RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 001179
(1131 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 = 990 bits (2562), Expect = 0.0
Identities = 293/1204 (24%), Positives = 474/1204 (39%), Gaps = 194/1204 (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 DLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVD 943
D+I+NPHA PSRMT+ ++E +A K +L G +DATPF + ++
Sbjct: 910 DVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTP---------------IE 954
Query: 944 ELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQ 1003
+L + G+ EV Y G G ++ I+ G VYYQ+L HMV+DK R+ G +
Sbjct: 955 QLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQI 1014
Query: 1004 ITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTAT 1063
+TRQP +GR R GG+RFGEMERD L+ G A LL DRL SD VC CG +
Sbjct: 1015 LTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYIGWY- 1073
Query: 1064 FIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITL 1123
+ K C + V + Y F+ L EL +M I L
Sbjct: 1074 -----------------DKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRL 1116
Query: 1124 QLGD 1127
L D
Sbjct: 1117 ILED 1120
>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 = 645 bits (1666), Expect = 0.0
Identities = 323/1281 (25%), Positives = 495/1281 (38%), Gaps = 271/1281 (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------FRDRREGYTDKAVVIRCVRKD----QSSVTLKLYYLLNGSVRLGFW 176
++ RS+ F+ IR + S++ +KLY S
Sbjct: 213 -IAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSS---ART 268
Query: 177 LQGKEYLL----PVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKII 232
++ + P+ I+ +AL D EI H CYD + ++++
Sbjct: 269 IKATLPYIKQDIPIVIIFRALGIIPDGEILEH--ICYDVNDWQM------------LEML 314
Query: 233 LAEVQD-LSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFN 291
V+D + R L IG + G++ E A+ +++ H+ +
Sbjct: 315 KPCVEDGFVIQDRETALDFIGRRGTAL--GIKKEKRIQYAKDILQKEFLPHITQLEGFES 372
Query: 292 ----LLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLI 347
L +M+ +L D+ D + + L G L+ K + + + +
Sbjct: 373 RKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYM 432
Query: 348 QDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTV 407
Q +E FN+ +K I + ++ L TG Q + RAG +
Sbjct: 433 QRTVEEAHD----FNMKLAIN------AKTITSGLKYALATGNWGEQ-KKAMSSRAGVSQ 481
Query: 408 QAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMT 467
R + +S R + R+L WG +CP TP+G+ CGL+ +++
Sbjct: 482 VLNRYTYSSTLSHLRRT-NTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS 540
Query: 468 STCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVG 527
++ D I+ L GM P L V P V ++G G
Sbjct: 541 LMSCISVGTDP-----------MPIITFLSEWGMEP-LEDYVPHQSPDATRVFVNGVWHG 588
Query: 528 VIPSSEIEKVVAHLRRLKVSAA-----SVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFV 582
V +++ LR L+ S+I D E L +FT +
Sbjct: 589 VH--RNPARLMETLRTLRRKGDINPEVSMIRDIREKE------------LKIFTDAGRVY 634
Query: 583 RPV-----------------------------RNISLPSEESQN-----------IELIG 602
RP+ ++I E+ + +E I
Sbjct: 635 RPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYID 694
Query: 603 PFEQVFMEIRC--------------PDGGDGGRR-----NAFPATHEEIHPTGMLSVVAN 643
E+ + I D +R +A TH EIHP+ +L V A+
Sbjct: 695 AEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAAS 754
Query: 644 LTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGI 703
+ P+ DHNQSPRN YQ M KQ MG + R D L PQ P+ T
Sbjct: 755 IIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKF 814
Query: 704 DEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN-KVDRG 762
E P G NAIVA+ Y+GY+ ED+MI+N+SS+DRG+ +++ G +
Sbjct: 815 RELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETF 874
Query: 763 QKLFRRN--KDAKSLHSVIDSDGLPYVGQMIHPGEPYC------------SIYDKTTNSW 808
+K R N + + +D DGL G + + +S
Sbjct: 875 EKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSK 934
Query: 809 RTNSR--KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQ 866
R S + +E+ VD V V N L + +R R T+ P IGDKF+SRHGQKG
Sbjct: 935 RDASTPLRSTENGIVDQVLVT-TNQDGL-KFVKVRVRTTKIPQIGDKFASRHGQKGTIGI 992
Query: 867 LWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSV 926
+ DMPF+ G+ PDLIINPHA PSRMT+A L+E + +K +L G DA+PF
Sbjct: 993 TYRREDMPFT-AEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPF---- 1047
Query: 927 KKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLR 986
+ V+ + ++LR G+ G EV+Y+G G +L +IF GP YYQRLR
Sbjct: 1048 -----------TDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLR 1096
Query: 987 HMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSD 1046
HMV DK R+ G M +TRQP++GR R GG+RFGEMERD ++AHGAA L +RL SD
Sbjct: 1097 HMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASD 1156
Query: 1047 YHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYV 1106
+C +CG + + C C + + +PY
Sbjct: 1157 AFRVHICGICGLM--TVIAKLNHN---------------QFECKGCDNKIDIYQIHIPYA 1199
Query: 1107 FRYLAAELAAMNIKITLQLGD 1127
+ L EL AMNI L
Sbjct: 1200 AKLLFQELMAMNITPRLYTDR 1220
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 460 bits (1185), Expect = e-143
Identities = 184/517 (35%), Positives = 264/517 (51%), Gaps = 53/517 (10%)
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 GDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGG 910
GDKF+SRHGQKG + DMPFS G+ PD+IINPHA PSRMT+A L+E +K
Sbjct: 966 GDKFASRHGQKGTIGMTYRHEDMPFS-AQGIVPDIIINPHAIPSRMTVAHLVECQLSKVS 1024
Query: 911 SLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTE 970
+L G DATPF + V+ + ++LR+ GF G EV+Y G G +
Sbjct: 1025 ALSGFEGDATPF---------------TDVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRK 1069
Query: 971 LTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLA 1030
L ++F+GP YYQRL+H+V DK R+ G + +TRQP++GR R GG+RFGEMERD ++
Sbjct: 1070 LVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQIS 1129
Query: 1031 HGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCH 1090
HG + +L +RL CSD + VC +CG + A++ C
Sbjct: 1130 HGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKK------------------DSYECR 1171
Query: 1091 ACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLGD 1127
+CQ V +PY + L EL +MNI L +
Sbjct: 1172 SCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTKN 1208
Score = 196 bits (500), Expect = 3e-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
>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 = 112 bits (283), Expect = 2e-25
Identities = 73/233 (31%), Positives = 100/233 (42%), Gaps = 45/233 (19%)
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 --AAKGGSLH--------------GKFMDATPFANSVKKTNGDTGTDESKSLVDELGEML 949
A + + K+ G D+ + V E L
Sbjct: 891 GLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKL 950
Query: 950 RTC-----------GFNYHGVEVLYSGVYGTELTCEIFIGPV-----YYQRLRHMVSDKF 993
G VLY G T E GP+ + +L HMV DK
Sbjct: 951 GLVTPGKTPEEQLKELFLQGKVVLYDG-----RTGEPIEGPIVVGQMFIMKLYHMVEDKM 1005
Query: 994 QVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSD 1046
RSTG IT+QP+ G+ + GG RFGEME +L A+GAA+ L + L SD
Sbjct: 1006 HARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSD 1058
Score = 30.7 bits (70), Expect = 3.3
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 = 87.9 bits (218), Expect = 1e-17
Identities = 74/233 (31%), Positives = 99/233 (42%), Gaps = 54/233 (23%)
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 KGGSLHGKFM--------DATPFANSVKKTNGDTGTDES-KSLVD--------------- 943
KG M F D + D
Sbjct: 1122 KGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMP 1181
Query: 944 ------------ELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPV-----YYQRLR 986
E+ E+L+ G LY G T E F PV Y +L
Sbjct: 1182 IATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDG-----RTGEQFERPVTVGYMYMLKLN 1236
Query: 987 HMVSDKFQVRSTG--TMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLL 1037
H+V DK RSTG ++ +T+QP+ G+ + GG RFGEME +L A+GAAY L
Sbjct: 1237 HLVDDKMHARSTGSYSL--VTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1287
Score = 33.5 bits (77), Expect = 0.56
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
>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 = 76.2 bits (187), Expect = 5e-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 = 69.7 bits (170), Expect = 5e-12
Identities = 106/626 (16%), Positives = 181/626 (28%), Gaps = 205/626 (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 IIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK 908
IG R C + +P+ +P S + D + N PS ML S+
Sbjct: 305 FIG----VR------CYEAYPNTSLPPS----ILEDSLENNEGVPS----PML--SI--S 342
Query: 909 GGSLHGKFMDATPFANSVKKTNGDTGTDE--SKSLVDELGEMLRTCGFNYHGVEVLYSGV 966
+ + V KTN + SLV N
Sbjct: 343 N-------LTQEQVQDYVNKTNSHLPAGKQVEISLV------------N----------- 372
Query: 967 YGTELTCEIFI--GPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEME 1024
+ + GP Q L + + ++ +DQ +R P RK RF +
Sbjct: 373 -----GAKNLVVSGPP--QSLYGLNLTLRKAKAPSGLDQ-SRIPFSERKLKFSNRFLPVA 424
Query: 1025 R---DSLLAHGAAYLLHDRLH-----TCSD-----YHV---ADVCSLCGSVLTATFIHPQ 1068
LL + + D + D Y +D+ L GS+
Sbjct: 425 SPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS-------- 476
Query: 1069 KRAIREIGGLP---PARAPKKVTCHA 1091
+R + I LP K T H
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKAT-HI 501
Score = 58.5 bits (141), 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 = 31.6 bits (71), Expect = 1.8
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 = 31.6 bits (71), Expect = 1.9
Identities = 35/192 (18%), Positives = 54/192 (28%), Gaps = 70/192 (36%)
Query: 832 KNLPQKANIRFRHTRNPIIGDKFSS---RHGQKG--VCSQLWPDIDMPFSGVTGMRPDLI 886
N P I F + I + +S+ G +++ +I+ + T +
Sbjct: 1666 INNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGL 1725
Query: 887 INPHAF--PSRMTIAMLLESVAA------KGGSLHGKFMDATPFANSVKKTNGDTGTDES 938
++ F P A+ L AA KG FA G S
Sbjct: 1726 LSATQFTQP-----ALTLMEKAAFEDLKSKGLIPADAT-----FA-------G-----HS 1763
Query: 939 KSLVDELGEMLRTCGFNYHGVEVLYS------GVYGTELTCEIFIGPVYYQR---LRHMV 989
LGE Y+ V E E+ V+Y R ++ V
Sbjct: 1764 ------LGE---------------YAALASLADVMSIESLVEV----VFY-RGMTMQVAV 1797
Query: 990 SDKFQVRSTGTM 1001
RS M
Sbjct: 1798 PRDELGRSNYGM 1809
>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 = 73.0 bits (178), Expect = 5e-13
Identities = 98/667 (14%), Positives = 191/667 (28%), Gaps = 222/667 (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 +
Sbjct: 292 DHHSMTL-----TPD-EVKSLL---------LKY-----------------------LDC 313
Query: 502 IPS-LPKLVKSGPPAVLSVLLDGRVVGVIPS-------SEIEKVVAHLRRLKVSAASVIP 553
P LP+ V + P LS++ + + +K+ ++ S + P
Sbjct: 314 RPQDLPREVLTTNPRRLSII--AESIRDGLATWDNWKHVNCDKL---TTIIESSLNVLEP 368
Query: 554 DDLEVGYVPLSLGGAYPGLYLFTSPPKFVR-PVRNISL-----PSEESQNI--ELI---- 601
+ + LS +F P P +SL + + +L
Sbjct: 369 AEYRKMFDRLS---------VF---PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL 416
Query: 602 ---GPFE------QVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQ 652
P E +++E++ + A H I + + +
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENE-------YALHRSI-----VDHYNIPKTFDSDDL 464
Query: 653 SPRN------------MYQCQMAKQTMGFSVQALKFR-ADQKLYHLQTPQTP-------I 692
P + + ++ F + L FR +QK+ H T +
Sbjct: 465 IPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL 524
Query: 693 VRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDL 752
+ Y Y D P + A+L + +E+ +I +K + + + I L
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAILDFL-PKIEENLICSK--------YTDLLR---IAL 572
Query: 753 SDDGNKV 759
+ +
Sbjct: 573 MAEDEAI 579
>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 = 34.3 bits (78), Expect = 0.13
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 1046 DYHVAD-VCSLCGSVLTATFI--HPQKRA 1071
+ D VC+LCG VL+ + + R
Sbjct: 37 RFSEGDVVCALCGLVLSDKLVDTRSEWRT 65
>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 = 9/33 (27%), Positives = 15/33 (45%), Gaps = 6/33 (18%)
Query: 1093 QTSKGMETVAMPYVFRYLAAELA-AMNIKITLQ 1124
Q K ++ Y A + A A+ IK T++
Sbjct: 20 QALKKLQASLKLY-----ADDSAPALAIKATME 47
Score = 30.3 bits (67), Expect = 1.9
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
>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 = 30.9 bits (71), 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
>3ixv_A Hemocyanin AA6 chain; HC, phenolxoidase activity, tyrosinase (TY),
catecholoxidase (CO), enzyme, SDS, cryo-EM, single
particle analysis; 6.80A {Androctonus australis} PDB:
3ixw_A
Length = 626
Score = 29.9 bits (67), Expect = 5.3
Identities = 16/64 (25%), Positives = 22/64 (34%), Gaps = 11/64 (17%)
Query: 954 FNYHGVEVLYSGVYGTELTCEIFIGPVY----------YQRLRHMVSDKFQVRSTGTMDQ 1003
F Y+ + V + T IF+ P Y QR + DKF T +
Sbjct: 438 FTYN-IVVENNSGAEKHSTVRIFLAPKYDELNNKLEPDEQRRLFIELDKFFYTLTPGKNT 496
Query: 1004 ITRQ 1007
I R
Sbjct: 497 IVRN 500
>2z6g_A B-catenin; FULL-length, beta-catenin, cell adhesion; 3.40A {Danio
rerio}
Length = 780
Score = 30.0 bits (67), Expect = 6.3
Identities = 18/104 (17%), Positives = 35/104 (33%), Gaps = 9/104 (8%)
Query: 1022 EMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHP-QKRAIREIGGLPP 1080
EM ++++ H ++ LH S + + L + P +RE G +P
Sbjct: 478 EMAQNAVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLA---LCPANHAPLREQGAIPR 534
Query: 1081 -----ARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNI 1119
RA + + V + + A A++I
Sbjct: 535 LVQLLVRAHQDTQRRTSMGGTQQQFVEGVRMEEIVEACTGALHI 578
>1zb7_A Neurotoxin; hexxh metalloprotease; HET: FLC; 2.35A {Clostridium
botulinum}
Length = 455
Score = 29.4 bits (65), Expect = 7.1
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 0.407
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: 17,567,469
Number of extensions: 1101449
Number of successful extensions: 2334
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2268
Number of HSP's successfully gapped: 32
Length of query: 1131
Length of database: 6,701,793
Length adjustment: 104
Effective length of query: 1027
Effective length of database: 3,798,009
Effective search space: 3900555243
Effective search space used: 3900555243
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)