RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 046825
(1208 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 = 685 bits (1768), Expect = 0.0
Identities = 250/839 (29%), Positives = 375/839 (44%), Gaps = 147/839 (17%)
Query: 228 PSGFKKQKDLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVV 287
P F +++ L PSD+++ +EK+ E++ E+ + + L V+
Sbjct: 161 PYNFYEERKEGVAKLTPSDIRERLEKVPESDVEILGYDP--------TTSRPEWMILTVL 212
Query: 288 LVPPIKFRLPSKGGDSV-MEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQ 346
VPPI R + E T L +++ N L + ++ +I W LQ
Sbjct: 213 PVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKES-IDAGAPQLIIEDLWDLLQY 271
Query: 347 SVNVLFD----GKNAAGQRDMAS--GICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPY 400
V FD G + R + Q L+ KEG FR L GKRV+++ R+VISPDP
Sbjct: 272 HVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPN 331
Query: 401 LAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNK 460
++++E+G+P A LT PER+TPWN+ KLR +ING + PGA + +
Sbjct: 332 ISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYV 391
Query: 461 KMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHV 520
K R + + G +V RHL DGDVVL NRQP+LH+ S+MAH
Sbjct: 392 KDRKEL-----------------ASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHR 434
Query: 521 VRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGD 580
VRVLKG T R++ C YNADFDGDEMN+H PQ E + AEA I+ + + P G
Sbjct: 435 VRVLKG-LTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGG 493
Query: 581 PLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQ 640
P+ QD+I A LLT K T L ++E Q+L + +
Sbjct: 494 PIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGVA----------------------DVK 531
Query: 641 EVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSD 700
L PAI P +TGKQV++A LP+DF
Sbjct: 532 IDLGE-PAILAPREYYTGKQVVSAF------------------LPKDF------------ 560
Query: 701 RKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLV 760
N G+ + ++ + E + ++I L+
Sbjct: 561 ---NFHGQANVSSG-----------------------PRLCKNEDCPHDSYVVIKNGILL 594
Query: 761 RGVIDKAQF---ADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLIL 817
GV DK ++H + + Y L+ L R+F F+++ GFT ++D+ +
Sbjct: 595 EGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQGFTMRLEDVSLG 654
Query: 818 KDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRG-----GGDAAV 872
D ++E N + ++ + I+K G G
Sbjct: 655 DDVKKEIYNEIDRAKVEVDNL---------------------IQKYKNGELEPIPGRTLE 693
Query: 873 AYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLG 932
+ + L+K + + N+ +M +GA+GS +N Q+++ LG
Sbjct: 694 ESLENYILDTLDK-----LRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLG 748
Query: 933 QQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVD 992
QQ + G+R+ R +TLP F P+D +P A GFI F TGL+P E +FH GREGLVD
Sbjct: 749 QQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVD 808
Query: 993 TAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFD 1051
TAV+TS+SGY+QR LI L L+ YD +VR G ++Q YG+DGV ++ D
Sbjct: 809 TAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGVFPMYSAHGKTVD 867
Score = 92.6 bits (230), Expect = 4e-19
Identities = 38/153 (24%), Positives = 52/153 (33%), Gaps = 6/153 (3%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRK 60
C TCG CPGHFGHI+LV PV + +Y LK C C K S E+EK R
Sbjct: 58 CPTCGNTLGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRI 117
Query: 61 LELIIKGDIIAAKSLDLDLPSESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSL 120
I K AA +E C + + N + +
Sbjct: 118 YNAIKKRWPSAA-----RRLTEYVKKTAMKAQVCPHCGEKQFKIKLEKPYNFYEERKEGV 172
Query: 121 QFAEAKLALLQFLKIETTKCGNCKAKNPRISKP 153
+ K+ + +P S+P
Sbjct: 173 AKLTPSDIRERLEKVPESDV-EILGYDPTTSRP 204
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 699 bits (1805), Expect = 0.0
Identities = 306/1164 (26%), Positives = 474/1164 (40%), Gaps = 233/1164 (20%)
Query: 133 LKIETTKCGNCKAKNPRISKPTFGWIHMNGMPHADIRA--NLIRGCNLGETFSGGEEEKD 190
KI C NC S P F P + A N+ + + +T G D
Sbjct: 102 KKILECVCWNCGKLKIDSSNPKFNDTQRYRDPKNRLNAVWNVCKTKMVCDT--GLSAGSD 159
Query: 191 LGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSGPLLPSDVKDI 250
S+ A H G Q T + + G+ G + L P +V I
Sbjct: 160 NFDLSNPSANMGHGGCGA---AQPTIRKDGLRLWGSWKRGKDESDLPEKRLLSPLEVHTI 216
Query: 251 IEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSK-GGDSVMEHPQ 309
+ + + A + V+ VPP R G S E
Sbjct: 217 FTHISSEDLAHLGLNE--------QYARPDWMIITVLPVPPPSVRPSISVDGTSRGEDDL 268
Query: 310 TVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDMAS---- 365
T LS +++AN + + A ++ LQ V D + A + +
Sbjct: 269 THKLSDIIKANANVRRC-EQEGAPAHIVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRP 327
Query: 366 --GICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVT 423
I L+ KEG R LMGKRV+++ R+VI+ DP L+++E+G+P A LTYPE VT
Sbjct: 328 LKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVT 387
Query: 424 PWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKD 483
P+N+ +L++ + NG + HPGA + + RI + +
Sbjct: 388 PYNIYQLQELVRNGPDEHPGAKYIIRD---------TGERIDLRYHKRAGDIPL------ 432
Query: 484 SDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNAD 543
G V RH++DGDVV+ NRQP+LHK S+M H +RV+ T R++ + S YNAD
Sbjct: 433 ----RYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPY-STFRLNLSVTSPYNAD 487
Query: 544 FDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFL 603
FDGDEMN+H PQ E +RAE I Q V P + P+ ++QD + + +D FL
Sbjct: 488 FDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFL 547
Query: 604 NRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVIT 663
R+ ++ +LP P I KP+ LWTGKQ+++
Sbjct: 548 TRNAVMNIMLW---------------------VPDWDGILP-PPVILKPKVLWTGKQILS 585
Query: 664 AVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKK 723
+ +P+ R + DKQS D G
Sbjct: 586 LI------------------IPKGINLIRDD-DKQSLSNPTDSG---------------- 610
Query: 724 KEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQF--ADYGLVHTVQEL 781
+LI +++ GV+DK + GLVHT+ +
Sbjct: 611 ----------------------------MLIENGEIIYGVVDKKTVGASQGGLVHTIWKE 642
Query: 782 YGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLE 841
G + + R+ +L +GF+ G+ D + D +E + + +
Sbjct: 643 KGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARR-------Q 695
Query: 842 ALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLL 901
E A+ + +LK E +R F+ K++ LN+ +
Sbjct: 696 VAECIQDAQHN--RLKPEPGMTLR-------ESFEAKVSRILNQ-----ARDNAGRSAEH 741
Query: 902 KPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPR 961
N + M +G+KGS +N Q+S+ +GQQ +EGKR+P +TLP F D +P
Sbjct: 742 SLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPE 801
Query: 962 AGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYS 1021
+ GFI + +L GL PQE++FH MAGREGL+DTAVKT+ +GY+QR L+K +E + + YD +
Sbjct: 802 SRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGT 861
Query: 1022 VRDADGSIVQFCYGEDGVDVHQTS-------------FISKF------------------ 1050
VR+A G I+QF YGEDG+D F K+
Sbjct: 862 VRNAMGDIIQFAYGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSI 921
Query: 1051 -------------------DALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQ 1091
D + +G ++ + ++ ++ + +
Sbjct: 922 ENDSSVQDLLDEEYTQLVADRELLCKFIFPKGDARWPLPVNVQRIIQNALQIFHLEAKKP 981
Query: 1092 LDASNAYIMELPDALKDN-------------AEKFADKFLSNEMAKQDFLKLVKHKFVLS 1138
D + I+ + L + A + + +K V ++ L+
Sbjct: 982 TDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRLN 1041
Query: 1139 LAQPGEPVGL------------------LASQSVGEPSTQMTLNTFHLAGRGEMNVTLGI 1180
+G LA+QS+GEP+TQMTLNTFH AG NVTLG+
Sbjct: 1042 KVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGV 1101
Query: 1181 PRLQEILTIASKDIKTPVITCPLL 1204
PRL+EIL +K+IKTP +T L+
Sbjct: 1102 PRLKEILN-VAKNIKTPSLTIYLM 1124
Score = 89.7 bits (222), Expect = 5e-18
Identities = 32/159 (20%), Positives = 48/159 (30%), Gaps = 36/159 (22%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRK 60
C+TCG+ CPGHFGHI+L PV++ + + +L+ +C+ C K + +
Sbjct: 69 CQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQ 128
Query: 61 LELIIKGDIIAAKSLDLDLPSESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSL 120
K + A ++ K C DN P
Sbjct: 129 RYRDPKNRLNAVWNV---------------CKTKMVCDT-GLSAGSDNFDLSNPSAN--- 169
Query: 121 QFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIH 159
G C A P I K
Sbjct: 170 -----------------MGHGGCGAAQPTIRKDGLRLWG 191
>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 = 618 bits (1595), Expect = 0.0
Identities = 230/831 (27%), Positives = 355/831 (42%), Gaps = 162/831 (19%)
Query: 231 FKKQKDLFSG------PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGH-SIFF 283
+KK + L ++ +I + + +F GF +
Sbjct: 185 WKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTS---------LGFNEVFSRPEWMI 235
Query: 284 LGVVLVPPIKFRLPSKGGDS-VMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWM 342
L + VPP R +S E T L+ +L+ANI L + I
Sbjct: 236 LTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETL-EHNGAPHHAIEEAES 294
Query: 343 NLQQSVNVLFD----GKNAAGQRDMAS--GICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ V D G+ A Q+ I L+ KEG R LMGKRV+++ R+VIS
Sbjct: 295 LLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVIS 354
Query: 397 PDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRL 456
DP L ++++G+P A LTYPE VTP+N+ +L + NG HPGA + +
Sbjct: 355 GDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRD------ 408
Query: 457 PPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFE-GKMVYRHLQDGDVVLVNRQPTLHKPS 515
RI L S+ + D + + G V RH+ D D VL NRQP+LHK S
Sbjct: 409 ---SGDRID----LRYSK-------RAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMS 454
Query: 516 IMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVR 575
+MAH V+V+ T R++ + S YNADFDGDEMN+H PQ E +RAE + Q V
Sbjct: 455 MMAHRVKVIPY-STFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVS 513
Query: 576 PSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLI 635
P + P ++QD + LT +DTF+ D+ +LY
Sbjct: 514 PQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYW--------------------- 552
Query: 636 SRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNA 695
V+P PAI KP+PLW+GKQ+++ +P RF+
Sbjct: 553 VPDWDGVIP-TPAIIKPKPLWSGKQILSVA------------------IPNGIHLQRFDE 593
Query: 696 DKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIY 755
+ +LI
Sbjct: 594 GTT---------------------------------------------LLSPKDNGMLII 608
Query: 756 KNDLVRGVIDKAQF--ADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDD 813
++ GV++K ++ GL+H V G L + ++ +L +GF+ G+ D
Sbjct: 609 DGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGD 668
Query: 814 LLILKDKERERKNHLHGS----EEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGD 869
+ RE + + ++ K L + G + + +
Sbjct: 669 TIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRE-SFEDNV--------- 718
Query: 870 AAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISS 929
++ ++ L N + M +G+KGS +N Q+S+
Sbjct: 719 -------VRFLNEARDKAGRLAEVNLKDL--------NNVKQMVMAGSKGSFINIAQMSA 763
Query: 930 HLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREG 989
+GQQ +EGKR+ +TLP F D++P + GF+ + +L GL PQE++FH M GREG
Sbjct: 764 CVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREG 823
Query: 990 LVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVD 1040
L+DTAVKT+ +GY+QR L+K LE + + YD + R++ G+++QF YGEDG+D
Sbjct: 824 LIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMD 874
Score = 113 bits (284), Expect = 2e-25
Identities = 47/114 (41%), Positives = 67/114 (58%), Gaps = 3/114 (2%)
Query: 1091 QLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLA 1150
Q DA + L L + ++ + A L ++ +F+ S+ PGE VG+LA
Sbjct: 1011 QRDAVTLFCCLLRSRLATR--RVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLA 1068
Query: 1151 SQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLL 1204
+QS+GEP+TQMTLNTFH AG VT G+PRL+EIL +K++KTP +T L
Sbjct: 1069 AQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILN-VAKNMKTPSLTVYLE 1121
Score = 86.7 bits (214), Expect = 4e-17
Identities = 22/114 (19%), Positives = 42/114 (36%), Gaps = 4/114 (3%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKC--- 57
C+TC + CPGHFGHIDL PV++ + + + +C C
Sbjct: 67 CQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQAL 126
Query: 58 -VRKLELIIKGDIIAAKSLDLDLPSESSNPEDSDVSNKSSCSMVTPRGNYDNVR 110
++ + K+ + S + + + ++ C P D ++
Sbjct: 127 AIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLK 180
>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 = 137 bits (347), Expect = 5e-35
Identities = 43/113 (38%), Positives = 60/113 (53%), Gaps = 3/113 (2%)
Query: 1093 DASNAYIMELPDALKDNAEKF--ADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLA 1150
+ LP + ++ + + L L ++ L PGE +G++A
Sbjct: 15 EKVKQASNILPQKIVEDLKNLISNKEVLVTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVA 74
Query: 1151 SQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPL 1203
+QSVGEP TQMTL TFH AG E+NVTLG+PRL EI+ A K TP++T L
Sbjct: 75 AQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVD-AKKVPSTPMMTIYL 126
>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 = 122 bits (309), Expect = 1e-29
Identities = 39/213 (18%), Positives = 70/213 (32%), Gaps = 27/213 (12%)
Query: 241 PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGH-SIFFLGVVLVPPIKFRLPSK 299
L+P++V+D +EK+ + + + G + L V+ VPP+ R PS
Sbjct: 241 RLMPTEVRDWLEKIPD---KDLPLL------GLDPEKSRPEWMVLTVLPVPPVTAR-PSI 290
Query: 300 --GGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNA 357
E T L +++ N L + +I W LQ V + +
Sbjct: 291 TLETGIRAEDDLTHKLVDIIRINNRLKQN-IEAGAPQLIIEDLWDLLQYHVTTYINNEAP 349
Query: 358 AGQRDMAS------GICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPY 411
+ Q L+ KEG FR L G + A +
Sbjct: 350 GVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGGAGSGAGSGSVLARA-------AFEIT 402
Query: 412 FALRLTYPERVTPWNVVKLRDSIINGAEIHPGA 444
E+ N+ + ++++ G + H
Sbjct: 403 VQHLFEAAEKGEVDNLNGVIENVLIGQKHHHHH 435
Score = 75.9 bits (187), Expect = 2e-14
Identities = 26/64 (40%), Positives = 38/64 (59%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRK 60
C+TCG R CPGHFGHI+L PV + +Y +L+ C C K + E+E+ ++K
Sbjct: 121 CETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKK 180
Query: 61 LELI 64
+EL
Sbjct: 181 IELA 184
>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 = 73.1 bits (180), Expect = 5e-13
Identities = 69/344 (20%), Positives = 114/344 (33%), Gaps = 109/344 (31%)
Query: 892 INELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTL- 950
+ + + + N + +M SGA+G+ +Q+ G R G L
Sbjct: 744 VTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLC---------GMR------G--LM 786
Query: 951 --PSFHPWDWAPRAGGFIIDR-----FLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYL 1003
PS G + F GL EY+ R+G DTA++T+ SGYL
Sbjct: 787 QKPS-----------GETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYL 835
Query: 1004 QRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRG 1063
R L+ ++++ VR+AD C + V F R R
Sbjct: 836 TRKLV------DVAHEIVVREAD------CGTTKYISV------PLFQMDEVTRTLRLRK 877
Query: 1064 RNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMA 1123
R+ + + GR + + ++LS E
Sbjct: 878 RSDI-----ESGLYGR------------------VLAR--EVEALGRRLEEGRYLSLEDV 912
Query: 1124 KQDFLKLVKHKF-------VL---------------SLAQPGEPV------GLLASQSVG 1155
+ L L+ PV G++A++S+G
Sbjct: 913 HFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSM-ARPVSIGEAVGVVAAESIG 971
Query: 1156 EPSTQMTLNTFHLAG-RGEMNVTLGIPRLQEILTIASKDIKTPV 1198
EP TQ+T+ TFH G ++T G+PR+ E+ K +
Sbjct: 972 EPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFEARRPKAKAVI 1015
Score = 69.6 bits (171), Expect = 5e-12
Identities = 32/87 (36%), Positives = 53/87 (60%), Gaps = 15/87 (17%)
Query: 503 VLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAE 562
VL+NR PTLH+ I A +++G +++++H C +NADFDGD+M VH P ++AE
Sbjct: 440 VLLNRAPTLHRLGIQAFQPVLVEG-QSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 498
Query: 563 A-------YNIVNANNQYVRPSNGDPL 582
A +N+++ P++G+PL
Sbjct: 499 ARIQMLSAHNLLS-------PASGEPL 518
Score = 63.1 bits (154), Expect = 5e-10
Identities = 30/80 (37%), Positives = 46/80 (57%), Gaps = 8/80 (10%)
Query: 344 LQQSVNVLFDG-------KNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ++V+ + D N +R + S + +L K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 314 LQEAVDAVIDNGRRGSPVTNPGSERPLRS-LTDILSGKQGRFRQNLLGKRVDYSGRSVIV 372
Query: 397 PDPYLAVNEIGIPPYFALRL 416
P L +++ G+P AL L
Sbjct: 373 VGPQLKLHQCGLPKRMALEL 392
>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 = 69.4 bits (170), Expect = 7e-12
Identities = 32/87 (36%), Positives = 53/87 (60%), Gaps = 15/87 (17%)
Query: 503 VLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAE 562
VL+NR PTLH+ I A +++G +++++H C +NADFDGD+M VH P ++AE
Sbjct: 700 VLLNRAPTLHRLGIQAFQPVLVEG-QSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 758
Query: 563 A-------YNIVNANNQYVRPSNGDPL 582
A +N+++ P++G+PL
Sbjct: 759 ARIQMLSAHNLLS-------PASGEPL 778
Score = 63.3 bits (154), Expect = 5e-10
Identities = 31/80 (38%), Positives = 45/80 (56%), Gaps = 8/80 (10%)
Query: 344 LQQSVNVLFDG-------KNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ++V+ L D N R + S + +L K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 574 LQEAVDALLDNGRRGAPVTNPGSDRPLRS-LTDILSGKQGRFRQNLLGKRVDYSGRSVIV 632
Query: 397 PDPYLAVNEIGIPPYFALRL 416
P L +++ G+P AL L
Sbjct: 633 VGPQLKLHQCGLPKRMALEL 652
Score = 62.1 bits (151), Expect = 1e-09
Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 1139 LAQPGEPVGLLASQSVGEPSTQMTLNTFHLAG-RGEMNVTLGIPRLQEILTIASKDIKTP 1197
GE VG++A+QS+GEP TQ+T+ TFH G G ++T G+PR+ E+ K
Sbjct: 1214 PVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAV 1273
Query: 1198 V 1198
+
Sbjct: 1274 I 1274
Score = 49.0 bits (117), Expect = 1e-05
Identities = 32/128 (25%), Positives = 48/128 (37%), Gaps = 37/128 (28%)
Query: 886 HTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMV 945
T+ V + + + N + +M SGA+G+ +Q+ G R
Sbjct: 998 ETTEKVTQAVF-KNFEENYPFNPLYVMAQSGARGNPQQIRQLC---------GLR----- 1042
Query: 946 SGKTL---PSFHPWDWAPRAGGFIIDR-----FLTGLRPQEYYFHCMAGREGLVDTAVKT 997
G L PS G + F GL EY+ R+G DTA++T
Sbjct: 1043 -G--LMQKPS-----------GETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRT 1088
Query: 998 SRSGYLQR 1005
+ SGYL R
Sbjct: 1089 ADSGYLTR 1096
>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 = 65.0 bits (159), Expect = 1e-10
Identities = 36/93 (38%), Positives = 53/93 (56%), Gaps = 15/93 (16%)
Query: 503 VLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAE 562
VL+NR PTLH+ I A +++G K +++H C+ YNADFDGD+M VH P ++ E
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE 479
Query: 563 AY-------NIVNANNQYVRPSNGDPLRSLIQD 588
A NI++ P+NG+P+ QD
Sbjct: 480 ARALMMSTNNILS-------PANGEPIIVPSQD 505
Score = 60.7 bits (148), Expect = 2e-09
Identities = 31/79 (39%), Positives = 51/79 (64%), Gaps = 7/79 (8%)
Query: 344 LQQSVNVLFD----GK--NAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
LQ++V+ L D G+ + +R + S + +++ K+G FRQ L+GKRV+Y+ RSVI+
Sbjct: 299 LQEAVDALLDNGRRGRAITGSNKRPLKS-LADMIKGKQGRFRQNLLGKRVDYSGRSVITV 357
Query: 398 DPYLAVNEIGIPPYFALRL 416
PYL +++ G+P AL L
Sbjct: 358 GPYLRLHQCGLPKKMALEL 376
Score = 56.9 bits (138), Expect = 4e-08
Identities = 18/59 (30%), Positives = 34/59 (57%)
Query: 1138 SLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKT 1196
+ GE +G++A+QS+GEP TQ+T+ TFH+ G +++ +I ++K+
Sbjct: 907 HIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKS 965
Score = 49.6 bits (119), Expect = 7e-06
Identities = 41/148 (27%), Positives = 59/148 (39%), Gaps = 48/148 (32%)
Query: 902 KPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTL---PSFHPWDW 958
K N I +M SGA+GS +Q++ G R G L P
Sbjct: 715 KQVSFNSIYMMADSGARGSAAQIRQLA---------GMR------G--LMAKPD------ 751
Query: 959 APRAGGFIIDR-----FLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLEC 1013
G II+ F GL +Y+ R+GL DTA+KT+ SGYL R L+
Sbjct: 752 -----GSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLV----- 801
Query: 1014 LKISYDYSVRDADGSIVQFCYGEDGVDV 1041
++ D V + D C +G+ +
Sbjct: 802 -DVAQDLVVTEDD------CGTHEGIMM 822
>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 = 53.9 bits (129), Expect = 4e-07
Identities = 89/544 (16%), Positives = 163/544 (29%), Gaps = 200/544 (36%)
Query: 188 EKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQ-------KGSGAVPSGFKKQKDLFSG 240
E +D+ H+ DT + + F K+ S
Sbjct: 92 ENCYLEGNDI-----HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKK----SN 142
Query: 241 PLLPSDVKD-------------IIEKLWENEFEL-------CSFISDMQQQGFGKKAGHS 280
L V + + +E EL + D+
Sbjct: 143 SALFRAVGEGNAQLVAIFGGQGNTDDYFE---ELRDLYQTYHVLVGDL------------ 187
Query: 281 IFFLGVVLVPPIK-----FRLPSKGGD--SVMEHPQTVLLSKVLQANIYLANAYVNQPDN 333
I F L I+ ++ ++G + +E+P YL + ++ P
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTP------DKDYLLSIPISCP-- 239
Query: 334 AKVIVARWMNLQQSVNVLFDGKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRS 393
+I + Q + + +LL G R L G +
Sbjct: 240 --LIG-----VIQLAHYVV--------------TAKLLGFTPGELRSYLKG--ATGHSQG 276
Query: 394 VIS----------PDPYLAVNE-------IGIPPYFALR--LTYPERVTPWNVVKLRDSI 434
+++ +++V + IG +R YP P ++++ DS+
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAITVLFFIG------VRCYEAYPNTSLPPSILE--DSL 328
Query: 435 INGAEIHP-------GATH-----YLDKLSTMRLPPNKKMRISI--GRK----------- 469
N E P T Y++K ++ LP K++ IS+ G K
Sbjct: 329 ENN-EGVPSPMLSISNLTQEQVQDYVNKTNS-HLPAGKQVEISLVNGAKNLVVSGPPQSL 386
Query: 470 --LDTS-RGAIVQPGKD-SDNEFEG---KMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVR 522
L+ + R A G D S F K R L V P H ++
Sbjct: 387 YGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFL----PVAS---P-FHSH-LLVPASD 437
Query: 523 VLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPL 582
++ + N F+ ++ + P V Y+ + ++ +R +G
Sbjct: 438 LINKD---------LVKNNVSFNAKDIQI--P---V-----YDTFDGSD--LRVLSGSIS 476
Query: 583 RSLIQDHIVSA-----ALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFT-----GKPGQR 632
++ D I+ K T + L + G +SGLG T G G R
Sbjct: 477 ERIV-DCIIRLPVKWETTTQFKATHI-------LDFGPG-GASGLGVLTHRNKDGT-GVR 526
Query: 633 VLIS 636
V+++
Sbjct: 527 VIVA 530
Score = 47.0 bits (111), Expect = 4e-05
Identities = 74/466 (15%), Positives = 141/466 (30%), Gaps = 158/466 (33%)
Query: 227 VPSG---FKKQ-KDLFSGPLLPSDVKDIIEKLWENEF----ELCS----FISDMQQQGFG 274
VP+ Q ++ F+ +LP + ++E EL ++S + +
Sbjct: 22 VPTASFFIASQLQEQFNK-ILPEPTEGFAA---DDEPTTPAELVGKFLGYVSSLVEPS-- 75
Query: 275 KKAGHSIFFLGVVLVPPIKFR---LPSKGGD--SV-----MEHPQTVLLSKVLQANIYLA 324
K G L + L +F L +G D ++ E+ T++ +K L N A
Sbjct: 76 -KVGQFDQVLNLCLT---EFENCYL--EGNDIHALAAKLLQENDTTLVKTKELIKNYITA 129
Query: 325 NAYVNQPDNAKVIVARWMNLQQSVN-------VLFDGKNAAGQ----------RDM---- 363
+P + K A L ++V +F G GQ RD+
Sbjct: 130 RIMAKRPFDKKSNSA----LFRAVGEGNAQLVAIF-G----GQGNTDDYFEELRDLYQTY 180
Query: 364 ASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALR--LTYPER 421
+ L++ + ++ R+ + + + L P
Sbjct: 181 HVLVGDLIKF---------SAETLSELIRTTLDAEKVF-------TQGLNILEWLENPSN 224
Query: 422 VTPWNVVKLRDSIINGAEI-HP--GAT---HYLDKLSTMRLPPNKKMRISIGRKLDTSRG 475
TP + I P G HY+ + P ++R + S+G
Sbjct: 225 -TP------DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP-GELRSYLKGATGHSQG 276
Query: 476 ---AIVQPGKDSDNEF----------------EGKMVYRHLQDGDVVLVNRQPTLHK--- 513
A+ DS F Y + + P++ +
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNT--------SLPPSILEDSL 328
Query: 514 ------PSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDE-VSRAEAYNI 566
PS M + + + + ++ + ++ N H P + V + +
Sbjct: 329 ENNEGVPSPMLSISNLTQ--EQVQDYV------------NKTNSHLPAGKQVEIS----L 370
Query: 567 VNANNQYVRPSNGDP--LRSLIQDHIVSAALLTKKDTFLNRDEFCQ 610
VN V +G P L L + A + D +R F +
Sbjct: 371 VNGAKNLV--VSGPPQSLYGLNL-TLRKAKAPSGLDQ--SRIPFSE 411
Score = 40.4 bits (94), Expect = 0.004
Identities = 46/295 (15%), Positives = 80/295 (27%), Gaps = 116/295 (39%)
Query: 932 GQQELEGKRVPRMVSGKTL----PSF-HPWDWAPRAGGFIIDRFLTGLR--------PQE 978
G QE +G M G L + W+ RA D + G P
Sbjct: 1625 GSQE-QG-----M--GMDLYKTSKAAQDVWN---RADNHFKDTY--GFSILDIVINNPVN 1671
Query: 979 YYFHCMAGREGLVDTAVKTSRSGYL----QRCLIKNLECLKISYDYSVRDADGSIVQFCY 1034
H G +G K R Y + + L+ KI ++ + + +
Sbjct: 1672 LTIH-FGGEKG------KRIRENYSAMIFETIVDGKLKTEKI-----FKEINEHSTSYTF 1719
Query: 1035 GEDGVDVHQTSF---------ISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIY 1085
+ + T F + F+ L + +G F G H
Sbjct: 1720 RSEKGLLSATQFTQPALTLMEKAAFEDL--KSKGLIPADATFA--G-H------------ 1762
Query: 1086 KKCS-GQ---LDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKH--KFVLSL 1139
S G+ L AS A +M + +++V + +
Sbjct: 1763 ---SLGEYAAL-ASLADVMSIESL----------------------VEVVFYRGMTMQVA 1796
Query: 1140 AQPGEPVGLLASQSVGEPSTQMTLNTFHLAGR-GEMNVTLGIPRLQEILTIASKD 1193
E +G + M +A G + + LQ ++ K
Sbjct: 1797 VPRDE---------LGRSNYGM------IAINPGRVAASFSQEALQYVVERVGKR 1836
Score = 40.4 bits (94), Expect = 0.005
Identities = 67/368 (18%), Positives = 104/368 (28%), Gaps = 167/368 (45%)
Query: 160 MNGM------PHA-DI--RANLIRGCNLGETFSGGEEEKDLGASSDV--DAPETHSFNGT 208
M GM A D+ RA+ G FS D+ + P + +
Sbjct: 1631 M-GMDLYKTSKAAQDVWNRADNHFKDTYG--FS----------ILDIVINNPVNLTIH-- 1675
Query: 209 FPGTQDTAAR-RHQKGSGA-VPSGFKKQKDLFSGPLLPSDVKDIIEKL----WENEFELC 262
F G + R + + G K + +F K+I E + +E L
Sbjct: 1676 FGGEKGKRIRENYSAMIFETIVDGKLKTEKIF---------KEINEHSTSYTFRSEKGLL 1726
Query: 263 ---------------SFISDMQQQGFGKK----AGHSIFFLGVVLVPPIKFRLPSKGGDS 303
+ D++ +G AGHS LG
Sbjct: 1727 SATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHS---LG------------------ 1765
Query: 304 VMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDM 363
E Y A +A M+++ V V+F R
Sbjct: 1766 --E---------------Y----------AALASLADVMSIESLVEVVF-------YR-- 1789
Query: 364 ASGICQLLEKKEGLFRQKLMGK----RVNYACRSVISPDPYLAVNEIGIPPYF---ALRL 416
G+ Q + + R NY +A+N + F AL+
Sbjct: 1790 ------------GMTMQVAVPRDELGRSNYGM---------IAINPGRVAASFSQEALQ- 1827
Query: 417 TYPERV---TPWNVVKLRDSIIN----GAEI----HPGATHYLDKLSTMRLPPNKKMRIS 465
ERV T W V I+N + A LD ++ + L K +I
Sbjct: 1828 YVVERVGKRTGWLV-----EIVNYNVENQQYVAAGDLRA---LDTVTNV-LNFIKLQKID 1878
Query: 466 IGRKLDTS 473
I +L S
Sbjct: 1879 I-IELQKS 1885
Score = 33.5 bits (76), Expect = 0.53
Identities = 25/149 (16%), Positives = 41/149 (27%), Gaps = 73/149 (48%)
Query: 2 KTCGQRQFL---CPGH---------------------FGHIDLVVPVYNP---------- 27
K +FL P H F D+ +PVY+
Sbjct: 413 KLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLS 472
Query: 28 --LLFNLLYTLLKRICFF--CHHFKAS-----------------RREVE-KCVRKLELII 65
+ ++ +++ + FKA+ R + VR
Sbjct: 473 GSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVR------ 526
Query: 66 KGDIIAAKSLDLDLPSESSNPEDSDVSNK 94
+I A +LD NP+D D K
Sbjct: 527 ---VIVAGTLD-------INPDD-DYGFK 544
Score = 31.2 bits (70), Expect = 2.6
Identities = 34/212 (16%), Positives = 64/212 (30%), Gaps = 70/212 (33%)
Query: 478 VQPGKDSD---------NEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEK 528
V+P K EFE +L+ D+ H ++ A +++ + +
Sbjct: 72 VEPSKVGQFDQVLNLCLTEFEN----CYLEGNDI---------H--ALAAKLLQ--ENDT 114
Query: 529 TLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQD 588
TL Y A + A + + SN R++ +
Sbjct: 115 TLVKTKELIKNY--------------------ITARIM--AKRPFDKKSNSALFRAVGEG 152
Query: 589 HIVSAALL----TKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLP 644
+ A+ D F +E + LY T LI S + +
Sbjct: 153 NAQLVAIFGGQGNTDDYF---EEL-RDLYQ-----------TYHVLVGDLIKFSAETLSE 197
Query: 645 LLPAIWKPEPLWT-GKQVITAVLNHITRGRPP 675
L+ E ++T G ++ L + + P
Sbjct: 198 LIRTTLDAEKVFTQGLNIL-EWLENPSN-TPD 227
>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 = 52.2 bits (124), Expect = 1e-06
Identities = 82/594 (13%), Positives = 172/594 (28%), Gaps = 188/594 (31%)
Query: 267 DMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANA 326
+ + + K I V K V + P+++L + + +I
Sbjct: 10 ETGEHQYQYK---DILS---VFEDAFVDNFDCK---DVQDMPKSILSKEEID-HI----- 54
Query: 327 YVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDMASGICQLLEKKEGLFRQKLMGK- 385
+ D LF LL K+E + QK + +
Sbjct: 55 -IMSKDA-----------VSGTLRLFW---------------TLLSKQEEMV-QKFVEEV 86
Query: 386 -RVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGA 444
R+NY +L P +T ++ RD + N ++
Sbjct: 87 LRINY---------KFLMSP-------IKTEQRQPSMMTR-MYIEQRDRLYNDNQV---- 125
Query: 445 THYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQ----PGKDS-------DNEFEGKM- 492
K + RL P K+R ++ +L ++ ++ GK + + KM
Sbjct: 126 ---FAKYNVSRLQPYLKLRQAL-LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD 181
Query: 493 --VY----RHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDG 546
++ ++ + VL Q L++ + T R ++
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQ----------IDPNWTSRSDHS---------SN 222
Query: 547 DEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRD 606
++ +H Q E+ R + + Y L L+ ++ +A + F
Sbjct: 223 IKLRIHSIQAELRR------LLKSKPYENC-----L--LVLLNVQNAKAW---NAFNLS- 265
Query: 607 EFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVL 666
C++L +++ + + L P E K ++ L
Sbjct: 266 --CKIL----LTTRFKQVTDFLSAATTTHISLDHHSMTLTP----DE----VKSLLLKYL 311
Query: 667 NHITRGRP-------PFVVERGGKLPQDFFKTRFNADKQSDR-KKNDKGKLSKTNKMHKD 718
+ + P P + + +D T D K + KL+ +
Sbjct: 312 DCRPQDLPREVLTTNPRRLSIIAESIRDGLAT-------WDNWKHVNCDKLTTIIES--- 361
Query: 719 KSGKKKEVVEGKPGEEKEAEKNKS---KEKELSEEKLLIYKNDLVRGVIDKAQFADYGLV 775
V+E P E ++ S + L + D+++ +
Sbjct: 362 ----SLNVLE--PAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMV--------- 406
Query: 776 HTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLH 829
V +L+ S + + Q T + + + + E + LH
Sbjct: 407 -VVNKLHKY-------SLVEK------QPKESTISIPSIYLELKVKLENEYALH 446
Score = 51.4 bits (122), Expect = 2e-06
Identities = 76/641 (11%), Positives = 177/641 (27%), Gaps = 167/641 (26%)
Query: 596 LTKKD-TFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEP 654
KD + D F V + + +++S+ L
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL-------- 67
Query: 655 LWT----GKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLS 710
WT ++++ + + R F++ KT + +
Sbjct: 68 FWTLLSKQEEMVQKFVEEVLRINYKFLMSP--------IKTEQR-----QPSMMTRMYIE 114
Query: 711 KTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKEL-SEEKLLIY------KNDLVRGV 763
+ ++++ D K V + K + EL + +LI K + V
Sbjct: 115 QRDRLYNDNQVFAKYNVS----RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDV 170
Query: 764 I--DKAQFADYGLVH--TVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILK- 818
K Q + ++ N+ T+L L +L + L+
Sbjct: 171 CLSYKVQCKMDFKIFWLNLKN---CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI 227
Query: 819 DKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMK 878
+ L + + + L + + ++ F++
Sbjct: 228 HSIQAELRRL-----LKSKPYENCLLV-----LLNVQNAKAWN------------AFNLS 265
Query: 879 ----MTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQ- 933
+T++ V + L + + + +T K + +L
Sbjct: 266 CKILLTTR-----FKQVTDFLSAATTTHISLDHHSMTLTPDEVKS------LLLKYLDCR 314
Query: 934 -QEL--EGKRV-PRMVS--GKTLPSFHP-WD-WAPRAGGF-----IIDRFLTGLRP---Q 977
Q+L E PR +S +++ WD W + II+ L L P +
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDGLATWDNW--KHVNCDKLTTIIESSLNVLEPAEYR 372
Query: 978 EYYFHCMAGREG--------------LVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVR 1023
+ + ++ + V + + L++ K + ++
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE-----KQPKESTIS 427
Query: 1024 DADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDK----------GSH 1073
+ E+ +H+ S + ++ + + G H
Sbjct: 428 IPSIYLELKVKLENEYALHR-SIVDHYNIPKTFD------SDDLIPPYLDQYFYSHIGHH 480
Query: 1074 TFVMGRNQE-----MIY-------KKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNE 1121
+ + M++ +K A NA + + L+ + + N+
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNA-SGSILNTLQQ-LKFYKPYICDND 538
Query: 1122 MAKQ-------DFL-----KLVKHKFV----LSLAQPGEPV 1146
+ DFL L+ K+ ++L E +
Sbjct: 539 PKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAI 579
Score = 47.5 bits (112), Expect = 3e-05
Identities = 96/599 (16%), Positives = 161/599 (26%), Gaps = 218/599 (36%)
Query: 248 KDIIEKLWEN---EFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFR-------LP 297
KDI+ + F+ C + DM + K+ I ++ L
Sbjct: 19 KDILSVFEDAFVDNFD-CKDVQDMPKSILSKEEIDHI-----IMSKDAVSGTLRLFWTLL 72
Query: 298 SKGGDSVMEHPQTVLLSKVLQANIY--LANAY---VNQP----------------DN--- 333
SK + V + + +VL+ N Y L + QP DN
Sbjct: 73 SKQEEMVQK-----FVEEVLRIN-YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126
Query: 334 AKVIVARW----------MNLQQSVNVLFDGKNAAG--------------QRDMASGI-- 367
AK V+R + L+ + NVL DG +G Q M I
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186
Query: 368 -----CQ----LLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTY 418
C +LE + L Q + N+ RS S + L ++ I LR
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQ--IDP--NWTSRSDHSSNIKLRIHSI----QAELRRLL 238
Query: 419 PERVTP---------WN--VVK--------L---RD-SIINGA-----------EIHPGA 444
+ N L R + +
Sbjct: 239 KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298
Query: 445 TH---------YLDKLSTMRLPPNKK----MRIS-IGRKLDTSRGAIVQPGKDSDNEFEG 490
T YLD LP R+S I + +D ++
Sbjct: 299 TPDEVKSLLLKYLD-CRPQDLPREVLTTNPRRLSIIAESI-----------RDGLATWDN 346
Query: 491 KMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMN 550
++H+ ++ T+ + S+ VL+ R + S +
Sbjct: 347 ---WKHVN------CDKLTTIIESSL-----NVLE-PAEYRKMFDRLSVFPPS------- 384
Query: 551 VHFPQD-------EVSRAEAYNIVNANNQYVRPS--NGDPLRSLIQDHIVSAALLTKKD- 600
H P +V +++ +V N+ + S P S I + L K +
Sbjct: 385 AHIPTILLSLIWFDVIKSDVMVVV---NKLHKYSLVEKQPKESTISIPSIYLELKVKLEN 441
Query: 601 ------TFLNRDEFCQLLYSSGVSSSGLG----SFTGKPGQRVLISRSEQEVLPLLPAI- 649
+ ++ + S + L S G L + E + L +
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG----HHLKNIEHPERMTLFRMVF 497
Query: 650 ----W------KPEPLWTGKQVITAVL-------NHITRGRPPFVVERGGKLPQDFFKT 691
+ W I L +I P + ER DF
Sbjct: 498 LDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKY--ERLVNAILDFLPK 554
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 38.0 bits (87), Expect = 0.006
Identities = 11/38 (28%), Positives = 14/38 (36%), Gaps = 16/38 (42%)
Query: 369 QLLEKKEGLFRQKLMGKRVNYACRSVISPD--PYLAVN 404
Q L+K + KL YA D P LA+
Sbjct: 20 QALKKLQA--SLKL------YA------DDSAPALAIK 43
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.4 bits (73), Expect = 0.61
Identities = 11/64 (17%), Positives = 21/64 (32%), Gaps = 20/64 (31%)
Query: 701 RKKNDKGKLSKTNKMHKDKSGKKK--EVVEGKPGE------------EKEAEKNKSKEKE 746
R++ K +L + D + K E E + EK N+ +K
Sbjct: 91 REEQRK-RLQE-----LDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKA 144
Query: 747 LSEE 750
++
Sbjct: 145 FYQQ 148
>3jql_A Phospholipase A2 isoform 3; phospholipase A2, hexapeptide, hydrolase,
calcium, disulfide bond, lipid degradation,
metal-binding, secreted; 1.20A {Naja sagittifera} PDB:
1mf4_A 3jq5_A 1ln8_A 3jti_A 3nju_A* 3osh_A* 3q4y_A 1t37_A
1zm6_A 3gci_A 1yxl_A 1oxr_A 1td7_A* 1sz8_A 1a3d_A 1a3f_A
1psh_A 2osh_A 1poa_A 1pob_A* ...
Length = 119
Score = 30.2 bits (68), Expect = 1.6
Identities = 13/78 (16%), Positives = 23/78 (29%), Gaps = 12/78 (15%)
Query: 969 RFLTGLRPQEYYF----HCMAGREG----LVDTAVKTSRSGYLQRCLIKNLECLKISYDY 1020
+ R + +C G G +D +T + Y C Y
Sbjct: 10 QCTVPSRSWADFADYGCYCGKGGSGTPVDDLDRCCQTHDNCY--NEAENISGCRPYFKTY 67
Query: 1021 SVRDADGSIVQFCYGEDG 1038
S G++ C G++
Sbjct: 68 SYECTQGTLT--CKGDNN 83
>3euw_A MYO-inositol dehydrogenase; protein structure initiative II (PSI II),
NYSGXRC, MYO-inosi dehydrogenase, oxidoreductase,
tetramer; 2.30A {Corynebacterium glutamicum}
Length = 344
Score = 30.4 bits (69), Expect = 4.0
Identities = 16/96 (16%), Positives = 23/96 (23%), Gaps = 31/96 (32%)
Query: 942 PRMVSGKTL-PSFHPWDWAPRAGGFIID---------RFLTGLRPQEYY-----FHCMAG 986
+ + P+ P D+ +GG D RF + F
Sbjct: 146 LEQLVIISRDPAPAPKDYIAGSGGIFRDMTIHDLDMARFFVPNIVEVTATGANVFSQEIA 205
Query: 987 REGLVDTA-------------VKTSRS---GYLQRC 1006
D + SR GY QR
Sbjct: 206 EFNDYDQVIVTLRGSKGELINIVNSRHCSYGYDQRL 241
>3ezy_A Dehydrogenase; structural genomics, unknown function, PSI-2, protein
structure initiative; 2.04A {Thermotoga maritima}
Length = 344
Score = 30.3 bits (69), Expect = 4.1
Identities = 21/83 (25%), Positives = 29/83 (34%), Gaps = 31/83 (37%)
Query: 955 PWDWAPRAGGFIID---------RFLTGLRPQEYY------FHCMAGREGLVDTAVKT-- 997
P D+ +GG +D R++ G +E + G+ G VDTAV
Sbjct: 159 PLDYIRVSGGIFLDMTIHDFDMARYIMGEEVEEVFADGSVLVDEEIGKAGDVDTAVVVLR 218
Query: 998 -----------SRS---GYLQRC 1006
SR GY QR
Sbjct: 219 FKSGALGVIDNSRRAVYGYDQRI 241
>1nkw_Y 50S ribosomal protein L31; ribosome, large subunit, X- RAY
structure, peptidyl-transferase, peptide bond formation;
3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB:
1nwx_Y* 1nwy_Y* 1pnu_Y 1pny_Y 1sm1_Y* 1vor_1 1vou_1
1vow_1 1voy_1 1vp0_1 1xbp_Y* 1yl3_4 2b66_4 2b9n_4 2b9p_4
Length = 73
Score = 27.6 bits (62), Expect = 5.1
Identities = 13/50 (26%), Positives = 18/50 (36%), Gaps = 17/50 (34%)
Query: 654 PLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKK 703
P WTG++ T GR V++ F RF + KK
Sbjct: 41 PFWTGEERFLD-----TEGR----VDK--------FNKRFGDSYRRGSKK 73
>1z05_A Transcriptional regulator, ROK family; structural genomics, protein
structure initiative, midwest center for structural
genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP:
a.4.5.63 c.55.1.10 c.55.1.10
Length = 429
Score = 29.6 bits (67), Expect = 7.2
Identities = 6/26 (23%), Positives = 12/26 (46%)
Query: 881 SQLNKHTSSSVINELLSEGLLKPTGK 906
S+L + + + EL+ L+ T
Sbjct: 63 SELAPASITKITRELIDAHLIHETTV 88
>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2,
protein structure initiative, joint center structural
genomics, JCSG; 2.46A {Thermotoga maritima} SCOP:
a.4.5.63 c.55.1.10 c.55.1.10
Length = 380
Score = 29.5 bits (67), Expect = 8.0
Identities = 5/26 (19%), Positives = 9/26 (34%)
Query: 881 SQLNKHTSSSVINELLSEGLLKPTGK 906
L K T + L +G++
Sbjct: 43 LGLTKTTVGEIAKIFLEKGIVVEEKD 68
>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA
binding P helix-turn-helix, phosphotransferase system;
2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10
c.55.1.10 PDB: 3bp8_A
Length = 406
Score = 29.2 bits (66), Expect = 8.5
Identities = 5/26 (19%), Positives = 14/26 (53%)
Query: 881 SQLNKHTSSSVINELLSEGLLKPTGK 906
+QL + + +++E+L L++
Sbjct: 40 AQLAPASITKIVHEMLEAHLVQELEI 65
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
0.318 0.135 0.401
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: 18,375,157
Number of extensions: 1140531
Number of successful extensions: 2276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2230
Number of HSP's successfully gapped: 52
Length of query: 1208
Length of database: 6,701,793
Length adjustment: 104
Effective length of query: 1104
Effective length of database: 3,798,009
Effective search space: 4193001936
Effective search space used: 4193001936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.6 bits)