RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13798
(614 letters)
>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 = 53/252 (21%), Positives = 95/252 (37%), Gaps = 15/252 (5%)
Query: 220 PAFGAGTTTSGQGFGGFGTGTATFGSTNTSTGGLFGSGGTTTAQPGFGSSAFG-TPSAPT 278
P +G+ + G GF TS G +G T+ PGFG S+ G +P++PT
Sbjct: 1494 PLVDSGSNDAMAG--GFTAYGGADYGEATSPFGAYGEAPTS---PGFGVSSPGFSPTSPT 1548
Query: 279 PAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAP 338
+ SPA+ T+ +PT+ + + T S S SPS + + ++
Sbjct: 1549 YSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1608
Query: 339 SGGLNFGTPTTQATSAFGTPTQSTGLSFGNFNSGLTFGAP--SGGLNFGTPTTQATSAFG 396
S + +P+ TS +PT + S + S + +P TS
Sbjct: 1609 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSY 1668
Query: 397 TPTQSTGLSFGPPFLFRSNETTATLDACVQSFGSTTPAQGFGSTAQTGLSFGTPSATQAS 456
+PT + P + + T+ + ++ T+P+ S G S G+P+ +
Sbjct: 1669 SPTSPSYSPTSPSY----SPTSPSYSPTSPNYSPTSPSY---SPTSPGYSPGSPAYSPKQ 1721
Query: 457 GGFSFGGGTAPQ 468
+
Sbjct: 1722 DEQKHNENENSR 1733
Score = 50.5 bits (120), Expect = 2e-06
Identities = 51/268 (19%), Positives = 88/268 (32%), Gaps = 19/268 (7%)
Query: 217 ATQPAFGAGTTTSGQGFGGFGTGTATFGS-TNTSTGGLFGSGGTTTAQPGFGSSAFGTPS 275
+ SG S S +GG T A
Sbjct: 1465 GQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFG 1524
Query: 276 APTPAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGLTF 335
A A SP FG ++ +PT+ + + T S S SPS + + ++
Sbjct: 1525 AYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1584
Query: 336 GAPSGGLNFGTPTTQATSAFGTPTQSTG--LSFGNFNSGLTFGAPSGGLNFGTPTTQATS 393
S + +P+ TS +PT + S + ++ S + +P+ TS
Sbjct: 1585 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1644
Query: 394 AFGTPTQSTGLSFGPPFLFRSNETTATLDACVQSFGSTTPAQGFGSTAQTGLSFGTPSAT 453
+PT S S P + T+ + S+ T+P+ S + + S P+ +
Sbjct: 1645 PSYSPT-SPSYSPTSPAY---SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS---PNYS 1697
Query: 454 QASGGFSFGGGTAPQTGGLNFGTPTSTQ 481
S +S T+P +P S
Sbjct: 1698 PTSPSYS---PTSPG------YSPGSPA 1716
Score = 47.8 bits (113), Expect = 1e-05
Identities = 49/306 (16%), Positives = 92/306 (30%), Gaps = 40/306 (13%)
Query: 232 GFGGFGTGTATFGSTNT-STGGLFGSGGTTTAQPGFGSSAFGTPSAPTPAFGSPAFGSTN 290
G T S + P S + + A+G +G
Sbjct: 1461 EIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEAT 1520
Query: 291 TFGTPTTQQ--STGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAPSGGLNFGTPT 348
+ + S GFG G S SP+ + + + S + +P+
Sbjct: 1521 SPFGAYGEAPTSPGFGVSS-----------PGFSPTSPTYSPTSPAYSPTSPSYSPTSPS 1569
Query: 349 TQATSAFGTPTQSTGLSFGNFNSGL--TFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSF 406
TS +PT + S ++ S + +P+ TS +PT
Sbjct: 1570 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP----- 1624
Query: 407 GPPFLFRSNETTATLDACVQSFGSTTPAQGFGSTAQTGLSFGTPSATQASGGFSFGGGTA 466
+ T+ + S+ T+P+ S S +P+ + S +S T+
Sbjct: 1625 ------SYSPTSPSYSPTSPSYSPTSPSY---SPTSPSYSPTSPAYSPTSPSYS---PTS 1672
Query: 467 PQTGGLNFGTPTSTQQPLFGAPATTAQTGFSFGTPAATSQPSVGFGAAATTQSVGFGAPA 526
P +PTS + +S +P + S S G+ + S
Sbjct: 1673 PS------YSPTSPSYSPTSPSYSPTSPNYSPTSP-SYSPTSPGYSPGSPAYSPKQDEQK 1725
Query: 527 TSQSVT 532
+++
Sbjct: 1726 HNENEN 1731
Score = 39.7 bits (92), Expect = 0.003
Identities = 50/305 (16%), Positives = 102/305 (33%), Gaps = 40/305 (13%)
Query: 60 LQSTQPEVQYLKERHLQLRQTYLKDSTNVFDVERGGRDTKL-PRDVEGPSPF--SAGFSF 116
+ + V+Y+ E+ + + + E G + L +D SP S
Sbjct: 1444 MIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDA 1503
Query: 117 GSTATQPAFGAGTTTSGQGFGGFGSATARLCNSIGSPAFGSTNTFGTPTTQQSTGFGGFG 176
+ GA + FG +G A + SP F T+ +PT+ +
Sbjct: 1504 MAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSY 1563
Query: 177 TSTHLVHLVLSRQLPLRLDFHLAPQQHSQHLWAGFSFGSTATQPAFGAGTTTSGQGFGGF 236
+ T S + T P++ + + +
Sbjct: 1564 SPT--------------------------------SPSYSPTSPSYSPTSPSYSPTSPSY 1591
Query: 237 GTGTATFGSTNTSTGGLFGSGGTTTAQPGFG-SSAFGTPSAPTPAFGSPAFGSTNTFGTP 295
+ ++ TS S + P + +S +P++P+ + SP++ T+ +P
Sbjct: 1592 SPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1649
Query: 296 TTQQ-STGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAPSGGLNFGTPTTQATSA 354
T+ S + ++ PT S SPS + + ++ S + +P+ TS
Sbjct: 1650 TSPSYSPTSPAYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSP 1708
Query: 355 FGTPT 359
+P
Sbjct: 1709 GYSPG 1713
Score = 39.7 bits (92), Expect = 0.004
Identities = 43/230 (18%), Positives = 77/230 (33%), Gaps = 29/230 (12%)
Query: 198 LAPQQHSQHLWAGFS--FGSTATQPAFGAGTTTSGQGFGGFGTGTATFGSTNTSTGGLFG 255
L FS S + G T G +G + +G TS G
Sbjct: 1479 LVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVS 1538
Query: 256 SGGTTTAQPGFG--SSAFG-------------TPSAPTPAFGSPAFGSTNTFGTPTTQQS 300
S G + P + S A+ +P++P+ + SP++ T+ +PT+
Sbjct: 1539 SPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1598
Query: 301 TGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAPSGGLNFGTPTTQATSAFGTPTQ 360
+ + T S S SPS + + ++ S + +P+ TS +PT
Sbjct: 1599 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1658
Query: 361 STGLSFGNFNSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSFGPPF 410
+ S + +P+ TS +PT + P +
Sbjct: 1659 P------------AYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNY 1696
Score = 34.3 bits (78), Expect = 0.16
Identities = 27/120 (22%), Positives = 39/120 (32%), Gaps = 5/120 (4%)
Query: 476 TPTSTQQPLFGAPATTAQTGFSFGTPAATSQPSVGFGAAATTQSVGFGAPATSQSVTFGA 535
TP S + L A +P S + T ATS +G
Sbjct: 1471 TPYSNESGLVNADLDVKDELMF--SPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGE 1528
Query: 536 QPASQPSVGFGAPATTQTGLSFGAPATSQPALSFGSSATGQAAGFSFGSSAPASSQPSLS 595
P S P G +P + T S TS S + + +S S + + + PS S
Sbjct: 1529 APTS-PGFGVSSPGFSPT--SPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1585
Score = 30.1 bits (67), Expect = 2.9
Identities = 50/295 (16%), Positives = 85/295 (28%), Gaps = 25/295 (8%)
Query: 274 PSAPTPAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGL 333
P G + + + F P SG + +
Sbjct: 1455 PEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFS--PLVDSG--------SNDAM 1504
Query: 334 TFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSFGNFNSGLTFGAPSGGLNFGTPTTQATS 393
G + G T A+G S G G++ S +PT+ A S
Sbjct: 1505 AGGFTAYGGADYGEATSPFGAYGEAPTSPG-------FGVSSPGFSPTSPTYSPTSPAYS 1557
Query: 394 AFGTPTQSTGLSFGPPFLFRSNETTATLDACVQSFGSTTPAQGFGSTAQTGLSFGTPSAT 453
T S+ P S T+ + S+ T+P+ S + S +PS +
Sbjct: 1558 PTSPSYSPTSPSYSPTSPSYS-PTSPSYSPTSPSYSPTSPSYSPTSPSY---SPTSPSYS 1613
Query: 454 QASGGFSFGGGTAPQTGGLNFGTPTSTQQPLFGAPATTAQTGFSFGTPA--ATSQPSVGF 511
S +S + T +PTS + +S +PA TS
Sbjct: 1614 PTSPSYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPT 1671
Query: 512 GAAATTQSVGFGAPATSQSVTFGAQPASQPSVGFGAPATTQTGLSFGAPATSQPA 566
+ + S + + S S T + PS +P + ++ Q
Sbjct: 1672 SPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKH 1726
>3t98_B Nucleoporin NUP58/NUP45; NUP62 complex, nuclear import,
coiled-coil, HE hairpin, FG-repeat, NPC, nuclear
tranport, TRA channel, karyopherin; 2.50A {Rattus
norvegicus} PDB: 2osz_A
Length = 93
Score = 46.1 bits (109), Expect = 1e-06
Identities = 15/46 (32%), Positives = 28/46 (60%)
Query: 41 ELYQTMRRVHDAVVSVAGSLQSTQPEVQYLKERHLQLRQTYLKDST 86
+L M++++ V++A LQS V+ LKE++L R+ +L D+
Sbjct: 48 DLSMAMQKIYQTFVALAAQLQSIHENVKVLKEQYLSYRKMFLGDAG 93
>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 = 2e-05
Identities = 51/252 (20%), Positives = 88/252 (34%), Gaps = 14/252 (5%)
Query: 209 AGFSFGSTATQPAFGAGTTTSGQGFGGFGTGTATFGSTNTSTGGLFGSGGTTTAQPGFGS 268
A FS + G G TS S G P +
Sbjct: 1503 AAFS--PLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSP 1560
Query: 269 SAFGTPSAPTPAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPST 328
S+ G ++P SP++ T+ +PT+ + + T S S SPS
Sbjct: 1561 SSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSY 1620
Query: 329 TQSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSFGNFNSGLTFGAPSGGLNFGTPT 388
+ + ++ S + +P+ TS +PT S S + ++ S + +P+
Sbjct: 1621 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYS----PTSPSYSPTSPSYSPTSPS 1675
Query: 389 TQATSAFGTPTQSTGLSFGPPFLFRSNETTATLDACVQSFGSTTPAQGFGSTAQTGLSFG 448
TS +PT S S P + T+ + S+ T+P+ S + + S
Sbjct: 1676 YSPTSPSYSPT-SPSYSPTSPSY---SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS-- 1729
Query: 449 TPSATQASGGFS 460
PS + S +S
Sbjct: 1730 -PSYSPTSPSYS 1740
Score = 46.6 bits (110), Expect = 3e-05
Identities = 54/304 (17%), Positives = 101/304 (33%), Gaps = 25/304 (8%)
Query: 200 PQQHSQHLWAGFSFGSTATQPAFGAGTTTSGQGFGGFGTGTATFGSTNTSTGGLFGSGGT 259
P + T P + SG + + FG G
Sbjct: 1466 PTLAGSGMGTSQLPEGAGT-PYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGL 1524
Query: 260 TTAQPGFGSSAFGTPSAPTPAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQS 319
A + ++P + SP +G T+ +P++ + + S+ PT
Sbjct: 1525 LGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPT--- 1581
Query: 320 GLSFNSPSTTQSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSFGNFNSGLTFGAPS 379
SPS + + ++ S + +P+ ATS +PT S S + ++ S
Sbjct: 1582 -----SPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPT-SPSYS----PTSPSYSPTS 1631
Query: 380 GGLNFGTPTTQATSAFGTPTQSTGLSFGPPFLFRSNETTATLDACVQSFGSTTPAQGFGS 439
+ +P+ TS +PT S S P + T+ + S+ T+P+ S
Sbjct: 1632 PSYSPTSPSYSPTSPSYSPT-SPSYS---PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1687
Query: 440 TAQTGLS-FGTPSATQASGGFSFGGGTAPQTGGLNFGTPTSTQQPLFGAPATTAQTGFSF 498
+ + S +P++ S T+P PTS + +S
Sbjct: 1688 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS------PTSPSYSPTSPSYSPTSPSYSP 1741
Query: 499 GTPA 502
+P+
Sbjct: 1742 TSPS 1745
Score = 44.7 bits (105), Expect = 9e-05
Identities = 50/296 (16%), Positives = 86/296 (29%), Gaps = 16/296 (5%)
Query: 225 GTTTSGQGFGGFGTGTAT-FGSTNTSTGGLFGSGGTTTAQPGFGSSAFGTPSAPTPAFGS 283
SG G G T + + G GS P + G
Sbjct: 1467 TLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLG 1526
Query: 284 PAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAPSGGLN 343
A T + G + S SP+ S ++ S
Sbjct: 1527 AASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTS---- 1582
Query: 344 FGTPTTQATSAFGTPTQSTGLSFGNFNSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTG 403
P+ TS +PT S S + + T + S +PT+ + S T
Sbjct: 1583 ---PSYSPTSPSYSPT-SPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1638
Query: 404 LSFGPPFLFRSNETTATLDACVQSFGSTTPAQGFGSTAQTGLSFGTPSATQASGGFSFGG 463
S+ P S + T + + S +P S S +PS + S +S
Sbjct: 1639 PSYSPT----SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS--- 1691
Query: 464 GTAPQTGGLNFGTPTSTQQPLFGAPATTAQTGFSFGTPAATSQPSVGFGAAATTQS 519
T+P + ++ +P+ + + T + S S + + + S
Sbjct: 1692 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1747
Score = 37.7 bits (87), Expect = 0.014
Identities = 60/319 (18%), Positives = 101/319 (31%), Gaps = 26/319 (8%)
Query: 238 TGTATFG---STNTSTGGLFGSGGTTTAQPGFGSSAFGTPSAPTPAFGSPAFGSTNTFGT 294
GT F + G+ T A G G+S A TP SP S
Sbjct: 1442 MGTGAFDIYLDQDMLMNYSLGTAVPTLAGSGMGTSQLP-EGAGTPYERSPMVDSGFVGSP 1500
Query: 295 PTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAPSGGLNFGTPTTQATSA 354
S G G G + S + + G S + +P TS
Sbjct: 1501 DAAAFSPLVQGGSEGREGFGDYGLLG----AASPYKGVQSPGYTSPFSSAMSPGYGLTSP 1556
Query: 355 FGTPTQSTGLSFGNFNSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSFGPPFLFRS 414
+P+ S G S + S + +P+ TS +PT + P + S
Sbjct: 1557 SYSPS-----SPGYSTSP-AYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATS 1610
Query: 415 NETTATLDACVQSFGSTTPAQ-GFGSTAQTGLSFGTPSATQASGGFSFGGGTAPQTGGLN 473
+ T + + S +P + T+ S +PS + S +S + T
Sbjct: 1611 PSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPTSPSYSPTSPSYSPTS--P 1667
Query: 474 FGTPTSTQQPLFGAPATTAQTGFSFGTPAATSQPSVGFGAAATTQSVGFGAPATSQSVTF 533
+PTS + +S T + S S + + + S +P+ S +
Sbjct: 1668 SYSPTSPSYSPTSPSYSPTSPSYS-PTSPSYSPTSPSYSPTSPSYSP--TSPSYSPT--- 1721
Query: 534 GAQPASQPSVGFGAPATTQ 552
P+ P+ +P +
Sbjct: 1722 --SPSYSPTSPSYSPTSPS 1738
Score = 33.1 bits (75), Expect = 0.33
Identities = 29/176 (16%), Positives = 49/176 (27%), Gaps = 10/176 (5%)
Query: 425 VQSFGSTTPAQGFGSTAQTGLSFGTPSATQASGGFSFGGGTAPQTGGLNFGTP--TSTQQ 482
+ ++ T + + T G F +P +
Sbjct: 1456 LMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAF-SPLVQGGSE 1514
Query: 483 PLFGAPATTAQTGFSFGTPAATSQPSVGFGAAATTQSVGFGAPATSQSVTFGAQPASQPS 542
G S + + F +A + + S + PA PS
Sbjct: 1515 GREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPS 1574
Query: 543 VGFGAPATTQTGLSFGAPATS--QPALSFGS---SATGQAAGFSFGSSAPASSQPS 593
+P T S +P+ S P+ S S SAT + + S +P S S
Sbjct: 1575 SPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYS 1628
>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets,
alpha helices, AMY amyloidosis, blood coagulation,
disease mutation, glycoprot phosphoprotein; HET: NAG NDG
BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A*
2a45_G*
Length = 562
Score = 44.1 bits (103), Expect = 1e-04
Identities = 49/308 (15%), Positives = 89/308 (28%), Gaps = 9/308 (2%)
Query: 210 GFSFGSTATQPAFGAGTTTSGQGFGGFGTGTATFGSTNTSTGGLFGSGGTTTAQPG-FGS 268
GST+ + + G + +G++ GST G G+GGT T +PG G
Sbjct: 250 ITRGGSTSYGTGSETESPRNPSSAGSWNSGSSGPGSTGNRNPGSSGTGGTATWKPGSSGP 309
Query: 269 SAFGTPSAPTPAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPST 328
+ G+ ++ + GS + + +T + G + G ++ S
Sbjct: 310 GSTGSWNSGSSGTGSTGNQNPGSPRPGST-GTWNPGSSERGSAGHWTSESSVSGSTGQWH 368
Query: 329 TQSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLS-FGNFNSGLTFGAPSGGLNFGTP 387
++SG +F S G P F + + +++ +
Sbjct: 369 SESG-SFRPDSPGSGNARPNNPDWGTFEEVSGNVSPGTRREYHTEKLVTSKGDKELRTGK 427
Query: 388 TTQATSAFGTPTQSTGLSFGPPFLFRSNETTATLDACVQSFGSTTPAQGFGST-----AQ 442
+ + T +S + + T + GS P T
Sbjct: 428 EKVTSGSTTTTRRSCSKTVTKTVIGPDGHKEVTKEVVTSEDGSDCPEAMDLGTLSGIGTL 487
Query: 443 TGLSFGTPSATQASGGFSFGGGTAPQTGGLNFGTPTSTQQPLFGAPATTAQTGFSFGTPA 502
G P S G + + T+ + T S P
Sbjct: 488 DGFRHRHPDEAAFFDTASTGKTFPGFFSPMLGEFVSETESRGSESGIFTNTKESSSHHPG 547
Query: 503 ATSQPSVG 510
PS G
Sbjct: 548 IAEFPSRG 555
Score = 32.2 bits (72), Expect = 0.59
Identities = 25/206 (12%), Positives = 53/206 (25%), Gaps = 11/206 (5%)
Query: 209 AGFSFGSTATQPAFGAGTTTSGQGFGGFGTGTATFGSTNTSTGGLFGSGGTTTAQPGFGS 268
+ + + +P G G T+ + ++ SG PG G+
Sbjct: 324 STGNQNPGSPRPGSTGTWNPGSSERGSAGHWTSESSVSGSTGQWHSESGSFRPDSPGSGN 383
Query: 269 SAFGT-------PSAPTPAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGL 321
+ + + G+ T T + G ++ + T++S
Sbjct: 384 ARPNNPDWGTFEEVSGNVSPGTRREYHTEKLVTSKGDKELRTGKEKVTSGSTTTTRRSCS 443
Query: 322 SFNSPSTTQSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSFGNFNS----GLTFGA 377
+ + + + + G G + F
Sbjct: 444 KTVTKTVIGPDGHKEVTKEVVTSEDGSDCPEAMDLGTLSGIGTLDGFRHRHPDEAAFFDT 503
Query: 378 PSGGLNFGTPTTQATSAFGTPTQSTG 403
S G F + F + T+S G
Sbjct: 504 ASTGKTFPGFFSPMLGEFVSETESRG 529
Score = 32.2 bits (72), Expect = 0.65
Identities = 46/311 (14%), Positives = 79/311 (25%), Gaps = 11/311 (3%)
Query: 298 QQSTGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAPSGGLNFGTPTTQATSAFGT 357
Q G + + G + S SG G+ + + GT
Sbjct: 237 QMRMELERPGGNEITRGGSTSYGTGSETESPRNPSSAGSWNSGSSGPGSTGNRNPGSSGT 296
Query: 358 PTQSTG--LSFGNFNSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSFGPPFLFRSN 415
+T S G ++G SG + G + T T + G S ++
Sbjct: 297 GGTATWKPGSSGPGSTGSWNSGSSGTGSTGNQNPGSPRPGSTGTWNPGSSERGSAGHWTS 356
Query: 416 ETTATLDACVQSFGSTTPAQGFGSTAQTGLSFGTPSATQASGGFSFGGGTAPQTGGLNFG 475
E++ + S G G G P+ G +P T
Sbjct: 357 ESSVS-----GSTGQWHSESGSFRPDSPGSGNARPNNPDWGTFEEVSGNVSPGTRREYHT 411
Query: 476 TPTSTQQPLFGAPATTAQTGFSFGTPAATSQPSVGFGAAATTQSVGFGAPATSQSVTFGA 535
T + + T+ T G ++ V
Sbjct: 412 EKLVTS----KGDKELRTGKEKVTSGSTTTTRRSCSKTVTKTVIGPDGHKEVTKEVVTSE 467
Query: 536 QPASQPSVGFGAPATTQTGLSFGAPATSQPALSFGSSATGQAAGFSFGSSAPASSQPSLS 595
+ P + L A F +++TG+ F + S
Sbjct: 468 DGSDCPEAMDLGTLSGIGTLDGFRHRHPDEAAFFDTASTGKTFPGFFSPMLGEFVSETES 527
Query: 596 FGAAIWIFSNR 606
G+ IF+N
Sbjct: 528 RGSESGIFTNT 538
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 36.6 bits (84), Expect = 0.031
Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 21/75 (28%)
Query: 553 TGLSFGAP-----ATS--QPALSFGSSATGQA-------------AGFSFGS-SAPASSQ 591
T +F + AT QPAL+ A + AG S G +A AS
Sbjct: 1715 TSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLA 1774
Query: 592 PSLSFGAAIWIFSNR 606
+S + + + R
Sbjct: 1775 DVMSIESLVEVVFYR 1789
Score = 34.6 bits (79), Expect = 0.11
Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 19/77 (24%)
Query: 323 FNSPSTTQSGLTFGAPSGGLNFGTPTTQ----ATS---------AFGTPTQST--GLSFG 367
F + + TF + G L+ T TQ P +T G S G
Sbjct: 1707 FKEINEHSTSYTFRSEKGLLSA-TQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLG 1765
Query: 368 NFNSGLTFGAPSGGLNF 384
+ + L + + ++
Sbjct: 1766 EY-AALA--SLADVMSI 1779
>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 = 35.2 bits (80), Expect = 0.076
Identities = 23/131 (17%), Positives = 32/131 (24%), Gaps = 5/131 (3%)
Query: 467 PQTGGLNFGTPTSTQQPL-FGAPATTAQTGFSFGTPAATSQPSVGFGAAATTQSVGF--- 522
PQ T QQP F P A G S+G Q +V +
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69
Query: 523 -GAPATSQSVTFGAQPASQPSVGFGAPATTQTGLSFGAPATSQPALSFGSSATGQAAGFS 581
+ + + P V A Q + G P Q + +A
Sbjct: 70 HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129
Query: 582 FGSSAPASSQP 592
P
Sbjct: 130 QNMRPMNQLYP 140
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.8 bits (71), Expect = 0.33
Identities = 9/23 (39%), Positives = 10/23 (43%), Gaps = 3/23 (13%)
Query: 552 QTGLSFGAPATSQPALSFGSSAT 574
Q L A S PAL+ AT
Sbjct: 26 QASLKLYAD-DSAPALAI--KAT 45
Score = 31.1 bits (69), Expect = 0.48
Identities = 6/21 (28%), Positives = 11/21 (52%), Gaps = 5/21 (23%)
Query: 584 SS----APASSQPSLSFGAAI 600
+S A S+ P+L+ A +
Sbjct: 27 ASLKLYADDSA-PALAIKATM 46
>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 = 32.4 bits (73), Expect = 0.46
Identities = 19/118 (16%), Positives = 29/118 (24%), Gaps = 7/118 (5%)
Query: 478 TSTQQPLFGAPATTAQTGFSFGTPAATSQPSVGFGAAATTQSVGFGAPATSQSVTFGAQP 537
+ + G P+A+ + AA V PA A
Sbjct: 4 SHHHHH---HSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPP---PAPA 57
Query: 538 ASQPSVGFGAPATTQTGLS-FGAPATSQPALSFGSSATGQAAGFSFGSSAPASSQPSL 594
A P + Q L P T+ A + + A + P L
Sbjct: 58 AGNPPDTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVPGL 115
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos
taurus} SCOP: i.9.1.1
Length = 390
Score = 29.8 bits (66), Expect = 2.7
Identities = 21/178 (11%), Positives = 36/178 (20%), Gaps = 3/178 (1%)
Query: 187 SRQLPLRLDFHLAPQ-QHSQHLWAGFSFGSTATQPAFGAGTTTSGQGFGGFGTGTATFGS 245
+ + Q Q + W G +G +
Sbjct: 210 MSTITGPVPREFKSQLQEAPLEWKALLEMQQTKMVLETFGGDGHARG--DSVSQGTGLAP 267
Query: 246 TNTSTGGLFGSGGTTTAQPGFGSSAFGTPSAPTPAFGSPAFGSTNTFGTPTTQQSTGFGG 305
+ G G G GSS P P P G+ T
Sbjct: 268 GSPRKPGTSSIGNVNPGSYGPGSSGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNPGRPEP 327
Query: 306 FGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTG 363
T+ + +P + G +G + ++ S
Sbjct: 328 GSAGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNTGSSGSSSFRPDSSGHGNIRPSSPD 385
>2ahu_A Putative enzyme YDIF; COA transferase, glutamyl thioester,
structural genomi montreal-kingston bacterial structural
genomics initiative; 1.90A {Escherichia coli} SCOP:
c.124.1.3 c.124.1.2 PDB: 2ahv_A* 2ahw_A*
Length = 531
Score = 29.6 bits (67), Expect = 3.3
Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 305 GFGTSTFGSQPTQQSGLSFNSPSTTQSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGL 364
G G + ++ G + + T ++G G S G+ FG + +Q
Sbjct: 308 GVGIADGIGLVAREEGCADDFILTVETGPIGGITSQGIAFGA-NVNTRAILDMTSQ---- 362
Query: 365 SFGNFNSG 372
F ++ G
Sbjct: 363 -FDFYHGG 369
>3ntn_A USPA1; beta roll, trimeric autotransporter proteins, outer membrane
membrane protein; 2.20A {Moraxella catarrhalis}
Length = 220
Score = 28.5 bits (63), Expect = 5.7
Identities = 16/78 (20%), Positives = 23/78 (29%)
Query: 221 AFGAGTTTSGQGFGGFGTGTATFGSTNTSTGGLFGSGGTTTAQPGFGSSAFGTPSAPTPA 280
A G+ T F G+ T + + L G A S+ G S A
Sbjct: 84 AIGSNNTVKKGQQNVFILGSNTDTTNAQNGSVLLGHNTAGKAATIVNSAEVGGLSLTGFA 143
Query: 281 FGSPAFGSTNTFGTPTTQ 298
S T + G +
Sbjct: 144 GASKTGNGTVSVGKKGKE 161
>3few_X Colicin S4; cell lysis, Y-RAY, cell killing, immune system; 2.45A
{Escherichia coli}
Length = 505
Score = 28.7 bits (63), Expect = 6.2
Identities = 22/90 (24%), Positives = 31/90 (34%), Gaps = 27/90 (30%)
Query: 228 TSGQGFGGFGTGTATFGSTNTSTGGLFGSGGTTT--------AQPGFGSSAFGTPSAP-- 277
T+G+ GG G G N S G+ GG+ + +Q G+G S P P
Sbjct: 11 TAGESMGGTGANLNQQGGNNNSNSGVHWGGGSGSGNGGREHGSQTGWGWSKTNNPDVPPY 70
Query: 278 -----------------TPAFGSPAFGSTN 290
TP +G P G +
Sbjct: 71 VDDNGQVRITITNGLVKTPVYGVPGAGGNS 100
>3a69_A Flagellar HOOK protein FLGE; the bacterial flagellar motor,
universal joint, bacterial flagellum, motor protein;
7.10A {Salmonella enterica subsp}
Length = 402
Score = 28.3 bits (63), Expect = 7.3
Identities = 17/156 (10%), Positives = 29/156 (18%)
Query: 350 QATSAFGTPTQSTGLSFGNFNSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLSFGPP 409
+ +T S + + + T S G +
Sbjct: 137 TIPNTLMAAKSTTTASMQINLNSTDPVPSKTPFSVSDADSYNKKGTVTVYDSQGNAHDMN 196
Query: 410 FLFRSNETTATLDACVQSFGSTTPAQGFGSTAQTGLSFGTPSATQASGGFSFGGGTAPQT 469
F + S A ST G + + A
Sbjct: 197 VYFVKTKDNEWAVYTHDSSDPAATAPTTASTTLKFNENGILESGGTVNITTGTINGATAA 256
Query: 470 GGLNFGTPTSTQQPLFGAPATTAQTGFSFGTPAATS 505
+ Q T Q G+ G +
Sbjct: 257 TFSLSFLNSMQQNTGANNIVATNQNGYKPGDLVSYQ 292
Score = 28.3 bits (63), Expect = 7.3
Identities = 28/158 (17%), Positives = 47/158 (29%), Gaps = 2/158 (1%)
Query: 208 WAGFSFGSTATQPAFGAGTTTSGQGFGGFGTGTATFGSTNTSTGGLFGSGGTTTAQPGFG 267
+ T Q A A T T TA+ ST + + +
Sbjct: 118 YPATGTPPTIQQGANPAPITIPNTLMAAKSTTTASMQINLNSTDPVPSKTPFSVSDAD-- 175
Query: 268 SSAFGTPSAPTPAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPS 327
S + G+ + T + + + T + L FN
Sbjct: 176 SYNKKGTVTVYDSQGNAHDMNVYFVKTKDNEWAVYTHDSSDPAATAPTTASTTLKFNENG 235
Query: 328 TTQSGLTFGAPSGGLNFGTPTTQATSAFGTPTQSTGLS 365
+SG T +G +N T T + S + Q+TG +
Sbjct: 236 ILESGGTVNITTGTINGATAATFSLSFLNSMQQNTGAN 273
>3lz8_A Putative chaperone DNAJ; structure genomics, structural genomics,
PSI-2, protein STRU initiative; 2.90A {Klebsiella
pneumoniae subsp} PDB: 2kqx_A
Length = 329
Score = 28.4 bits (64), Expect = 8.0
Identities = 9/71 (12%), Positives = 12/71 (16%), Gaps = 6/71 (8%)
Query: 213 FGSTATQPAFGAGTTTSGQGFGGFGTGTATFGST-NTSTGGLFGSGGTTTAQPGFGSSAF 271
P FG T Q + F ++ G A G
Sbjct: 92 LWQHRNDPGFGRQRQTHEQSYSQQD-----FDDIFSSMFGQQAHQRRRQHAARGHDLEIE 146
Query: 272 GTPSAPTPAFG 282
Sbjct: 147 VAVFLEETLAE 157
>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
fusion, viral P glycoprotein B, HSV-1, membrane; HET:
NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
3nwd_A*
Length = 703
Score = 28.4 bits (63), Expect = 9.9
Identities = 15/83 (18%), Positives = 24/83 (28%), Gaps = 2/83 (2%)
Query: 274 PSAP-TPAFGSPAFGSTNTFGTPTTQQSTGFGGFGTSTFGSQPTQQSGLSFNSPSTTQSG 332
P+AP +P A + G P T G T + ++ + P
Sbjct: 2 PAAPTSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPK-NPTPPRPAGDN 60
Query: 333 LTFGAPSGGLNFGTPTTQATSAF 355
T A L +A +
Sbjct: 61 ATVAAGHATLREHLRDIKAENTD 83
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.314 0.129 0.391
Gapped
Lambda K H
0.267 0.0507 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,750,359
Number of extensions: 516103
Number of successful extensions: 1119
Number of sequences better than 10.0: 1
Number of HSP's gapped: 976
Number of HSP's successfully gapped: 140
Length of query: 614
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 515
Effective length of database: 3,937,614
Effective search space: 2027871210
Effective search space used: 2027871210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 60 (27.4 bits)