RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3015
(1791 letters)
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A
2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Length = 880
Score = 523 bits (1349), Expect = e-164
Identities = 133/399 (33%), Positives = 197/399 (49%), Gaps = 54/399 (13%)
Query: 71 NQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTR--THSTHPDDE 128
+E+ IL + + +P IL P+ +TGKQV S +P + N S+ P
Sbjct: 517 TKEEAQQILG-VADVKIDLGEPAILAPREYYTGKQVVSAFLPKDFNFHGQANVSSGPRLC 575
Query: 129 DSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSS-GSLLHICFLELGHEVCGRFYGNI 187
+ P D+ VV+++G LL G+ KK++G S+LH E E N+
Sbjct: 576 KN----EDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNL 631
Query: 188 QTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHS 247
V ++ L+G ++ + D EI I +AK +V +IQK N +LEP PG
Sbjct: 632 FRVFIRFVELQGFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPG-- 689
Query: 248 IGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILN 307
TL ++ EN + L+
Sbjct: 690 --------------------------------------------RTLEESLENYILDTLD 705
Query: 308 DARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRT 367
R G A K L +N M G++GS +NI+Q+ A +GQQ+V G+RI G+ RT
Sbjct: 706 KLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRT 765
Query: 368 LPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK 427
LPHF D PE+RGF+ +S+ GL P+E FFHA GGREGL+DTAV+T+++GY+QRRLI
Sbjct: 766 LPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLIN 825
Query: 428 AMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQR 466
A+ + YD TVR+ G++IQ+ YG+DG+ H +
Sbjct: 826 ALSDLRAEYDGTVRSLYGEVIQVAYGDDGVFPMYSAHGK 864
Score = 180 bits (459), Expect = 3e-46
Identities = 51/125 (40%), Positives = 71/125 (56%), Gaps = 4/125 (3%)
Query: 1009 AQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068
Q+ A +GQQ+V G+RI G+ RTLPHF D PE+RGF+ +S+ GL P+E FFHA
Sbjct: 741 TQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAA 800
Query: 1069 GGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFD 1128
GGREGL+DTAV+T+++ + L ++ YD TV E + V Y
Sbjct: 801 GGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYD----GTVRSLYGEVIQVAYGDDGVF 856
Query: 1129 PTRIS 1133
P +
Sbjct: 857 PMYSA 861
Score = 79.1 bits (195), Expect = 9e-15
Identities = 21/48 (43%), Positives = 31/48 (64%)
Query: 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQR 639
GY+QRRLI A+ + YD TVR+ G++IQ+ YG+DG+ H +
Sbjct: 817 GYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGVFPMYSAHGK 864
Score = 69.1 bits (169), Expect = 1e-11
Identities = 14/62 (22%), Positives = 26/62 (41%)
Query: 1489 VENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTV 1548
+ I + + IITP+ P++G QD ++ +T + L K A + +
Sbjct: 476 AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGVADVKIDLG 535
Query: 1549 IP 1550
P
Sbjct: 536 EP 537
Score = 69.1 bits (169), Expect = 1e-11
Identities = 20/45 (44%), Positives = 33/45 (73%)
Query: 28 PYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQ 72
P + ILG DP +RP+WM++TVLPVPP+++RP++++ R +
Sbjct: 188 PESDVEILGYDPTTSRPEWMILTVLPVPPITIRPSIMIESGIRAE 232
>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 = 517 bits (1333), Expect = e-154
Identities = 204/423 (48%), Positives = 264/423 (62%), Gaps = 55/423 (13%)
Query: 71 NQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDS 130
+Q++N+L ++P WDG +P P I+KPKPLW+GKQ+ S+ IP +++ R
Sbjct: 542 ELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDE-------- 593
Query: 131 GPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTV 190
+SP D +++ G ++ G++ KK++G+S+G L+H+ E G +VC + +GNIQ V
Sbjct: 594 -GTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKV 652
Query: 191 VNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGI 250
VN WLL G S GIGDTIAD T EI I +AK+ V++V ++A L G
Sbjct: 653 VNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHG----- 707
Query: 251 GDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDAR 310
TLR++FE+ V R LN+AR
Sbjct: 708 -----------------------------------------MTLRESFEDNVVRFLNEAR 726
Query: 311 DKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPH 370
DK G A+ +L + NN+K MV+AGSKGS INI+Q+ ACVGQQ+VEGKRI FGF RTLPH
Sbjct: 727 DKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPH 786
Query: 371 FIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAME 430
F KDDY PES+GFVENSYL GLTP EFFFHAMGGREGLIDTAVKTAETGYIQRRL+KA+E
Sbjct: 787 FSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALE 846
Query: 431 SVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERP 490
+MVHYD T RNS+G +IQ YGEDG+ +E Q +DT+ S FE +YR D N
Sbjct: 847 DIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDH 906
Query: 491 TLR 493
TL
Sbjct: 907 TLD 909
Score = 434 bits (1116), Expect = e-125
Identities = 185/521 (35%), Positives = 281/521 (53%), Gaps = 44/521 (8%)
Query: 953 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVI 1012
+ G++++ + A +A LF CL+RS L T+ V + YRL+ +AF+W++ IE +F ++ V
Sbjct: 1000 LRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVH 1059
Query: 1013 ACVGQQNVEGKRIPFGFRKRTLPHFIKDDYG--------PESRGFVENSYLAGLTPSEFF 1064
+ + I + TL F P + + N TPS
Sbjct: 1060 PGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEIL-NVAKNMKTPSLTV 1118
Query: 1065 FHAMGGREGLIDTAVKTAETVNVL------VFLFQVTANTAIYYDPDPQNTVIPEDQEFV 1118
+ L E ++ L VT + IYYDPDP++TVIPED+E +
Sbjct: 1119 Y--------LEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEII 1170
Query: 1119 NVYYEMPDFDP----TRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFND 1174
+++ + D + + SPWLLR+ELDR M DK LTM + E+I F +DL I+++
Sbjct: 1171 QLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSE 1230
Query: 1175 DNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYM 1234
DN EKL++R R++ DA + E+D L+ IE ML ++TL+G+E I +V M
Sbjct: 1231 DNDEKLIIRCRVVRPKS------LDAETEAEEDHMLKKIENTMLENITLRGVENIERVVM 1284
Query: 1235 HLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVL 1294
R + + +GE+ +W+LETDG +L +V++ +DP R ++N +I +VL
Sbjct: 1285 M-----KYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVL 1339
Query: 1295 GIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMR 1354
GIEA R ++ KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG NR +TGALMR
Sbjct: 1340 GIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMR 1399
Query: 1355 CSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLA 1414
CSFEETV++L +A A AE D RGVSEN+I+GQ+ +GTG FD+++D E +
Sbjct: 1400 CSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKI 1459
Query: 1415 TGMMGGPAGMFF------GSAATPSSIPGPPAWYPIHIAIS 1449
T + G G G + + P+ + S
Sbjct: 1460 TEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS 1500
Score = 215 bits (549), Expect = 3e-56
Identities = 99/402 (24%), Positives = 164/402 (40%), Gaps = 33/402 (8%)
Query: 567 MRCSFEETV--DVLMDAAAHAEADPMRGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLR 624
+R + E T V + + + + DP I E + +H+ + +
Sbjct: 1134 IRSAIEHTTLKSVTIASEIYYDPDPRSTVIPED----EEIIQLHFSLLDEEAEQSFD--Q 1187
Query: 625 YGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNED--VLRELMGSGDV 682
L E D + E + ++ + N++ ++R +
Sbjct: 1188 QSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKS 1247
Query: 683 ISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDV-ISELEKEWEKLCEDREALREIFSS 741
+ + DH K + LR + V + + +++ + E
Sbjct: 1248 LDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLE 1307
Query: 742 GESNVVLPCNLMEVIFILQRWKLWGNENLRF----LCKIIFVL---SVRKSVEKEMNTVL 794
+ NL EV + G + R I+ VL + R ++ KE+ V+
Sbjct: 1308 TDG-----VNLSEV------MTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVI 1356
Query: 795 QFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHA 854
G YVNYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV++L +A A A
Sbjct: 1357 ASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASA 1416
Query: 855 EADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFGSAAT 914
E D RGVSEN+I+GQ+ +GTG FD+++D E + T + G G +
Sbjct: 1417 ELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNE 1476
Query: 915 PSSMSPQMTPW--AQSTPAYNALMSPGAA--MTPGGPGFSPS 952
++ + +P ++ + A T G
Sbjct: 1477 SGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGE 1518
Score = 151 bits (381), Expect = 1e-36
Identities = 96/278 (34%), Positives = 128/278 (46%), Gaps = 14/278 (5%)
Query: 1009 AQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068
AQ+ ACVGQQ+VEGKRI FGF RTLPHF KDDY PES+GFVENSYL GLTP EFFFHAM
Sbjct: 759 AQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAM 818
Query: 1069 GGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDP---DPQNTVIP----EDQEFVNVY 1121
GGREGLIDTAVKTAET + L + + ++YD + VI ED +
Sbjct: 819 GGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDG-MDAAH 877
Query: 1122 YEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLV 1181
E D S + ++ E + GD + D+ ++LV
Sbjct: 878 IEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLV 937
Query: 1182 -----LRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHL 1236
LR + ++ + +++ I+ SD+T++ I K
Sbjct: 938 KDRKFLR-EVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQEN 996
Query: 1237 PQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSE 1274
K II + L + +VL E
Sbjct: 997 LLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQE 1034
Score = 149 bits (376), Expect = 6e-36
Identities = 69/274 (25%), Positives = 112/274 (40%), Gaps = 47/274 (17%)
Query: 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFE 651
GYIQRRL+KA+E +MVHYD T RNS+G +IQ YGEDG+ +E Q +DT+ S FE
Sbjct: 835 GYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFE 894
Query: 652 DKYRFDPSNERQLRRIFNEDVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLREL 711
+YR D N + E+
Sbjct: 895 KRYRVDLLNTD-----------------------------------HTLDPSLLESGSEI 919
Query: 712 MGSGDVISELEKEWEKLCEDREALREIFSSGESNVVLPCNLMEVIFILQRWKLWGNENLR 771
+G + L++E+++L +DR+ LRE+F GE+N LP N+ +I Q+ +
Sbjct: 920 LGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPS 979
Query: 772 FLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHL---MAITRHGIN 828
L VL V+ E + + + N + A+ + L + + +
Sbjct: 980 DLTIKDIVLGVKDLQEN-LLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLT 1038
Query: 829 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGV 862
+Q +F+ + + + P V
Sbjct: 1039 KQ--------AFDWVLSNIEAQFLRSVVHPGEMV 1064
Score = 130 bits (328), Expect = 2e-30
Identities = 46/77 (59%), Positives = 58/77 (75%)
Query: 516 SVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETV 575
++ KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV
Sbjct: 1347 ALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETV 1406
Query: 576 DVLMDAAAHAEADPMRG 592
++L +A A AE D RG
Sbjct: 1407 EILFEAGASAELDDCRG 1423
Score = 108 bits (270), Expect = 2e-23
Identities = 64/246 (26%), Positives = 103/246 (41%), Gaps = 55/246 (22%)
Query: 1462 TLKTFLEMKDFKKPPQKGFGLLTLTLMV----ENIHVTPRQIITPQNNRPVMGIVQDTLT 1517
TL TF G +T V E ++V + + TP +
Sbjct: 1080 TLNTF---------HFAGVASKKVTSGVPRLKEILNVA-KNMKTPSLTVYLEPGHAADQE 1129
Query: 1518 AVRKMTKR--DVFLDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDP----TRIS 1571
+ + L VT + IYYDPDP++TVIPED+E + +++ + D + + S
Sbjct: 1130 QAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQS 1189
Query: 1572 PWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFG 1631
PWLLR+ELDR M DK LTM + E+I F
Sbjct: 1190 PWLLRLELDRAAM----------------------------NDKDLTMGQVGERIKQTFK 1221
Query: 1632 DDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEED-------AVDKMEDDMFLRCIEETDR 1684
+DL I+++DN EKL++R R++ + E + + M +++ LR +E +R
Sbjct: 1222 NDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIER 1281
Query: 1685 SFVKVD 1690
+
Sbjct: 1282 VVMMKY 1287
Score = 72.0 bits (176), Expect = 2e-12
Identities = 27/64 (42%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 1489 VENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTV 1548
+ + P QI++PQ+N+P MGIVQDTL +RK+T RD F++ +Y+ PD + V
Sbjct: 501 LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDW-DGV 559
Query: 1549 IPED 1552
IP
Sbjct: 560 IPTP 563
Score = 67.8 bits (165), Expect = 4e-11
Identities = 18/45 (40%), Positives = 29/45 (64%)
Query: 28 PYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQ 72
++ LG + F+RP+WM++T LPVPP VRP++ + S R +
Sbjct: 215 SVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGE 259
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 515 bits (1328), Expect = e-153
Identities = 215/419 (51%), Positives = 266/419 (63%), Gaps = 55/419 (13%)
Query: 71 NQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDS 130
+ +MNI++++P WDG +P P ILKPK LWTGKQ+ SLIIP +N+ R
Sbjct: 548 TRNAVMNIMLWVPDWDGILPPPVILKPKVLWTGKQILSLIIPKGINLIRDDDKQS----- 602
Query: 131 GPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTV 190
+P D+ +++E+G ++ G++ KK++G S G L+H + E G E+C F+ IQ V
Sbjct: 603 ----LSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFFNGIQRV 658
Query: 191 VNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGI 250
VN WLL G SIGIGDTIAD T E+ +K+A+ V E IQ A + L+P PG
Sbjct: 659 VNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGM---- 714
Query: 251 GDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDAR 310
TLR++FE +V+RILN AR
Sbjct: 715 ------------------------------------------TLRESFEAKVSRILNQAR 732
Query: 311 DKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPH 370
D G SA+ SL + NN+K MV AGSKGS INISQ+ ACVGQQ VEGKRIPFGF+ RTLPH
Sbjct: 733 DNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPH 792
Query: 371 FIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAME 430
F KDD PESRGF+ENSYL GLTP EFFFHAM GREGLIDTAVKTAETGYIQRRL+KAME
Sbjct: 793 FPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAME 852
Query: 431 SVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNER 489
VMV YD TVRN++G +IQ YGEDGL VE+Q D++ LS K+FE KYR D +R
Sbjct: 853 DVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDR 911
Score = 451 bits (1160), Expect = e-131
Identities = 216/529 (40%), Positives = 297/529 (56%), Gaps = 50/529 (9%)
Query: 953 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVI 1012
G D++++ NATLLFQ L+RS K V YRL+ AFEW++GE+E RFQQA V
Sbjct: 1003 FRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRLNKVAFEWIMGEVEARFQQAVVS 1062
Query: 1013 ACVGQQNVEGKRIPFGFRKRTLPHFIKDDYG--------PESRGFVENSYLAGLTPSEFF 1064
+ + I + TL F P + + N TPS
Sbjct: 1063 PGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIL-NVAKNIKTPSLTI 1121
Query: 1065 FHAMGGREGLIDTAVKTAETVNVL------VFLFQVTANTAIYYDPDPQNTVIPEDQEFV 1118
+ L+ + + L VT+ T I+YDPDPQ+TVI ED++FV
Sbjct: 1122 Y--------LMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFV 1173
Query: 1119 NVYYEMPDFDP----TRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFND 1174
++ +PD + + SPWLLR+ELDR +M DKKL+M ++ KI F DL I+++
Sbjct: 1174 EAFFAIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSE 1233
Query: 1175 DNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYM 1234
DNA+KL++R RI+ DD K ED + +E+D+FL+ IE +ML ++L+G+ I +VYM
Sbjct: 1234 DNADKLIIRCRIIRDDDRK---AEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYM 1290
Query: 1235 HLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVL 1294
K + E G F+ +W+LETDG +L + ++ VD RT+SN EI Q+L
Sbjct: 1291 M-----EHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQIL 1345
Query: 1295 GIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMR 1354
GIEA R ++ KE+ V++F G YVNYRHLALLCDVMT++GHLMAITRHGINR +TGALMR
Sbjct: 1346 GIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMR 1405
Query: 1355 CSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKD---GIEI 1411
CSFEETV++LMDAAA E D +G+SENI++GQL MGTG FD+ LD + + G +
Sbjct: 1406 CSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDMLMNYSLGTAV 1465
Query: 1412 PLATGMMGGPAGMFFGSAATPSS-----------IPGPPAWYPIHIAIS 1449
P G G A TP P A+ P+ S
Sbjct: 1466 PTLAGSGMGT-SQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGGS 1513
Score = 229 bits (585), Expect = 1e-60
Identities = 87/175 (49%), Positives = 108/175 (61%), Gaps = 6/175 (3%)
Query: 782 VRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFE 841
R ++ KE+ V++F G YVNYRHLALLCDVMT++GHLMAITRHGINR +TGALMRCSFE
Sbjct: 1350 TRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFE 1409
Query: 842 ETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKD---GIEIPLAT 898
ETV++LMDAAA E D +G+SENI++GQL MGTG FD+ LD + + G +P
Sbjct: 1410 ETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDMLMNYSLGTAVPTLA 1469
Query: 899 GMMGGPAGMFFGSAATPSSMSPQMTPWAQSTPAYNALMSPGA-AMTPGGPGFSPS 952
G G A TP SP + +P A SP + G GF
Sbjct: 1470 GSGMGT-SQLPEGAGTPYERSPMVDSGFVGSPDA-AAFSPLVQGGSEGREGFGDY 1522
Score = 160 bits (405), Expect = 2e-39
Identities = 86/221 (38%), Positives = 121/221 (54%), Gaps = 9/221 (4%)
Query: 1009 AQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068
+Q+ ACVGQQ VEGKRIPFGF+ RTLPHF KDD PESRGF+ENSYL GLTP EFFFHAM
Sbjct: 765 SQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAM 824
Query: 1069 GGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDP---DPQNTVI----PEDQEFVNVY 1121
GREGLIDTAVKTAET + L + + + YD + +I ED
Sbjct: 825 AGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDG-LDATL 883
Query: 1122 YEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISE-KINAGFGDDLNCIFNDDNAEKL 1180
E FD R+S + M D+ L++ + + ++ D L+ + A++
Sbjct: 884 VEYQVFDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSIENDSSVQDLLDEEYTQLVADRE 943
Query: 1181 VLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDM 1221
+L I D++ + +++ + + +EA +D+
Sbjct: 944 LLCKFIFPKGDARWPLPVNVQRIIQNALQIFHLEAKKPTDL 984
Score = 139 bits (352), Expect = 4e-33
Identities = 69/272 (25%), Positives = 104/272 (38%), Gaps = 46/272 (16%)
Query: 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFE 651
GYIQRRL+KAME VMV YD TVRN++G +IQ YGEDGL VE+Q D++ LS K+FE
Sbjct: 841 GYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSLRLSTKQFE 900
Query: 652 DKYRFDPSNERQLRRIFNEDVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLREL 711
KYR D +R L +
Sbjct: 901 KKYRIDLMEDRSLSLYMENSIE-------------------------------------- 922
Query: 712 MGSGDVISELEKEWEKLCEDREALR-EIFSSGESNVVLPCNLMEVIFILQRWKLWGNENL 770
V L++E+ +L DRE L IF G++ LP N+ +I + +
Sbjct: 923 -NDSSVQDLLDEEYTQLVADRELLCKFIFPKGDARWPLPVNVQRIIQNALQIFHLEAKKP 981
Query: 771 RFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQ 830
L + + + + K + + + ++ A L + +
Sbjct: 982 TDLLPSDIINGLNELIAK-LTIFRGSDRITRDVQNNATLLFQILLRSKF-----AVKRVI 1035
Query: 831 DTGALMRCSFEETVDVLMDAAAHAEADPMRGV 862
L + +FE + + A P V
Sbjct: 1036 MEYRLNKVAFEWIMGEVEARFQQAVVSPGEMV 1067
Score = 134 bits (338), Expect = 2e-31
Identities = 55/78 (70%), Positives = 67/78 (85%)
Query: 515 TSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEET 574
+++ KE+ V++F G YVNYRHLALLCDVMT++GHLMAITRHGINR +TGALMRCSFEET
Sbjct: 1352 SALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEET 1411
Query: 575 VDVLMDAAAHAEADPMRG 592
V++LMDAAA E D +G
Sbjct: 1412 VEILMDAAASGEKDDCKG 1429
Score = 120 bits (302), Expect = 3e-27
Identities = 66/203 (32%), Positives = 102/203 (50%), Gaps = 37/203 (18%)
Query: 1497 RQIITPQNNRPVMGIVQDTLTAVRKMTKR--DVFLDKVTANTAIYYDPDPQNTVIPEDQE 1554
+ I TP +M + + + + + L VT+ T I+YDPDPQ+TVI ED++
Sbjct: 1112 KNIKTPSLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKD 1171
Query: 1555 FVNVYYEMPDFDP----TRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPL 1610
FV ++ +PD + + SPWLLR+ELDR +M
Sbjct: 1172 FVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKM-------------------------- 1205
Query: 1611 SPTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKM 1670
DKKL+M ++ KI F DL I+++DNA+KL++R RI+ DD K ED + +
Sbjct: 1206 --LDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRK---AEDDDNMI 1260
Query: 1671 EDDMFLRCIEETDRSFVKVDFVE 1693
E+D+FL+ IE + + V
Sbjct: 1261 EEDVFLKTIEGHMLESISLRGVP 1283
Score = 73.6 bits (180), Expect = 5e-13
Identities = 41/132 (31%), Positives = 63/132 (47%), Gaps = 24/132 (18%)
Query: 1489 VENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTV 1548
++ I + P+QI++PQ+N+PVMGIVQDTL VRK + RD FL +
Sbjct: 507 IQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTR----------------- 549
Query: 1549 IPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNT 1608
+N+ +PD+D P I + T K++ I + IN DD +
Sbjct: 550 ----NAVMNIMLWVPDWDGILPPPV---ILKPKVLWTGKQILSLIIPKGINLIRDDDKQS 602
Query: 1609 PLSPTDKKLTME 1620
+PTD + +E
Sbjct: 603 LSNPTDSGMLIE 614
Score = 69.7 bits (170), Expect = 8e-12
Identities = 22/45 (48%), Positives = 35/45 (77%)
Query: 28 PYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQ 72
E+ LG++ ++ARPDWM++TVLPVPP SVRP++ + G++R +
Sbjct: 221 SSEDLAHLGLNEQYARPDWMIITVLPVPPPSVRPSISVDGTSRGE 265
Score = 31.2 bits (70), Expect = 4.2
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 904 PAGMFFGSAATPSSMSPQMTP-WAQSTPAYNALMSPGAAMTPGGPGFSPS 952
P + +PSS +P + S+P+Y+ SP +P P +SP+
Sbjct: 1549 PGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSP-TSPS--YSPTSPSYSPT 1595
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C
4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Length = 395
Score = 235 bits (601), Expect = 2e-68
Identities = 72/280 (25%), Positives = 129/280 (46%), Gaps = 38/280 (13%)
Query: 1122 YEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLV 1181
+ I+ + ++LD + + DK +T++ + + IN + ++ N +
Sbjct: 150 ENVVSSTSIDIASMSIILQLDNEMLKDKGVTVDDVKKAINRLKLGEFVIDESEGNTLNIS 209
Query: 1182 LRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDS 1241
D + + + + ++GI+ I + + +
Sbjct: 210 FA--------------------NIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE- 248
Query: 1242 KKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRK 1301
+++ TDG++L VLS + VD + +N+I EI +V GIEA R+
Sbjct: 249 -----------------YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAARE 291
Query: 1302 SVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETV 1361
+ +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV
Sbjct: 292 IIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTV 351
Query: 1362 DVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 1401
L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 352 KHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTMR 391
Score = 180 bits (457), Expect = 2e-49
Identities = 56/292 (19%), Positives = 117/292 (40%), Gaps = 18/292 (6%)
Query: 594 IQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDK 653
++ + +D V + ++ E+ + +++ + + +
Sbjct: 117 PSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKD 176
Query: 654 YRFDPSNERQLRRIFNEDVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMG 713
+ ++ G+ ++ + + +LR ++ + G
Sbjct: 177 KGVTVDDVKKAINRLKLGEFVIDESEGNTLNISFANIDSIAALFKLRDKILNTKIKGIKG 236
Query: 714 SGDVISELEKEWEKLCEDREALREIFSSGESNVV-LPCNLMEVIFILQRWKLWGNENLRF 772
I + + + + D L + S ++ + N + I +++G E
Sbjct: 237 IKRAIVQKKGDEYIILTDGSNLSGVLSVKGVDIAKVETNNIREIE-----EVFGIE---- 287
Query: 773 LCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDT 832
+ R+ + +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ +
Sbjct: 288 --------AAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKN 339
Query: 833 GALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 884
L R +FE TV L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 340 SVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTMR 391
Score = 129 bits (324), Expect = 6e-32
Identities = 30/77 (38%), Positives = 45/77 (58%)
Query: 516 SVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETV 575
+ +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV
Sbjct: 292 IIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTV 351
Query: 576 DVLMDAAAHAEADPMRG 592
L+DAAA + + +G
Sbjct: 352 KHLLDAAARGDVEEFKG 368
Score = 50.1 bits (119), Expect = 4e-06
Identities = 2/59 (3%), Positives = 19/59 (32%)
Query: 953 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQV 1011
+ ++ + A+ + + L + + ++ + + + + + +
Sbjct: 6 DEKDKSYLEEKVKQASNILPQKIVEDLKNLISNKEVLVTRDEIDKIFDLAIKEYSEGLI 64
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 79.9 bits (196), Expect = 6e-15
Identities = 110/793 (13%), Positives = 220/793 (27%), Gaps = 267/793 (33%)
Query: 680 GDVISELEKEMVDHFSWKQ----LRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREAL 735
D++S E VD+F K + I +++ + ++ S D +S + + L +E +
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 736 REIFSSGESNVVLPCNLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQ 795
+ F VL N F++ K + + M T
Sbjct: 79 VQKFVEE----VLRINYK---FLMSPIK-------------------TEQRQPSMMTR-- 110
Query: 796 FYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAE 855
+Y+ R D + + ++ ++R + L A E
Sbjct: 111 ---MYIEQR------DRLYNDNQV--FAKYNVSR-----------LQPYLKLRQAL--LE 146
Query: 856 ADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFGSAATP 915
P + V +I G + G + + C + M +F
Sbjct: 147 LRPAKNV---LIDG----VL-GSGKTWVALDVCLS---YKVQCKM---DFKIF------- 185
Query: 916 SSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGFSPSVAGEDQLSKQANENATLLFQCLV 975
W ++ +P E L LL+Q +
Sbjct: 186 ---------W----------LNLKNCNSP-----------ETVLEMLQK----LLYQ--I 209
Query: 976 RSTLCTKL-VAENYRLSSEAFEWLVGEIENRFQQAQVIAC--VGQQNVEGKRI--PFGFR 1030
++ + N +L + E+ + C V NV+ + F
Sbjct: 210 DPNWTSRSDHSSNIKLR---IHSIQAELRRLLKSKPYENCLLV-LLNVQNAKAWNAFNLS 265
Query: 1031 KRTL----PHFIKDDYGPESRGFVE-NSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV 1085
+ L + D + + + + LTP E
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE------------------VKS-- 305
Query: 1086 NVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRIS--PWLLRIELDR 1143
L Y D PQ+ +P E+ +P R+S +R L
Sbjct: 306 -----LL------LKYLDCRPQD--LPR---------EVLTTNPRRLSIIAESIRDGLAT 343
Query: 1144 ----KRMTDKKLTMEAISEKINA--------GFGDDLNCIFNDD-NAEKLVLRIRIMNSD 1190
K + KLT I +N F D L+ +F + ++L + +
Sbjct: 344 WDNWKHVNCDKLT-TIIESSLNVLEPAEYRKMF-DRLS-VFPPSAHIPTILLSLIWFDVI 400
Query: 1191 DSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITES 1250
D V+K+ +E + + + K ++
Sbjct: 401 K---SDVMVVVNKLHK---YSLVEKQPKE----------STISIPSIYLELKVKL----- 439
Query: 1251 GEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICE------IFQVLG--IEAVRKS 1302
+ +L + + + P S+D+ + +G ++ +
Sbjct: 440 ------------ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHP 487
Query: 1303 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1362
+ F +++++R L K I +G+++ +
Sbjct: 488 ERMTL-----FRMVFLDFRFLE-------QK-----IRHDSTAWNASGSIL--------N 522
Query: 1363 VLMDAAAH----AEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMM 1418
L + + DP N I+ LP++ +L+ K D + I L
Sbjct: 523 TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEE---NLICS--KYTDLLRIALMA--- 574
Query: 1419 GGPAGMFFGSAAT 1431
F A
Sbjct: 575 --EDEAIFEEAHK 585
Score = 73.3 bits (179), Expect = 6e-13
Identities = 106/720 (14%), Positives = 215/720 (29%), Gaps = 206/720 (28%)
Query: 1015 VGQQNVEGKRIPFGFRKRTLPHFIKD-DYGPESRGFVENSYLAGLTPSEFFFHAMGGREG 1073
G+ + K I F F+ + D V++ + L+ E
Sbjct: 11 TGEHQYQYKDILSVF----EDAFVDNFDCK-----DVQDMPKSILSKEE----------- 50
Query: 1074 LIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRIS 1133
ID + + + V+ + LF + + V Q+FV ++
Sbjct: 51 -IDHIIMSKDAVSGTLRLFWTLLSK-------QEEMV----QKFVEEVLR-INY------ 91
Query: 1134 PWLL-RIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNA--EKLVLRIRIMNSD 1190
+L+ I + + E+ + + D N +F N + L++R
Sbjct: 92 KFLMSPI---KTEQRQPSMMTRMYIEQRDRLYND--NQVFAKYNVSRLQPYLKLR----- 141
Query: 1191 DSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITES 1250
A+ ++ + + G+ GK ++ L S K +
Sbjct: 142 --------QALLELRPAKNV-----------LIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Query: 1251 GEFKAIADWL---LETDGTSLMKVLSE--RDVDPVRTFSNDICEIFQVLGIEAVRKSVEK 1305
F WL +++++L + +DP T +D + L I +++ + +
Sbjct: 183 KIF-----WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK-LRIHSIQAELRR 236
Query: 1306 EMNTVLQFYGLYVNYRHLALLC--DVMTAKGHLMA---------ITRHGINRQDTGALMR 1354
L Y N LL +V AK A TR +Q T L
Sbjct: 237 -----LLKSKPYEN----CLLVLLNVQNAK-AWNAFNLSCKILLTTR---FKQVTDFL-- 281
Query: 1355 CSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPR-MGTGCFDLLLDAEKCKDGIEIPL 1413
S T + +D ++ + + L + + DL + P
Sbjct: 282 -SAATTTHISLD-------HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT-----NPR 328
Query: 1414 ATGMMGGPAGMFFGSAATPSSIPGPPAW-YPIHIAISLLSRFTTVI--CIYTLKTFLEMK 1470
++ S G W H+ + TT+I + L+ E +
Sbjct: 329 RLSIIAE------------SIRDGLATWDNWKHVNCD---KLTTIIESSLNVLEP-AEYR 372
Query: 1471 D-FKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIV------QDTLTAVRKMT 1523
F + L++ + H+ ++ ++ D + V K+
Sbjct: 373 KMFDR----------LSVFPPSAHIPTI----------LLSLIWFDVIKSDVMVVVNKLH 412
Query: 1524 KRDVFLDKVTANTAIYYDPDPQ-NTVIPEDQE------FVNVYYEMPDFDPTRISP---- 1572
K + ++K + P + + E V+ Y FD + P
Sbjct: 413 KYSL-VEK-QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLD 470
Query: 1573 ----WLLRIELDRKRMTDKKLTMEA-------ISEKI-NAGFGDDLNTPLSPT--DKKLT 1618
+ L ++ + +KI + + + + T K
Sbjct: 471 QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFY 530
Query: 1619 MEAISEKINAGFGDDLNCI--FNDDNAEKLV-------LRIRIMNSDDSKMQDEEDAVDK 1669
I + + +N I F E L+ LRI +M D++ ++ V +
Sbjct: 531 KPYICDNDPK-YERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 65.6 bits (159), Expect = 1e-10
Identities = 74/615 (12%), Positives = 180/615 (29%), Gaps = 169/615 (27%)
Query: 214 YLEIQMAIKKAK-EDVIEVIQKAHNMDLE-------PTP-------GHSIGIGDTIADPQ 258
+++ + + + +D++ V + A + + P H I D ++
Sbjct: 6 HMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVS--G 63
Query: 259 TYLEIQMAIKKAKEDVIEVIQKAHNMD---------LEPTPGNTLRQTFENQVNRILNDA 309
T + K +E V + +++ ++ E + + + + Q +R+ ND
Sbjct: 64 TLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 310 ---------RDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIAC-VGQQNVEGKRI 359
R + +++L E K +++ G GS +A V ++
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSG---KTWVALDVCLSYKVQCKM 180
Query: 360 PFG-----FRKR-----------TLPHFIKDDYGPESRGFVENSYLAGLTPSEF--FFHA 401
F + L + I ++ S +E +
Sbjct: 181 DFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS 240
Query: 402 MGGREGLI---DTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGE--DG 456
L+ + V+ A+ A C + L+ R+ + D
Sbjct: 241 KPYENCLLVLLN--VQNAKA-------WNAFN-----LSCKI------LLTTRFKQVTDF 280
Query: 457 LCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNV-----SSLRR-VVNSKPLLIG 510
L H +D +++ P + L L R V+ + P +
Sbjct: 281 LSAATTTHISLDHHSMT---------LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331
Query: 511 -CWKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMR- 568
+ ++ + +VN L ++ + +N + A R
Sbjct: 332 IIAESI---RDGLATWDNW-KHVNCDKLT----------TIIESS---LNVLEP-AEYRK 373
Query: 569 ----CS-FEETVDVLMDA-----AAHAEADPMR---GYIQRRLIK---AMESVMVHYDCT 612
S F + + ++D M + L++ ++ +
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP---- 429
Query: 613 VRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYR----FDPSNERQLRR-- 666
I L +++ H+ D Y FD +
Sbjct: 430 -------SIYLEL-----------KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Query: 667 -IFNEDV--LRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGS-GDVISELE 722
++ L+ + + ++ +D F + + ++I ++ GS + + +L+
Sbjct: 472 YFYSHIGHHLKN-IEHPERMTLFRMVFLD-FRFLE-QKIRHDSTAWNASGSILNTLQQLK 528
Query: 723 KEWEKLCEDREALRE 737
++ D + E
Sbjct: 529 F-YKPYICDNDPKYE 542
Score = 41.0 bits (95), Expect = 0.004
Identities = 86/563 (15%), Positives = 168/563 (29%), Gaps = 168/563 (29%)
Query: 20 YAWYVVP--------------YPYEESIILGMDPKFA-----RPD--WMLVTVLPVPPLS 58
Y + + P Y + + + FA R L L L
Sbjct: 91 YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQAL----LE 146
Query: 59 VRPA--VVMHGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVN 116
+RPA V++ G + G +GK + + +
Sbjct: 147 LRPAKNVLIDG------------VL-----G--------------SGKTW--VAL----D 169
Query: 117 MTRTHSTHPDDEDSGPYQWISPG---DTKVVVEH-GSLLMGI---LCKKSLGTSSGSL-L 168
+ ++ D + W++ + V+E LL I +S +S+ L +
Sbjct: 170 VCLSYKVQ-CKMDFKIF-WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI 227
Query: 169 HICFLELGHEVCGRFYGNIQTVVNN-W-------------LLLEGHSIGIGDTIADPQTY 214
H EL + + Y N V+ N +LL + D ++ T
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTT 287
Query: 215 LEIQMAIKKA--KEDVIEVIQKAHNMDLEPTP-----GH----SIGIGDTIADP----QT 259
++V ++ K + + P + SI I ++I D
Sbjct: 288 HISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI-IAESIRDGLATWDN 346
Query: 260 YLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFEN------------QVNRIL- 306
+ + + + +I+ + N LEP R+ F+ + ++
Sbjct: 347 WKHVN------CDKLTTIIESSLN-VLEP---AEYRKMFDRLSVFPPSAHIPTILLSLIW 396
Query: 307 -----NDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN-------- 353
+D K SL E K S I+I + + +
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQP---------KESTISIPSIYLELKVKLENEYALHR 447
Query: 354 --VEGKRIPFGFRKRTLPHFIKDDYGPESRGF----VENSYLAGLTPSEFF-FHAMGGRE 406
V+ IP F L D Y G +E+ L F F + +
Sbjct: 448 SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK- 506
Query: 407 GLIDTAVKTAETGYIQRRL--IKAMESVMVHYDCTVRNSVGQLIQ--LRYGEDGLCGEAV 462
+ + +G I L +K + + D V ++ + E+ +C
Sbjct: 507 -IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICS--- 562
Query: 463 EHQRIDTVALSHKK---FEDKYR 482
++ + +AL + FE+ ++
Sbjct: 563 KYTDLLRIALMAEDEAIFEEAHK 585
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase
subunit A', DNA-directed...; transcription, fusion
protein, chimera protein, multiprotein; 3.30A
{Pyrococcus furiosus}
Length = 436
Score = 69.7 bits (171), Expect = 3e-12
Identities = 19/45 (42%), Positives = 34/45 (75%)
Query: 28 PYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQ 72
P ++ +LG+DP+ +RP+WM++TVLPVPP++ RP++ + R +
Sbjct: 255 PDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAE 299
>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 = 60.8 bits (147), Expect = 5e-09
Identities = 74/379 (19%), Positives = 126/379 (33%), Gaps = 124/379 (32%)
Query: 137 SPGDTKVVVEHGSLLMGILCKKS-------LGTSSGSLLHICFLELGH-----EVCGRFY 184
+ D + V G ++ L S L + S I ++L H ++ G
Sbjct: 201 TTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP 260
Query: 185 GNIQTVVNNWLLLEGHSIGI--GDTIADPQTYLEIQMAIKKAKEDVIEVI-------QKA 235
G +++ + GHS G+ IA+ ++ ++++KA I V+ +A
Sbjct: 261 GELRSYLKG---ATGHSQGLVTAVAIAETDSWESFFVSVRKA----ITVLFFIGVRCYEA 313
Query: 236 H-NMDLEPTPGH-SIGIGDTIADPQTYLEIQM-AIKK-AKEDVIEVIQKAHNMDLEPTPG 291
+ N L P+ S+ + + P M +I +E V + + K N L
Sbjct: 314 YPNTSLPPSILEDSLENNEGVPSP-------MLSISNLTQEQVQDYVNKT-NSHLPA--- 362
Query: 292 NTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGS----KGSNINISQVIA 347
QV I SL N K +VV+G G N+ + + A
Sbjct: 363 -------GKQVE-I--------------SL--VNGAKNLVVSGPPQSLYGLNLTLRKAKA 398
Query: 348 CVGQ-QNVEGKRIPFGFRK-----RTLP-----HFIKDDYGPESRGFVENSYLAG----- 391
G Q+ RIPF RK R LP H S L
Sbjct: 399 PSGLDQS----RIPFSERKLKFSNRFLPVASPFH---------S------HLLVPASDLI 439
Query: 392 ---LTPSEFFFHAMGGREGLIDTAVKTAETGY--------IQRRLIKAMESVMVHYDCTV 440
L + F+A + + V G I R++ + + V ++ T
Sbjct: 440 NKDLVKNNVSFNA----KDI-QIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTT 494
Query: 441 RNSVGQLIQLRYGEDGLCG 459
+ ++ +G G G
Sbjct: 495 QFKATHILD--FGPGGASG 511
Score = 59.3 bits (143), Expect = 1e-08
Identities = 100/642 (15%), Positives = 184/642 (28%), Gaps = 207/642 (32%)
Query: 360 PFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETG 419
P TL H G +E+ L P+ FF A L + K
Sbjct: 8 PL-----TLSH-----------GSLEHVLL---VPTASFFIA----SQLQEQFNKI---- 40
Query: 420 YIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVE----HQRIDTVALSHK 475
L + E + T + +L+ ++ G VE Q + L
Sbjct: 41 -----LPEPTEGFAADDEPT---TPAELV-GKF--LGYVSSLVEPSKVGQFDQVLNLCLT 89
Query: 476 KFEDKY-----------RFDPSNERPTLRNVSSLR-----RVVNSKPL-------LIGCW 512
+FE+ Y + N+ ++ ++ R++ +P L
Sbjct: 90 EFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL---- 145
Query: 513 KLTSVEKEMNTV-LQFYG-------------LYVNYRHL-ALLCDVMTAKGHLMAITRHG 557
+V + + F G LY Y L L L + R
Sbjct: 146 -FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAE--TLSELIRT- 201
Query: 558 INRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGYIQRRLIKAMESV-------MVHYD 610
D + F + +++ ++ + P + Y L+ S + HY
Sbjct: 202 --TLDAEKV----FTQGLNI-LEWLENPSNTPDKDY----LLSIPISCPLIGVIQLAHYV 250
Query: 611 CTVRN---SVGQLIQLRYGEDGLCGEAVEHQRIDTVALSH-KKFEDKYRFDPSNERQLRR 666
T + + G+L G G + + + VA++ +E F S + +
Sbjct: 251 VTAKLLGFTPGELRSYLKGATG-HSQGL----VTAVAIAETDSWES---FFVSVRKAITV 302
Query: 667 IFNEDVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMG--------SGDVI 718
+F +G + + L ED L G S
Sbjct: 303 LF-------FIGV---------RCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQ 346
Query: 719 SELEKEWEKLCEDREALREIFSS---GESNVVL---PCNLMEVIFILQRWKLWGNENLRF 772
+++ K A +++ S G N+V+ P +L + L++ K +
Sbjct: 347 EQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD--- 403
Query: 773 LCKIIFVLSVRKSVEKEMNTVLQFYGLYVN--YRHLALLCDV------------MTAKGH 818
+I F S RK +F L V + H LL ++
Sbjct: 404 QSRIPF--SERKLK-----FSNRF--LPVASPF-HSHLLVPASDLINKDLVKNNVSFNAK 453
Query: 819 LMAI----TRHGINRQD-----TGALMRCSFEETVDVLMDAAAHAEA------DPMRGVS 863
+ I T G + + + ++ C V + +A P
Sbjct: 454 DIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK--WETTTQFKATHILDFGP----- 506
Query: 864 ENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPA 905
G +G L K G+ + +A + P
Sbjct: 507 -----GGASGLGV-----LTHRNKDGTGVRVIVAGTLDINPD 538
Score = 56.2 bits (135), Expect = 1e-07
Identities = 108/599 (18%), Positives = 172/599 (28%), Gaps = 209/599 (34%)
Query: 645 LSHKKFEDKYRFD-PSNE----RQLRRIF--------------NEDV-LRELMGS--GDV 682
LSH E + P+ QL+ F +E EL+G G V
Sbjct: 11 LSHGSLE--HVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYV 68
Query: 683 ISELEKEMVDHFSW--KQLRRIFNEDVLR---------ELMGSGDVISELEKEWEK---- 727
S +E V F F L +L+ D KE K
Sbjct: 69 SSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYIT 128
Query: 728 --LCEDRE-------ALREIFSSGESNVVLPCNLMEVIFILQRWKLWGNENLRFLCKIIF 778
+ R AL G + +V IF Q GN + F
Sbjct: 129 ARIMAKRPFDKKSNSALFRAVGEGNAQLVA-------IFGGQ-----GNTDDYF------ 170
Query: 779 VLSVRKSVEKEMNTVLQFYGLYVNYRHL-ALLCDVMTAKGHLMAITRHGINRQDTGALMR 837
+E L+ LY Y L L L + R D +
Sbjct: 171 ---------EE----LR--DLYQTYHVLVGDLIKFSAE--TLSELIRT---TLDAEKV-- 208
Query: 838 CSFEETVDV---LMDAAAHAEAD-----PMRGVSENII-MGQLPRMGTGCFDLLLDAEKC 888
F + +++ L + + + D P +S +I + QL + +
Sbjct: 209 --FTQGLNILEWLENPSNTPDKDYLLSIP---ISCPLIGVIQL-----AHYVVTAKLLGF 258
Query: 889 KDGIEIPLATGMMGGPAGMFFGSAATPSSMSPQMTPWA----QSTPAYNALMS------- 937
G G G G+ A + + W A L
Sbjct: 259 TPGELRSYLKGATGHSQGLV---TAVAIAETDS---WESFFVSVRKAITVLFFIGVRCYE 312
Query: 938 --PGAAMTP-----------GGPGFSP--SVAG--EDQLSKQANE-NATLLFQCLVRSTL 979
P ++ P G P SP S++ ++Q+ N+ N+ L +
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVP--SPMLSISNLTQEQVQDYVNKTNSHLP----AGKQV 366
Query: 980 CTKLV--AENYRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHF 1037
LV A+N +S + L G + ++A+ + + Q RIPF RK F
Sbjct: 367 EISLVNGAKNLVVSGPP-QSLYG-LNLTLRKAKAPSGLDQ-----SRIPFSERK---LKF 416
Query: 1038 IKDDYGPESRGFVENSYLAGLTPSEFFFHA--MGGREGLIDTAVK------TAETVNVLV 1089
N +L +P FH+ + LI+ + A+ + + V
Sbjct: 417 -------------SNRFLPVASP----FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV 459
Query: 1090 FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMP---------------DFDPTRIS 1133
+ +T D + I E V+ +P DF P S
Sbjct: 460 Y------DTFDGSDLRVLSGSISER--IVDCIIRLPVKWETTTQFKATHILDFGPGGAS 510
Score = 52.0 bits (124), Expect = 2e-06
Identities = 120/718 (16%), Positives = 215/718 (29%), Gaps = 252/718 (35%)
Query: 57 LSVRPAVVMHGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTG----KQVFSLIIP 112
S RP + HGS +L P + ++ F+ I+P
Sbjct: 4 YSTRPLTLSHGSLE---------------------HVLLVPTASFFIASQLQEQFNKILP 42
Query: 113 GNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLL---MGILCKKSLGTSSGSLLH 169
T DDE + P E L+ +G + + G
Sbjct: 43 -----EPTEGFAADDEPTTP------------AE---LVGKFLGYVSSLVEPSKVGQFDQ 82
Query: 170 ICFLELGHEVCGRFYGNIQTVVNNWLLLEG---HSIGIGDTIADPQTYLEIQMAIK---K 223
+ L L F LEG H++ + T ++ + IK
Sbjct: 83 VLNLCLTE-----FENCY---------LEGNDIHALAAKLLQENDTTLVKTKELIKNYIT 128
Query: 224 AKEDVIEVIQKAHNMDL-EPTPGHSIGI-------GDTIADPQTYL-EIQMAIKKAKEDV 274
A+ K N L + + G+T Y E++ + V
Sbjct: 129 ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNT----DDYFEELRDLYQTYHVLV 184
Query: 275 IEVIQKAHNM--DLEPTPGNTLRQTFEN--QVNRILNDARDKTGGSAKKSLTEYNNLKAM 330
++I+ + +L T + + F + L + + +Y L
Sbjct: 185 GDLIKFSAETLSELIRTTLDA-EKVFTQGLNILEWLENPSNTPD-------KDY--L--- 231
Query: 331 VVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLA 390
+I IS + V Q L H++ + L
Sbjct: 232 -------LSIPISCPLIGVIQ----------------LAHYVVT------------AKLL 256
Query: 391 GLTPSEFFFHAMG--GR-EGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQL 447
G TP E + G G +GL+ TAV AET + ES + +VR ++ L
Sbjct: 257 GFTPGELRSYLKGATGHSQGLV-TAVAIAET--------DSWES----FFVSVRKAITVL 303
Query: 448 IQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPT--LRNVSSLRRVVNSK 505
+ G+ ++ +L ED + + P+ L ++S+L +
Sbjct: 304 FFI-----GVRC----YEAYPNTSLPPSILEDS--LENNEGVPSPML-SISNLTQE---- 347
Query: 506 PLLIGCWKLTSVEKEMNTVL----QFY-GLYVN-YRHLALLCDVMTAKGH---LMAITRH 556
++ + N+ L Q L VN ++L V++ G L +
Sbjct: 348 -------QVQDYVNKTNSHLPAGKQVEISL-VNGAKNL-----VVS--GPPQSLYGLNLT 392
Query: 557 --------GINRQDTGALMRCSFEE----------TVDV------LMDAAAHAEADPMRG 592
G++ Q R F E V L+ A+ D ++
Sbjct: 393 LRKAKAPSGLD-QS-----RIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKN 446
Query: 593 YIQRRLIKAME-SVMVHYD-------CTVRNSVGQ-LIQLRYGEDGLCGEAVEHQRIDTV 643
+ A + + V YD + S+ + ++ + V+ +
Sbjct: 447 NVS---FNAKDIQIPV-YDTFDGSDLRVLSGSISERIVDC------IIRLPVKWETTTQF 496
Query: 644 ALSHKKFEDKYRFDPSNERQLRRIFNEDVLRELMGSG-DVI--SELEKEMVDHFSWKQ 698
+H D F P L + + R G+G VI L+ D + +KQ
Sbjct: 497 KATH--ILD---FGPGGASGLGVLTH----RNKDGTGVRVIVAGTLDINPDDDYGFKQ 545
Score = 52.0 bits (124), Expect = 2e-06
Identities = 35/255 (13%), Positives = 72/255 (28%), Gaps = 79/255 (30%)
Query: 665 RRIFNE--DVLRELMG-S-GDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISE 720
+ ++N + ++ G S D++ + HF ++ +RI RE +
Sbjct: 1643 QDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRI------RENYSAMI---- 1692
Query: 721 LEKEWEKLCEDREALREIFSSGESNVVLPCNLMEVIFILQRWKLWGNENLRFLCKI---- 776
+E + + + +IF + + F + L +
Sbjct: 1693 ----FETIVDGKLKTEKIFKE------INEHSTSYTF-------RSEKGLLSATQFTQPA 1735
Query: 777 IFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGH-------LMAITRHGINR 829
+ ++ L+ GL A GH L ++
Sbjct: 1736 LTLMEK------AAFEDLKSKGLIPADATFA---------GHSLGEYAALASL------- 1773
Query: 830 QDTGALMRCSFEETVDVLM---DAAAHAEADPMRGVSENIIMGQLP-RMGTGCFDLLLDA 885
+ S E V+V+ A G S ++ P R+
Sbjct: 1774 --ADVM---SIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASF-----SQ 1823
Query: 886 EKCKDGIE-IPLATG 899
E + +E + TG
Sbjct: 1824 EALQYVVERVGKRTG 1838
Score = 44.3 bits (104), Expect = 5e-04
Identities = 43/249 (17%), Positives = 71/249 (28%), Gaps = 90/249 (36%)
Query: 1224 QGIEAIGKVYM--HLPQTDSKKRIIITESGEFKAI---ADW-LLETDGTSLMKVLSERDV 1277
QG + G M L +T S + + AD +T G S++ ++
Sbjct: 1624 QGSQEQG---MGMDLYKT----------SKAAQDVWNRADNHFKDTYGFSILDIVIN--- 1667
Query: 1278 DPVR-TF------SNDICEIFQVLGIEA------VRKSVEKEMN---TVLQFYG----L- 1316
+PV T I E + + E + + KE+N T F L
Sbjct: 1668 NPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS 1727
Query: 1317 -------------YVNYRHL----ALLCDVMTAKGH-------LMAITRHGINRQDTGAL 1352
+ L + D A GH L ++ +
Sbjct: 1728 ATQFTQPALTLMEKAAFEDLKSKGLIPADATFA-GHSLGEYAALASLA---------DVM 1777
Query: 1353 MRCSFEETVDVLM---DAAAHAEADPMRGVSENIIMGQLP-RMGTGCFDLLLDAEKCKDG 1408
S E V+V+ A G S ++ P R+ E +
Sbjct: 1778 ---SIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASF-----SQEALQYV 1829
Query: 1409 IE-IPLATG 1416
+E + TG
Sbjct: 1830 VERVGKRTG 1838
Score = 43.5 bits (102), Expect = 7e-04
Identities = 69/408 (16%), Positives = 116/408 (28%), Gaps = 162/408 (39%)
Query: 1431 TPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKTFLEMKDFKKPPQKGFGLLTLTLMVE 1490
PS+ P Y + I IS P L+ + +
Sbjct: 221 NPSNTPDKD--YLLSIPISC------------------------P------LIGVIQLA- 247
Query: 1491 NIHVTPRQI-ITPQNNRPVM----GIVQDTLTA--VRKMTKRDVFLDKVTANTAI----- 1538
+ VT + + TP R + G Q +TA + + + F + AI
Sbjct: 248 HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFV--SVRKAITVLFF 305
Query: 1539 -------YYDPDPQNTVIPED-QEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLT 1590
Y P ++ P ++ + +P SP +L I LT
Sbjct: 306 IGVRCYEAY---PNTSLPPSILEDSLENNEGVP-------SP-MLSI---------SNLT 345
Query: 1591 MEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKIN-------AGFGDDLNCIFNDDNA 1643
E + + + + N+ L P K++ IS +N +G L
Sbjct: 346 QEQVQDYV-----NKTNSHL-PAGKQV---EIS-LVNGAKNLVVSGPPQSL--------- 386
Query: 1644 EKLVLRIRIMNSDDSKMQDE--------------------------EDAVDKMEDDMFLR 1677
L L +R + Q A D + D+
Sbjct: 387 YGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDL--- 443
Query: 1678 CIEETDRSFVKVDFVEP-KDLVEWKTLLKQMHSDFCLAQIIKCIPTLSRHLGSDCSSNEK 1736
+ + SF D P D + L ++ S +I+ CI L E
Sbjct: 444 --VKNNVSFNAKDIQIPVYDTFDGSDL--RVLSGSISERIVDCIIRLPVKW-------ET 492
Query: 1737 -VRYGKLHIPEIFFRTLIIVILLRLFLHF-PLKLYGFGDIFDTRSQNG 1782
++ HI L F P G G + R+++G
Sbjct: 493 TTQFKATHI-----------------LDFGPGGASGLGVLTH-RNKDG 522
Score = 43.1 bits (101), Expect = 0.001
Identities = 98/636 (15%), Positives = 183/636 (28%), Gaps = 215/636 (33%)
Query: 1026 PFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV 1085
P TL H G +E+ L P+ FF A L +
Sbjct: 8 PL-----TLSH-----------GSLEHVLL---VPTASFFIA----SQLQEQ-------- 36
Query: 1086 NVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVY--YEMPDFDPTRISPW--LLRIEL 1141
F + T + D T E V + Y +P+++ + +L + L
Sbjct: 37 ----FNKILPEPTEGFAADDEPTTPA----ELVGKFLGYVSSLVEPSKVGQFDQVLNLCL 88
Query: 1142 DRKRMTDKKLTMEAISEKINAGF--GDDLNCI---FNDDNAEKLVLRIRIMNSDDSKMQD 1196
+ G+D++ + +N LV ++ + +
Sbjct: 89 TE----------------FENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 1197 EEDAVDKMEDDMFLRCIEANMLSDMTL---QGI------E--AIGKVYMHLPQTDSKKRI 1245
+ DK + R + + + QG E + + Y L +
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVG-----DL 187
Query: 1246 IITESGEFKAIADWLLETD-----GTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVR 1300
I + + L+ + G ++++ L P + + L +
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDY----------LLSIPI- 236
Query: 1301 KSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEET 1360
S + V+Q +Y V+TAK G + + ++ + +
Sbjct: 237 -SCP--LIGVIQL----AHY--------VVTAK-------LLGFTPGELRSYLKGATGHS 274
Query: 1361 VDVLMDAAAHAEADPMRGVSENI--IMGQLPRMGTGC---F-DLLLDAEKCKDGIEIPLA 1414
++ A A AE D ++ + L +G C + + L +D +E
Sbjct: 275 QGLVT-AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLE---- 329
Query: 1415 TGMMGGPAGMFFGSAATPSSIPGPP------------AWYPI--HIAISLL-SRFTTVIC 1459
G P+ M SI + P + ISL+ V+
Sbjct: 330 -NNEGVPSPML--------SISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVS 380
Query: 1460 IYTLKTFLEMKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAV 1519
PPQ L L L + Q+ P +
Sbjct: 381 --------------GPPQ---SLYGLNLTLRKAKAPSGLD---QSRIPF---------SE 411
Query: 1520 RKMTKRDVFLDKVTANTAIYYDP------DPQNTVIPEDQEFVNVYYE-----MPDFDPT 1568
RK+ + FL V + P P + +I +D NV + +P +D
Sbjct: 412 RKLKFSNRFL-PVAS-------PFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTF 463
Query: 1569 --------------RISPWLLRIELDRKRMTDKKLT 1590
RI ++R+ + + T K T
Sbjct: 464 DGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKAT 499
Score = 42.7 bits (100), Expect = 0.001
Identities = 55/306 (17%), Positives = 95/306 (31%), Gaps = 113/306 (36%)
Query: 445 GQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFED------KYRFDPSNERPTLRNVSSL 498
G+ I+ Y + E + D + K F++ Y F L
Sbjct: 1681 GKRIRENY--SAMIFETIV----DGKLKTEKIFKEINEHSTSYTFRSEKGL--------L 1726
Query: 499 RRVVNSKPLLIGCWKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGH-------LM 551
++P L +EK L+ GL A GH L
Sbjct: 1727 SATQFTQPAL-----TL-MEKAAFEDLKSKGLIPADATFA---------GHSLGEYAALA 1771
Query: 552 AITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGYIQRRLIKAMESVMVHYDC 611
++ + S E V+V+ RG M+ V V D
Sbjct: 1772 SLA---------DVM---SIESLVEVV-----FY-----RG-------MTMQ-VAVPRDE 1801
Query: 612 TVRNSVGQLIQLRYGE--DGLCGEAVEHQRIDTVALSHKKF-EDKYRFDPSNERQLRRIF 668
R++ G +I + G EA++ ++ V E N +
Sbjct: 1802 LGRSNYG-MIAINPGRVAASFSQEALQ-YVVERVGKRTGWLVE------IVN-------Y 1846
Query: 669 NED----VLRELMGSGDVISELEK--EMVDHFSWKQLRRIFNEDVLRELMGSGDVISELE 722
N + V +GD+ + L+ +++ L++I D++ EL S +S LE
Sbjct: 1847 NVENQQYVA-----AGDLRA-LDTVTNVLNFIK---LQKI---DII-ELQKS---LS-LE 1889
Query: 723 KEWEKL 728
+ L
Sbjct: 1890 EVEGHL 1895
Score = 40.8 bits (95), Expect = 0.006
Identities = 35/185 (18%), Positives = 61/185 (32%), Gaps = 77/185 (41%)
Query: 199 GHSIG-------IGDTIADPQTYLEIQMAIKKAKEDVIEV-------IQKAHNMDLEPTP 244
GHS+G + D + I E ++EV +Q A P
Sbjct: 1761 GHSLGEYAALASLAD-------VMSI--------ESLVEVVFYRGMTMQVA-------VP 1798
Query: 245 GHSIGIGDT--IA-DPQTYLEIQMAIKKAKED---VIEVIQKAHNMDLEPTPGNTLRQTF 298
+G + IA +P ++A ++E V+E + K +E
Sbjct: 1799 RDELGRSNYGMIAINPG-----RVAASFSQEALQYVVERVGKRTGWLVEI---------- 1843
Query: 299 ENQVNRILNDARDKT---GG--SAKKSLTEY-NNLKAMVVAGSKGSNINISQVIACVGQQ 352
VN N ++ G A ++T N +K I+I ++ + +
Sbjct: 1844 ---VN--YN-VENQQYVAAGDLRALDTVTNVLNFIKLQ--------KIDIIELQKSLSLE 1889
Query: 353 NVEGK 357
VEG
Sbjct: 1890 EVEGH 1894
Score = 36.6 bits (84), Expect = 0.11
Identities = 32/210 (15%), Positives = 47/210 (22%), Gaps = 94/210 (44%)
Query: 869 GQLPRMGTG--CFDLLLDA----EKCKDGIEIPLATGMMGGPAGMFFGSAATPSSMSPQM 922
G+ R F+ ++D EK I + G+
Sbjct: 1681 GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS------------A 1728
Query: 923 TPWAQSTPA-------------------------------YNALMSPGAAMTPGGPGFSP 951
T + Q PA Y AL S M+
Sbjct: 1729 TQFTQ--PALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMS-----I-- 1779
Query: 952 SVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAE------NYR------------LSSE 993
E + ++F R V NY S E
Sbjct: 1780 ----ESLVE--------VVFY---RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQE 1824
Query: 994 AFEWLVGEIENRFQQAQVIA---CVGQQNV 1020
A +++V + R I QQ V
Sbjct: 1825 ALQYVVERVGKRTGWLVEIVNYNVENQQYV 1854
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 57.7 bits (140), Expect = 3e-08
Identities = 46/205 (22%), Positives = 86/205 (41%), Gaps = 53/205 (25%)
Query: 247 SIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFE---NQVN 303
+IGI D P+ +++A + I++A+ M T +QV
Sbjct: 689 TIGIDD-AVIPEEKQRY---LEEADRKL-RQIEQAYEMGF---------LTDRERYDQVI 734
Query: 304 RILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQV------IACVGQQNV 354
++ + +K + + E +N L M +G++G+ I Q+ +
Sbjct: 735 QLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQ-----KP 789
Query: 355 EGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVK 414
G+ +P ++ +S+ GLT E+F + G R+G DTA++
Sbjct: 790 SGETFE-------VP--VR------------SSFREGLTVLEYFISSHGARKGGADTALR 828
Query: 415 TAETGYIQRRLIK-AMESVMVHYDC 438
TA++GY+ R+L+ A E V+ DC
Sbjct: 829 TADSGYLTRKLVDVAHEIVVREADC 853
Score = 46.1 bits (110), Expect = 1e-04
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 839 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1180 SFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1218
Score = 46.1 bits (110), Expect = 1e-04
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1394
SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1180 SFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1218
Score = 37.3 bits (87), Expect = 0.060
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTAE 1083
GLT E+F + G R+G DTA++TA+
Sbjct: 805 GLTVLEYFISSHGARKGGADTALRTAD 831
Score = 34.2 bits (79), Expect = 0.59
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 43 RPDWMLVTVLPVPPLSVRPAVVMHG 67
RP+WM++ +PV P +RP V + G
Sbjct: 248 RPEWMILEAVPVLPPDLRPMVQVDG 272
Score = 30.3 bits (69), Expect = 7.4
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 570 SFEETVDVLMDAAAHAEADPMRGY----IQRRLIKA 601
SF+ T VL +AA + D + G I RLI A
Sbjct: 1180 SFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPA 1215
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 56.7 bits (137), Expect = 7e-08
Identities = 46/207 (22%), Positives = 90/207 (43%), Gaps = 53/207 (25%)
Query: 245 GHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFE---NQ 301
G +IGI D P+ + +++A +++ I++A+ M T +Q
Sbjct: 946 GITIGIDD-AVIPEEKKQY---LEEADRKLLQ-IEQAYEMGF---------LTDRERYDQ 991
Query: 302 VNRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQV------IACVGQQ 352
+ ++ + +K + K+ E +N L M +G++G+ I Q+ +
Sbjct: 992 ILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQ----- 1046
Query: 353 NVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTA 412
G+ +P ++ +S+ GLT E+F + G R+G DTA
Sbjct: 1047 KPSGETFE-------VP--VR------------SSFREGLTVLEYFISSHGARKGGADTA 1085
Query: 413 VKTAETGYIQRRLIK-AMESVMVHYDC 438
++TA++GY+ R+L+ E V+ DC
Sbjct: 1086 LRTADSGYLTRKLVDVTHEIVVREADC 1112
Score = 46.3 bits (110), Expect = 1e-04
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 839 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1439 SFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Score = 46.3 bits (110), Expect = 1e-04
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1394
SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1439 SFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Score = 37.4 bits (87), Expect = 0.059
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTAE 1083
GLT E+F + G R+G DTA++TA+
Sbjct: 1064 GLTVLEYFISSHGARKGGADTALRTAD 1090
Score = 34.8 bits (80), Expect = 0.33
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 43 RPDWMLVTVLPVPPLSVRPAVVMHG 67
RP+WM++ +PV P +RP V + G
Sbjct: 508 RPEWMILEAVPVLPPDLRPMVQVDG 532
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 53.8 bits (130), Expect = 6e-07
Identities = 22/49 (44%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 391 GLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-AMESVMVHYDC 438
GL ++F G R+GL DTA+KTA +GY+ RRL+ A + V+ DC
Sbjct: 766 GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDC 814
Score = 45.3 bits (108), Expect = 2e-04
Identities = 19/39 (48%), Positives = 27/39 (69%)
Query: 839 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ET VL +AA + D +RG+ EN+I+G+L GTG
Sbjct: 1324 SFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Score = 45.3 bits (108), Expect = 2e-04
Identities = 19/39 (48%), Positives = 27/39 (69%)
Query: 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1394
SF+ET VL +AA + D +RG+ EN+I+G+L GTG
Sbjct: 1324 SFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Score = 38.0 bits (89), Expect = 0.036
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTAE 1083
GL ++F G R+GL DTA+KTA
Sbjct: 766 GLNVLQYFISTHGARKGLADTALKTAN 792
Score = 33.4 bits (77), Expect = 0.81
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 43 RPDWMLVTVLPVPPLSVRPAV 63
+P+WM++TVLPV P +RP V
Sbjct: 233 KPEWMILTVLPVLPPDLRPLV 253
>3fd5_A Selenide, water dikinase 1; selenophosphate synthetase, SELD,
ATP-binding, nucleotide-binding, selenium, transferase;
HET: AP2; 1.90A {Homo sapiens} PDB: 3fd6_A*
Length = 394
Score = 35.7 bits (82), Expect = 0.15
Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 18/102 (17%)
Query: 192 NNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIG 251
N + L+ G P+T + + + +E + + I IG
Sbjct: 310 NMFGLMHGT---------CPETSGGLLICL--PREQAARFCAEIKSPKYGEGHQAWI-IG 357
Query: 252 DTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNT 293
+ I I K + +IEV + ++ PTPG T
Sbjct: 358 -IVEKGNRTARI---IDKPR--IIEVAPQVATQNVNPTPGAT 393
>3saj_A Glutamate receptor 1; rossman fold, ION channel, membrane,
transport protein; HET: NAG BMA MAN; 2.50A {Rattus
norvegicus}
Length = 384
Score = 34.0 bits (77), Expect = 0.49
Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 8/86 (9%)
Query: 689 EMVDHFSWKQLRRIFNED--------VLRELMGSGDVISELEKEWEKLCEDREALREIFS 740
++DH+ W+ I++ D VL ++ + R +++
Sbjct: 121 SIIDHYKWQTFVYIYDADRGLSVLQRVLDTAAEKNWQVTAVNILTTTEEGYRMLFQDLEK 180
Query: 741 SGESNVVLPCNLMEVIFILQRWKLWG 766
E VV+ C + IL +
Sbjct: 181 KKERLVVVDCESERLNAILGQIVKLE 206
>3nyb_A Poly(A) RNA polymerase protein 2; polya RNA polymerase, zinc
knuckle protein, RNA surveillance binds to TRF4P/AIR2P
heterodimer; 2.70A {Saccharomyces cerevisiae}
Length = 323
Score = 32.8 bits (74), Expect = 0.91
Identities = 19/109 (17%), Positives = 42/109 (38%), Gaps = 9/109 (8%)
Query: 679 SGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALREI 738
++ L E+ D ++ R E +R IS + + ++L D + +
Sbjct: 14 QKEISDWLTFEIKDFVAYISPSR--EEIEIRN-----QTISTIREAVKQLWPDADL--HV 64
Query: 739 FSSGESNVVLPCNLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVE 787
F S +++ LP + ++ + + NL L + ++ VE
Sbjct: 65 FGSYSTDLYLPGSDIDCVVTSELGGKESRNNLYSLASHLKKKNLATEVE 113
>1y63_A LMAJ004144AAA protein; structural genomics, protein structure
initiative, PSI, SGPP structural genomics of pathogenic
protozoa consortium; HET: ADP; 1.70A {Leishmania major}
SCOP: c.37.1.1
Length = 184
Score = 32.0 bits (72), Expect = 0.96
Identities = 22/151 (14%), Positives = 45/151 (29%), Gaps = 28/151 (18%)
Query: 1149 KKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDM 1208
K E I+ +++ + ++ D+ + +E+D D++ D
Sbjct: 23 KTSMAEMIAAELD-----GFQHLEVGKLVKENHFYTEYDTELDTHIIEEKD-EDRLLD-- 74
Query: 1209 FLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSL 1268
M M +G + L +++ L T L
Sbjct: 75 -------FMEPIMVSRGNHVVDYHSSELFPERWFHMVVV-------------LHTSTEVL 114
Query: 1269 MKVLSERDVDPVRTFSNDICEIFQVLGIEAV 1299
+ L++R + N EI + EA
Sbjct: 115 FERLTKRQYSEAKRAENMEAEIQCICEEEAR 145
>2rr7_A Dynein heavy chain 9; microtubule-binding, stalk head, MTBD,
antiparallel coil, motor protein, DSH; NMR {Chlamydomonas
reinhardtii}
Length = 155
Score = 31.5 bits (72), Expect = 1.4
Identities = 24/104 (23%), Positives = 37/104 (35%), Gaps = 16/104 (15%)
Query: 1468 EMKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDV 1527
E+K K PP + L E I + + +V D A +KM
Sbjct: 30 EVKGMKSPPA----GVRRVL--EAICIMKGVKPARVKDTASGRMVDDYWEASKKMLMEFD 83
Query: 1528 FLDKVTANTAIYYDPDPQNTVIPEDQ-EFVNVYYEMPDFDPTRI 1570
FLD + +D D IP + + + + P+F P I
Sbjct: 84 FLDSL-----RKFDKDH----IPPEVIVKIRPFAQDPEFQPKVI 118
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double
chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces
cerevisiae}
Length = 800
Score = 32.0 bits (73), Expect = 2.0
Identities = 33/183 (18%), Positives = 64/183 (34%), Gaps = 35/183 (19%)
Query: 1533 TANTAIYYDPD--PQNTVIPED-------QEFVNVYYEMPDFDPTRISPWLLRIELDRKR 1583
TA+T + +D D PQ + + V VY + ++ + +E +
Sbjct: 643 TADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLV-----SKDT-----VEEEVLE 692
Query: 1584 MTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDNA 1643
KK+ +E I+ G D + AI + FG +F +
Sbjct: 693 RARKKMILEYAI--ISLGVTDGNKYTKKNEPNAGELSAILK-----FGAGN--MFTATDN 743
Query: 1644 EKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEETDRSFVKVDFVEPKDLVEWKTL 1703
+K + + + D + ED V + EE + F D+ K ++W +
Sbjct: 744 QKKLEDLNL----DDVLNHAEDHVTTPDLGESHLGGEEFLKQFEVTDY---KADIDWDDI 796
Query: 1704 LKQ 1706
+ +
Sbjct: 797 IPE 799
Score = 31.3 bits (71), Expect = 3.5
Identities = 21/125 (16%), Positives = 46/125 (36%), Gaps = 27/125 (21%)
Query: 1095 TANTAIYYDPD--PQNTVIPED-------QEFVNVYYEMPDFDPTRISPWLLRIELDRKR 1145
TA+T + +D D PQ + + V VY + ++ + +E +
Sbjct: 643 TADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLV-----SKDT-----VEEEVLE 692
Query: 1146 MTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRI------RIMNSDDSKMQDEED 1199
KK+ +E I+ G D ++ + I + + D++ + E+
Sbjct: 693 RARKKMILEYAI--ISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDL 750
Query: 1200 AVDKM 1204
+D +
Sbjct: 751 NLDDV 755
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 31.2 bits (70), Expect = 2.1
Identities = 20/102 (19%), Positives = 30/102 (29%), Gaps = 37/102 (36%)
Query: 1187 MNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRII 1246
M + +S D+ ++ L C P+ I
Sbjct: 1 MMTRES--IDKRAGRRGPNLNIVLTC------------------------PECKVYPPKI 34
Query: 1247 ITESGEFKAIADWLLETDGTSLMKVLSERDVDPV---RTFSN 1285
+ E D + G VLS++ VD RTFSN
Sbjct: 35 VERFSE----GDVVCALCGL----VLSDKLVDTRSEWRTFSN 68
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 30.6 bits (69), Expect = 5.8
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 12/47 (25%)
Query: 1255 AIADWLLETDGTSLMK---VLSERDVDP--VRTFSNDICEI-FQVLG 1295
AI W T GT LM +++E ++ VRTFS E+ F +LG
Sbjct: 668 AIIGW---TRGTGLMSANNIIAE-GIEKMGVRTFSQK--EMAFNLLG 708
>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel,
protein turnover; NMR {Saccharomyces cerevisiae}
Length = 208
Score = 30.0 bits (67), Expect = 6.5
Identities = 13/69 (18%), Positives = 23/69 (33%), Gaps = 21/69 (30%)
Query: 1631 GDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEETDRSFVKVD 1690
D + +N + +L + K + ++ C+ ETD + D
Sbjct: 157 DDVIEISYNGKTFKIKILEV--------KPESSSKSI----------CVIETD---LVTD 195
Query: 1691 FVEPKDLVE 1699
F P VE
Sbjct: 196 FAPPVGYVE 204
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
0.321 0.137 0.408
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 28,120,735
Number of extensions: 1814259
Number of successful extensions: 3861
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3803
Number of HSP's successfully gapped: 84
Length of query: 1791
Length of database: 6,701,793
Length adjustment: 107
Effective length of query: 1684
Effective length of database: 3,714,246
Effective search space: 6254790264
Effective search space used: 6254790264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 64 (28.9 bits)