RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 002296
(940 letters)
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 715 bits (1847), Expect = 0.0
Identities = 222/988 (22%), Positives = 378/988 (38%), Gaps = 161/988 (16%)
Query: 12 LRELVRHHIESFDYMLDEGLSEMFD----------------------------------- 36
+ LVR H++S++ + L E+ D
Sbjct: 23 SKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRESDRGERE 82
Query: 37 ----HCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQK 92
R ++Y L + ++ E G P+MLK+ + K
Sbjct: 83 ISPMEARLRNLTYAAPLWLTMI--PVENNIEAEPEEVYIGDLPIMLKSAIDPISQYTLDK 140
Query: 93 LVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCV 152
L+ + E+ + GGYFI+NG ERV + N V T A +I
Sbjct: 141 LIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNR----VLVDTGKTGSNITHTAKIISST 196
Query: 153 RKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEK 212
+ VT++ L +G+ + F +P I+++AL D +I + D +
Sbjct: 197 AGYRVPVTIE--RLKDGTFHVSF--PAVPGKIPFVILMRALGILTDRDIVYAV--SLDPE 250
Query: 213 YKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAE 272
+ E + + Q S+ L IG G + E+ A+
Sbjct: 251 IQNE--------------LFPSLEQASSIANVDDALDFIGSRVAI---GQKRENRIEKAQ 293
Query: 273 TVIRDYIFVHL----NDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLI 328
+I Y HL +D K L + + K+ L D+ D N+ + L G L
Sbjct: 294 QIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLF 353
Query: 329 TIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKT 388
+ + +++ ++ K L + + + I L T
Sbjct: 354 ASLFRVAFKAFVKDLTYQLEKSKVRGRK----LALKALVR------PDIVTERIRHALAT 403
Query: 389 GRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGF 448
G + R G + +R N+L +S R V + R L WG
Sbjct: 404 GNW-------VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQ-PNFEARDLHGTQWGR 455
Query: 449 LCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIP----- 503
+CP TP+G GL+ ++ ++A + + + L +G++P
Sbjct: 456 MCPFETPEGPNSGLVKNLALMAQIAVGINE-----------KIVEKTLYEMGVVPVEEVI 504
Query: 504 ---SLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGY 560
+ ++ V+L+GR+VG + E++ +R + I D++ VG+
Sbjct: 505 RRVTEGGEDQNEYLKWSKVILNGRLVGYY--RDGEELAKKIRERRRKG--EISDEVNVGH 560
Query: 561 VPLSLGGAYPGLYLFTSPPKFVRPVRNIS-------------LPSEE--------SQNIE 599
+ +++ + RP+ +S L S IE
Sbjct: 561 IVTDFINE---VHVNCDSGRVRRPLIIVSNGNPLVTREDIEKLDSGSITFDDLVRQGKIE 617
Query: 600 LIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQ 659
+ E+ + TH EI +L + A++ PY +HNQSPRN YQ
Sbjct: 618 YLDAEEEENAYVALEP-----SDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQ 672
Query: 660 CQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAY 719
MAKQ +G + R D + + L PQ P+V+T G P G NAI+AV+++
Sbjct: 673 SAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISF 732
Query: 720 TGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN-KVDRGQKLFRRNKDAKS--LH 776
TGY+MED++I+N+SSV+RGM ++ + + + D+ + K +
Sbjct: 733 TGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYY 792
Query: 777 SVIDSDGLPYVGQMIHPGEPYCSIYDKTTN-----------SWRTNSR--KGSESVFVDY 823
+++ +G+ + G+ + R S + E VD
Sbjct: 793 RLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDL 852
Query: 824 VAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 883
V + + + +R R R P IGDKF+SRHGQKGV L P +DMP++ V G+ P
Sbjct: 853 VLIT--ETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYT-VKGVVP 909
Query: 884 DLIINPHAFPSRMTIAMLLESVAAKVVA 911
D+I+NPHA PSRMT+ ++E +A K A
Sbjct: 910 DVILNPHALPSRMTLGQIMEGIAGKYAA 937
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 420 bits (1081), Expect = e-130
Identities = 246/1062 (23%), Positives = 389/1062 (36%), Gaps = 233/1062 (21%)
Query: 15 LVRHHIESFDYMLDEGLSEMFD-------------------------------------- 36
LV ++SF+ +D L ++
Sbjct: 43 LVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMV 102
Query: 37 -------------HCRQAKISYTGKLMADVEFQYLDA-----------------GSPVVR 66
R ++Y+ L DV+ + +A
Sbjct: 103 NESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSES 162
Query: 67 ERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126
+ G+ P+ML+++ C+L A L LKE +MGGYFI+NG E+V
Sbjct: 163 GKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVL---------- 212
Query: 127 PMSMVRSS------FRDRREGYTDKAVVIRCV--RKDQSSVTLKLYYLLNGSVRLGFWLQ 178
++ RS+ F+ IR + + TL++
Sbjct: 213 -IAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKA 271
Query: 179 GKEYL---LPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAE 235
Y+ +P+ I+ +AL D EI H CYD + ++++
Sbjct: 272 TLPYIKQDIPIVIIFRALGIIPDGEILEH--ICYDVNDWQM------------LEMLKPC 317
Query: 236 VQD-LSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFN--- 291
V+D + R L IG + G++ E A+ +++ H+ +
Sbjct: 318 VEDGFVIQDRETALDFIGRRGTAL--GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKA 375
Query: 292 -LLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDE 350
L +M+ +L D+ D + + L G L+ K + + + +Q
Sbjct: 376 FFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRT 435
Query: 351 IENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAE 410
+E FN+ +K I + ++ L TG Q + RAG +
Sbjct: 436 VEEAHD----FNMKLAIN------AKTITSGLKYALATGNWGEQ-KKAMSSRAGVSQVLN 484
Query: 411 RLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTC 470
R + +S R + R+L WG +CP TP+G+ CGL+ +++
Sbjct: 485 RYTYSSTLSHLRRT-NTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMS 543
Query: 471 RVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIP 530
++ D I+ L GM P L V P V ++G GV
Sbjct: 544 CISVGTDP-----------MPIITFLSEWGMEP-LEDYVPHQSPDATRVFVNGVWHGVH- 590
Query: 531 SSEIEKVVAHLRRLKVSAA-----SVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPV 585
+++ LR L+ S+I D E L +FT + RP+
Sbjct: 591 -RNPARLMETLRTLRRKGDINPEVSMIRDIREKE------------LKIFTDAGRVYRPL 637
Query: 586 -----------------------------RNISLPSEESQN-----------IELIGPFE 605
++I E+ + +E I E
Sbjct: 638 FIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEE 697
Query: 606 QVFMEIRC--------------PDGGDGGRR-----NAFPATHEEIHPTGMLSVVANLTP 646
+ + I D +R +A TH EIHP+ +L V A++ P
Sbjct: 698 EESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIP 757
Query: 647 YSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEY 706
+ DHNQSPRN YQ M KQ MG + R D L PQ P+ T E
Sbjct: 758 FPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFREL 817
Query: 707 PTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN-KVDRGQKL 765
P G NAIVA+ Y+GY+ ED+MI+N+SS+DRG+ +++ G + +K
Sbjct: 818 PAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKP 877
Query: 766 FRRN--KDAKSLHSVIDSDGLPYVGQMIHPGEPYC------------SIYDKTTNSWRTN 811
R N + + +D DGL G + + +S R
Sbjct: 878 QRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDA 937
Query: 812 SR--KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWP 869
S + +E+ VD V V N L + +R R T+ P IGDKF+SRHGQKG +
Sbjct: 938 STPLRSTENGIVDQVLVT-TNQDGL-KFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYR 995
Query: 870 DIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVA 911
DMPF+ G+ PDLIINPHA PSRMT+A L+E + +KV A
Sbjct: 996 REDMPFT-AEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAA 1036
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 242 bits (619), Expect = 1e-66
Identities = 110/301 (36%), Positives = 155/301 (51%), Gaps = 20/301 (6%)
Query: 628 THEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQT 687
TH EIHP +L ++A++ P+ DHNQSPRN YQ M KQ MG + + R D L
Sbjct: 728 THCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYY 787
Query: 688 PQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQT 747
PQ P+ T + E P G NAIVA+L Y+GY+ ED++I+N++S+DRG+ Y+T
Sbjct: 788 PQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRT 847
Query: 748 ETIDLSDDGN-KVDRGQKLFRRNKDAK--SLHSVIDSDGLPYVGQMIHPGEPYC------ 798
T G ++ ++ R + ++ DGL G + +
Sbjct: 848 YTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPI 907
Query: 799 ------SIYDKTTNSWRTNSR--KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPII 850
++ R S + +ES VD V V ++ + +R R TR P I
Sbjct: 908 PLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVT--TNQEGLKFVKVRMRSTRIPQI 965
Query: 851 GDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVV 910
GDKF+SRHGQKG + DMPFS G+ PD+IINPHA PSRMT+A L+E +KV
Sbjct: 966 GDKFASRHGQKGTIGMTYRHEDMPFS-AQGIVPDIIINPHAIPSRMTVAHLVECQLSKVS 1024
Query: 911 A 911
A
Sbjct: 1025 A 1025
Score = 195 bits (497), Expect = 2e-51
Identities = 115/607 (18%), Positives = 199/607 (32%), Gaps = 122/607 (20%)
Query: 15 LVRHHIESFDYMLDEGLSEMFD-------------------------------------- 36
L R + SFD + + E+ D
Sbjct: 30 LARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTM 89
Query: 37 -------------HCRQAKISYTGKLMADVEFQ---------------YLDAGSPVVRER 68
R ++Y+ L D+ + +L +
Sbjct: 90 TEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSK 149
Query: 69 FNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPM 128
G+ P+ML++ C L G +L L E + GGYFI+NG E+V + + +
Sbjct: 150 VFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVI--IAQERSAANI 207
Query: 129 SMVRSSFRDRREGYTDKAVVIRCV--RKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLL-- 184
V F+ IR R + ++++ + + G ++ +
Sbjct: 208 VQV---FKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIRATLPYIRS 264
Query: 185 --PVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLT 242
P+ IV +AL D +I H CYD + + E +K + E +
Sbjct: 265 DIPIVIVFRALGVVPDRDILEH--ICYDPNDFQ---------MLEMMKPCIEEAFV--IQ 311
Query: 243 TRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHL----NDNNDKFNLLIFMLQ 298
+ L +IG+ G+ E A +++ + H+ K L +M+
Sbjct: 312 DKDIALDYIGKRGSTT--GVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIH 369
Query: 299 KLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKF 358
++ D+ D + + L G L+ + R K +Q +E N +
Sbjct: 370 RMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNRE-- 427
Query: 359 DFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFI 418
FNL K S I + L TG Q R G + R F +
Sbjct: 428 --FNLTLAVK------SNIITNGLRYSLATGNWGDQKRSM-VNRVGVSQVLNRYTFASTL 478
Query: 419 SFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDS 478
S R + G + R+L WG +CP TP+G+ CGL+ +++ V+ S
Sbjct: 479 SHLRRTNTPIGRDG-KLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPS 537
Query: 479 RGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVV 538
I+ L G+ L S P V ++G +GV + +
Sbjct: 538 -----------APIIEFLEEWGLET-LEDYNPSASPNATKVFVNGVWLGVH--RDPAHLT 583
Query: 539 AHLRRLK 545
LR L+
Sbjct: 584 ETLRSLR 590
>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 = 75.9 bits (186), Expect = 6e-14
Identities = 113/684 (16%), Positives = 193/684 (28%), Gaps = 281/684 (41%)
Query: 12 LRELVRHH--IE-SFD-----YMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSP 63
R L H +E + + L E F+ T AD E +P
Sbjct: 6 TRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEP---TEGFAADDEPT-----TP 57
Query: 64 VVRE---RF-----------NFGQFPVMLKT-----RRCHLQGADSQKLV-SLKEEAAEM 103
E +F GQF +L C+L+G D L L +E
Sbjct: 58 A--ELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEN--- 112
Query: 104 GGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTL-- 161
+ + +I +NY T + + R K +S
Sbjct: 113 ------DTTLVKTKELI---KNY---------------ITARIMAKRPFDKKSNSALFRA 148
Query: 162 ------KLYYLLNGSVRLGFWLQG--KEYLLPVGIVLKALVDTNDL-EIFNHLTCCYDEK 212
+L + G QG +Y +L +++ +
Sbjct: 149 VGEGNAQLVAIFGG--------QGNTDDYF-------------EELRDLY--------QT 179
Query: 213 YKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQ---------------- 256
Y LV + +K + +L T L + +
Sbjct: 180 YH--------VLVGDLIKFSAETLSELI-RTTLDAEKVFTQGLNILEWLENPSNTPDKDY 230
Query: 257 --------PVIDGLQSESYYAVAETV------IRDYI--------------FVHLNDNND 288
P+I +Q Y A+ + +R Y+ + D+ +
Sbjct: 231 LLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWE 290
Query: 289 KF-NLLIFMLQKLFSL-------VDHTSVSDNP--DSLQNQEILLPGHLITI--YLKEKL 336
F + + LF + +TS+ + DSL+N E +P +++I +E++
Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNE-GVPSPMLSISNLTQEQV 349
Query: 337 EDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTG 396
+D++ K N KQ+ S L G
Sbjct: 350 QDYVNK------------------TN-------SHLPAGKQVEIS----LVNGA------ 374
Query: 397 LDLQQR--AGYTVQAERLNFLRFISFFRAVHRGASFAGLRTT----SVRKLLPESWGFL- 449
+ +G LN + + + +GL + S RKL S FL
Sbjct: 375 ---KNLVVSGPPQSLYGLN--------LTLRKAKAPSGLDQSRIPFSERKLKF-SNRFLP 422
Query: 450 --CPVHTP-----------DGEPCGLLNHMTSTCRVASY--YDSRGNIRDFSKMRTSILR 494
P H+ D + + ++ Y +D ++R S SI
Sbjct: 423 VASPFHSHLLVPASDLINKDLVKNNVSFN-AKDIQIPVYDTFDGS-DLRVLS---GSISE 477
Query: 495 VLIGVGMIPSLP----KLVKS--------GPPAV--LSVL----LDGRVVGVIPSSEIEK 536
+ V I LP + GP L VL DG V VI + ++
Sbjct: 478 RI--VDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDI 535
Query: 537 VVAHLRRLKVSAASVIPDDLEVGY 560
PDD + G+
Sbjct: 536 N---------------PDD-DYGF 543
Score = 58.1 bits (140), Expect = 1e-08
Identities = 81/503 (16%), Positives = 145/503 (28%), Gaps = 168/503 (33%)
Query: 414 FLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLC--PVHT-----PDGEPCGLLNHM 466
FL ++S + F + + + E+ +L +H L+
Sbjct: 64 FLGYVSSLVEPSKVGQFDQVLNLCLTEF--EN-CYLEGNDIHALAAKLLQENDTTLVKT- 119
Query: 467 TSTCRVASYYDSRGNI-RDFSKMRTSIL---------RV-LI--GVGMIPS----LPKLV 509
+ +Y +R R F K S L ++ I G G L L
Sbjct: 120 KELIK--NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLY 177
Query: 510 KSGPPAVLSVLLD--GRVVGVIPSSEIEKVVAHLRRLKVSA----ASVIPDDLEVGYVPL 563
++ V L+ + + + ++ + L + S PD + +P+
Sbjct: 178 QTYHVLV-GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI 236
Query: 564 SLGGAYP--GL-----YLFT------SPPKFVRPVRNISL--------------PSEES- 595
S P G+ Y+ T +P + ++ + S ES
Sbjct: 237 SC----PLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESF 292
Query: 596 -QN----IEL---IGPFEQVFMEIRCPDGGDGGRRNAFPAT------------HEEIHPT 635
+ I + IG +RC A+P T + E P+
Sbjct: 293 FVSVRKAITVLFFIG--------VRC--------YEAYPNTSLPPSILEDSLENNEGVPS 336
Query: 636 GMLSVVANLT---------------PYSDH------NQSPRNMYQCQMAKQTMGFSVQAL 674
MLS ++NLT P N +N+ + G ++
Sbjct: 337 PMLS-ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVN-GAKNLVVSGPPQSLYGLNLTLR 394
Query: 675 KFRA----DQ--------KL------------YH--LQTPQTPIVRTNTYTKYGIDEYPT 708
K +A DQ KL +H L P + ++ + K + +
Sbjct: 395 KAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKD-LVKNNV-SFNA 452
Query: 709 GTNAIVAVLA-YTGYDM--EDAMILNKSSVDRGMCHGQIYQTETIDLS-----DDG-NKV 759
I V + G D+ I + VD + + T D G
Sbjct: 453 KDIQI-PVYDTFDGSDLRVLSGSIS-ERIVDC-IIRLPVKWETTTQFKATHILDFGPGGA 509
Query: 760 DRGQKLFRRNKDAKSLHSVIDSD 782
L RNKD + ++
Sbjct: 510 SGLGVLTHRNKDGTGVRVIVAGT 532
Score = 56.6 bits (136), Expect = 4e-08
Identities = 79/455 (17%), Positives = 141/455 (30%), Gaps = 146/455 (32%)
Query: 546 VSAASVIP-----DDLEVGY-VPLSLGGAYPGLY-LFTS--PPKFVRPVRNISLPSEESQ 596
+ A S P LE VP + L F P P + E +
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPE----PTEGFAADDEPTT 56
Query: 597 NIELIGPFEQVFMEIRCPDGGDGGRR-------NAFPAT---HEEIHPTGMLSVVANLTP 646
EL+G F ++ G F +IH ++ A L
Sbjct: 57 PAELVGKFLG-YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH-----ALAAKLLQ 110
Query: 647 YSDHNQSP-----RNMYQCQMAKQTMGFSVQ-----ALKFRADQ----KLYHL---QTPQ 689
+D +N A+ AL FRA +L + Q
Sbjct: 111 ENDTTLVKTKELIKNYIT---ARIMAKRPFDKKSNSAL-FRAVGEGNAQLVAIFGGQGN- 165
Query: 690 TPIVRTNTYTKYGIDE----YPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIY 745
T+ Y +E Y T + ++ ++ + + L ++++D +
Sbjct: 166 -----TDDY----FEELRDLYQTYHVLVGDLIKFSAETLSE---LIRTTLDA-----EKV 208
Query: 746 QTETIDLSDDGNKVDRGQKLFRRNKDAKS----LHSVIDSDGLPYVG--QMIHPGEPY-- 797
T+ +++ + + N L S+ S P +G Q+ H Y
Sbjct: 209 FTQGLNILE-----------WLENPSNTPDKDYLLSIPIS--CPLIGVIQLAH----YVV 251
Query: 798 -CSIYDKTTNSWRTNSRKGSESVFVDYV---AVDMKNS-----KNLPQKANIRFRHTRNP 848
+ T R+ + G+ V A+ +S ++ + + F
Sbjct: 252 TAKLLGFTPGELRSYLK-GATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF------ 304
Query: 849 IIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVA-- 906
IG R C + +P+ +P S + D + N PS ML S++
Sbjct: 305 FIG----VR------CYEAYPNTSLPPS----ILEDSLENNEGVPS----PML--SISNL 344
Query: 907 --AKVVAYME--NLWMQHHLQIQSRKLMEILGLMN 937
+V Y+ N HL +++ EI L+N
Sbjct: 345 TQEQVQDYVNKTN----SHLP-AGKQV-EI-SLVN 372
Score = 31.6 bits (71), Expect = 1.7
Identities = 54/359 (15%), Positives = 112/359 (31%), Gaps = 136/359 (37%)
Query: 62 SPVVRERFNFGQFPVMLKTRRC--HLQ---GADSQKLVSLKEEAAEMGGYFILNGLERVF 116
S ++ +N R H + G +V + +F +R+
Sbjct: 1639 SKAAQDVWN-----------RADNHFKDTYGFSILDIV--INNPVNLTIHFGGEKGKRI- 1684
Query: 117 RSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFW 176
++NY +M+ + D G + + + + +S T
Sbjct: 1685 ------RENY-SAMIFETIVD---GKLKTEKIFKEINEHSTSYT---------------- 1718
Query: 177 LQGKEYLL-------PVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAV-------G- 221
+ ++ LL P AL + F L K KG + G
Sbjct: 1719 FRSEKGLLSATQFTQP------ALT-LMEKAAFEDL---------KSKGLIPADATFAGH 1762
Query: 222 -----SPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVI--DGLQSESYYAVAETV 274
+ L S LA+V +S+ + ++ + + G Q + D L +Y +A
Sbjct: 1763 SLGEYAALAS------LADV--MSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINP 1814
Query: 275 IRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTS-----VSDNPDSLQNQEILLPGHLIT 329
R V + + + ++ + K T V+ N ++NQ+ + G L
Sbjct: 1815 GR----VAASFSQEALQYVVERVGK------RTGWLVEIVNYN---VENQQYVAAGDLRA 1861
Query: 330 IYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIK--KVMEKNPSKQIGTSIETML 386
+ + + + L +F L I ++ + ++ +E L
Sbjct: 1862 L---DTVTNVL------------------NFIKLQKIDIIELQKSLSLEE----VEGHL 1895
Score = 29.6 bits (66), Expect = 5.8
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 12/83 (14%)
Query: 832 KNLPQKANIRFRHTRNPIIGDKFSS---RHGQKG--VCSQLWPDIDMPFSGVTGMRPDLI 886
N P I F + I + +S+ G +++ +I+ + T +
Sbjct: 1666 INNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGL 1725
Query: 887 INPHAF--PSRMTIAMLLESVAA 907
++ F P A+ L AA
Sbjct: 1726 LSATQFTQP-----ALTLMEKAA 1743
>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 = 69.9 bits (170), Expect = 3e-12
Identities = 99/666 (14%), Positives = 191/666 (28%), Gaps = 220/666 (33%)
Query: 167 LNGSVRLGFWL---QGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSP 223
++G++RL FW + +E +++ V+ + L + + + +
Sbjct: 61 VSGTLRL-FWTLLSKQEE-------MVQKFVEEVLRINYKFLMSPIKTEQR-QPSMMTRM 111
Query: 224 LVSERVKIILAEVQDLS--LTTRLQCLQHIGEHFQPVIDGLQSESYYAV----------- 270
+ +R ++ + Q + +RLQ + + L+ +
Sbjct: 112 YIEQRDRL-YNDNQVFAKYNVSRLQPYLKLRQALL----ELRPAKNVLIDGVLGSGKTWV 166
Query: 271 AETVIRDYIFVHLNDNN---------DKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEI 321
A V Y D + ++ MLQKL +D + + D N I
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP-NWTSRSDHSSN--I 223
Query: 322 LLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTS 381
L H I L+ L+ + L+ ++N K ++ FNL+ K
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENCLLVLLNVQNA-KAWNAFNLS----------CK----- 267
Query: 382 IETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKL 441
+L T RF + TT+ L
Sbjct: 268 --ILLTT---------------------------RFKQVTDFL-------SAATTTHISL 291
Query: 442 LPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGM 501
S TPD E LL Y D R
Sbjct: 292 DHHSMTL-----TPD-EVKSLL---------LKYLDCR---------------------- 314
Query: 502 IPSLPKLVKSGPPAVLSVLLDGRVVGVIPS-------SEIEKVVAHLRRLKVSAASVIPD 554
LP+ V + P LS++ + + +K+ ++ S + P
Sbjct: 315 PQDLPREVLTTNPRRLSII--AESIRDGLATWDNWKHVNCDKL---TTIIESSLNVLEPA 369
Query: 555 DLEVGYVPLSLGGAYPGLYLFTSPPKFVR-PVRNISL-----PSEESQNI--ELI----- 601
+ + LS +F P P +SL + + +L
Sbjct: 370 EYRKMFDRLS---------VF---PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 602 --GPFE------QVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQS 653
P E +++E++ + A H I + + +
Sbjct: 418 EKQPKESTISIPSIYLELKVKLENE-------YALHRSI-----VDHYNIPKTFDSDDLI 465
Query: 654 PRN------------MYQCQMAKQTMGFSVQALKFR-ADQKLYHLQTPQTP-------IV 693
P + + ++ F + L FR +QK+ H T +
Sbjct: 466 PPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQ 525
Query: 694 RTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLS 753
+ Y Y D P + A+L + +E+ +I +K + + + I L
Sbjct: 526 QLKFYKPYICDNDPKYERLVNAILDFL-PKIEENLICSK--------YTDLLR---IALM 573
Query: 754 DDGNKV 759
+ +
Sbjct: 574 AEDEAI 579
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C*
3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Length = 1119
Score = 56.1 bits (136), Expect = 5e-08
Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 10/65 (15%)
Query: 850 IGDKFSSRHGQKGVCSQLWPDIDMPF--SGVTGMRP-DLIINPHAFPSRMTIAMLLESV- 905
+GDK ++RHG KGV +++ P DMP G P D+I+NP PSRM + +LE+
Sbjct: 835 VGDKLANRHGNKGVVAKILPVEDMPHLPDG----TPVDVILNPLGVPSRMNLGQILETHL 890
Query: 906 --AAK 908
A
Sbjct: 891 GLAGY 895
Score = 30.7 bits (70), Expect = 2.9
Identities = 24/102 (23%), Positives = 38/102 (37%), Gaps = 26/102 (25%)
Query: 20 IESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLK 79
++ +Y L E + CR+ ++Y L A ++ + D G E F G P+M +
Sbjct: 66 LDFLEYRLGEPPFPQDE-CREKDLTYQAPLYARLQLIHKDTGLIKEDEVF-LGHIPLMTE 123
Query: 80 TRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVIL 121
G FI+NG +RV S I
Sbjct: 124 D------------------------GSFIINGADRVIVSQIH 141
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 51.6 bits (124), Expect = 1e-06
Identities = 28/61 (45%), Positives = 38/61 (62%), Gaps = 4/61 (6%)
Query: 851 GDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES---VAA 907
GDK + RHG KGV S++ P DMP+ G D+++NP PSRM I +LE+ +AA
Sbjct: 1063 GDKMAGRHGNKGVISKINPIEDMPYDE-NGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Query: 908 K 908
K
Sbjct: 1122 K 1122
Score = 33.2 bits (76), Expect = 0.48
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475
VR + P +G +CP+ TP+G GL+N ++ + Y
Sbjct: 547 VRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEY 584
>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 = 30.3 bits (67), Expect = 1.8
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 18/44 (40%)
Query: 152 VRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVD 195
++K Q+S LKLY + S P + +KA ++
Sbjct: 22 LKKLQAS--LKLY--ADDSA-------------P-ALAIKATME 47
Score = 28.8 bits (63), Expect = 4.9
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 5/27 (18%)
Query: 672 QALK-FRADQKLYHLQTPQT-PIVRTN 696
QALK +A KLY + P +
Sbjct: 20 QALKKLQASLKLY---ADDSAPALAIK 43
>3ftd_A Dimethyladenosine transferase; KSGA, rossmann-like fold, RNA
methyltransferase, mtase, anti resistance,
methyltransferase, RNA-binding; 1.44A {Aquifex aeolicus}
PDB: 3ftc_A 3fte_A 3ftf_A* 3r9x_B*
Length = 249
Score = 30.5 bits (70), Expect = 2.1
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 279 IFVHLNDNNDKFNLLIFMLQK 299
I + N D L +FM+QK
Sbjct: 111 IIENTVYNKDCVPLAVFMVQK 131
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 3.7
Identities = 9/34 (26%), Positives = 16/34 (47%), Gaps = 7/34 (20%)
Query: 332 LKEK----LEDWLRKGKKLIQDEIENNG---KKF 358
+EK LE+W ++ + ++ NN K F
Sbjct: 112 WREKAKKDLEEWNQRQSEQVEKNKINNRIADKAF 145
>2wkj_A N-acetylneuraminate lyase; directed evolution, sialic acid
mimetics, aldolase, S base, carbohydrate metabolism,
N-acetylneuraminic acid LYAS; HET: KPI PYR; 1.45A
{Escherichia coli} PDB: 2wnq_A 2xfw_A* 2wpb_A* 2wnz_A*
2ygy_A* 2wo5_A* 2wnn_A* 3lbm_A 3lbc_A 3lcf_A 3lcl_A
3lcg_A 3lch_A 3lci_A 1hl2_A 1fdy_A 1fdz_A 1nal_1 3lcx_A
3lcw_A
Length = 303
Score = 28.9 bits (65), Expect = 8.1
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 1 MARKKSADFEPLRELVRHHIES 22
++++ D LR LV+ +I+
Sbjct: 23 FDQQQALDKASLRRLVQFNIQQ 44
>1zb7_A Neurotoxin; hexxh metalloprotease; HET: FLC; 2.35A {Clostridium
botulinum}
Length = 455
Score = 29.0 bits (64), Expect = 9.5
Identities = 23/134 (17%), Positives = 42/134 (31%), Gaps = 12/134 (8%)
Query: 764 KLFRR---NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVF 820
KLF R + L +I D +PY+G P + + + + + +
Sbjct: 94 KLFNRINSKPSGQRLLDMI-VDAIPYLGNASTPPDKFAANVANVSINKKIIQPGAE---- 148
Query: 821 VDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLW--PDIDMPFSGV 878
D + M N + T + I+ G G + P F+ V
Sbjct: 149 -DQIKGLMTNLIIFGPGPVLSDNFTDSMIMNGHSPISEGF-GARMMIRFCPSCLNVFNNV 206
Query: 879 TGMRPDLIINPHAF 892
+ I + A+
Sbjct: 207 QENKDTSIFSRRAY 220
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.137 0.405
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 14,560,500
Number of extensions: 906772
Number of successful extensions: 1816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1762
Number of HSP's successfully gapped: 32
Length of query: 940
Length of database: 6,701,793
Length adjustment: 103
Effective length of query: 837
Effective length of database: 3,825,930
Effective search space: 3202303410
Effective search space used: 3202303410
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.9 bits)