BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy3015
(1791 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 403 bits (1035), Expect = e-112, Method: Compositional matrix adjust.
Identities = 214/415 (51%), Positives = 261/415 (62%), Gaps = 55/415 (13%)
Query: 75 MMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQ 134
+MNI++++P WDG +P P ILKPK LWTGKQ+ SLIIP +N+ R DD+ S
Sbjct: 552 VMNIMLWVPDWDGILPPPVILKPKVLWTGKQILSLIIPKGINLIRD-----DDKQS---- 602
Query: 135 WISPGDTKVVVEHGSLLMGIXXXXXXXXXXXXXXHICFLELGHEVCGRFYGNIQTVVNNW 194
+P D+ +++E+G ++ G+ H + E G E+C F+ IQ VVN W
Sbjct: 603 LSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFFNGIQRVVNYW 662
Query: 195 LLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTI 254
LL HN G SIGIGDTI
Sbjct: 663 LL---------------------------------------HN-------GFSIGIGDTI 676
Query: 255 ADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTG 314
AD T E+ +K+A+ V E IQ A + L+P PG TLR++FE +V+RILN ARD G
Sbjct: 677 ADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAG 736
Query: 315 GSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKD 374
SA+ SL + NN+K MV AGSKGS INISQ+ ACVGQQ VEGKRIPFGF+ RTLPHF KD
Sbjct: 737 RSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKD 796
Query: 375 DYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMV 434
D PESRGF+ENSYL GLTP EFFFHAM GREGLIDTAVKTAETGYIQRRL+KAME VMV
Sbjct: 797 DDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMV 856
Query: 435 HYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNER 489
YD TVRN++G +IQ YGEDGL VE+Q D++ LS K+FE KYR D +R
Sbjct: 857 RYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDR 911
Score = 360 bits (925), Expect = 3e-99, Method: Compositional matrix adjust.
Identities = 208/467 (44%), Positives = 287/467 (61%), Gaps = 35/467 (7%)
Query: 955 GEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVIAC 1014
G D++++ NATLLFQ L+RS K V YRL+ AFEW++GE+E RFQQA V
Sbjct: 1005 GSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRLNKVAFEWIMGEVEARFQQAVVSPG 1064
Query: 1015 VGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGL--------------TP 1060
+ + I + TL F G + G+ TP
Sbjct: 1065 EMVGTLAAQSIGEPATQMTLNTF-------HYAGVSSKNVTLGVPRLKEILNVAKNIKTP 1117
Query: 1061 SEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNV 1120
S + M +D A K +T L VT+ T I+YDPDPQ+TVI ED++FV
Sbjct: 1118 S-LTIYLMPWIAANMDLA-KNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEA 1175
Query: 1121 YYEMPDFDPT----RISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDN 1176
++ +PD + + SPWLLR+ELDR +M DKKL+M ++ KI F DL I+++DN
Sbjct: 1176 FFAIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDN 1235
Query: 1177 AEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHL 1236
A+KL++R RI+ DD K +D+++ + E+D+FL+ IE +ML ++L+G+ I +VYM
Sbjct: 1236 ADKLIIRCRIIRDDDRKAEDDDNMI---EEDVFLKTIEGHMLESISLRGVPNITRVYMM- 1291
Query: 1237 PQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGI 1296
K + E G F+ +W+LETDG +L + ++ VD RT+SN EI Q+LGI
Sbjct: 1292 ----EHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQILGI 1347
Query: 1297 EAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCS 1356
EA R ++ KE+ V++F G YVNYRHLALLCDVMT++GHLMAITRHGINR +TGALMRCS
Sbjct: 1348 EATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCS 1407
Query: 1357 FEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1403
FEETV++LMDAAA E D +G+SENI++GQL MGTG FD+ LD +
Sbjct: 1408 FEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQD 1454
Score = 163 bits (413), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 86/187 (45%), Positives = 113/187 (60%), Gaps = 20/187 (10%)
Query: 773 LCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDT 832
+ +I+ + + R ++ KE+ V++F G YVNYRHLALLCDVMT++GHLMAITRHGINR +T
Sbjct: 1341 ILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAET 1400
Query: 833 GALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKD-- 890
GALMRCSFEETV++LMDAAA E D +G+SENI++GQL MGTG FD+ LD + +
Sbjct: 1401 GALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDMLMNYS 1460
Query: 891 -GIEIPLATXXXXXXXXXXXXXXXTPSSMSPQMTPWAQSTP-AYNALMSPGAAMTPGGPG 948
G +P S M P TP + ++ G +P
Sbjct: 1461 LGTAVP----------------TLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAA 1504
Query: 949 FSPSVAG 955
FSP V G
Sbjct: 1505 FSPLVQG 1511
Score = 140 bits (354), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 67/102 (65%), Positives = 77/102 (75%)
Query: 1009 AQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068
+Q+ ACVGQQ VEGKRIPFGF+ RTLPHF KDD PESRGF+ENSYL GLTP EFFFHAM
Sbjct: 765 SQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAM 824
Query: 1069 GGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTV 1110
GREGLIDTAVKTAET + L + + + YD +N +
Sbjct: 825 AGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAM 866
Score = 123 bits (308), Expect = 1e-27, Method: Compositional matrix adjust.
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 = 95.9 bits (237), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 61/156 (39%), Positives = 91/156 (58%), Gaps = 35/156 (22%)
Query: 1529 LDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPT----RISPWLLRIELDRKRM 1584
L VT+ T I+YDPDPQ+TVI ED++FV ++ +PD + + SPWLLR+ELDR +M
Sbjct: 1146 LSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKM 1205
Query: 1585 TDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDNAE 1644
DKKL+M ++ KI F DL T I+++DNA+
Sbjct: 1206 LDKKLSMSDVAGKIAESFERDLFT----------------------------IWSEDNAD 1237
Query: 1645 KLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIE 1680
KL++R RI+ DD K +D+++ + E+D+FL+ IE
Sbjct: 1238 KLIIRCRIIRDDDRKAEDDDNMI---EEDVFLKTIE 1270
Score = 95.5 bits (236), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 62/166 (37%), Positives = 87/166 (52%), Gaps = 40/166 (24%)
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 ++ E+ I N+ +++L
Sbjct: 901 KKYRIDLMEDRSL-SLYMEN-----------------------------SIENDSSVQDL 930
Query: 712 MGSGDVISELEKEWEKLCEDREAL-REIFSSGESNVVLPCNLMEVI 756
L++E+ +L DRE L + IF G++ LP N+ +I
Sbjct: 931 ---------LDEEYTQLVADRELLCKFIFPKGDARWPLPVNVQRII 967
Score = 63.5 bits (153), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 68/132 (51%), Gaps = 24/132 (18%)
Query: 1489 VENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTV 1548
++ I + P+QI++PQ+N+PVMGIVQDTL VRK + RD FL + N V
Sbjct: 507 IQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTR--------------NAV 552
Query: 1549 IPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNT 1608
+ N+ +PD+D P +L+ ++ T K++ I + IN DD +
Sbjct: 553 M-------NIMLWVPDWDGILPPPVILKPKV---LWTGKQILSLIIPKGINLIRDDDKQS 602
Query: 1609 PLSPTDKKLTME 1620
+PTD + +E
Sbjct: 603 LSNPTDSGMLIE 614
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 380 bits (976), Expect = e-105, Method: Compositional matrix adjust.
Identities = 202/420 (48%), Positives = 257/420 (61%), Gaps = 55/420 (13%)
Query: 73 EQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGP 132
+Q++N+L ++P WDG +P P I+KPKPLW+GKQ+ S+ IP +++ R DE +
Sbjct: 544 DQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRF------DEGT-- 595
Query: 133 YQWISPGDTKVVVEHGSLLMGIXXXXXXXXXXXXXXHICFLELGHEVCGRFYGNIQTVVN 192
+SP D +++ G ++ G+ H+ E G +VC + +GNIQ VVN
Sbjct: 596 -TLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVN 654
Query: 193 NWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGD 252
WLL HN G S GIGD
Sbjct: 655 FWLL---------------------------------------HN-------GFSTGIGD 668
Query: 253 TIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDK 312
TIAD T EI I +AK+ V++V ++A L G TLR++FE+ V R LN+ARDK
Sbjct: 669 TIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK 728
Query: 313 TGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFI 372
G A+ +L + NN+K MV+AGSKGS INI+Q+ ACVGQQ+VEGKRI FGF RTLPHF
Sbjct: 729 AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFS 788
Query: 373 KDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESV 432
KDDY PES+GFVENSYL GLTP EFFFHAMGGREGLIDTAVKTAETGYIQRRL+KA+E +
Sbjct: 789 KDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDI 848
Query: 433 MVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTL 492
MVHYD T RNS+G +IQ YGEDG+ +E Q +DT+ S FE +YR D N TL
Sbjct: 849 MVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTL 908
Score = 315 bits (807), Expect = 1e-85, Method: Compositional matrix adjust.
Identities = 180/478 (37%), Positives = 279/478 (58%), Gaps = 60/478 (12%)
Query: 955 GEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQA----- 1009
G++++ + A +A LF CL+RS L T+ V + YRL+ +AF+W++ IE +F ++
Sbjct: 1002 GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPG 1061
Query: 1010 QVIACVGQQN-----------------VEGKRIPFGF-RKRTLPHFIKDDYGPESRGFVE 1051
+++ + Q+ V K++ G R + + + K+ P ++E
Sbjct: 1062 EMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLE 1121
Query: 1052 NSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVI 1111
+ A ++ R + T +K+ VT + IYYDPDP++TVI
Sbjct: 1122 PGHAADQEQAKLI------RSAIEHTTLKS------------VTIASEIYYDPDPRSTVI 1163
Query: 1112 PEDQEFVNVYYEMPD------FDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFG 1165
PED+E + +++ + D FD + SPWLLR+ELDR M DK LTM + E+I F
Sbjct: 1164 PEDEEIIQLHFSLLDEEAEQSFD--QQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFK 1221
Query: 1166 DDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQG 1225
+DL I+++DN EKL++R R++ DA + E+D L+ IE ML ++TL+G
Sbjct: 1222 NDLFVIWSEDNDEKLIIRCRVVRPKSL------DAETEAEEDHMLKKIENTMLENITLRG 1275
Query: 1226 IEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSN 1285
+E I +V M R + + +GE+ +W+LETDG +L +V++ +DP R ++N
Sbjct: 1276 VENIERVVMM-----KYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTN 1330
Query: 1286 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 1345
+I +VLGIEA R ++ KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG N
Sbjct: 1331 SFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFN 1390
Query: 1346 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1403
R +TGALMRCSFEETV++L +A A AE D RGVSEN+I+GQ+ +GTG FD+++D E
Sbjct: 1391 RSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEE 1448
Score = 147 bits (370), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 69/102 (67%), Positives = 80/102 (78%)
Query: 1009 AQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068
AQ+ ACVGQQ+VEGKRI FGF RTLPHF KDDY PES+GFVENSYL GLTP EFFFHAM
Sbjct: 759 AQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAM 818
Query: 1069 GGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTV 1110
GGREGLIDTAVKTAET + L + + ++YD +N++
Sbjct: 819 GGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSL 860
Score = 134 bits (337), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 61/114 (53%), Positives = 86/114 (75%)
Query: 773 LCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDT 832
+ +++ + + R ++ KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG NR +T
Sbjct: 1335 IMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNT 1394
Query: 833 GALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 886
GALMRCSFEETV++L +A A AE D RGVSEN+I+GQ+ +GTG FD+++D E
Sbjct: 1395 GALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEE 1448
Score = 101 bits (252), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 59/165 (35%), Positives = 88/165 (53%), Gaps = 35/165 (21%)
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 D L+ +++ S E+
Sbjct: 895 KRYRVD---------LLNTD------------HTLDPSLLESGS--------------EI 919
Query: 712 MGSGDVISELEKEWEKLCEDREALREIFSSGESNVVLPCNLMEVI 756
+G + L++E+++L +DR+ LRE+F GE+N LP N+ +I
Sbjct: 920 LGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRII 964
Score = 100 bits (249), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 47/87 (54%), Positives = 61/87 (70%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV++L
Sbjct: 1350 KEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEIL 1409
Query: 579 MDAAAHAEADPMRGYIQRRLIKAMESV 605
+A A AE D RG + ++ M +
Sbjct: 1410 FEAGASAELDDCRGVSENVILGQMAPI 1436
Score = 92.0 bits (227), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 61/169 (36%), Positives = 90/169 (53%), Gaps = 43/169 (25%)
Query: 1529 LDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPD------FDPTRISPWLLRIELDRK 1582
L VT + IYYDPDP++TVIPED+E + +++ + D FD + SPWLLR+ELDR
Sbjct: 1143 LKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFD--QQSPWLLRLELDRA 1200
Query: 1583 RMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDN 1642
M DK LTM + E+I F +DL I+++DN
Sbjct: 1201 AMNDKDLTMGQV----------------------------GERIKQTFKNDLFVIWSEDN 1232
Query: 1643 AEKLVLRIRIM--NSDDSKMQDEED-AVDKMEDDMF----LRCIEETDR 1684
EKL++R R++ S D++ + EED + K+E+ M LR +E +R
Sbjct: 1233 DEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIER 1281
Score = 59.3 bits (142), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 38/122 (31%), Positives = 61/122 (50%), Gaps = 24/122 (19%)
Query: 1496 PRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTVIPEDQEF 1555
P QI++PQ+N+P MGIVQDTL +RK+T RD F+ E +
Sbjct: 508 PLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFI---------------------ELDQV 546
Query: 1556 VNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDK 1615
+N+ Y +PD+D +P +++ + + K++ AI I+ D+ T LSP D
Sbjct: 547 LNMLYWVPDWDGVIPTPAIIK---PKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDN 603
Query: 1616 KL 1617
+
Sbjct: 604 GM 605
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 380 bits (975), Expect = e-105, Method: Compositional matrix adjust.
Identities = 202/420 (48%), Positives = 257/420 (61%), Gaps = 55/420 (13%)
Query: 73 EQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGP 132
+Q++N+L ++P WDG +P P I+KPKPLW+GKQ+ S+ IP +++ R DE +
Sbjct: 544 DQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRF------DEGT-- 595
Query: 133 YQWISPGDTKVVVEHGSLLMGIXXXXXXXXXXXXXXHICFLELGHEVCGRFYGNIQTVVN 192
+SP D +++ G ++ G+ H+ E G +VC + +GNIQ VVN
Sbjct: 596 -TLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVN 654
Query: 193 NWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGD 252
WLL HN G S GIGD
Sbjct: 655 FWLL---------------------------------------HN-------GFSTGIGD 668
Query: 253 TIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDK 312
TIAD T EI I +AK+ V++V ++A L G TLR++FE+ V R LN+ARDK
Sbjct: 669 TIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK 728
Query: 313 TGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFI 372
G A+ +L + NN+K MV+AGSKGS INI+Q+ ACVGQQ+VEGKRI FGF RTLPHF
Sbjct: 729 AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFS 788
Query: 373 KDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESV 432
KDDY PES+GFVENSYL GLTP EFFFHAMGGREGLIDTAVKTAETGYIQRRL+KA+E +
Sbjct: 789 KDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDI 848
Query: 433 MVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTL 492
MVHYD T RNS+G +IQ YGEDG+ +E Q +DT+ S FE +YR D N TL
Sbjct: 849 MVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTL 908
Score = 316 bits (809), Expect = 1e-85, Method: Compositional matrix adjust.
Identities = 180/478 (37%), Positives = 279/478 (58%), Gaps = 60/478 (12%)
Query: 955 GEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQA----- 1009
G++++ + A +A LF CL+RS L T+ V + YRL+ +AF+W++ IE +F ++
Sbjct: 1002 GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPG 1061
Query: 1010 QVIACVGQQN-----------------VEGKRIPFGF-RKRTLPHFIKDDYGPESRGFVE 1051
+++ + Q+ V K++ G R + + + K+ P ++E
Sbjct: 1062 EMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLE 1121
Query: 1052 NSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVI 1111
+ A ++ R + T +K+ VT + IYYDPDP++TVI
Sbjct: 1122 PGHAADQEQAKLI------RSAIEHTTLKS------------VTIASEIYYDPDPRSTVI 1163
Query: 1112 PEDQEFVNVYYEMPD------FDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFG 1165
PED+E + +++ + D FD + SPWLLR+ELDR M DK LTM + E+I F
Sbjct: 1164 PEDEEIIQLHFSLLDEEAEQSFD--QQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFK 1221
Query: 1166 DDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQG 1225
+DL I+++DN EKL++R R++ DA + E+D L+ IE ML ++TL+G
Sbjct: 1222 NDLFVIWSEDNDEKLIIRCRVVRPKSL------DAETEAEEDHMLKKIENTMLENITLRG 1275
Query: 1226 IEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSN 1285
+E I +V M R + + +GE+ +W+LETDG +L +V++ +DP R ++N
Sbjct: 1276 VENIERVVMM-----KYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTN 1330
Query: 1286 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 1345
+I +VLGIEA R ++ KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG N
Sbjct: 1331 SFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFN 1390
Query: 1346 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1403
R +TGALMRCSFEETV++L +A A AE D RGVSEN+I+GQ+ +GTG FD+++D E
Sbjct: 1391 RSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEE 1448
Score = 146 bits (369), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 69/102 (67%), Positives = 80/102 (78%)
Query: 1009 AQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068
AQ+ ACVGQQ+VEGKRI FGF RTLPHF KDDY PES+GFVENSYL GLTP EFFFHAM
Sbjct: 759 AQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAM 818
Query: 1069 GGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTV 1110
GGREGLIDTAVKTAET + L + + ++YD +N++
Sbjct: 819 GGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSL 860
Score = 135 bits (339), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 66/138 (47%), Positives = 98/138 (71%), Gaps = 3/138 (2%)
Query: 751 NLMEVIFI--LQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLAL 808
NL EV+ + + +++ N + + +++ + + R ++ KE+ V+ G YVNYRH+AL
Sbjct: 1312 NLSEVMTVPGIDPTRIYTNSFIDIM-EVLGIEAGRAALYKEVYNVIASDGSYVNYRHMAL 1370
Query: 809 LCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIM 868
L DVMT +G L ++TRHG NR +TGALMRCSFEETV++L +A A AE D RGVSEN+I+
Sbjct: 1371 LVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVIL 1430
Query: 869 GQLPRMGTGCFDLLLDAE 886
GQ+ +GTG FD+++D E
Sbjct: 1431 GQMAPIGTGAFDVMIDEE 1448
Score = 102 bits (253), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 59/165 (35%), Positives = 88/165 (53%), Gaps = 35/165 (21%)
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 D L+ +++ S E+
Sbjct: 895 KRYRVD---------LLNTD------------HTLDPSLLESGS--------------EI 919
Query: 712 MGSGDVISELEKEWEKLCEDREALREIFSSGESNVVLPCNLMEVI 756
+G + L++E+++L +DR+ LRE+F GE+N LP N+ +I
Sbjct: 920 LGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRII 964
Score = 101 bits (251), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 55/119 (46%), Positives = 74/119 (62%), Gaps = 8/119 (6%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV++L
Sbjct: 1350 KEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEIL 1409
Query: 579 MDAAAHAEADPMRGYIQRRLIKAME-------SVMVHYDCTVRNSVGQLI-QLRYGEDG 629
+A A AE D RG + ++ M VM+ + V+ Q I ++ G+DG
Sbjct: 1410 FEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDG 1468
Score = 92.0 bits (227), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 61/169 (36%), Positives = 90/169 (53%), Gaps = 43/169 (25%)
Query: 1529 LDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPD------FDPTRISPWLLRIELDRK 1582
L VT + IYYDPDP++TVIPED+E + +++ + D FD + SPWLLR+ELDR
Sbjct: 1143 LKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFD--QQSPWLLRLELDRA 1200
Query: 1583 RMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDN 1642
M DK LTM + E+I F +DL I+++DN
Sbjct: 1201 AMNDKDLTMGQV----------------------------GERIKQTFKNDLFVIWSEDN 1232
Query: 1643 AEKLVLRIRIM--NSDDSKMQDEED-AVDKMEDDMF----LRCIEETDR 1684
EKL++R R++ S D++ + EED + K+E+ M LR +E +R
Sbjct: 1233 DEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIER 1281
Score = 59.3 bits (142), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 38/122 (31%), Positives = 61/122 (50%), Gaps = 24/122 (19%)
Query: 1496 PRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTVIPEDQEF 1555
P QI++PQ+N+P MGIVQDTL +RK+T RD F+ E +
Sbjct: 508 PLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFI---------------------ELDQV 546
Query: 1556 VNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDK 1615
+N+ Y +PD+D +P +++ + + K++ AI I+ D+ T LSP D
Sbjct: 547 LNMLYWVPDWDGVIPTPAIIK---PKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDN 603
Query: 1616 KL 1617
+
Sbjct: 604 GM 605
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
Length = 1732
Score = 380 bits (975), Expect = e-105, Method: Compositional matrix adjust.
Identities = 202/420 (48%), Positives = 257/420 (61%), Gaps = 55/420 (13%)
Query: 73 EQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGP 132
+Q++N+L ++P WDG +P P I+KPKPLW+GKQ+ S+ IP +++ R DE +
Sbjct: 544 DQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRF------DEGT-- 595
Query: 133 YQWISPGDTKVVVEHGSLLMGIXXXXXXXXXXXXXXHICFLELGHEVCGRFYGNIQTVVN 192
+SP D +++ G ++ G+ H+ E G +VC + +GNIQ VVN
Sbjct: 596 -TLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVN 654
Query: 193 NWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGD 252
WLL HN G S GIGD
Sbjct: 655 FWLL---------------------------------------HN-------GFSTGIGD 668
Query: 253 TIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDK 312
TIAD T EI I +AK+ V++V ++A L G TLR++FE+ V R LN+ARDK
Sbjct: 669 TIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK 728
Query: 313 TGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFI 372
G A+ +L + NN+K MV+AGSKGS INI+Q+ ACVGQQ+VEGKRI FGF RTLPHF
Sbjct: 729 AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFS 788
Query: 373 KDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESV 432
KDDY PES+GFVENSYL GLTP EFFFHAMGGREGLIDTAVKTAETGYIQRRL+KA+E +
Sbjct: 789 KDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDI 848
Query: 433 MVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTL 492
MVHYD T RNS+G +IQ YGEDG+ +E Q +DT+ S FE +YR D N TL
Sbjct: 849 MVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTL 908
Score = 315 bits (808), Expect = 1e-85, Method: Compositional matrix adjust.
Identities = 180/478 (37%), Positives = 279/478 (58%), Gaps = 60/478 (12%)
Query: 955 GEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQA----- 1009
G++++ + A +A LF CL+RS L T+ V + YRL+ +AF+W++ IE +F ++
Sbjct: 1002 GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPG 1061
Query: 1010 QVIACVGQQN-----------------VEGKRIPFGF-RKRTLPHFIKDDYGPESRGFVE 1051
+++ + Q+ V K++ G R + + + K+ P ++E
Sbjct: 1062 EMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLE 1121
Query: 1052 NSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVI 1111
+ A ++ R + T +K+ VT + IYYDPDP++TVI
Sbjct: 1122 PGHAADQEQAKLI------RSAIEHTTLKS------------VTIASEIYYDPDPRSTVI 1163
Query: 1112 PEDQEFVNVYYEMPD------FDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFG 1165
PED+E + +++ + D FD + SPWLLR+ELDR M DK LTM + E+I F
Sbjct: 1164 PEDEEIIQLHFSLLDEEAEQSFD--QQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFK 1221
Query: 1166 DDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQG 1225
+DL I+++DN EKL++R R++ DA + E+D L+ IE ML ++TL+G
Sbjct: 1222 NDLFVIWSEDNDEKLIIRCRVVRPKSL------DAETEAEEDHMLKKIENTMLENITLRG 1275
Query: 1226 IEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSN 1285
+E I +V M R + + +GE+ +W+LETDG +L +V++ +DP R ++N
Sbjct: 1276 VENIERVVMM-----KYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTN 1330
Query: 1286 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 1345
+I +VLGIEA R ++ KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG N
Sbjct: 1331 SFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFN 1390
Query: 1346 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1403
R +TGALMRCSFEETV++L +A A AE D RGVSEN+I+GQ+ +GTG FD+++D E
Sbjct: 1391 RSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEE 1448
Score = 146 bits (368), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 69/102 (67%), Positives = 80/102 (78%)
Query: 1009 AQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068
AQ+ ACVGQQ+VEGKRI FGF RTLPHF KDDY PES+GFVENSYL GLTP EFFFHAM
Sbjct: 759 AQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAM 818
Query: 1069 GGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTV 1110
GGREGLIDTAVKTAET + L + + ++YD +N++
Sbjct: 819 GGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSL 860
Score = 135 bits (339), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 66/138 (47%), Positives = 98/138 (71%), Gaps = 3/138 (2%)
Query: 751 NLMEVIFI--LQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLAL 808
NL EV+ + + +++ N + + +++ + + R ++ KE+ V+ G YVNYRH+AL
Sbjct: 1312 NLSEVMTVPGIDPTRIYTNSFIDIM-EVLGIEAGRAALYKEVYNVIASDGSYVNYRHMAL 1370
Query: 809 LCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIM 868
L DVMT +G L ++TRHG NR +TGALMRCSFEETV++L +A A AE D RGVSEN+I+
Sbjct: 1371 LVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVIL 1430
Query: 869 GQLPRMGTGCFDLLLDAE 886
GQ+ +GTG FD+++D E
Sbjct: 1431 GQMAPIGTGAFDVMIDEE 1448
Score = 102 bits (253), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 59/165 (35%), Positives = 88/165 (53%), Gaps = 35/165 (21%)
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 D L+ +++ S E+
Sbjct: 895 KRYRVD---------LLNTD------------HTLDPSLLESGS--------------EI 919
Query: 712 MGSGDVISELEKEWEKLCEDREALREIFSSGESNVVLPCNLMEVI 756
+G + L++E+++L +DR+ LRE+F GE+N LP N+ +I
Sbjct: 920 LGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRII 964
Score = 101 bits (251), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 55/119 (46%), Positives = 74/119 (62%), Gaps = 8/119 (6%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV++L
Sbjct: 1350 KEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEIL 1409
Query: 579 MDAAAHAEADPMRGYIQRRLIKAME-------SVMVHYDCTVRNSVGQLI-QLRYGEDG 629
+A A AE D RG + ++ M VM+ + V+ Q I ++ G+DG
Sbjct: 1410 FEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDG 1468
Score = 92.0 bits (227), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 61/169 (36%), Positives = 90/169 (53%), Gaps = 43/169 (25%)
Query: 1529 LDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPD------FDPTRISPWLLRIELDRK 1582
L VT + IYYDPDP++TVIPED+E + +++ + D FD + SPWLLR+ELDR
Sbjct: 1143 LKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFD--QQSPWLLRLELDRA 1200
Query: 1583 RMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDN 1642
M DK LTM + E+I F +DL I+++DN
Sbjct: 1201 AMNDKDLTMGQV----------------------------GERIKQTFKNDLFVIWSEDN 1232
Query: 1643 AEKLVLRIRIM--NSDDSKMQDEED-AVDKMEDDMF----LRCIEETDR 1684
EKL++R R++ S D++ + EED + K+E+ M LR +E +R
Sbjct: 1233 DEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIER 1281
Score = 59.3 bits (142), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 38/122 (31%), Positives = 61/122 (50%), Gaps = 24/122 (19%)
Query: 1496 PRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTVIPEDQEF 1555
P QI++PQ+N+P MGIVQDTL +RK+T RD F+ E +
Sbjct: 508 PLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFI---------------------ELDQV 546
Query: 1556 VNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDK 1615
+N+ Y +PD+D +P +++ + + K++ AI I+ D+ T LSP D
Sbjct: 547 LNMLYWVPDWDGVIPTPAIIK---PKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDN 603
Query: 1616 KL 1617
+
Sbjct: 604 GM 605
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 204 bits (519), Expect = 4e-52, Method: Compositional matrix adjust.
Identities = 137/387 (35%), Positives = 200/387 (51%), Gaps = 61/387 (15%)
Query: 91 QPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWIS---PGDTKVVVEH 147
+P IL P+ +TGKQV S +P + N + SGP + P D+ VV+++
Sbjct: 536 EPAILAPREYYTGKQVVSAFLPKDFNFHGQANV-----SSGPRLCKNEDCPHDSYVVIKN 590
Query: 148 GSLLMGIXXXXXXXXXXXXXXHICFLELGHEVCGRFYGNIQT-VVNNWLLLEGHSIGIGD 206
G LL G+ + GN Q + +WL+ E +S G
Sbjct: 591 GILLEGVFDK------------------------KAIGNQQPESILHWLIKE-YSDEYGK 625
Query: 207 TIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMA 266
+ D + I+ V + M LE + +GD + EI
Sbjct: 626 WLMDNLFRVFIRF-----------VELQGFTMRLE-----DVSLGDDVKK-----EIYNE 664
Query: 267 IKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNN 326
I +AK +V +IQK N +LEP PG TL ++ EN + L+ R G A K L +N
Sbjct: 665 IDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNF 724
Query: 327 LKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVEN 386
M G++GS +NI+Q+ A +GQQ+V G+RI G+ RTLPHF D PE+RGF+ +
Sbjct: 725 AYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYS 784
Query: 387 SYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQ 446
S+ GL P+E FFHA GGREGL+DTAV+T+++GY+QRRLI A+ + YD TVR+ G+
Sbjct: 785 SFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGE 844
Query: 447 LIQLRYGEDGLC------GEAVEHQRI 467
+IQ+ YG+DG+ G+ V+ RI
Sbjct: 845 VIQVAYGDDGVFPMYSAHGKTVDVNRI 871
Score = 96.7 bits (239), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/94 (47%), Positives = 63/94 (67%)
Query: 1010 QVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMG 1069
Q+ A +GQQ+V G+RI G+ RTLPHF D PE+RGF+ +S+ GL P+E FFHA G
Sbjct: 742 QMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAG 801
Query: 1070 GREGLIDTAVKTAETVNVLVFLFQVTANTAIYYD 1103
GREGL+DTAV+T+++ + L ++ YD
Sbjct: 802 GREGLVDTAVRTSQSGYMQRRLINALSDLRAEYD 835
Score = 48.1 bits (113), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 9/69 (13%)
Query: 578 LMDAAAHAEADPMRGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLC------ 631
L+D A GY+QRRLI A+ + YD TVR+ G++IQ+ YG+DG+
Sbjct: 806 LVDTAVRTSQS---GYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGVFPMYSAH 862
Query: 632 GEAVEHQRI 640
G+ V+ RI
Sbjct: 863 GKTVDVNRI 871
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 204 bits (518), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 136/387 (35%), Positives = 200/387 (51%), Gaps = 61/387 (15%)
Query: 91 QPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWIS---PGDTKVVVEH 147
+P IL P+ +TGKQV S +P + N + SGP + P D+ VV+++
Sbjct: 536 EPAILAPREYYTGKQVISAFLPKDFNFHGQANV-----SSGPRLCKNEDCPHDSYVVIKN 590
Query: 148 GSLLMGIXXXXXXXXXXXXXXHICFLELGHEVCGRFYGNIQT-VVNNWLLLEGHSIGIGD 206
G LL G+ + GN Q + +WL+ E +S G
Sbjct: 591 GILLEGVFDK------------------------KAIGNQQPESILHWLIKE-YSDEYGK 625
Query: 207 TIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMA 266
+ D + I+ V + M LE + +GD + EI
Sbjct: 626 WLMDNLFRVFIRF-----------VELQGFTMRLE-----DVSLGDDVKK-----EIYNE 664
Query: 267 IKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNN 326
I +AK +V +IQK N +LEP PG TL ++ EN + L+ R G A K L +N
Sbjct: 665 IDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNF 724
Query: 327 LKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVEN 386
M G++GS +NI+Q+ A +GQQ+V G+RI G+ RTLPHF D PE+RGF+ +
Sbjct: 725 AYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYS 784
Query: 387 SYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQ 446
S+ GL P+E FFHA GGREGL+DTAV+T+++GY+QRRLI A+ + YD TVR+ G+
Sbjct: 785 SFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGE 844
Query: 447 LIQLRYGEDGLC------GEAVEHQRI 467
++Q+ YG+DG+ G+ V+ RI
Sbjct: 845 VVQVAYGDDGVFPMYSAHGKTVDVNRI 871
Score = 97.1 bits (240), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 45/94 (47%), Positives = 63/94 (67%)
Query: 1010 QVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMG 1069
Q+ A +GQQ+V G+RI G+ RTLPHF D PE+RGF+ +S+ GL P+E FFHA G
Sbjct: 742 QMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAG 801
Query: 1070 GREGLIDTAVKTAETVNVLVFLFQVTANTAIYYD 1103
GREGL+DTAV+T+++ + L ++ YD
Sbjct: 802 GREGLVDTAVRTSQSGYMQRRLINALSDLRAEYD 835
Score = 47.4 bits (111), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 35/55 (63%), Gaps = 6/55 (10%)
Query: 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLC------GEAVEHQRI 640
GY+QRRLI A+ + YD TVR+ G+++Q+ YG+DG+ G+ V+ RI
Sbjct: 817 GYMQRRLINALSDLRAEYDGTVRSLYGEVVQVAYGDDGVFPMYSAHGKTVDVNRI 871
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 119 bits (299), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 85/270 (31%), Positives = 140/270 (51%), Gaps = 40/270 (14%)
Query: 1132 ISPWLLRIELDRKRMTDKKLTMEAISEKIN-AGFGDDLNCIFNDDNAEKLVLRIRIMNSD 1190
I+ + ++LD + + DK +T++ + + IN G+ F D +E L I N D
Sbjct: 160 IASMSIILQLDNEMLKDKGVTVDDVKKAINRLKLGE-----FVIDESEGTTLNISFANID 214
Query: 1191 DSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITES 1250
A+ K+ D + + ++GI+ I KR I+ +
Sbjct: 215 SIA------ALFKLRDKIL----------NTKIKGIKGI-------------KRAIVQKK 245
Query: 1251 GEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTV 1310
G+ ++++ TDG++L VLS + VD + +N+I EI +V GIEA R+ + +E++ V
Sbjct: 246 GD-----EYIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKV 300
Query: 1311 LQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAH 1370
L GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV L+DAAA
Sbjct: 301 LAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAAR 360
Query: 1371 AEADPMRGVSENIIMGQLPRMGTGCFDLLL 1400
+ + +GV ENII+G ++GTG +L +
Sbjct: 361 GDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
Score = 86.7 bits (213), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/115 (37%), Positives = 70/115 (60%)
Query: 769 NLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 828
N+R + ++ + + R+ + +E++ VL GL V+ RH+ L+ DVMT G + I RHG+
Sbjct: 276 NIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVT 335
Query: 829 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 883
+ L R +FE TV L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 336 GEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
Score = 64.7 bits (156), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 48/81 (59%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
+E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV L
Sbjct: 295 REISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHL 354
Query: 579 MDAAAHAEADPMRGYIQRRLI 599
+DAAA + + +G ++ +I
Sbjct: 355 LDAAARGDVEEFKGVVENIII 375
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 119 bits (297), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 85/270 (31%), Positives = 140/270 (51%), Gaps = 40/270 (14%)
Query: 1132 ISPWLLRIELDRKRMTDKKLTMEAISEKIN-AGFGDDLNCIFNDDNAEKLVLRIRIMNSD 1190
I+ + ++LD + + DK +T++ + + IN G+ F D +E L I N D
Sbjct: 160 IASMSIILQLDNEMLKDKGVTVDDVKKAINRLKLGE-----FVIDESEGNTLNISFANID 214
Query: 1191 DSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITES 1250
A+ K+ D + + ++GI+ I KR I+ +
Sbjct: 215 SIA------ALFKLRDKIL----------NTKIKGIKGI-------------KRAIVQKK 245
Query: 1251 GEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTV 1310
G+ ++++ TDG++L VLS + VD + +N+I EI +V GIEA R+ + +E++ V
Sbjct: 246 GD-----EYIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKV 300
Query: 1311 LQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAH 1370
L GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV L+DAAA
Sbjct: 301 LAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAAR 360
Query: 1371 AEADPMRGVSENIIMGQLPRMGTGCFDLLL 1400
+ + +GV ENII+G ++GTG +L +
Sbjct: 361 GDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
Score = 86.7 bits (213), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/115 (37%), Positives = 70/115 (60%)
Query: 769 NLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 828
N+R + ++ + + R+ + +E++ VL GL V+ RH+ L+ DVMT G + I RHG+
Sbjct: 276 NIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVT 335
Query: 829 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 883
+ L R +FE TV L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 336 GEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
Score = 64.7 bits (156), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 48/81 (59%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
+E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV L
Sbjct: 295 REISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHL 354
Query: 579 MDAAAHAEADPMRGYIQRRLI 599
+DAAA + + +G ++ +I
Sbjct: 355 LDAAARGDVEEFKGVVENIII 375
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
Length = 392
Score = 117 bits (294), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 63/158 (39%), Positives = 98/158 (62%), Gaps = 5/158 (3%)
Query: 1243 KRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKS 1302
KR I+ + G+ ++++ TDG++L VLS + VD + +N+I EI +V GIEA R+
Sbjct: 235 KRAIVQKKGD-----EYIILTDGSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREI 289
Query: 1303 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1362
+ +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV
Sbjct: 290 IIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVK 349
Query: 1363 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 1400
L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 350 HLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 387
Score = 86.7 bits (213), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/115 (37%), Positives = 70/115 (60%)
Query: 769 NLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 828
N+R + ++ + + R+ + +E++ VL GL V+ RH+ L+ DVMT G + I RHG+
Sbjct: 273 NIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVT 332
Query: 829 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 883
+ L R +FE TV L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 333 GEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 387
Score = 64.7 bits (156), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 48/81 (59%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
+E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV L
Sbjct: 292 REISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHL 351
Query: 579 MDAAAHAEADPMRGYIQRRLI 599
+DAAA + + +G ++ +I
Sbjct: 352 LDAAARGDVEEFKGVVENIII 372
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 395
Score = 117 bits (294), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 63/158 (39%), Positives = 98/158 (62%), Gaps = 5/158 (3%)
Query: 1243 KRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKS 1302
KR I+ + G+ ++++ TDG++L VLS + VD + +N+I EI +V GIEA R+
Sbjct: 238 KRAIVQKKGD-----EYIILTDGSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREI 292
Query: 1303 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1362
+ +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV
Sbjct: 293 IIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVK 352
Query: 1363 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 1400
L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 353 HLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
Score = 86.7 bits (213), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/115 (37%), Positives = 70/115 (60%)
Query: 769 NLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 828
N+R + ++ + + R+ + +E++ VL GL V+ RH+ L+ DVMT G + I RHG+
Sbjct: 276 NIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVT 335
Query: 829 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 883
+ L R +FE TV L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 336 GEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
Score = 64.7 bits (156), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 48/81 (59%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
+E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV L
Sbjct: 295 REISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHL 354
Query: 579 MDAAAHAEADPMRGYIQRRLI 599
+DAAA + + +G ++ +I
Sbjct: 355 LDAAARGDVEEFKGVVENIII 375
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 59.7 bits (143), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 65/266 (24%), Positives = 117/266 (43%), Gaps = 58/266 (21%)
Query: 204 IGDTIADPQTYLE-IQMAIKKAKEDVIEVIQKA------------------HNMDLEPTP 244
+G+ + D + E IQM + + K + +++ +A + L T
Sbjct: 595 VGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTS 654
Query: 245 GHSIGIGDTI--ADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQV 302
G +IGI D + + Q YLE A +K ++ I++A+ M T R+ + +QV
Sbjct: 655 GITIGIDDAVIPEEKQRYLE--EADRKLRQ-----IEQAYEMGF-----LTDRERY-DQV 701
Query: 303 NRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRI 359
++ + +K + K+ E +N L M +G++G+ I Q+ G
Sbjct: 702 IQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG--------- 752
Query: 360 PFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETG 419
++ G V +S+ GLT E+F + G R+G DTA++TA++G
Sbjct: 753 -----------LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSG 801
Query: 420 YIQRRLIK-AMESVMVHYDCTVRNSV 444
Y+ R+L+ A E V+ DC N +
Sbjct: 802 YLTRKLVDVAHEIVVREADCGTTNYI 827
Score = 39.3 bits (90), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 819 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1130 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1187
Score = 39.3 bits (90), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 1336 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1130 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1187
Score = 34.3 bits (77), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 1084
V +S+ GLT E+F + G R+G DTA++TA++
Sbjct: 766 VRSSFREGLTVLEYFISSHGARKGGADTALRTADS 800
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 59.7 bits (143), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 65/266 (24%), Positives = 117/266 (43%), Gaps = 58/266 (21%)
Query: 204 IGDTIADPQTYLE-IQMAIKKAKEDVIEVIQKA------------------HNMDLEPTP 244
+G+ + D + E IQM + + K + +++ +A + L T
Sbjct: 886 VGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTS 945
Query: 245 GHSIGIGDTI--ADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQV 302
G +IGI D + + Q YLE A +K ++ I++A+ M T R+ + +QV
Sbjct: 946 GITIGIDDAVIPEEKQRYLE--EADRKLRQ-----IEQAYEMGF-----LTDRERY-DQV 992
Query: 303 NRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRI 359
++ + +K + K+ E +N L M +G++G+ I Q+ G
Sbjct: 993 IQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG--------- 1043
Query: 360 PFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETG 419
++ G V +S+ GLT E+F + G R+G DTA++TA++G
Sbjct: 1044 -----------LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSG 1092
Query: 420 YIQRRLIK-AMESVMVHYDCTVRNSV 444
Y+ R+L+ A E V+ DC N +
Sbjct: 1093 YLTRKLVDVAHEIVVREADCGTTNYI 1118
Score = 39.3 bits (90), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 819 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Score = 39.3 bits (90), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 1336 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Score = 34.3 bits (77), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 1084
V +S+ GLT E+F + G R+G DTA++TA++
Sbjct: 1057 VRSSFREGLTVLEYFISSHGARKGGADTALRTADS 1091
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 57.8 bits (138), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 64/266 (24%), Positives = 116/266 (43%), Gaps = 58/266 (21%)
Query: 204 IGDTIADPQTYLE-IQMAIKKAKEDVIEVIQKA------------------HNMDLEPTP 244
+G+ + D + E IQM + + K + +++ +A + L T
Sbjct: 626 VGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTS 685
Query: 245 GHSIGIGDTI--ADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQV 302
G +IGI D + + Q YLE A +K ++ I++A+ M T R+ + +QV
Sbjct: 686 GITIGIDDAVIPEEKQRYLE--EADRKLRQ-----IEQAYEMGF-----LTDRERY-DQV 732
Query: 303 NRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRI 359
++ + +K + + E +N L M +G++G+ I Q+ G
Sbjct: 733 IQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG--------- 783
Query: 360 PFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETG 419
++ G V +S+ GLT E+F + G R+G DTA++TA++G
Sbjct: 784 -----------LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSG 832
Query: 420 YIQRRLIK-AMESVMVHYDCTVRNSV 444
Y+ R+L+ A E V+ DC N +
Sbjct: 833 YLTRKLVDVAHEIVVREADCGTTNYI 858
Score = 39.3 bits (90), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 819 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1161 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1218
Score = 39.3 bits (90), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 1336 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1161 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1218
Score = 34.7 bits (78), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 1084
V +S+ GLT E+F + G R+G DTA++TA++
Sbjct: 797 VRSSFREGLTVLEYFISSHGARKGGADTALRTADS 831
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 55.1 bits (131), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 97/217 (44%), Gaps = 39/217 (17%)
Query: 234 KAHNMDLEPTPGHSIGIGDTI--ADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPG 291
K + T G +IGI D + + + YLE +A +++ I++A+ M
Sbjct: 935 KYYGFTFSTTSGITIGIDDAVIPEEKKQYLE------EADRKLLQ-IEQAYEMGF----- 982
Query: 292 NTLRQTFENQVNRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQVIAC 348
T R+ + +Q+ ++ + +K + K+ E +N L M +G++G+ I Q+
Sbjct: 983 LTDRERY-DQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGL 1041
Query: 349 VGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGL 408
G ++ G V +S+ GLT E+F + G R+G
Sbjct: 1042 RG--------------------LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGG 1081
Query: 409 IDTAVKTAETGYIQRRLIKAMESVMVH-YDCTVRNSV 444
DTA++TA++GY+ R+L+ ++V DC N +
Sbjct: 1082 ADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYI 1118
Score = 39.7 bits (91), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 819 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Score = 39.7 bits (91), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 1336 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Score = 35.0 bits (79), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAI 1100
V +S+ GLT E+F + G R+G DTA++TA++ + L VT +
Sbjct: 1057 VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVV 1107
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 55.1 bits (131), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 97/217 (44%), Gaps = 39/217 (17%)
Query: 234 KAHNMDLEPTPGHSIGIGDTI--ADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPG 291
K + T G +IGI D + + + YLE +A +++ I++A+ M
Sbjct: 935 KYYGFTFSTTSGITIGIDDAVIPEEKKQYLE------EADRKLLQ-IEQAYEMGF----- 982
Query: 292 NTLRQTFENQVNRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQVIAC 348
T R+ + +Q+ ++ + +K + K+ E +N L M +G++G+ I Q+
Sbjct: 983 LTDRERY-DQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGL 1041
Query: 349 VGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGL 408
G ++ G V +S+ GLT E+F + G R+G
Sbjct: 1042 RG--------------------LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGG 1081
Query: 409 IDTAVKTAETGYIQRRLIKAMESVMVH-YDCTVRNSV 444
DTA++TA++GY+ R+L+ ++V DC N +
Sbjct: 1082 ADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYI 1118
Score = 39.7 bits (91), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 819 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Score = 39.7 bits (91), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 1336 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Score = 35.0 bits (79), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAI 1100
V +S+ GLT E+F + G R+G DTA++TA++ + L VT +
Sbjct: 1057 VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVV 1107
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1265
Score = 51.6 bits (122), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 63/261 (24%), Positives = 114/261 (43%), Gaps = 59/261 (22%)
Query: 204 IGDTIADPQTYLE-IQMAIKKAKEDVIEVIQKA------------------HNMDLEPTP 244
+G+ + D + E IQM + + K + +++ +A + L T
Sbjct: 626 VGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTS 685
Query: 245 GH-SIGIGDTI--ADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQ 301
G +IGI D + + Q YLE A +K ++ I++A+ M T R+ + +Q
Sbjct: 686 GIITIGIDDAVIPEEKQRYLE--EADRKLRQ-----IEQAYEMGF-----LTDRERY-DQ 732
Query: 302 VNRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKR 358
V ++ + +K + + E +N L M +G++G+ I Q+ G
Sbjct: 733 VIQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG-------- 784
Query: 359 IPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 418
++ G V +S+ GLT E+F + G R+G DTA++TA++
Sbjct: 785 ------------LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADS 832
Query: 419 GYIQRRLIK-AMESVMVHYDC 438
GY+ R+L+ A E V+ DC
Sbjct: 833 GYLTRKLVDVAHEIVVREADC 853
Score = 39.3 bits (90), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 819 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1162 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1219
Score = 39.3 bits (90), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 1336 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1162 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1219
Score = 34.3 bits (77), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 1084
V +S+ GLT E+F + G R+G DTA++TA++
Sbjct: 798 VRSSFREGLTVLEYFISSHGARKGGADTALRTADS 832
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 47.0 bits (110), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 37/122 (30%), Positives = 57/122 (46%), Gaps = 21/122 (17%)
Query: 324 YNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGF 383
+N++ M +G++GS I Q+ G + + K P G T P + F
Sbjct: 719 FNSIYMMADSGARGSAAQIRQL---AGMRGLMAK--PDGSIIET----------PITANF 763
Query: 384 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-AMESVMVHYDCTVRN 442
E GL ++F G R+GL DTA+KTA +GY+ RRL+ A + V+ DC
Sbjct: 764 RE-----GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHE 818
Query: 443 SV 444
+
Sbjct: 819 GI 820
Score = 44.3 bits (103), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 67/145 (46%), Gaps = 23/145 (15%)
Query: 1271 VLSERDVDPV-RTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQ------------FYGLY 1317
+L R V V R N++ +++++ G++ K +E + +L+ G
Sbjct: 1220 ILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQ 1279
Query: 1318 VNYRHLALLCDVMTAKGH--------LMAITRHGINRQDTGALMRCSFEETVDVLMDAAA 1369
V Y + + + A G L+ IT+ + + + SF+ET VL +AA
Sbjct: 1280 VEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESF--ISAASFQETTRVLTEAAV 1337
Query: 1370 HAEADPMRGVSENIIMGQLPRMGTG 1394
+ D +RG+ EN+I+G+L GTG
Sbjct: 1338 AGKRDELRGLKENVIVGRLIPAGTG 1362
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 838 CSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ET VL +AA + D +RG+ EN+I+G+L GTG
Sbjct: 1323 ASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Score = 32.0 bits (71), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 569 CSFEETVDVLMDAAAHAEADPMRGY----IQRRLIKAMESVMVHYDCTVRNSVGQ 619
SF+ET VL +AA + D +RG I RLI A H D R + G+
Sbjct: 1323 ASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGE 1377
Score = 31.6 bits (70), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYD 1103
+ ++ GL ++F G R+GL DTA+KTA + + L V + + D
Sbjct: 759 ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED 812
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 47.0 bits (110), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 37/122 (30%), Positives = 57/122 (46%), Gaps = 21/122 (17%)
Query: 324 YNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGF 383
+N++ M +G++GS I Q+ G + + K P G T P + F
Sbjct: 719 FNSIYMMADSGARGSAAQIRQL---AGMRGLMAK--PDGSIIET----------PITANF 763
Query: 384 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-AMESVMVHYDCTVRN 442
E GL ++F G R+GL DTA+KTA +GY+ RRL+ A + V+ DC
Sbjct: 764 RE-----GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHE 818
Query: 443 SV 444
+
Sbjct: 819 GI 820
Score = 44.3 bits (103), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 67/145 (46%), Gaps = 23/145 (15%)
Query: 1271 VLSERDVDPV-RTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQ------------FYGLY 1317
+L R V V R N++ +++++ G++ K +E + +L+ G
Sbjct: 1220 ILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQ 1279
Query: 1318 VNYRHLALLCDVMTAKGH--------LMAITRHGINRQDTGALMRCSFEETVDVLMDAAA 1369
V Y + + + A G L+ IT+ + + + SF+ET VL +AA
Sbjct: 1280 VEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESF--ISAASFQETTRVLTEAAV 1337
Query: 1370 HAEADPMRGVSENIIMGQLPRMGTG 1394
+ D +RG+ EN+I+G+L GTG
Sbjct: 1338 AGKRDELRGLKENVIVGRLIPAGTG 1362
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 838 CSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ET VL +AA + D +RG+ EN+I+G+L GTG
Sbjct: 1323 ASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Score = 32.0 bits (71), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 569 CSFEETVDVLMDAAAHAEADPMRGY----IQRRLIKAMESVMVHYDCTVRNSVGQ 619
SF+ET VL +AA + D +RG I RLI A H D R + G+
Sbjct: 1323 ASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGE 1377
Score = 31.6 bits (70), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYD 1103
+ ++ GL ++F G R+GL DTA+KTA + + L V + + D
Sbjct: 759 ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED 812
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 36.2 bits (82), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 23/37 (62%)
Query: 834 ALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQ 870
L R +FE TV L +AA E D + GV EN+++GQ
Sbjct: 393 VLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQ 429
Score = 36.2 bits (82), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 23/37 (62%)
Query: 1351 ALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQ 1387
L R +FE TV L +AA E D + GV EN+++GQ
Sbjct: 393 VLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQ 429
>pdb|3SE8|H Chain H, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc03 In Complex With Hiv-1 Gp120
Length = 233
Score = 34.7 bits (78), Expect = 0.46, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 98 KPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSG----PYQWISPGDT 141
KPLW G ++ + G V+MTR S PDD D G + ++P DT
Sbjct: 52 KPLW-GAVSYARQLQGRVSMTRQLSQDPDDPDWGVAYMEFSGLTPADT 98
>pdb|1JZQ|A Chain A, Isoleucyl-Trna Synthetase Complexed With Isoleucyl-
Adenylate Analogue
pdb|1JZS|A Chain A, Isoleucyl-trna Synthetase Complexed With Mupirocin
pdb|1ILE|A Chain A, Isoleucyl-Trna Synthetase
Length = 821
Score = 30.4 bits (67), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 10/100 (10%)
Query: 1230 GKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICE 1289
GK LP T + + E G F +AD++ + DGT + V F + E
Sbjct: 281 GKALEGLPYTPPYPQAL--EKGYFVVLADYVSQEDGTGI--------VHQAPAFGAEDLE 330
Query: 1290 IFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDV 1329
+V G+ ++ E+ V F GLY + A+L D+
Sbjct: 331 TARVYGLPLLKTVDEEGKLLVEPFKGLYFREANRAILRDL 370
>pdb|3V9P|A Chain A, Crystal Structure Of Thymidylate Kinase From Burkholderia
Thailandensis
pdb|3V9P|B Chain B, Crystal Structure Of Thymidylate Kinase From Burkholderia
Thailandensis
Length = 227
Score = 30.4 bits (67), Expect = 9.4, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 34/83 (40%), Gaps = 5/83 (6%)
Query: 1612 PTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKME 1671
P DK +EA+ + GF DL +F+ R + D K + E DA
Sbjct: 135 PRDK---LEALERWVQGGFQPDLTVLFDVPPQIASARRGAVRMPD--KFESESDAFFART 189
Query: 1672 DDMFLRCIEETDRSFVKVDFVEP 1694
+LR +E FV VD EP
Sbjct: 190 RAEYLRRAQEAPHRFVIVDSSEP 212
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 51,669,328
Number of Sequences: 62578
Number of extensions: 2128151
Number of successful extensions: 4646
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 4493
Number of HSP's gapped (non-prelim): 134
length of query: 1791
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1678
effective length of database: 7,902,023
effective search space: 13259594594
effective search space used: 13259594594
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)