RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8714
(562 letters)
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex,
single-stranded DNA, isomerase/DNA complex; HET: DNA;
2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A*
2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*
Length = 659
Score = 213 bits (545), Expect = 2e-61
Identities = 95/500 (19%), Positives = 183/500 (36%), Gaps = 72/500 (14%)
Query: 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP-KTVWRARFSAITDKDIKAAMWNL 163
+ +V D D+EG+ + EV++ ++ + + + + ++ A+ L
Sbjct: 93 HEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCL---INDLNPQAVERAIDRL 149
Query: 164 VKPNI-FE--ARSVDARQELDLRIGCAFTRYQT-KFFQGKYGDLDASLISYGPCQTPTLG 219
+ N F S AR D G TR T Y + +S G QTP LG
Sbjct: 150 -RSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGV----LSVGRVQTPVLG 204
Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNL-NGVAVSVTW-----------SRGHIFDKSTCNV 267
V R ++I F + ++ + + + W G + +
Sbjct: 205 LVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEH 264
Query: 268 FFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQ 326
+ + V +S++ P + L A+ G+ + + I ++LY T
Sbjct: 265 VVNRI-SGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETH 323
Query: 327 GYVSYPRTETT-----QYPENFDLVAVLRQQESSPDWGDHVREVLSNGI---SKPRKGKD 378
+++PR++ + ++ + V + N K
Sbjct: 324 KLITFPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKK------ 377
Query: 379 VGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTME 438
V H I PT ++ L + ++Y+ I R ++ C D V+ + V + +A F +
Sbjct: 378 VDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAK 437
Query: 439 AKYLLHPGFTGVMTWSAMKNE----SIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELI 494
A++L G+ ++ E +P GD + + ++VER+T PP + T++ L+
Sbjct: 438 ARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLL 497
Query: 495 SLME-----------------KHGIGTDA---SIPVHINNICQRNYVTVTSGRRLVPTSL 534
S M G+GT+A I I + +R ++T GR + T
Sbjct: 498 SAMTGIARFVQDKDLKKILRATDGLGTEATRAGI---IELLFKRGFLTK-KGRYIHSTDA 553
Query: 535 GIVLVHGYQKIDRELVEPTM 554
G L + + P M
Sbjct: 554 GKAL---FHSLPEMATRPDM 570
>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga
maritima} PDB: 2gaj_A*
Length = 633
Score = 145 bits (368), Expect = 3e-37
Identities = 113/483 (23%), Positives = 178/483 (36%), Gaps = 104/483 (21%)
Query: 100 LANEAKDCEFLVLWL--DCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIK 157
L + AK E L + D D+EGE I + + N+ R FS IT + I+
Sbjct: 70 LKDLAKKGE---LLIASDMDREGEAIAWHIARV------TNTLGRKNRIVFSEITPRVIR 120
Query: 158 AAMWNLVKPNIFEARSVD--------ARQELDLRIGCAFTRYQ------TKFFQGKYGDL 203
A+ N R +D AR+ LD +G Y F
Sbjct: 121 EAVKN--------PREIDMKKVRAQLARRILDRIVG-----YSLSPVLWRNFKSNL---- 163
Query: 204 DASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKS 263
S G Q+ TL +R +I F P+ Y +T+N +G+ + FD
Sbjct: 164 -----SAGRVQSATLKLVCDREREILRFVPKKYH--RITVNFDGLTAEIDVKEKKFFDAE 216
Query: 264 TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
T K ++ + V + + S K P+ T L + A S LG M IA++L
Sbjct: 217 T----LKEIQSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQL 272
Query: 324 Y--------TQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGI----- 370
Y +++Y RT++T+ S + R +++
Sbjct: 273 YEGVETKDGHIAFITYMRTDSTRV---------------SDYAKEEARNLITEVFGEEYV 317
Query: 371 -SKPRKGKDVGD----HPPITPTKLATRT------QLDGDAWRLYDYIVRHFIGTLCGDL 419
SK + K H I PT + T L+ D +LY+ I + F+ +
Sbjct: 318 GSKRERRKSNAKIQDAHEAIRPTNV-FMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPS 376
Query: 420 VYTQKVAKFSVADEMFTMEAKY--LLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM 477
Y + D + + + G+ V W +N F+ G+ + VK+
Sbjct: 377 QYEETRFVLRTKDGKYRFKGTVLKKIFDGYEKV--WKTERNTGEFPFEEGESVKPVVVKI 434
Query: 478 VERKTTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSL 534
E++T P TE L+ ME+ GIG T AS I + R Y+ L PT +
Sbjct: 435 EEQETKPKPRYTEGSLVKEMERLGIGRPSTYAST---IKLLLNRGYIKK-IRGYLYPTIV 490
Query: 535 GIV 537
G V
Sbjct: 491 GSV 493
>1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA;
1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X*
1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A*
3pwt_A* 3px7_A* 1ecl_A 1cy9_A* 1cyy_A*
Length = 592
Score = 136 bits (346), Expect = 1e-34
Identities = 113/479 (23%), Positives = 180/479 (37%), Gaps = 90/479 (18%)
Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159
L A+ + + L D D+EGE I + + E I + R F+ IT I+ A
Sbjct: 96 LKQLAEKADHIYLATDLDREGEAIAWHLREV----IGGD-DARYSRVVFNEITKNAIRQA 150
Query: 160 MWNLVKPNIFEARSVD--------ARQELDLRIGCAFTRYQ------TKFFQGKYGDLDA 205
++ AR+ +D +G Y K +G
Sbjct: 151 FNK--------PGELNIDRVNAQQARRFMDRVVG-----YMVSPLLWKKIARGL------ 191
Query: 206 SLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG---VAVSVTWSRG---HI 259
S G Q+ + VER +I+ F PE +W +D + +A+ VT
Sbjct: 192 ---SAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRP 248
Query: 260 FDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQA-LNTVELMRVASSGLGMGPHHAMQ 318
+K +EK ++ +V++ + + KP A T L + AS+ LG G M
Sbjct: 249 VNKEQTQAAVSLLEKARY-SVLEREDKPTTS-KPGAPFITSTLQQAASTRLGFGVKKTMM 306
Query: 319 IAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGI------SK 372
+A+RLY GY++Y RT++T S D + VR +S+
Sbjct: 307 MAQRLYEAGYITYMRTDSTNL---------------SQDAVNMVRGYISDNFGKKYLPES 351
Query: 373 PRKGKDVGD----HPPITPTKLATRT-----QLDGDAWRLYDYIVRHFIGTLCGDLVYTQ 423
P + + I P+ + ++ DA +LY I R F+ Y
Sbjct: 352 PNQYASKENSQEAREAIRPSDV-NVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDS 410
Query: 424 KVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNES--IPDFKPGDLIPIQSVKMVERK 481
D + L G+T VM +E +P GD + + + +
Sbjct: 411 TTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHF 470
Query: 482 TTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSLGIV 537
T PP +E+ L+ +EK GIG T ASI I+ I R YV V RR +G +
Sbjct: 471 TKPPARFSEASLVKELEKRGIGRPSTYASI---ISTIQDRGYVRVE-NRRFYAEKMGEI 525
>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea,
helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16
c.37.1.16 e.10.1.1 PDB: 1gl9_B*
Length = 1054
Score = 136 bits (344), Expect = 8e-34
Identities = 101/534 (18%), Positives = 177/534 (33%), Gaps = 121/534 (22%)
Query: 50 LFKMTSVCGHI---------MGLD----FTSKYNNWDKVDPL------ELFSCPTEKREA 90
+ +T+ GH+ G+ F Y + + + SCP E
Sbjct: 546 VLMVTASIGHVVDLITNRGFHGVLVNGRFVPVYASIKRCRDCGYQFTEDRESCPKCGSEN 605
Query: 91 TP-KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFS 149
L A D EF+++ D D EGE I +++ ++ V RA F
Sbjct: 606 VDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNL------LSGCGAVKRAEFH 659
Query: 150 AITDKDIKAAMWNLVKPNIFEARSVDA---RQELDLRIGCAFT---RYQTKFFQGKYGDL 203
+T + I A+ + + V A R+ D IG F + +F
Sbjct: 660 EVTRRAILEALES---LRDVDENLVKAQVVRRIEDRWIG--FVLSQKLWERF--NNRN-- 710
Query: 204 DASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKS 263
+S G QT LG+ ++R + R +
Sbjct: 711 ----LSAGRAQTLVLGWIIDRFQESRERRKIAIV-------------------------R 741
Query: 264 TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
++ + E+E +T+ V+ + +T T ++ A+ L MQIA+ L
Sbjct: 742 DFDLVLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDANRILKFSVKQTMQIAQEL 801
Query: 324 YTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK------ 377
+ G ++Y RT++T+ S +E L + G+
Sbjct: 802 FENGLITYHRTDSTRV---------------SDVGQRIAKEYLGDDFVGREWGESGAHEC 846
Query: 378 ----DVGDHP---PITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSV 430
+ + L + + LYD I R F+ + C K
Sbjct: 847 IRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEF 906
Query: 431 ADEM----FTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPD 486
+ + A+ + + V +P VK +
Sbjct: 907 DGKTAEEERIVRAEGRAYELYRAVW-----VKNELPTGTFR-------VKAEVKSVPKVL 954
Query: 487 YLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSLGIV 537
T+SE+I +M++ GIG T A+I ++ + RNYV R++PT LGI
Sbjct: 955 PFTQSEIIQMMKERGIGRPSTYATI---VDRLFMRNYVVE-KYGRMIPTKLGID 1004
>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 = 64.7 bits (157), Expect = 5e-11
Identities = 79/471 (16%), Positives = 152/471 (32%), Gaps = 144/471 (30%)
Query: 130 AVRHQININSPKTVW------RARFSAI----TDK----DIKAAMWNLVKPNI-FEARSV 174
++ H + + P + + +F+ I T+ D LV + + + V
Sbjct: 15 SLEHVLLV--PTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLV 72
Query: 175 D-----ARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIR 229
+ ++ L + T ++ + +G D+ A TL V+ + I+
Sbjct: 73 EPSKVGQFDQV-LNL--CLTEFENCYLEGN--DIHALAAKLLQENDTTL---VKTKELIK 124
Query: 230 TFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDV---QSS 286
+ A + FDK + + F+AV E + +V + Q +
Sbjct: 125 NY----I-----------TARIMA---KRPFDKKSNSALFRAVG-EGNAQLVAIFGGQGN 165
Query: 287 TKS---------KTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETT 337
T +T + +L++ + AE L +
Sbjct: 166 TDDYFEELRDLYQTYHVLVG--DLIKFS--------------AETL--SELIRTTLDAEK 207
Query: 338 QYPENFDLVAVLRQQESSPDWGDHVREVL-SNGISKPRKGKDVGDHPPITPTKLATRTQL 396
+ + +++ L ++PD ++ L S IS P L QL
Sbjct: 208 VFTQGLNILEWLENPSNTPD-----KDYLLSIPISCP----------------LIGVIQL 246
Query: 397 DGDAW-----RLYDYIVRHFIGTLCGDLVYTQKV---AKFSVAD--EMFTMEAKYLLHPG 446
A +L + L G ++Q + + D E F + + +
Sbjct: 247 ---AHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL 303
Query: 447 F-TGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDY------LTESELISLMEK 499
F GV + A N S+P P +E P LT+ ++ + K
Sbjct: 304 FFIGVRCYEAYPNTSLP--------PSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNK 355
Query: 500 HGIGTDASIP----VHINNIC-QRNYVTVTSGRRLVPTSLGIVLVHGYQKI 545
T++ +P V I+ + +N V V+ G P SL L +K
Sbjct: 356 ----TNSHLPAGKQVEISLVNGAKNLV-VS-GP---PQSL-YGLNLTLRKA 396
Score = 33.5 bits (76), Expect = 0.23
Identities = 41/311 (13%), Positives = 80/311 (25%), Gaps = 99/311 (31%)
Query: 9 VPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLV-LFKMTSVCGH--IMGLDF 65
+P S P LI ++ + + + P G+L K + + +
Sbjct: 234 IPIS-----CP-LIGVIQLAHYVV-TAKLLGF-TP--GELRSYLKGATGHSQGLVTAV-A 282
Query: 66 TSKYNNWDK-----VDPLE-LFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKE 119
++ ++W+ + LF EA P LP + D +
Sbjct: 283 IAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILE------------DSLEN 330
Query: 120 GENI-CFEVMEAVRH----QININSPKTVWRARFSAITDKDIKAAMWNLVKPNIF----- 169
E + M ++ + Q+ V + K ++ ++ N
Sbjct: 331 NEGVPSP--MLSISNLTQEQVQ----DYVNKTNSHLPAGKQVEISLVN--GAKNLVVSGP 382
Query: 170 ---------EARSVDARQELD-----------------LRIGCAF-TRYQTKFFQGKYGD 202
R A LD L + F + D
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKD 442
Query: 203 LDASLISYGPCQTPTLGFCVER----HDKIRTFKPEPYWLLDLTLNLNGVAVS--VTWSR 256
L + +S+ + V D +R ++ + + V W
Sbjct: 443 LVKNNVSFNAKD---IQIPVYDTFDGSD-LRVLSGS------ISERIVDCIIRLPVKWET 492
Query: 257 G------HIFD 261
HI D
Sbjct: 493 TTQFKATHILD 503
>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 = 56.0 bits (134), Expect = 2e-08
Identities = 85/577 (14%), Positives = 162/577 (28%), Gaps = 196/577 (33%)
Query: 64 DFTSKYNNWDKVD-PLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGEN 122
F ++ D D P + S K E + +A + W K E
Sbjct: 28 AFVDNFDCKDVQDMPKSILS----KEEIDHIIMSK-----DAVSGTLRLFWTLLSK-QEE 77
Query: 123 ICFEVMEAVRHQININSPKTVWRARF---SAITDKDIKA--AMWNLVKPNIFEARSVDAR 177
+ + +E V +IN + + S +T I+ ++N + F +V +R
Sbjct: 78 MVQKFVEEV-LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV--FAKYNV-SR 133
Query: 178 QE--LDLR-------------------IG--------CAFTRYQTKFFQGKYGDLDASLI 208
+ L LR G C + Q K + +
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF------WL 187
Query: 209 SYGPCQTPTL------GFCV-------ERHDKI---------------RTFKPEPYW--L 238
+ C +P R D R K +PY L
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247
Query: 239 LDLTLNLNGVAVSVTWSRGHI--FD---------KSTCNVFFKAVEKEKHVTVVDVQSS- 286
L L V + F+ + F + H+++ +
Sbjct: 248 LVL----LNV-----QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298
Query: 287 TKSKTKP---QALNTV--ELMRVASSGLGMGPHHAMQIAERL--------YTQGYVSYPR 333
T + K + L+ +L R + P IAE + + +V+ +
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTT---NPRRLSIIAESIRDGLATWDNWK-HVNCDK 354
Query: 334 TETT-------QYP----ENFDLVAVLRQQESSPD------WGDHVREVLSNGISKPRKG 376
T P + FD ++V P W D ++ + ++K K
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414
Query: 377 KDVGDHPP-----ITPTKLATRTQLDG------------------DAWRL---------Y 404
V P I L + +L+ D+ L Y
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY 474
Query: 405 DYIVRHFIGTLCGDLVYTQKVAKFSVA--DEMFTMEAKYLLHPGFTGVMTWSAMKNESIP 462
+I H + +++ F + D F +E K ++++S
Sbjct: 475 SHIGHHLKNIE-----HPERMTLFRMVFLDFRF-LEQK---------------IRHDSTA 513
Query: 463 DFKPGDLIP-IQSVKMVERKTTPPDYLTESELISLME 498
G ++ +Q +K + D E + ++++
Sbjct: 514 WNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD 550
Score = 39.5 bits (91), Expect = 0.004
Identities = 39/278 (14%), Positives = 76/278 (27%), Gaps = 99/278 (35%)
Query: 27 PLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTE 86
P + + + P L S+ + D + ++NW V+ +
Sbjct: 319 PRE----VLTTN----PR----RL----SIIAESIR-DGLATWDNWKHVN--------CD 353
Query: 87 KREATPKLKLPAFLANEAKDC--EFLV--------------LWLDCDKEGENICFEVMEA 130
K + L E + V +W D K +VM
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS------DVMVV 407
Query: 131 VRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIF--EARSVDARQELDLRIGCAF 188
V ++S + +K K + ++ P+I+ ++ L I
Sbjct: 408 VNKL-----------HKYSLV-EKQPKESTISI--PSIYLELKVKLENEYALHRSI---V 450
Query: 189 TRYQT--KFFQGKYGD--LDASLISYGPCQTPTLGF---CVERHDKIRTFKPEPYWLLDL 241
Y F LD S+ +G +E +++ F LD
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSH-------IGHHLKNIEHPERMTLF---RMVFLDF 500
Query: 242 -----TLNLNGVAVSVTWS-----------RGHIFDKS 263
+ + A + + S + +I D
Sbjct: 501 RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDND 538
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 35.1 bits (80), Expect = 0.044
Identities = 22/113 (19%), Positives = 41/113 (36%), Gaps = 33/113 (29%)
Query: 62 GLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFL---ANEAKDCEFLVLWLDCDK 118
G+ Y++ K + ++ +K + P +++ + L + K +FLV+
Sbjct: 117 GMAIQVNYSSEVKENSVD----SDDKAKVPPLIRIVSGLELSDTKQKGKKFLVI----AY 168
Query: 119 EG-ENICFEV--MEAVRHQIN-----------INSPKTVWRARFSAITDKDIK 157
E ENI E+ E + + N +N T W D K
Sbjct: 169 EPFENIAIELPPNEILFSENNDMDNNNDGVDELNKKCTFW--------DAISK 213
>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 = 32.2 bits (72), Expect = 0.24
Identities = 8/23 (34%), Positives = 9/23 (39%), Gaps = 2/23 (8%)
Query: 203 LDASLISYGPCQTPTLGF--CVE 223
L ASL Y P L +E
Sbjct: 25 LQASLKLYADDSAPALAIKATME 47
>2ljw_A ALR2454 protein; novel fold, structural genomics, northeast
structural genomi consortium, NESG, PSI-biology, protein
structure initiative function; NMR {Nostoc SP}
Length = 110
Score = 29.9 bits (67), Expect = 0.79
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 14/70 (20%)
Query: 318 QIAERLYTQ---GYV---SYPRTETTQYPENFDLVAVLRQQESSPDWG--DHVREVLSNG 369
+ +++ Q Y+ S+P ET +Y E+ D VA G V+ ++
Sbjct: 24 RTQGKIFLQVMWKYLEQASFPMNET-EYQEHLDSVA-----NYLHALGGAVQVKTFITQT 77
Query: 370 ISKPRKGKDV 379
+PR GK V
Sbjct: 78 KERPRLGKAV 87
>3eol_A Isocitrate lyase; seattle structural center for infectious disease,
ssgcid; 2.00A {Brucella melitensis} PDB: 3oq8_A 3e5b_A
3p0x_A*
Length = 433
Score = 31.4 bits (70), Expect = 0.90
Identities = 10/67 (14%), Positives = 24/67 (35%), Gaps = 6/67 (8%)
Query: 311 MGPHHAM-----QIAERLYTQGYVSYPRTETTQYPENFDLVAVLR-QQESSPDWGDHVRE 364
+ H + ++A + +Y + ++ D + Q+E + D V
Sbjct: 348 LAGFHQLNYGMFELARGYKDRQMAAYSELQQAEFAAEADGYTATKHQREVGTGYFDAVSL 407
Query: 365 VLSNGIS 371
++ G S
Sbjct: 408 AITGGQS 414
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 29.1 bits (65), Expect = 5.5
Identities = 17/161 (10%), Positives = 37/161 (22%), Gaps = 7/161 (4%)
Query: 354 SSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIG 413
S P G + S + + + Q+ + +
Sbjct: 1218 SVPAPGKGILTTAREHHSSVKYASPNLNMKYRKRQLVTREAQIKDWVENELEALKLEAEE 1277
Query: 414 TLCGDLV--YTQKVAKFSVADEMFTMEAKYLLH-PGFTGVMTWSAMKNESIPDFKPGDLI 470
D ++ + E A+ + + ++ G I
Sbjct: 1278 IPSEDQNEFLLERTREIHNEAESQLRAAQQQWGNDFYKRDPRIAPLRGALA---TYGLTI 1334
Query: 471 PIQSVKMVERKTTPPDYLTESELI-SLMEKHGIGTDASIPV 510
V +T + ES I +M+ G +
Sbjct: 1335 DDLGVASFHGTSTKANDKNESATINEMMKHLGRSEGNPVIG 1375
>3i4e_A Isocitrate lyase; structural genomics, seattle structural genomics
center for infectious disease, ssgcid; 2.69A
{Burkholderia pseudomallei}
Length = 439
Score = 28.5 bits (63), Expect = 6.7
Identities = 9/78 (11%), Positives = 23/78 (29%), Gaps = 7/78 (8%)
Query: 312 GPHHAM-----QIAERLYTQGYVSYPRTETTQYPENFDLVAVLR-QQESSPDWGDHVREV 365
HA+ +A ++ + ++ ++ Q+E + D V +
Sbjct: 354 AGFHALNYSMFNLAHGYARTQMSAFVELQQAEFAAADKGFTAVKHQREVGTGYFDAVTQT 413
Query: 366 LSNGIS-KPRKGKDVGDH 382
+ S G +
Sbjct: 414 VEREASTTALHGSTEDEQ 431
>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 = 28.1 bits (62), Expect = 6.9
Identities = 14/79 (17%), Positives = 20/79 (25%), Gaps = 32/79 (40%)
Query: 84 PTEKREATPKLKLPAFLANEAKDCEFLVLWLDC----------DKEGENICFE---VMEA 130
P L N C +C EG+ +C V+
Sbjct: 8 DKRAGRRGPNL-------NIVLTCP------ECKVYPPKIVERFSEGDVVCALCGLVLSD 54
Query: 131 VRHQININSPKTVWRARFS 149
++ S WR FS
Sbjct: 55 --KLVDTRSE---WRT-FS 67
>1dqu_A Isocitrate lyase; beta barrel; 2.80A {Emericella nidulans} SCOP:
c.1.12.7
Length = 538
Score = 28.3 bits (62), Expect = 8.2
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 314 HHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLR-QQESSPDWGDHVREVLSNGIS 371
+ A+ QG +Y E Q PE + V V+ Q+ S ++ D++ ++++ G+S
Sbjct: 466 LISDTFAKAYAKQGMRAY--GELVQEPEMANGVDVVTHQKWSGANYVDNMLKMITGGVS 522
>1ylm_A Hypothetical protein BSU32300; MCSG, structural genomics,
hypothetical cytosolic protein, PSI, protein structure
initiative; 1.83A {Bacillus subtilis subsp}
Length = 144
Score = 27.3 bits (60), Expect = 8.5
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 537 VLVHGYQKIDRELVEPTMR 555
LV Y D + ++
Sbjct: 98 TLVQQYLLADSGELYRLIK 116
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
0.320 0.136 0.416
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,699,285
Number of extensions: 518450
Number of successful extensions: 1040
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1021
Number of HSP's successfully gapped: 24
Length of query: 562
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 463
Effective length of database: 3,937,614
Effective search space: 1823115282
Effective search space used: 1823115282
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: 60 (27.4 bits)