RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 001092
(1159 letters)
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 1393 bits (3606), Expect = 0.0
Identities = 429/1223 (35%), Positives = 647/1223 (52%), Gaps = 112/1223 (9%)
Query: 24 PVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIV-----------S 72
+ D + ++ F + L +Q L SF+ FV +++IV + +
Sbjct: 10 ETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQG 69
Query: 73 GIDPSIFLRFKDVRIGQPSMT-VDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT-- 129
+ + F + + +P+MT DG + + P RL ++TY++P+ V++
Sbjct: 70 DVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADS 129
Query: 130 -----------EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFI 178
E+ E + V IG+IPIMLRS C+L G ++EL L ECP D GGYFI
Sbjct: 130 NVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFI 189
Query: 179 IKGTEKVLLIQEQLSKNRVIIDTDKKGNINA--SVTSSTETVKSKTVIQMEK-------- 228
I G+EKV++ QE+ + N V + + A + S S+ + M+
Sbjct: 190 INGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE 249
Query: 229 ---GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDP---RYSALLLPSIEECAN 282
+ L IPI++V +A+G+ D+++++ + DP + ++ P IEE
Sbjct: 250 NSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFV 309
Query: 283 LDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVA 342
I ++ AL+Y+ + T G R A IL+ L ++ K F++
Sbjct: 310 --IQDKDIALDYIGKRGS--TTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLG 365
Query: 343 VMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKP 402
M+ RM+ L + DD+D+ G KRL+L+G L++ LF LF+ M +V K + +
Sbjct: 366 YMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETN 425
Query: 403 SRSSRFDLSQFIVRDSITVGLERTLSTGNF-DVKRFKMHRKGMTQVLARLSFIGTLGHMT 461
F+L+ + + IT GL +L+TGN+ D KR ++R G++QVL R +F TL H+
Sbjct: 426 RE---FNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLR 482
Query: 462 RVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLIS 521
R + + K++ PR L + WGM+CP +TPEG+ACGLVKNL+LM++V+ P+I
Sbjct: 483 RTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIE 542
Query: 522 LCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVS 581
G+E LE + +PN+ V NG+ LG HR P + +R LRR I VS
Sbjct: 543 FLEEWGLETLEDYNPS--ASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVS 600
Query: 582 VFVNEKQRCVYIASDGGRVCRPLVIAD-------KGISRIKEHHMKELLDGVR------- 627
+ + +++ + + +D GR+CRPL I D +G I++ H+++L++
Sbjct: 601 IVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPE 660
Query: 628 ---SFDDFLREGLIEYLDVNEENNALIALYEGDATPDT---------------------- 662
+ + GLIEYLD EE +IA+ D
Sbjct: 661 QRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAP 720
Query: 663 -------THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDS 715
TH EI P ILG++A +IP+P HNQSPRNTYQ AMGKQAMG N RMD+
Sbjct: 721 NPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDT 780
Query: 716 LLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFG 775
+ +L YPQ+PL TTR++E + + +L AGQNA VA++ YSGY+ ED+I+MN++S+DRG
Sbjct: 781 MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLF 840
Query: 776 RCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEI 835
R I + YT +K + + RP R+ RM+ + L+DDGL APG
Sbjct: 841 RSIFYRTYTDQEKKIGMTVMEEFERPVRSTTL--RMKHGTYD-----KLEDDGLIAPGTR 893
Query: 836 IKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGD 895
+ D+ I K +P+ + R + E+ +VD+V + +++ G
Sbjct: 894 VSGEDIIIGKTAPIPLDHEELGQ-RTQLHAKRDVSTPLRST--ESGIVDQVMVTTNQEGL 950
Query: 896 LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRM 955
+K +R TR P++GDKF+SRHGQKG G + ED PFS +GI PD+I+NPH PSRM
Sbjct: 951 KFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRM 1010
Query: 956 TVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGI 1015
TV ++E K G + F + TVE++S+ L HGF G +++Y G
Sbjct: 1011 TVAHLVECQLSKVSALSGFEGDATPFTD-----VTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Query: 1016 TGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERD 1075
TG L A +F+GP YYQ+LKH+V DK+HAR GP +LTRQP EGR+R+GGLR GEMERD
Sbjct: 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERD 1125
Query: 1076 CLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLP 1135
C I++G S ++ ERL SD + V VC +CGL+ ++K + C +C+N S + LP
Sbjct: 1126 CQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLP 1185
Query: 1136 YACKLLIQELQSMNIVPRLKLAE 1158
YA KLL QEL SMNI PRL
Sbjct: 1186 YAAKLLFQELMSMNIAPRLFTKN 1208
>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 = 1383 bits (3580), Expect = 0.0
Identities = 429/1246 (34%), Positives = 653/1246 (52%), Gaps = 112/1246 (8%)
Query: 1 MGLMQVEGSPKDEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGI 60
M + DE + +AP+ + D + ++ F + +GLV Q LDSFN FV+ +
Sbjct: 1 MSDLANSEKYYDEDPYGFEDESAPI-TAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL 59
Query: 61 RKIVRANDRIV-----------SGIDPSIFLRFKDVRIGQPSMT-VDGVSEKLNPHMCRL 108
+ I+ + ++ I + F + + +P + DGV+ L P RL
Sbjct: 60 QDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARL 119
Query: 109 SDMTYAAPILVNIEYVQGS---------------HTEKTTMEKNDVVIGRIPIMLRSCRC 153
++TY++ + V+++ + E V IGR+PIMLRS C
Sbjct: 120 RNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNC 179
Query: 154 VLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASV-- 211
L E++L +L ECP D GGYFII G+EKVL+ QE+ + N V + + + V
Sbjct: 180 YLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAE 239
Query: 212 TSSTETVKSKTVIQME----------KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261
S S+ + ++ + L + IPI+++ +A+G+ D E+++
Sbjct: 240 IRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILE 299
Query: 262 MVGRDP---RYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSI 318
+ D + +L P +E+ I +E AL+++ + G R A I
Sbjct: 300 HICYDVNDWQMLEMLKPCVEDG--FVIQDRETALDFIGRRGT--ALGIKKEKRIQYAKDI 355
Query: 319 LRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSL 378
L+ FL ++ K F++ M+ R++ L++ DD+D+ G KRL+L+G L++
Sbjct: 356 LQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQ 415
Query: 379 LFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFK 438
LF+ LFK + ++ + + + + F++ I +IT GL+ L+TGN+ ++
Sbjct: 416 LFKTLFKKLTKDIFRYMQRTVEEAHD---FNMKLAINAKTITSGLKYALATGNWGEQKKA 472
Query: 439 M-HRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEA 497
M R G++QVL R ++ TL H+ R + + K++ PR L + WG++CP +TPEG+A
Sbjct: 473 MSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQA 532
Query: 498 CGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKH 557
CGLVKNL+LM+ ++ + P+I+ G+E LE + +P++ V NG+ G H
Sbjct: 533 CGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQ--SPDATRVFVNGVWHGVH 590
Query: 558 RRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGIS----- 612
R P + +R LRR G I VS+ + +++ + I +D GRV RPL I + S
Sbjct: 591 RNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKE 650
Query: 613 -RIKEHHMKELLDGVR-------------SFDDFLREGLIEYLDVNEENNALIALYEGDA 658
++++ H+ +L+ ++ L EGL+EY+D EE + LIA+ D
Sbjct: 651 LKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDL 710
Query: 659 TPDT------------------------THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQ 694
P TH EI P ILGV A +IP+P HNQSPRNTYQ
Sbjct: 711 EPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQ 770
Query: 695 CAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSY 754
AMGKQAMG N RMD++ +L YPQ+PL TTR +E + + +L AGQNA VA+ Y
Sbjct: 771 SAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACY 830
Query: 755 SGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQVV 814
SGY+ ED+++MN+SS+DRG R + + Y +KY S ++ +P RT +
Sbjct: 831 SGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTY 890
Query: 815 HHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYK 874
LDDDGL APG + DV I K +P+ + R A +
Sbjct: 891 DK-------LDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQ-RTAYHSKRDASTPLR 942
Query: 875 GPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFP 934
E +VD+V + ++++G +K +R T+ P++GDKF+SRHGQKG G ++ED P
Sbjct: 943 ST--ENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMP 1000
Query: 935 FSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESI 994
F+ GI PDLI+NPH PSRMTV +IE L K G S F + TVE I
Sbjct: 1001 FTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTD-----ITVEGI 1055
Query: 995 SETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLT 1054
S+ L +HG+ G +++Y+G TG L A IF GP YYQ+L+HMV DK+HAR GP +LT
Sbjct: 1056 SKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLT 1115
Query: 1055 RQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYY-NH 1113
RQP EGR+R+GGLR GEMERDC+IA+GA+ + ERLM +SD F V +C +CGL+
Sbjct: 1116 RQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKL 1175
Query: 1114 KLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLAEA 1159
C C N +I + +PYA KLL QEL +MNI PRL +
Sbjct: 1176 NHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRS 1221
>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 = 1363 bits (3530), Expect = 0.0
Identities = 410/1144 (35%), Positives = 636/1144 (55%), Gaps = 48/1144 (4%)
Query: 30 DKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQ 89
++++++ + K +GLV+QHLDS+N FV +++I+ I + I P + +R +RIG+
Sbjct: 12 ERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEI-PGLKVRLGKIRIGK 70
Query: 90 PSMT-VDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIML 148
P + D +++P RL ++TYAAP+ + + V+ E +V IG +PIML
Sbjct: 71 PRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVEN----NIEAEPEEVYIGDLPIML 126
Query: 149 RSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNI- 207
+S + +L +GE P DPGGYFI+ G+E+V++ QE L+ NRV++DT K G+
Sbjct: 127 KSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTGSNI 186
Query: 208 --NASVTSSTETVKSKTVIQMEK-GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG 264
A + SST + I+ K G ++ KIP +++M+A+G+ +D+++V V
Sbjct: 187 THTAKIISSTAGYRVPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTDRDIVYAVS 246
Query: 265 RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFL 324
DP L PS+E+ ++ I + AL+++ +V G +R +A I+ FL
Sbjct: 247 LDPEIQNELFPSLEQASS--IANVDDALDFIGSRVA---IGQKRENRIEKAQQIIDKYFL 301
Query: 325 ANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLF 384
++ ++ R K +Y+A + +++E L + DDKD+ NKRL L+G L + LF F
Sbjct: 302 PHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAF 361
Query: 385 KTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGM 444
K + ++ ++ R + L + D +T + L+TGN+ R G+
Sbjct: 362 KAFVKDLTYQLEKSKV---RGRKLALKALVRPDIVTERIRHALATGNW-----VGGRTGV 413
Query: 445 TQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504
+Q+L R +++ L H+ RV + + R L +QWG +CP +TPEG GLVKNL
Sbjct: 414 SQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNL 473
Query: 505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELH-------NPNSFLVIFNGLILGKH 557
ALM + E + Y +GV +E + VI NG ++G +
Sbjct: 474 ALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYY 533
Query: 558 RRPKCFADVMRKLRRAGKIGEFVSV--FVNEKQRCVYIASDGGRVCRPLVIADKGISRIK 615
R + A +R+ RR G+I + V+V V + V++ D GRV RPL+I G +
Sbjct: 534 RDGEELAKKIRERRRKGEISDEVNVGHIVTDFINEVHVNCDSGRVRRPLIIVSNGNPLVT 593
Query: 616 EHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGV 675
+++L G +FDD +R+G IEYLD EE NA +AL D TP+ TH+EI ILG+
Sbjct: 594 REDIEKLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEHTHLEIWSPAILGI 653
Query: 676 IAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIEL 735
A +IPYP HNQSPRNTYQ AM KQA+G A N R D+ +LL YPQRPL+ TR +++
Sbjct: 654 TASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDI 713
Query: 736 VGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTS 795
+GY AG NA +AV+S++GY++ED+I+MN+SS++RG R + Y+ KY
Sbjct: 714 IGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQE 773
Query: 796 DRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSI 855
D+I+ P+ G + + L+D+G+ +P +K DV I K SP
Sbjct: 774 DKIVMPEPGVRGYKGKEYYRL-------LEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEF 826
Query: 856 MSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFS 915
+ + R + GE +VD V + G+ +K +R R P +GDKF+
Sbjct: 827 KELSPEQA--KRDTSIVTRH--GEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFA 882
Query: 916 SRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRF 975
SRHGQKGV G ++ Q D P++ +G+ PD+I+NPH PSRMT+G+++E + GK G
Sbjct: 883 SRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNI 942
Query: 976 HYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLK 1035
+ F + +E + ++K+G+ + ++ Y G TG +++ I+ G +YYQKL
Sbjct: 943 VDATPFYK-----TPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLH 997
Query: 1036 HMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSD 1095
HMV DK+HAR GP +LTRQPTEGRAR GGLR GEMERDCLI +G +ML+ +RL+ +SD
Sbjct: 998 HMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSD 1057
Query: 1096 PFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLK 1155
+ VC CG +G+Y+ +C + N+ + + YA KLLIQEL SM I PRL
Sbjct: 1058 RTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLI 1117
Query: 1156 LAEA 1159
L +
Sbjct: 1118 LEDR 1121
>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 = 169 bits (431), Expect = 7e-43
Identities = 131/472 (27%), Positives = 211/472 (44%), Gaps = 108/472 (22%)
Query: 744 GQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKK--YTAIN-QKYANSTSDRILR 800
GQN VA+M + GY+ EDAIV++ + ++K+ YT+I+ ++Y D
Sbjct: 669 GQNVLVAIMPFDGYNFEDAIVIS----EE------LLKRDFYTSIHIERYEIEARD---- 714
Query: 801 PDRTGPGAERM--QVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSP 858
T G ER+ + H S L LD++G+ G +KP D+ + + S
Sbjct: 715 ---TKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGR----------TSF 761
Query: 859 TGQTDS-------------RYRSARQT-YKGPDGET-CVVDRVALCSDKNGD-------L 896
G+++ + R + T + P GE VV V L G
Sbjct: 762 KGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVRE 821
Query: 897 CIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMT 956
++ + R+ ++GDK ++RHG KGV I+ ED P G D+I+NP G PSRM
Sbjct: 822 VVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMN 881
Query: 957 VGKMIELLGGKAGVSCGR--------------------FHYGSAFGEPSGHADTVESISE 996
+G+++E G AG G+ + FG+ G V+
Sbjct: 882 LGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREV 941
Query: 997 TLVKH------------------GFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMV 1038
+++ GK ++Y G TG P++ I +G ++ KL HMV
Sbjct: 942 EVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMV 1001
Query: 1039 LDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFE 1098
DKMHAR +GP ++T+QP G+A+ GG R GEME L AYGA+ + E L + SD
Sbjct: 1002 EDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSD--- 1058
Query: 1099 VQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNI 1150
+ G Y +K G+++ +P + ++L++ELQ++ +
Sbjct: 1059 ----DIEGRNAAYEAIIK---------GEDVPEPSVPESFRVLVKELQALAL 1097
Score = 82.0 bits (203), Expect = 8e-16
Identities = 105/550 (19%), Positives = 199/550 (36%), Gaps = 171/550 (31%)
Query: 35 LPEFLKVRGLVKQHLDSFNYFV----------NTGIRKIVRANDRIVSGIDPSIFLR--F 82
LP ++ Q ++S+ + N GI+ R I L F
Sbjct: 15 LPPLTEI-----Q-VESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDF 68
Query: 83 KDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIG 142
+ R+G+P D E CR D+TY AP+ ++ + H + +++++V +G
Sbjct: 69 LEYRLGEPPFPQD---E------CREKDLTYQAPLYARLQLI---HKDTGLIKEDEVFLG 116
Query: 143 RIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNR-VIIDT 201
IP+M G FII G ++V++ Q S D
Sbjct: 117 HIPLM------------------------TEDGSFIINGADRVIVSQIHRSPGVYFTPDP 152
Query: 202 DKKGNINASVTSSTET-------VKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGME 254
+ G AS+ + V+ V+ M+ K +K P++++++ +G +
Sbjct: 153 ARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNK---------RKFPLVLLLRVLGYD 203
Query: 255 SDQEVVQMVGRDPRYSALLLPSI----EECANLDIY---------TQEKALEYLEGKV-- 299
+ ++ L+ S+ E A + ++ ++KA+ Y+ G +
Sbjct: 204 QETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIAD 263
Query: 300 -KRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRM-----VEAML 353
+R G GR + + + F F V L + + A +
Sbjct: 264 PRRYDLG-----EAGR-YKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGV 317
Query: 354 NKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTV---------------DII 398
+DD D++GN+R+ G+L+ D F+ ++ + + V ++
Sbjct: 318 PGHEVDDIDHLGNRRIRTVGELM----TDQFRVGLARLARGVRERMLMGSEDSLTPAKLV 373
Query: 399 LSKPSRSSRFD------LSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQV--LA- 449
S+P ++ + LSQF + L+
Sbjct: 374 NSRPLEAAIREFFSRSQLSQF------------------------------KDETNPLSS 403
Query: 450 -----RLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504
R+S +G G +TR F+ V R + + +G +CP +TPEG GL+ +L
Sbjct: 404 LRHKRRISALGP-GGLTRERAGFD----V---RDVHRTHYGRICPVETPEGANIGLITSL 455
Query: 505 ALMTHVTTDE 514
A + DE
Sbjct: 456 A--AYARVDE 463
>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 = 106 bits (267), Expect = 2e-23
Identities = 71/235 (30%), Positives = 101/235 (42%), Gaps = 49/235 (20%)
Query: 898 IKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTV 957
+K + RR + GDK + RHG KGV I ED P+ E G D+++NP G PSRM +
Sbjct: 1050 VKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNI 1109
Query: 958 G----------------KMIELLGGKAGVSCGRFHYGSAFGEPSGHADTV---------- 991
G K+ +L + V+ R A+ + V
Sbjct: 1110 GQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEV 1169
Query: 992 -----------------------ESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGP 1028
I E L +G+ +Y G TG + + +G
Sbjct: 1170 MRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGY 1229
Query: 1029 IYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGAS 1083
+Y KL H+V DKMHAR +G ++T+QP G+A+ GG R GEME L AYGA+
Sbjct: 1230 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1284
Score = 59.3 bits (144), Expect = 7e-09
Identities = 59/251 (23%), Positives = 100/251 (39%), Gaps = 69/251 (27%)
Query: 32 FQLLPEFLKVRGLVKQHLDSFNYFV------NTGIRKIVRANDRIVSGIDPSIFLRFKDV 85
F P+ L V L+ LDSF F+ G+ R+ I S + L++
Sbjct: 15 FGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSY-SGNSELQYVSY 73
Query: 86 RIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPI-----LVNIEYVQGSHTEKTTMEKNDVV 140
R+G+P V E C++ +TY+AP+ LV E T K E+ +V
Sbjct: 74 RLGEPVFDVQ---E------CQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQ-EVY 123
Query: 141 IGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNR---V 197
+G IP+M G F+I GTE+V I QL R V
Sbjct: 124 MGEIPLMT------------------------DNGTFVINGTERV--IVSQLH--RSPGV 155
Query: 198 IIDTDKKGNINASVTSSTETVKSKTVIQM----------EKGKMYLLLNQFVKKIPIMVV 247
D+DK SS + + + +I K +++ +++ +K+P ++
Sbjct: 156 FFDSDKG-----KTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDR-RRKLPATII 209
Query: 248 MKAMGMESDQE 258
++A+ ++Q
Sbjct: 210 LRALNYTTEQI 220
Score = 47.0 bits (112), Expect = 4e-05
Identities = 41/187 (21%), Positives = 75/187 (40%), Gaps = 48/187 (25%)
Query: 341 VAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMI-----------S 389
+ VM +++++ K +DD D++GN+R+ G++ F +
Sbjct: 426 IDVM-KKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDL 484
Query: 390 EVQKTVDIILSKPSRSSRFD------LSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKG 443
+ D+I +KP ++ + LSQF + + KR
Sbjct: 485 DTLMPQDMINAKPISAAVKEFFGSSQLSQF---------MVQNNPLSEITHKR------- 528
Query: 444 MTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKN 503
R+S +G G +TR FE R + P+ +G +CP +TPEG GL+ +
Sbjct: 529 ------RISALGP-GGLTRERAGFEV-------RDVHPTHYGRVCPIETPEGPNIGLINS 574
Query: 504 LALMTHV 510
L++
Sbjct: 575 LSVYAQT 581
Score = 40.5 bits (95), Expect = 0.004
Identities = 29/111 (26%), Positives = 52/111 (46%), Gaps = 18/111 (16%)
Query: 741 LGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAIN-QKYANSTSDRIL 799
L GQN VA M ++GY+ ED+I++++ R + ++T I+ Q+ A + D
Sbjct: 794 LALGQNMRVAFMPWNGYNFEDSILVSE--------RVVQEDRFTTIHIQELACVSRD--- 842
Query: 800 RPDRTGPGAERM--QVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESP 848
T G E + + + L LD+ G+ G + D+ + K +P
Sbjct: 843 ----TKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Score = 33.2 bits (76), Expect = 0.67
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 23/87 (26%)
Query: 638 IEYLDVNEENNALIAL-------------------YEGD---ATPDT-THIEIEPFTILG 674
I YL EE N +IA +G+ + D ++++ ++
Sbjct: 603 IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 662
Query: 675 VIAGLIPYPHHNQSPRNTYQCAMGKQA 701
V A LIP+ H+ + R M +QA
Sbjct: 663 VGASLIPFLEHDDANRALMGANMQRQA 689
>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 = 77.8 bits (191), Expect = 2e-14
Identities = 119/738 (16%), Positives = 200/738 (27%), Gaps = 287/738 (38%)
Query: 426 TLSTGNFDVKRFKMHRKGMTQVLARLSFI---GTLGHMTRVSPQFEKSRKVSGPRALQPS 482
TLS G+ + + + +++ QF K P +P+
Sbjct: 10 TLSHGSLEH-----------------VLLVPTASFFIASQLQEQFNKIL----P---EPT 45
Query: 483 QWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCL--GVEDLE--LLSGEE 538
+ D P A LV + +V++ E + L + + E L G +
Sbjct: 46 E--GFAADDEPTTPA-ELV--GKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND 100
Query: 539 LHN-------------PNSFLVI---FNGLILGKHRRPKCFADVMRKLRRAGKIGE--FV 580
+H + +I I+ K K L RA G V
Sbjct: 101 IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS---ALFRAVGEGNAQLV 157
Query: 581 SVF---------VNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDD 631
++F E + +Y LV I E + EL+ +
Sbjct: 158 AIFGGQGNTDDYFEELRD-LYQTY------HVLV--GDLIKFSAET-LSELIRTTLDAEK 207
Query: 632 FLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPH------- 684
+GL ++ E L TPD ++ P + +I G+I H
Sbjct: 208 VFTQGL----NILE------WLENPSNTPDKDYLLSIPIS-CPLI-GVIQLAHYVVTAKL 255
Query: 685 HNQSPRNTYQCAMGKQAMGN-------IA-------FNQLCRMDSLLYLLVYPQRPLLTT 730
+P G IA F + + +L +
Sbjct: 256 LGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVS--VRKAITVLFF-------- 305
Query: 731 RTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKY 790
+G A Y + +I+ + SL+ G
Sbjct: 306 -----IGV----RCYEA------YPNTSLPPSIL--EDSLENNEGV-------------- 334
Query: 791 ANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLE 850
P P M + SNL + + + N P
Sbjct: 335 ----------P---SP----MLSI--SNLTQEQVQ--------DYVN----KTNSHLPAG 363
Query: 851 TRGSIMSPTGQTDSRYRSARQ---TYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRR 907
+ I S A+ + GP +L L + R +
Sbjct: 364 KQVEI--------SLVNGAKNLVVS--GP--------PQSLYG-----LNLTL--RKAKA 398
Query: 908 PELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGF-PSRMTVGKMIELLGG 966
P D Q PFSER + + F P
Sbjct: 399 PSGLD-----------------QSRIPFSERKLKFS-----NRFLP-------------- 422
Query: 967 KAGVSCGRFHYGSAFGEPSGH-ADTVESISETLVKHGFSYNGKDM---IYSGITGCPLQA 1022
V+ FH S + I++ LVK+ S+N KD+ +Y G L+
Sbjct: 423 ---VAS-PFH--------SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRV 470
Query: 1023 Y-----------IFMGPIYYQKLKHM----VLDKMHARGSGPRV-MLTRQPTEGRARNGG 1066
I P+ ++ +LD G + +LT + +G G
Sbjct: 471 LSGSISERIVDCIIRLPVKWETTTQFKATHILD--FGPGGASGLGVLTHRNKDGT----G 524
Query: 1067 LRV---GEMERDCLIAYG 1081
+RV G ++ + YG
Sbjct: 525 VRVIVAGTLDINPDDDYG 542
Score = 52.4 bits (125), Expect = 1e-06
Identities = 101/619 (16%), Positives = 190/619 (30%), Gaps = 189/619 (30%)
Query: 315 AFSILRDVFLANVPVHNNNF----RPKCFYVAVMLRR---MVEAMLNKDAMDDKDYVGNK 367
S L++ F +P F P A ++ + V +++ + D V N
Sbjct: 29 IASQLQEQFNKILPEPTEGFAADDEPTT--PAELVGKFLGYVSSLVEPSKVGQFDQVLNL 86
Query: 368 RLE------LSGQ----LVSLLFEDLFKTMISEVQKTVDII-------------LSKPSR 404
L L G L + L ++ T++ KT ++I K S
Sbjct: 87 CLTEFENCYLEGNDIHALAAKLLQENDTTLV----KTKELIKNYITARIMAKRPFDKKSN 142
Query: 405 SSRFDLSQFIVRDSITVGLERTLST----GN----FD--VKRFKMHRKGMTQVLARLSFI 454
S+ F ++ G + ++ GN F+ ++ + + ++ +
Sbjct: 143 SALF--------RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSA-- 192
Query: 455 GTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDE 514
TL + R + EK + L +W + P +TP+ + L + ++
Sbjct: 193 ETLSELIRTTLDAEKVF----TQGLNILEW-LENPSNTPDKDY------LLSIP-IS--- 237
Query: 515 EEGPLISL----CYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKL 570
PLI + Y + + L P G ++
Sbjct: 238 --CPLIGVIQLAHYVVTAKLLGF-------TPGELRSYLKGATG-------HSQGLV--- 278
Query: 571 RRAGKIGEFVSV------FVNEKQRCV----YIASDGGRV--CRP-LVIADKGISRIKEH 617
++ F ++ + +I G R P + + E+
Sbjct: 279 -----TAVAIAETDSWESFFVSVRKAITVLFFI---GVRCYEAYPNTSLPPSILEDSLEN 330
Query: 618 ------HMKELLDGVRSFDDFLREGLIEYLD-VNE---ENNAL-IALYEGDATPDTTHIE 666
M L + + +E + +Y++ N + I+L G
Sbjct: 331 NEGVPSPM--L--SIS---NLTQEQVQDYVNKTNSHLPAGKQVEISLVNG---AKN---- 376
Query: 667 IEPFTILGVIAGLIPYP----HHNQSPRNTYQCAMGK-QAMGNIAFNQLCR--MDSLLYL 719
V++G P N + R + G Q+ I F++ R S +L
Sbjct: 377 ---L----VVSG---PPQSLYGLNLTLRK-AKAPSGLDQS--RIPFSE--RKLKFSNRFL 421
Query: 720 LVY-P-QRPLLT--TRTI--ELVGYDKLGAGQNATVAVMSYSGYDIEDAIVM--NKSSLD 771
V P LL + I +LV + ++ + V YD D + S+
Sbjct: 422 PVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV-----YDTFDGSDLRVLSGSIS 476
Query: 772 RGFGRCIVVKKYTAIN-QKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDG-- 828
CI+ + + + IL D GPG L D G
Sbjct: 477 ERIVDCIIRL---PVKWETTTQFKATHIL--D-FGPGG----ASGLGVLTHRNKDGTGVR 526
Query: 829 LAAPGEI-IKPNDVYINKE 846
+ G + I P+D Y K+
Sbjct: 527 VIVAGTLDINPDDDYGFKQ 545
Score = 42.7 bits (100), Expect = 0.001
Identities = 45/285 (15%), Positives = 84/285 (29%), Gaps = 98/285 (34%)
Query: 125 QGSHTE---KTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAE---LARLGECPLD-----P 173
QGS + + + + V + A+ G LD P
Sbjct: 1624 QGSQEQGMGMDLYKTSKAA-----------QDVW---NRADNHFKDTYGFSILDIVINNP 1669
Query: 174 GGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGN-----INASVTSSTETVKSKTVIQMEK 228
I G EK I+E S +I +T G I + + + + EK
Sbjct: 1670 VNLTIHFGGEKGKRIRENYSA--MIFETIVDGKLKTEKIFKEINEHS----TSYTFRSEK 1723
Query: 229 GKMYLLLN-Q---FVKKIPIMVVMKAMGMESDQ---------EVVQMVGRDPRYSALLLP 275
G + Q + + +K+ G+ E Y+AL
Sbjct: 1724 GLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGE----------YAAL--- 1770
Query: 276 SIEECANLDIYTQEKALEYLE--GKVKRSTFGSPPNDREGRA-FSILRDVFLANVPVHNN 332
+ D+ + E +E + G + + P D GR+ + +
Sbjct: 1771 ----ASLADVMSIESLVEVVFYRGMTMQV---AVPRDELGRSNYGM-------------- 1809
Query: 333 NFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVS 377
+A+ R+ + + + YV + + +G LV
Sbjct: 1810 --------IAINPGRVAASF----SQEALQYVVERVGKRTGWLVE 1842
Score = 40.0 bits (93), Expect = 0.006
Identities = 39/251 (15%), Positives = 81/251 (32%), Gaps = 71/251 (28%)
Query: 54 YFVNTGIRKIVRAN-DRIV--SGIDPSIFLR--FKDVRIGQPSMTVDGVSEKLNPHMCRL 108
+F ++I R N ++ + +D + FK++ S T L+
Sbjct: 1675 HFGGEKGKRI-RENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS------ 1727
Query: 109 SDMT-YAAPILVNIEYVQGSHTEKTTMEKNDVVI---------------GRIPI-----M 147
T + P L +E + + D + I +
Sbjct: 1728 --ATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEV 1785
Query: 148 LRSCRCVLYGK--------DEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVII 199
+ R G DE + G ++PG E + + E++ K
Sbjct: 1786 VFY-R----GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGK----- 1835
Query: 200 DTDKKG------NINASVTSSTETVKSKTVIQMEKGKMYLLLNQF-VKKIPIMVVMKAMG 252
+ G N N + + V + + ++ + +LN ++KI I+ + K++
Sbjct: 1836 ---RTGWLVEIVNYNVE---NQQYVAAGDLRALDT--VTNVLNFIKLQKIDIIELQKSLS 1887
Query: 253 MESDQEVVQMV 263
+E EV +
Sbjct: 1888 LE---EVEGHL 1895
Score = 40.0 bits (93), Expect = 0.006
Identities = 63/434 (14%), Positives = 117/434 (26%), Gaps = 189/434 (43%)
Query: 249 KAMGME--SDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGS 306
+ MGM+ + Q D++ +A + + T+G
Sbjct: 1629 QGMGMDLYKTSKAAQ----------------------DVW--NRADNHF-----KDTYG- 1658
Query: 307 PPNDREGRAFSILRDVFLANVP----VHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKD 362
FSIL D+ + N P +H + K +R AM+ + +D
Sbjct: 1659 ---------FSIL-DIVINN-PVNLTIHFGGEKGK------RIRENYSAMIFETIVDG-- 1699
Query: 363 YVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQF----IVRDS 418
L E +FK I+E + +QF +
Sbjct: 1700 --------------KLKTEKIFKE-INE--HSTSYTFRSE--KGLLSATQFTQPALT--- 1737
Query: 419 ITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIG-TLGHMTRVSPQFEKSRKVSGPR 477
+ F+ + KG+ A +F G +LG E +
Sbjct: 1738 -------LMEKAAFED----LKSKGLIPADA--TFAGHSLG---------EYA------- 1768
Query: 478 ALQPSQWGMLCPCDTPEGEACGLVKN--LALMTHVTTDEEEGPLISLCYCLGVEDLELLS 535
AL S ++ + E +V + + V DE +
Sbjct: 1769 ALA-SLADVM----SIE-SLVEVVFYRGMTMQVAVPRDELGRSNYGMIAI---------- 1812
Query: 536 GEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKL--RRAGKIGEFVSVFVNEKQRCVYI 593
NP F+ + ++ + R + G V + VN Y
Sbjct: 1813 -----NPGRVAASFS-------------QEALQYVVERVGKRTGWLVEI-VN------Y- 1846
Query: 594 ASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENN-ALIA 652
+ + V A G ++ L + + L+ + +I
Sbjct: 1847 NVENQQY----VAA--G-------DLRAL------------DTVTNVLNFIKLQKIDIIE 1881
Query: 653 LYEGDATPDTTHIE 666
L + +E
Sbjct: 1882 L------QKSLSLE 1889
Score = 33.9 bits (77), Expect = 0.37
Identities = 33/239 (13%), Positives = 65/239 (27%), Gaps = 102/239 (42%)
Query: 39 LKVRGL----VKQHLDSFNY------------------FVNTG-----------IRKIVR 65
L + L V+ +++ N V +G +RK
Sbjct: 339 LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKA-- 396
Query: 66 ANDRIVSGID----------PSIFLRFKDVRIGQP--SMTVDGVSEKLNPHMCRLSDMTY 113
+ SG+D RF + + P S + S+ +N + + +++++
Sbjct: 397 ---KAPSGLDQSRIPFSERKLKFSNRF--LPVASPFHSHLLVPASDLINKDLVK-NNVSF 450
Query: 114 AAPIL---VNIEYVQGSHTE--KTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGE 168
A + V Y T + + RI C++
Sbjct: 451 NAKDIQIPV---Y----DTFDGSDLRVLSGSISERI------VDCII------------R 485
Query: 169 CPLD----------------PGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASV 211
P+ PGG G + + + RVI+ N +
Sbjct: 486 LPVKWETTTQFKATHILDFGPGG---ASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDY 541
Score = 32.3 bits (73), Expect = 1.2
Identities = 70/447 (15%), Positives = 127/447 (28%), Gaps = 149/447 (33%)
Query: 5 QVEGSPKD--EQLPDKQKL----AAPVKSVVDK-FQLLPEFLKVRGLVKQHLDSFNYFVN 57
Q G+ D E+L + L V ++ + L E L++ LD+ F
Sbjct: 163 Q--GNTDDYFEEL---RDLYQTYHVLVGDLIKFSAETLSE------LIRTTLDAEKVFTQ 211
Query: 58 TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLN-----PH---MCRLS 109
G++ +L + + +S L H +L
Sbjct: 212 ---------------GLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLL 256
Query: 110 DMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRS------------------- 150
T P + Y++G T +V S
Sbjct: 257 GFT---PGELR-SYLKG-----ATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIG 307
Query: 151 CRCVL-YGKDEAELARLGECPLDPG-GY----FIIKGTEKVLLIQEQLSKNRVIIDTDKK 204
RC Y + L + L+ G I + + Q+ ++K + K+
Sbjct: 308 VRCYEAYPNTSLPPSILEDS-LENNEGVPSPMLSISNLTQEQV-QDYVNKTNSHLPAGKQ 365
Query: 205 ---GNINAS----VTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQ 257
+N + V+ +++ LN ++K KA DQ
Sbjct: 366 VEISLVNGAKNLVVSGPPQSLYG--------------LNLTLRKA------KA-PSGLDQ 404
Query: 258 EVVQMVGRDPRYSALLLP-----------SIEECANLDIYTQEKAL--EYLEGKVKRSTF 304
+ R ++S LP + N D+ + + ++ V TF
Sbjct: 405 SRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVY-DTF 463
Query: 305 -GSPPNDREGRAFSILRDVF--LANVPVH---NNNFRPK---CF------YVAVMLRRMV 349
GS + R SI + + +PV F+ F + V+ R
Sbjct: 464 DGS--DLRVLSG-SISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNK 520
Query: 350 E---------AMLNKDAMDDKDYVGNK 367
+ L+ + DD G K
Sbjct: 521 DGTGVRVIVAGTLDINPDDD---YGFK 544
>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 = 62.9 bits (152), Expect = 5e-10
Identities = 78/470 (16%), Positives = 136/470 (28%), Gaps = 140/470 (29%)
Query: 18 KQKLAAPVKSVV--DKFQLLPEF----LKVR-----GLVKQHLDSFNYFVNTGIRKIVRA 66
K +A V K Q +F L ++ V + L Y ++
Sbjct: 163 KTWVAL---DVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH 219
Query: 67 NDRIVSGIDPSIFLRFKDVRIGQP---SMTV-DGVS-----EKLNPHMCRLSDMTYAAPI 117
+ I I SI + + +P + V V N C+ I
Sbjct: 220 SSNIKLRIH-SIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS-CK---------I 268
Query: 118 LVNIEYVQGSHTEKTTMEKN--DVVIG--RIPIMLRSCRCVLYGKDEAE--LARLGECPL 171
L+ TT K D + I L L DE + L + +C
Sbjct: 269 LL------------TTRFKQVTDFLSAATTTHISLDHHSMTLT-PDEVKSLLLKYLDCRP 315
Query: 172 D--P-----GGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVI 224
P + +I E + D K N + K T+I
Sbjct: 316 QDLPREVLTTNPRRLS------IIAESIRDGLATWDNWKHVNCD----------KLTTII 359
Query: 225 QM--------EKGKMYLLLNQFVK--KIPIMVVM---KAMGMESDQEVVQ------MVGR 265
+ E KM+ L+ F IP +++ + VV +V +
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK 419
Query: 266 DPRYSALLLPSI--EECANLDIYTQ--EKALE-Y-LEGKVKRSTFGSPPND--------- 310
P+ S + +PSI E L+ ++ Y + P D
Sbjct: 420 QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
Query: 311 -----REGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDD----- 360
++ R VFL +FR ++ +R A ++ +
Sbjct: 480 HLKNIEHPERMTLFRMVFL--------DFR----FLEQKIRHDSTAWNASGSILNTLQQL 527
Query: 361 ---KDYVGNKRLELSGQLVSLLFEDLFK----TMISEVQKTVDIILSKPS 403
K Y+ + + +LV+ + + L K + S+ + I L
Sbjct: 528 KFYKPYICDNDPKYE-RLVNAILDFLPKIEENLICSKYTDLLRIALMAED 576
Score = 60.6 bits (146), Expect = 3e-09
Identities = 100/702 (14%), Positives = 217/702 (30%), Gaps = 201/702 (28%)
Query: 34 LLPEFLK--VRGLVKQHLDSF--NYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQ 89
+L F V + + + I I+ + D VSG +F +
Sbjct: 21 ILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDA-VSGTL-RLFWTLLS----K 74
Query: 90 PSMTVDG-VSEKLNPH----MCRLSDMTYAAPILVNIEYVQGS---HTEKTTMEKNDVVI 141
V V E L + M + P ++ Y++ + + K +V
Sbjct: 75 QEEMVQKFVEEVLRINYKFLMSPIKT-EQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR 133
Query: 142 GRIPIMLRSC--------RCVLYG-----KD--EAELARLG--ECPLDPGGYFIIKG--- 181
+ + LR ++ G K ++ +C +D +++
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN 193
Query: 182 -TEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMY---LL--- 234
E VL + ++L ++ + + + ++++ +++++ + K K Y LL
Sbjct: 194 SPETVLEMLQKLL-YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL-KSKPYENCLLVLL 251
Query: 235 -------LNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYT 287
N F I++ + ++V + S++ + T
Sbjct: 252 NVQNAKAWNAFNLSCKILLTTR------FKQVTDFLSAATTTH----ISLDH--HSMTLT 299
Query: 288 QEKALEYLEGKVKRSTFGSPPNDREG--RAFSILRDVFLANVPVHNNNFRPKCFYVAVM- 344
++ L + P R SI+ + + + +N++ +V
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE-SIRDGLATWDNWK----HVNCDK 354
Query: 345 LRRMVEAMLNK-DAMDDKDYVGNKRLELSGQLVSLLFEDL--FKTMISEVQKTVDIILSK 401
L ++E+ LN + + + F+ L F + I
Sbjct: 355 LTTIIESSLNVLEPAEYRKM----------------FDRLSVF-------PPSAHI---- 387
Query: 402 PSRSSRFDLSQFIV-RDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLG-H 459
P+ LS ++ D I + ++ K+H+ + + + T+
Sbjct: 388 PTIL----LS--LIWFDVIKSDVMVVVN---------KLHKYSL---VEKQPKESTISIP 429
Query: 460 MTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPL 519
E K+ AL + +++ H
Sbjct: 430 SI----YLELKVKLENEYAL-----------------------HRSIVDHYN-------- 454
Query: 520 ISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEF 579
I + ++L P ++ +G H ++ + ++ F
Sbjct: 455 IPKTFD----------SDDLIPPYLDQYFYS--HIGHH---------LKNIEHPERMTLF 493
Query: 580 VSVFVN-----EKQRCVYIASDG-GRVCRPLVIADKGISRIKEHHMK-ELLDGVRSFDDF 632
VF++ +K R A + G + L I ++ K E L V + DF
Sbjct: 494 RMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERL--VNAILDF 551
Query: 633 LR---EGLI--EYLDVNEENNALIAL-YEGDATPDTTHIEIE 668
L E LI +Y D+ IAL E +A + H +++
Sbjct: 552 LPKIEENLICSKYTDLLR-----IALMAEDEAIFEEAHKQVQ 588
Score = 54.1 bits (129), Expect = 3e-07
Identities = 89/741 (12%), Positives = 183/741 (24%), Gaps = 276/741 (37%)
Query: 381 EDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTG---NFD--VK 435
+D+ K+++S ++ +D I+ S + + +++ + N+ +
Sbjct: 39 QDMPKSILS--KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMS 96
Query: 436 RFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRA----------LQPSQW- 484
K ++ + + +I + + F K VS + L+P++
Sbjct: 97 PIKTEQRQPS--MMTRMYIEQRDRLYNDNQVFAK-YNVSRLQPYLKLRQALLELRPAKNV 153
Query: 485 ---GMLCPCDTPEGEACGLVKN-LALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELH 540
G+L G G K +AL ++ ++
Sbjct: 154 LIDGVL-------G--SG--KTWVAL-------------------------DVCLSYKVQ 177
Query: 541 NPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRV 600
F + + L L P+ V+ L ++ I +
Sbjct: 178 CKMDFKIFW--LNLKNCNSPE---TVLEML----------------QKLLYQIDPNW--- 213
Query: 601 CRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATP 660
+ H + + S LR L N L+ L
Sbjct: 214 ------------TSRSDHSSNIKLRIHSIQAELRR----LLKSKPYENCLLVL---LNVQ 254
Query: 661 DTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLL 720
+ AFN C++
Sbjct: 255 NAKAWN---------------------------------------AFNLSCKI------- 268
Query: 721 VYPQRPLLTTRTIELVGYDKLGAGQNATVAVM----------------SYSGYDIED--- 761
LLTTR ++ D L A +++ Y +D
Sbjct: 269 ------LLTTRFKQVT--DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR 320
Query: 762 --------AIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPD----------- 802
+ + S+ G K +S +L P
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380
Query: 803 ----------------RTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKE 846
++ M VV+ + L+ I +Y+ +
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ----PKESTISIPSIYLELK 436
Query: 847 SPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCI-----KFL 901
LE ++ +RS Y P SD + +
Sbjct: 437 VKLENEYAL----------HRSIVDHYNIPK---------TFDSDDLIPPYLDQYFYSHI 477
Query: 902 IRHTRRPELGDKFSS-RHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKM 960
H + E ++ + R + DF F E+ I H + G +
Sbjct: 478 GHHLKNIEHPERMTLFRM--------VFL--DFRFLEQKIR-------HDSTAWNASGSI 520
Query: 961 IELLGGKAGVSCGRFH-YGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCP 1019
+ L + Y + + E + ++ F ++ +
Sbjct: 521 LNTL--------QQLKFYKPYICD---NDPKYERLVNAILD--FLPKIEENLICSKYTDL 567
Query: 1020 LQAYIFM---GPIYYQKLKHM 1037
L+ M I+ + K +
Sbjct: 568 LR-IALMAEDEAIFEEAHKQV 587
Score = 44.5 bits (104), Expect = 2e-04
Identities = 39/264 (14%), Positives = 78/264 (29%), Gaps = 70/264 (26%)
Query: 617 HHMK-ELLDGVRSFDDFL---REGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTI 672
HHM E + + D L + ++ D + + ++ + + HI + +
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL---SKEEIDHIIMSKDAV 61
Query: 673 LGV--IAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF--NQL---CRMDSLLYLL----- 720
G + + Q + + N F + + R S++ +
Sbjct: 62 SGTLRLFWTL-----LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR 116
Query: 721 --------VYPQ----RP---------LLTTRTIELVG-YDKLGAGQNATVAVMSYSGYD 758
V+ + R LL R + V LG+G+ VA+ Y
Sbjct: 117 DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK-TWVALDVCLSYK 175
Query: 759 IEDAIVMNKSSLDRG-----FGRCIVVKKYTAINQK-YANSTSDRILRPDRTGPGAERMQ 812
++ +D C + + QK + R D + R+
Sbjct: 176 VQCK-------MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH 228
Query: 813 VVHH--SNLL--------LLILDD 826
+ LL LL+L +
Sbjct: 229 SIQAELRRLLKSKPYENCLLVLLN 252
Score = 42.5 bits (99), Expect = 0.001
Identities = 48/342 (14%), Positives = 99/342 (28%), Gaps = 129/342 (37%)
Query: 11 KDEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRI 70
+ + LP + P + ++ E ++ L +++ + + K+ +
Sbjct: 314 RPQDLPREVLTTNPR--RLS---IIAESIR------DGLATWDNWKHVNCDKLTTIIESS 362
Query: 71 VSGIDP----------SIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRL-SDMTYAAPILV 119
++ ++P S+F I P++ + + D+ + ++V
Sbjct: 363 LNVLEPAEYRKMFDRLSVFP--PSAHI--PTIL-----------LSLIWFDVIKSDVMVV 407
Query: 120 NIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAEL-ARLGEC--------- 169
+ + S EK I I + ++E L + +
Sbjct: 408 VNKLHKYSLVEK------QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461
Query: 170 ------PLDPGGYF---------IIKGTEKVLLIQEQL-------SKNRVIIDTDKKGNI 207
LD YF I+ E++ L + K I N
Sbjct: 462 DDLIPPYLD--QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK---IRHDSTAWNA 516
Query: 208 NASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDP 267
+ S+ + T+ Q++ K Y+ N DP
Sbjct: 517 SGSILN--------TLQQLKFYKPYICDN-----------------------------DP 539
Query: 268 RYSALL------LPSIEE----CANLDIYTQEKALEYLEGKV 299
+Y L+ LP IEE D+ AL + +
Sbjct: 540 KYERLVNAILDFLPKIEENLICSKYTDLL--RIALMAEDEAI 579
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor,
transferase-transcription complex; 2.91A {Thermus
aquaticus}
Length = 188
Score = 47.5 bits (114), Expect = 5e-06
Identities = 32/149 (21%), Positives = 57/149 (38%), Gaps = 48/149 (32%)
Query: 49 LDSFNYFV----------NTGIRKIVRANDRIVSGIDPS--IFLRFKDVRIGQPSMTVDG 96
++S+ + N GI+ + I G + L F + RIG P + D
Sbjct: 8 VESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQD- 66
Query: 97 VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLY 156
E CR D+TY AP+ ++ + H + +++++V +G +P+M
Sbjct: 67 --E------CREKDLTYQAPLYARLQLI---HKDTGLIKEDEVFLGHLPLMT-------- 107
Query: 157 GKDEAELARLGECPLDPGGYFIIKGTEKV 185
G FII G ++V
Sbjct: 108 ----------------EDGSFIINGADRV 120
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.1 bits (69), Expect = 1.1
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 6/31 (19%)
Query: 288 QEKALEYLEGKVKRSTFGSPPNDREGRAFSI 318
+++AL+ L+ +K S P A +I
Sbjct: 18 EKQALKKLQASLKLYADDSAP------ALAI 42
>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax
volcanii}
Length = 74
Score = 29.2 bits (65), Expect = 1.4
Identities = 11/53 (20%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 635 EGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQ 687
L+ +D++ + L +G P+ +E++ +L +I G + + HH+
Sbjct: 24 ADLVRAVDLSPHE--VTVLVDGRPVPEDQSVEVDRVKVLRLIKGGLEHHHHHH 74
>2cm2_A Tyrosine-protein phosphatase non-receptor type 1; polymorphism,
phosphorylation, endoplasmic reticulum, oxidation,
hydrolase, acetylation; 1.5A {Homo sapiens} SCOP:
c.45.1.2 PDB: 2cm3_A 2cmb_A* 2cmc_A* 2cne_A* 3a5j_A
2cma_A 3a5k_A 3eu0_A 3sme_A 2azr_A* 2b07_A* 2h4g_A*
2h4k_A* 2hb1_A* 2qbp_A* 2qbq_A* 2qbr_A* 2qbs_A* 2zmm_A*
2zn7_A* ...
Length = 304
Score = 29.9 bits (68), Expect = 4.7
Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 413 FIVRDSITVGLERTLSTGNFDVKRF--KM--HRKGMTQVLARLSFI 454
F + D+ + +++ + D+K+ +M R G+ Q +L F
Sbjct: 231 FCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFS 276
>3t5o_A Complement component C6; macpf, MAC, membrane attack complex, innate
IMMU system, blood, membrane, cytolysin, immune SYST;
HET: NAG FUL FUC BGC MAN; 2.87A {Homo sapiens} PDB:
4a5w_B* 4e0s_B*
Length = 913
Score = 29.5 bits (65), Expect = 8.1
Identities = 8/39 (20%), Positives = 18/39 (46%)
Query: 1111 YNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMN 1149
++ GIC T K+ + ++P + + E+Q+
Sbjct: 188 LDNSFTGGICKTVKSSRTSNPYRVPANLENVGFEVQTAE 226
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.5 bits (63), Expect = 9.3
Identities = 10/47 (21%), Positives = 14/47 (29%), Gaps = 21/47 (44%)
Query: 486 MLCP-C---------DTPEGE----ACGLVKNLALMTHVTTDEEEGP 518
+ CP C EG+ CGLV L + +
Sbjct: 22 LTCPECKVYPPKIVERFSEGDVVCALCGLV----LSDKL---VDTRS 61
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 0.138 0.407
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: 17,844,685
Number of extensions: 1140725
Number of successful extensions: 2069
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2006
Number of HSP's successfully gapped: 36
Length of query: 1159
Length of database: 6,701,793
Length adjustment: 104
Effective length of query: 1055
Effective length of database: 3,798,009
Effective search space: 4006899495
Effective search space used: 4006899495
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: 63 (28.3 bits)