II largest... 41 0.004
>sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II largest subunit (RPB1)
Length = 1970
Score = 46.2 bits (108), Expect = 1e-04
Identities = 53/213 (24%), Positives = 83/213 (38%), Gaps = 6/213 (2%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAY--TNPISEKPKAPRKQPPVI 224
T+ Y +PS +PS SP S SP+Y T+P S P +P P
Sbjct: 1632 TSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSP-SYSPTS 1689
Query: 225 AQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL--TGPIYFNSSPESS 398
S + P + P ++P S ++P+ T P Y +SP S
Sbjct: 1690 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYS 1749
Query: 399 TYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTRPIGAPPRPIS 578
S TP + +Y +YSP SP+ + + N S P+ P T P +P P
Sbjct: 1750 PTSPNYTPTS--PSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSP---TSPSYSPTSPSY 1804
Query: 579 THGHGAQRPHATSGRHRNPNSHKRNSNSLKPST 677
+ P + + +P S+ +S S P++
Sbjct: 1805 SPSSPRYTPQSPTYTPSSP-SYSPSSPSYSPTS 1836
Score = 43.1 bits (100), Expect = 0.001
Identities = 49/186 (26%), Positives = 64/186 (34%), Gaps = 26/186 (13%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAYT-NPISEKPKAPRKQP---- 215
T+ Y +PS +PS SP S QSP YT + S P +P P
Sbjct: 1779 TSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPK 1838
Query: 216 --PVIAQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL---------T 362
P S P + PK++P S + P T
Sbjct: 1839 YTPTSPSYSPSSPEYTPASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPT 1898
Query: 363 GPIYFNSSPESSTYSQEKTPDNIKN-----TYKAAP---LNYSPGSPHASKSMDNISSMI 518
P+Y +SP+ S S +P + K TY YSP SP S + S
Sbjct: 1899 SPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTS 1958
Query: 519 PAIEPD 536
PAI PD
Sbjct: 1959 PAISPD 1964
Score = 32.3 bits (72), Expect = 1.8
Identities = 31/121 (25%), Positives = 49/121 (40%)
Frame = +3
Query: 315 FTPKPTRNSSSNPNLTGPIYFNSSPESSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKS 494
+ P P S + + T P Y SP T Q + +Y +YSP SP+ S +
Sbjct: 1581 YIPSPGGAMSPSYSPTSPAYEPRSPGGYT-PQSPSYSPTSPSYSPTSPSYSPTSPNYSPT 1639
Query: 495 MDNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQRPHATSGRHRNPNSHKRNSNSLKPS 674
+ S P+ P T P +P P + + P + S +P S+ S S P+
Sbjct: 1640 SPSYSPTSPSYSP---TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPT 1695
Query: 675 T 677
+
Sbjct: 1696 S 1696
>sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II largest subunit (RPB1)
Length = 1970
Score = 46.2 bits (108), Expect = 1e-04
Identities = 53/213 (24%), Positives = 83/213 (38%), Gaps = 6/213 (2%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAY--TNPISEKPKAPRKQPPVI 224
T+ Y +PS +PS SP S SP+Y T+P S P +P P
Sbjct: 1632 TSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSP-SYSPTS 1689
Query: 225 AQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL--TGPIYFNSSPESS 398
S + P + P ++P S ++P+ T P Y +SP S
Sbjct: 1690 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYS 1749
Query: 399 TYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTRPIGAPPRPIS 578
S TP + +Y +YSP SP+ + + N S P+ P T P +P P
Sbjct: 1750 PTSPNYTPTS--PSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSP---TSPSYSPTSPSY 1804
Query: 579 THGHGAQRPHATSGRHRNPNSHKRNSNSLKPST 677
+ P + + +P S+ +S S P++
Sbjct: 1805 SPSSPRYTPQSPTYTPSSP-SYSPSSPSYSPTS 1836
Score = 43.1 bits (100), Expect = 0.001
Identities = 49/186 (26%), Positives = 64/186 (34%), Gaps = 26/186 (13%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAYT-NPISEKPKAPRKQP---- 215
T+ Y +PS +PS SP S QSP YT + S P +P P
Sbjct: 1779 TSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPK 1838
Query: 216 --PVIAQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL---------T 362
P S P + PK++P S + P T
Sbjct: 1839 YTPTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPT 1898
Query: 363 GPIYFNSSPESSTYSQEKTPDNIKN-----TYKAAP---LNYSPGSPHASKSMDNISSMI 518
P+Y +SP+ S S +P + K TY YSP SP S + S
Sbjct: 1899 SPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTS 1958
Query: 519 PAIEPD 536
PAI PD
Sbjct: 1959 PAISPD 1964
Score = 32.3 bits (72), Expect = 1.8
Identities = 31/121 (25%), Positives = 49/121 (40%)
Frame = +3
Query: 315 FTPKPTRNSSSNPNLTGPIYFNSSPESSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKS 494
+ P P S + + T P Y SP T Q + +Y +YSP SP+ S +
Sbjct: 1581 YIPSPGGAMSPSYSPTSPAYEPRSPGGYT-PQSPSYSPTSPSYSPTSPSYSPTSPNYSPT 1639
Query: 495 MDNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQRPHATSGRHRNPNSHKRNSNSLKPS 674
+ S P+ P T P +P P + + P + S +P S+ S S P+
Sbjct: 1640 SPSYSPTSPSYSP---TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPT 1695
Query: 675 T 677
+
Sbjct: 1696 S 1696
>sp|P11414|RPB1_CRIGR DNA-directed RNA polymerase II largest subunit (RPB1)
Length = 467
Score = 46.2 bits (108), Expect = 1e-04
Identities = 53/213 (24%), Positives = 83/213 (38%), Gaps = 6/213 (2%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAY--TNPISEKPKAPRKQPPVI 224
T+ Y +PS +PS SP S SP+Y T+P S P +P P
Sbjct: 129 TSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSP-SYSPTS 186
Query: 225 AQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL--TGPIYFNSSPESS 398
S + P + P ++P S ++P+ T P Y +SP S
Sbjct: 187 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYS 246
Query: 399 TYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTRPIGAPPRPIS 578
S TP + +Y +YSP SP+ + + N S P+ P T P +P P
Sbjct: 247 PTSPNYTPTS--PSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSP---TSPSYSPTSPSY 301
Query: 579 THGHGAQRPHATSGRHRNPNSHKRNSNSLKPST 677
+ P + + +P S+ +S S P++
Sbjct: 302 SPSSPRYTPQSPTYTPSSP-SYSPSSPSYSPTS 333
Score = 43.1 bits (100), Expect = 0.001
Identities = 49/186 (26%), Positives = 64/186 (34%), Gaps = 26/186 (13%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAYT-NPISEKPKAPRKQP---- 215
T+ Y +PS +PS SP S QSP YT + S P +P P
Sbjct: 276 TSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPK 335
Query: 216 --PVIAQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL---------T 362
P S P + PK++P S + P T
Sbjct: 336 YTPTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPT 395
Query: 363 GPIYFNSSPESSTYSQEKTPDNIKN-----TYKAAP---LNYSPGSPHASKSMDNISSMI 518
P+Y +SP+ S S +P + K TY YSP SP S + S
Sbjct: 396 SPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTS 455
Query: 519 PAIEPD 536
PAI PD
Sbjct: 456 PAISPD 461
Score = 32.3 bits (72), Expect = 1.8
Identities = 31/121 (25%), Positives = 49/121 (40%)
Frame = +3
Query: 315 FTPKPTRNSSSNPNLTGPIYFNSSPESSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKS 494
+ P P S + + T P Y SP T Q + +Y +YSP SP+ S +
Sbjct: 78 YIPSPGGAMSPSYSPTSPAYEPRSPGGYT-PQSPSYSPTSPSYSPTSPSYSPTSPNYSPT 136
Query: 495 MDNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQRPHATSGRHRNPNSHKRNSNSLKPS 674
+ S P+ P T P +P P + + P + S +P S+ S S P+
Sbjct: 137 SPSYSPTSPSYSP---TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPT 192
Query: 675 T 677
+
Sbjct: 193 S 193
>sp|Q01443|SSP2_PLAYO Sporozoite surface protein 2 precursor
Length = 827
Score = 45.8 bits (107), Expect = 2e-04
Identities = 52/214 (24%), Positives = 84/214 (39%), Gaps = 6/214 (2%)
Frame = +3
Query: 51 NNTNYKYGKLNPSDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVIAQ 230
NN N NP++ N P+ S P+ +P+ ++P NP KP P P
Sbjct: 364 NNPNNPNNPNNPNNPNN-PNDPSNPNNPNPKK---RNPKRRNPNKPKPNKPNPNKP---N 416
Query: 231 KSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNLTGPIYFNSSPESSTYSQ 410
++ N N P + NE P KP N SNPN P + E S ++
Sbjct: 417 PNEPSNPNKPNPNEPSNPNKPNPNE-PSNPNKPNPNEPSNPNKPNPNEPLNPNEPSNPNE 475
Query: 411 EKTPDNIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTRP--IGAPPRPIS-- 578
P+ N + + N P +P+ + + S+ P K + P P P++
Sbjct: 476 PSNPNAPSNPNEPSNPN-EPSNPNEPSNPNEPSNPNEPSNPKKPSNPNEPSNPNEPLNPN 534
Query: 579 --THGHGAQRPHATSGRHRNPNSHKRNSNSLKPS 674
++ + P+ S P++ K SN +PS
Sbjct: 535 EPSNPNEPSNPNEPS-NPEEPSNPKEPSNPNEPS 567
>sp|Q6BQ20|ATG13_DEBHA Autophagy-related protein 13
Length = 837
Score = 44.3 bits (103), Expect = 5e-04
Identities = 45/192 (23%), Positives = 74/192 (38%), Gaps = 3/192 (1%)
Frame = +3
Query: 99 NTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVIAQKSKKDNANPPPRRDFX 278
N S+ P PQ++ SP++ P + ++P + K + +PP +F
Sbjct: 361 NNASMSLSPCSSGPQTVTEDSPSHNKPSANTTPIVSQRPTINPFKVGSISTSPPATTNFG 420
Query: 279 XXXXXXENELPKFTPKPTRNSSSNPNLTGPIYFNSSPESSTYSQEKTP--DNIKNTYKAA 452
+ L + + S+SN +L + S SST + P +N N +
Sbjct: 421 G------SSLERKVSITSNKSASNASLAAMLRNPRSSTSSTNTTANIPIANNNSNNQYNS 474
Query: 453 PLNYSPGSPHASKSMDNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQRPHA-TSGRHR 629
S S H S + +++ PD + PR S+ G A R + TSGR
Sbjct: 475 TFPRSVSSSHGSNLAHDNDNLLGFSNPDNTSN----TPRFSSSFGSRASRRFSNTSGRQS 530
Query: 630 NPNSHKRNSNSL 665
+ S N SL
Sbjct: 531 SLPSGNMNDTSL 542
>sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II largest subunit
Length = 1852
Score = 44.3 bits (103), Expect = 5e-04
Identities = 53/225 (23%), Positives = 81/225 (36%), Gaps = 14/225 (6%)
Frame = +3
Query: 45 ELNNTNYKYGKLNPSDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQP--- 215
+ + T+ Y +PS +P+ +G+SP +S S + T+P S P +P P
Sbjct: 1581 QFSMTSPHYSPTSPSYSPTSPA-----AGQSP---VSPSYSPTSP-SYSPTSPSYSPTSP 1631
Query: 216 ---PVIAQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL--TGPIYFN 380
P S + P + P ++P R S ++P T P Y
Sbjct: 1632 SYSPTSPSYSPTSPSYSPTSPSYSPSSPSYSPSSPSYSPSSPRYSPTSPTYSPTSPTYSP 1691
Query: 381 SSPE----SSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTR 548
+SP S TYS Y + YSP SP S + + S P P
Sbjct: 1692 TSPTYSPTSPTYSPTSPSYESGGGYSPSSPKYSPSSPTYSPTSPSYSPTSPQYSPTSPQY 1751
Query: 549 PIGAPPRPISTHGHGAQRPHATSGRHRNPNS--HKRNSNSLKPST 677
+P S+ + P S +P S + S S PS+
Sbjct: 1752 SPSSPTYTPSSPTYNPTSPRGFSSPQYSPTSPTYSPTSPSYTPSS 1796
Score = 38.5 bits (88), Expect = 0.025
Identities = 53/231 (22%), Positives = 79/231 (34%), Gaps = 29/231 (12%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAYT-NPISEKPKAPRKQP---- 215
T+ Y +PS +PS SP S SP+Y+ + S P +PR P
Sbjct: 1622 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPSSPSYSPSSPSYSPSSPRYSPTSPT 1681
Query: 216 -----PVIAQKSKKDNANPP---PRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL--TG 365
P + S + P P PK++P S ++P+ T
Sbjct: 1682 YSPTSPTYSPTSPTYSPTSPTYSPTSPSYESGGGYSPSSPKYSPSSPTYSPTSPSYSPTS 1741
Query: 366 PIYFNSSPESSTYSQEKTPDN-----------IKNTYKAAPLNYSPGSPHASKSMDNISS 512
P Y +SP+ S S TP + Y YSP SP + S S
Sbjct: 1742 PQYSPTSPQYSPSSPTYTPSSPTYNPTSPRGFSSPQYSPTSPTYSPTSPSYTPSSPQYSP 1801
Query: 513 MIPAIEPDKKTRP-IGAPPRPISTHGHGAQRPHATSGRHRNPNSHKRNSNS 662
P P +P A P S + ++ + +P+S + NS
Sbjct: 1802 TSPTYTPSPSEQPGTSAQYSPTSPTYSPSSPTYSPASPSYSPSSPTYDPNS 1852
Score = 34.3 bits (77), Expect = 0.47
Identities = 26/99 (26%), Positives = 40/99 (40%)
Frame = +3
Query: 339 SSSNPNLTGPIYFNSSPESSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSMDNISSMI 518
SS ++T P Y +SP S S + +Y +YSP SP S + + S
Sbjct: 1578 SSPQFSMTSPHYSPTSPSYSPTSPAAGQSPVSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1637
Query: 519 PAIEPDKKTRPIGAPPRPISTHGHGAQRPHATSGRHRNP 635
P+ P T P +P P + + P + S +P
Sbjct: 1638 PSYSP---TSPSYSPTSPSYSPSSPSYSPSSPSYSPSSP 1673
>sp|P24152|EXTN_SORBI Extensin precursor (Proline-rich glycoprotein)
Length = 283
Score = 42.7 bits (99), Expect = 0.001
Identities = 50/183 (27%), Positives = 60/183 (32%), Gaps = 8/183 (4%)
Frame = +3
Query: 84 PSDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVIAQ------KSKKD 245
P +H+ TP + +P + T S KPK+P PP A S K
Sbjct: 64 PKEHKPTPPTYTPSPKPTPPPATPKPTPPTYTPSPKPKSPVYPPPPKASTPPTYTPSPKP 123
Query: 246 NANPPPRRDFXXXXXXXENELPKFT--PKPTRNSSSNPNLTGPIYFNSSPESSTYSQEKT 419
A PP P +T PKP P T P+Y + T T
Sbjct: 124 PATKPPTYPTPKPPATKPPTPPVYTPSPKPPVTKPPTPKPTPPVYTPNPKPPVTKPPTHT 183
Query: 420 PDNIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQ 599
P T K P Y+P SP K P P K P P P ST H
Sbjct: 184 PSPKPPTSKPTPPVYTP-SPKPPKPSP------PTYTPTPK--PPATKP-PTSTPTHPKP 233
Query: 600 RPH 608
PH
Sbjct: 234 TPH 236
>sp|P23253|TCNA_TRYCR Sialidase (Neuraminidase) (NA) (Major surface antigen)
Length = 1162
Score = 42.7 bits (99), Expect = 0.001
Identities = 42/199 (21%), Positives = 71/199 (35%), Gaps = 2/199 (1%)
Frame = +3
Query: 87 SDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVIAQKSKKDNANPPPR 266
S TPS + S S S + S A++ P + + P S + P
Sbjct: 930 SSAHGTPSTPADSSAHSTPSTPADSSAHSTPSTPADSSAHSTPSTPVDSSAHSTPSTPAD 989
Query: 267 RDFXXXXXXXENELPKFTPKPTRNSSSNPNLTGPIYFNSSPESSTYSQEKTPDNIKNTYK 446
+ TP +SS++ + P+ +SS +S TP + ++
Sbjct: 990 SSAHSTPSTPADSSAHSTPSTPADSSAHSTPSTPV------DSSAHSTPSTPAD--SSAH 1041
Query: 447 AAPLNYSPGSPHASKS--MDNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQRPHATSG 620
P + S H++ S +D+ + P+ D G P P + H A S
Sbjct: 1042 GTPSTPADSSAHSTPSTPVDSSAHSTPSTPADSSAH--GTPSTPADSSAHSTPSTPADSS 1099
Query: 621 RHRNPNSHKRNSNSLKPST 677
H P++ +S PST
Sbjct: 1100 AHGTPSTPADSSAHSTPST 1118
Score = 42.4 bits (98), Expect = 0.002
Identities = 45/205 (21%), Positives = 74/205 (36%), Gaps = 8/205 (3%)
Frame = +3
Query: 87 SDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVIAQKSKKDNANPPPR 266
S TPS + S S S + S A+ P + + P S + P
Sbjct: 762 SSAHGTPSTPADSSAHSTPSTPADSSAHGTPSTPVDSSAHSTPSTPVDSSAHGTPSTPVD 821
Query: 267 RDFXXXXXXXENELPKFTPKPTRNSS--SNPNLTGPIYFNSSP----ESSTYSQEKTPDN 428
+ TP +SS S P+ +S+P +SS + TP
Sbjct: 822 SSAHSTPSTPVDSSAHGTPSTPVDSSAHSTPSTPADSSAHSTPSTPADSSAHGTPSTP-- 879
Query: 429 IKNTYKAAPLNYSPGSPHASKS--MDNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQR 602
+ ++ + P + S H++ S +D+ + P+ D G P P+ + HG
Sbjct: 880 VDSSAHSTPSTPADSSAHSTPSTPVDSSAHSTPSTPADSSAH--GTPSTPVDSSAHGTPS 937
Query: 603 PHATSGRHRNPNSHKRNSNSLKPST 677
A S H P++ +S PST
Sbjct: 938 TPADSSAHSTPSTPADSSAHSTPST 962
Score = 40.4 bits (93), Expect = 0.007
Identities = 46/205 (22%), Positives = 73/205 (35%), Gaps = 8/205 (3%)
Frame = +3
Query: 87 SDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVIAQKSKKDNANPPPR 266
S TPS S S S + S A++ P + + P A S + P
Sbjct: 870 SSAHGTPSTPVDSSAHSTPSTPADSSAHSTPSTPVDSSAHSTPSTPADSSAHGTPSTPVD 929
Query: 267 RDFXXXXXXXENELPKFTPKPTRNSS--SNPNLTGPIYFNSSP----ESSTYSQEKTPDN 428
+ TP +SS S P+ +S+P +SS +S TP +
Sbjct: 930 SSAHGTPSTPADSSAHSTPSTPADSSAHSTPSTPADSSAHSTPSTPVDSSAHSTPSTPAD 989
Query: 429 IKNTYKAAPLNYSPGSPHASKSM--DNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQR 602
++ + P + S H++ S D+ + P+ D P P + HG
Sbjct: 990 --SSAHSTPSTPADSSAHSTPSTPADSSAHSTPSTPVDSSAH--STPSTPADSSAHGTPS 1045
Query: 603 PHATSGRHRNPNSHKRNSNSLKPST 677
A S H P++ +S PST
Sbjct: 1046 TPADSSAHSTPSTPVDSSAHSTPST 1070
Score = 40.0 bits (92), Expect = 0.009
Identities = 44/223 (19%), Positives = 79/223 (35%)
Frame = +3
Query: 9 QQGDAGTSSRMTELNNTNYKYGKLNPSDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISE 188
++ D T S +T N Y +LN + R + ++ S S A++ P +
Sbjct: 544 KRSDMPTISHVTVNNVLLYNRRQLNTEEIRTLFLSQDLIGTEAHMDSSSDSSAHSTPSTP 603
Query: 189 KPKAPRKQPPVIAQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNLTGP 368
+ P S + P + TP +SS++ + P
Sbjct: 604 ADSSAHSTPSTPVDSSAHSTPSTPADSSAHGTPSTPVDSSAHGTPSTPADSSAHGTPSTP 663
Query: 369 IYFNSSPESSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTR 548
+ +SS +S TP + + + +P +P +D+ + P+ D
Sbjct: 664 V------DSSAHSTPSTPVD-------SSAHSTPSTP-----VDSSAHGAPSTPADSSAH 705
Query: 549 PIGAPPRPISTHGHGAQRPHATSGRHRNPNSHKRNSNSLKPST 677
G P P+ + HG A S H P++ +S PST
Sbjct: 706 --GTPSTPVDSSAHGTPSTPADSSAHSTPSTPADSSAHSTPST 746
Score = 38.9 bits (89), Expect = 0.019
Identities = 45/219 (20%), Positives = 78/219 (35%), Gaps = 8/219 (3%)
Frame = +3
Query: 45 ELNNTNYKYGKLNPSDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVI 224
+L T + S +TPS + S S S S A++ P + + P
Sbjct: 580 DLIGTEAHMDSSSDSSAHSTPSTPADSSAHSTPSTPVDSSAHSTPSTPADSSAHGTPSTP 639
Query: 225 AQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNLTGPIYFN-----SSP 389
S + P + TP +SS++ + P+ + S+P
Sbjct: 640 VDSSAHGTPSTPADSSAHGTPSTPVDSSAHSTPSTPVDSSAHSTPSTPVDSSAHGAPSTP 699
Query: 390 -ESSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSM--DNISSMIPAIEPDKKTRPIGA 560
+SS + TP + ++ P + S H++ S D+ + P+ D
Sbjct: 700 ADSSAHGTPSTP--VDSSAHGTPSTPADSSAHSTPSTPADSSAHSTPSTPADSSAH--ST 755
Query: 561 PPRPISTHGHGAQRPHATSGRHRNPNSHKRNSNSLKPST 677
P P+ + HG A S H P++ +S PST
Sbjct: 756 PSTPVDSSAHGTPSTPADSSAHSTPSTPADSSAHGTPST 794
Score = 37.0 bits (84), Expect = 0.073
Identities = 42/198 (21%), Positives = 70/198 (35%), Gaps = 1/198 (0%)
Frame = +3
Query: 87 SDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVIAQKSKKDNANPPPR 266
S TPS S S S S A+ P + + P S + P
Sbjct: 786 SSAHGTPSTPVDSSAHSTPSTPVDSSAHGTPSTPVDSSAHSTPSTPVDSSAHGTPSTPVD 845
Query: 267 RDFXXXXXXXENELPKFTPKPTRNSSSNPNLTGPIYFNSSPESSTYSQEKTP-DNIKNTY 443
+ TP +SS++ + P+ +SS +S TP D+ ++
Sbjct: 846 SSAHSTPSTPADSSAHSTPSTPADSSAHGTPSTPV------DSSAHSTPSTPADSSAHST 899
Query: 444 KAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTRPIGAPPRPISTHGHGAQRPHATSGR 623
+ P++ S S ++ + D+ + P+ D G P P + H A S
Sbjct: 900 PSTPVDSSAHSTPSTPA-DSSAHGTPSTPVDSSAH--GTPSTPADSSAHSTPSTPADSSA 956
Query: 624 HRNPNSHKRNSNSLKPST 677
H P++ +S PST
Sbjct: 957 HSTPSTPADSSAHSTPST 974
>sp|P04050|RPB1_YEAST DNA-directed RNA polymerase II largest subunit (RNA polymerase II
subunit 1) (B220)
Length = 1733
Score = 41.6 bits (96), Expect = 0.003
Identities = 47/182 (25%), Positives = 68/182 (37%), Gaps = 2/182 (1%)
Frame = +3
Query: 24 GTSSRMTELNNTNYKYGKLNPSDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAP 203
G S + T+ Y +PS +PS SP S S SP T+P S P +P
Sbjct: 1541 GFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSP--TSP-SYSPTSP 1596
Query: 204 RKQPPVIAQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL--TGPIYF 377
P S + P + P ++P S ++P+ T P Y
Sbjct: 1597 -SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1655
Query: 378 NSSPESSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDKKTRPIG 557
+SP S S +P + +Y +YSP SP S + N S P+ P G
Sbjct: 1656 PTSPAYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPG 1713
Query: 558 AP 563
+P
Sbjct: 1714 SP 1715
Score = 38.9 bits (89), Expect = 0.019
Identities = 42/160 (26%), Positives = 59/160 (36%), Gaps = 12/160 (7%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAY--TNPISEKPKAPRKQP--- 215
T+ Y +PS +PS SP S SP+Y T+P S P +P P
Sbjct: 1566 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPTSP 1624
Query: 216 ---PVIAQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL--TGPIYFN 380
P S + P + P ++P S ++P+ T P Y
Sbjct: 1625 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSP 1684
Query: 381 SSPESSTYSQEKTPDNIKNTYKAAPLNYSPGSPHASKSMD 500
+SP S S +P + +Y YSPGSP S D
Sbjct: 1685 TSPSYSPTSPNYSPTS--PSYSPTSPGYSPGSPAYSPKQD 1722
>sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II largest subunit
Length = 1853
Score = 41.2 bits (95), Expect = 0.004
Identities = 42/164 (25%), Positives = 59/164 (35%), Gaps = 5/164 (3%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQSIISQSPAYTNPISEKPKAPRKQPPVIAQKS 236
T+ Y +PS +PS S S S + T+P P +P+ P
Sbjct: 1703 TSPTYSPTSPSYEGYSPSSPKYSPSSPTYSPTSPSYSPTSP-QYSPTSPQYSPSSPTYTP 1761
Query: 237 KKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNLTGPIYFNSSPESSTYSQEK 416
NP R F P+++P +S + T P Y SSP+ S S
Sbjct: 1762 SSPTYNPTSPRAFSS---------PQYSP-----TSPTYSPTSPSYTPSSPQYSPTSPTY 1807
Query: 417 TPD-----NIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEP 533
TP N Y + YSP SP S + + S P +P
Sbjct: 1808 TPSPADQPGTSNQYSPSSPTYSPSSPTYSPASPSYSPSSPTYDP 1851
Score = 40.4 bits (93), Expect = 0.007
Identities = 48/202 (23%), Positives = 73/202 (36%), Gaps = 19/202 (9%)
Frame = +3
Query: 57 TNYKYGKLNPSDHRNTPSIMSIPSGKSPQS--IISQSPAY--TNPISEKPKAPRKQP--- 215
T+ Y +PS +PS SP S SP+Y T+P S P +PR P
Sbjct: 1626 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPSSPRYSPTSP 1684
Query: 216 ------PVIAQKSKKDNANPPPRRDFXXXXXXXENELPKFTPKPTRNSSSNPNL--TGPI 371
P + S + P PK++P S ++P+ T P
Sbjct: 1685 TYSPTSPTYSPTSPTYSPTSPTYSPTSPSYEGYSPSSPKYSPSSPTYSPTSPSYSPTSPQ 1744
Query: 372 YFNSSPESSTYSQEKTPD----NIKNTYKAAPLNYSPGSPHASKSMDNISSMIPAIEPDK 539
Y +SP+ S S TP N + + YSP SP S + + + P P
Sbjct: 1745 YSPTSPQYSPSSPTYTPSSPTYNPTSPRAFSSPQYSPTSPTYSPTSPSYTPSSPQYSPTS 1804
Query: 540 KTRPIGAPPRPISTHGHGAQRP 605
T +P +++ + P
Sbjct: 1805 PTYTPSPADQPGTSNQYSPSSP 1826
Database: Non-redundant SwissProt sequences
Posted date: Dec 6, 2005 7:40 AM
Number of letters in database: 68,354,980
Number of sequences in database: 184,735
Database: swissprot.01
Posted date: Dec 6, 2005 8:18 AM
Number of letters in database: 66,202,850
Number of sequences in database: 184,431
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 100,556,716
Number of Sequences: 369166
Number of extensions: 2135343
Number of successful extensions: 7985
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 7001
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 7707
length of database: 68,354,980
effective HSP length: 110
effective length of database: 48,034,130
effective search space used: 8838279920
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)