RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12447
(551 letters)
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA
replication, DNA-BI DNA-directed DNA polymerase,
exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A
{Saccharomyces cerevisiae}
Length = 919
Score = 375 bits (964), Expect = e-120
Identities = 178/544 (32%), Positives = 243/544 (44%), Gaps = 148/544 (27%)
Query: 4 QQTSDKWSRAP-PPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTME 62
+ + R P + +P I FQQI E I +VR FGVT E
Sbjct: 25 EHDLSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKDENT-----STVVRFFGVTSE 79
Query: 63 GNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIV 122
G+SV C+V GF YLYV AP ++ + ++ + A+ +E+V
Sbjct: 80 GHSVLCNVTGFKNYLYVPAPNSSDANDQEQINKFVHY--------LNETFDHAIDSIEVV 131
Query: 123 QKQTVFGFWGEELENFLKIT----------------ESVFPTFPTHTYKAFESNIDFDIR 166
KQ+++G+ G+ F KI + NI + +R
Sbjct: 132 SKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNSWFSNGTTTYDNIAYTLR 191
Query: 167 FMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDV 226
MVD IVG +WI +P GK+ + + VS CQLE+ ++ ++++H E
Sbjct: 192 LMVDCGIVGMSWITLPKGKYSMIEPNN-------RVSSCQLEVSINYRNLIAHPAE---- 240
Query: 227 STDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENI 286
G+WS APLRI+SFDIECAGR G+FP+P +DP+IQIAN+ GA +
Sbjct: 241 -----------GDWSHTAPLRIMSFDIECAGRIGVFPEPEYDPVIQIANVVSIAGAKKP- 288
Query: 287 FVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAP 346
F++NVFTLNTC+P
Sbjct: 289 -----------------------------------------------FIRNVFTLNTCSP 301
Query: 347 IVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLG 406
I GS + TE E+L W FI ++DPD+ GYN NFD PYL+NRAK
Sbjct: 302 ITGSMIFSHATEEEMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLNRAKA---------- 351
Query: 407 RVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDS 466
L V +F + GR+K ++ IK+S
Sbjct: 352 --------------------------------------LKVNDFPYFGRLKTVKQEIKES 373
Query: 467 FIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSII 526
SK G RE K +N +GR+ DLL + REYKLRSYTLN+VS HFL EQKEDV +SII
Sbjct: 374 VFSSKAYGTRETKNVNIDGRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKEDVHYSII 433
Query: 527 SDLQ 530
SDLQ
Sbjct: 434 SDLQ 437
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A
{Human herpesvirus 1} PDB: 1dml_B*
Length = 1193
Score = 330 bits (847), Expect = e-101
Identities = 95/550 (17%), Positives = 172/550 (31%), Gaps = 132/550 (24%)
Query: 4 QQTSDKWSRAPPPELNPKEDKIVFQQISIEHYT-------GEPIPGMP-GSQLKPVPIVR 55
+ S W VF I + ++
Sbjct: 82 PRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEHAYGMRAAQFHARFMDAITPTGTVIT 141
Query: 56 MFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFK---EALNRAIIADMRGNKDEI 112
+ G+T EG+ V HV+G Y Y++ + CRA + E + A+ + I
Sbjct: 142 LLGLTPEGHRVAVHVYGTRQYFYMNKEEVDRHLQCRAPRDLCERMAAALRESPGASFRGI 201
Query: 113 QEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPTFPT------HTYKAFESNIDFDIR 166
E+V++ V+ + F ++ K +E +D R
Sbjct: 202 SADHFEAEVVERTDVYYYETRP-ALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVDATTR 260
Query: 167 FMVD-NDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEID 225
F++D V W + PG+ Q + +E + + D++
Sbjct: 261 FILDNPGFVTFGWYRLKPGRNNTLAQP---RAPMAFGTSSDVEFNCTADNLA-------- 309
Query: 226 VSTDDIVSHAPEGEWSKVAPLRILSFDIEC-AGRKG--IFPDPNH--DPIIQIANMCISQ 280
EG S + +++ FDIEC AG + FP H D +IQI+ +
Sbjct: 310 ----------IEGGMSDLPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDL 359
Query: 281 GASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFT 340
+ + +F+L +C ++
Sbjct: 360 S-TTALEHVLLFSLGSC-----------------------------------DLPESHLN 383
Query: 341 LNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
+ V+ +E E+L + +++ P+ TGYNI NFD+P+L+ + +
Sbjct: 384 ELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFLLAKLTDIYKV 443
Query: 401 NFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIR 460
GR+ R V + I KR
Sbjct: 444 PLDGYGRMN-GRGVFRVWDIGQSHFQKR-------------------------------- 470
Query: 461 SVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKED 520
I G V D+ ++ + KL SY LN+V+ L+++K+D
Sbjct: 471 ------------------SKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKD 512
Query: 521 VQHSIISDLQ 530
+ + I
Sbjct: 513 LSYRDIPAYY 522
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET:
DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5
e.8.1.1
Length = 847
Score = 294 bits (754), Expect = 3e-90
Identities = 75/526 (14%), Positives = 142/526 (26%), Gaps = 164/526 (31%)
Query: 15 PPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVHGFS 74
L ++ ++ + ++ Y G+ + ++F + G
Sbjct: 4 REWLEEAQENKIYFLLQVD-YDGKK----------GKAVCKLFDKETQKIYALYDNTGHK 52
Query: 75 PYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFGFWGEE 134
PY V + + ++ + +E V K + + +
Sbjct: 53 PYFLVDLEPDKVGKIPKIVRD------------------PSFDHIETVSKIDPYTWNKFK 94
Query: 135 LENFLKITESVFPTFP---THTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQ 191
KI KA+E++I + +M D ++ + GK +
Sbjct: 95 ---LTKIVVRDPLAVRRLRNDVPKAYEAHIKYFNNYMYDIGLIPGMPYVVKNGKLES--- 148
Query: 192 HKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSF 251
+ +++ + D ++ + + +++ ++ ++
Sbjct: 149 ---VYLSLDEKDVEEIKKAFADSDEMTRQMAVDWLPIFE----------TEIPKIKRVAI 195
Query: 252 DIEC-AGRKGIFPDPNHD--PIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICC 308
DIE KG PD PII IA S G + + V N +N
Sbjct: 196 DIEVYTPVKGRIPDSQKAEFPIISIALAG-SDGLKK-VLVLNRNDVNEG----------- 242
Query: 309 KTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAF 368
+ G V TE ELL ++
Sbjct: 243 -----------------------------------SVKLDGISVERFNTEYELLGRFFDI 267
Query: 369 IRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKR 428
+ + I +N +FD PY+ RA LG I GK
Sbjct: 268 LL--EYPIVLTFNGDDFDLPYIYFRALKLG----------------YFPEEIPIDVAGKD 309
Query: 429 ENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVC 488
E K +L + I+
Sbjct: 310 EAK--------------------YLAGLH-----------------------IDLYKFFF 326
Query: 489 FDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALL 534
+ E K Y L++V+ L K V ++IS L + L
Sbjct: 327 NKAVRNYAFEGKYNEYNLDAVAKALLGTSKVKV-DTLISFLDVEKL 371
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA
repair, DNA-binding; HET: DNA DOC DCP; 1.92A
{Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A*
3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*
Length = 786
Score = 216 bits (552), Expect = 7e-62
Identities = 56/481 (11%), Positives = 119/481 (24%), Gaps = 183/481 (38%)
Query: 52 PIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDE 111
V + T G + + ++ A + + I+ +G
Sbjct: 22 TEVSFWLATDNG-PLQVTLAPQESVAFIPADQVPR-----------AQHILQGEQG---- 65
Query: 112 IQEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPTFPTHTYKAFESNIDFDIRFMVDN 171
+ L ++ +Q V+G + + + +E+++ R++++
Sbjct: 66 FRLTPLALKDFHRQPVYGLYCRAHRQLMNYEK----RLREGGVTVYEADVRPPERYLMER 121
Query: 172 DIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDI 231
I W+E + +L+
Sbjct: 122 FITSPVWVEGDMHNGT--------------IVNARLKP---------------------- 145
Query: 232 VSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNV 291
PL+ +S DIE ++ CI V +
Sbjct: 146 -------HPDYRPPLKWVSIDIETTRHGELY--------------CIGLEGCGQRIVYML 184
Query: 292 FTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQ 351
N A + +
Sbjct: 185 GPEN-----------------------------------------------GDASSLDFE 197
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDI 411
+ + +LL+K +A+ DPD+ G+N+ FD L A+ + LGR
Sbjct: 198 LEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPL--RLGRDN-- 253
Query: 412 RSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSK 471
S ++ ++ G +
Sbjct: 254 ------SELEWREHGFKNGVF--------------------------------------- 268
Query: 472 QMGKRENKTINFEGRVCFDLLFVLLRE-YKLRSYTLNSVSYHFLQEQKE-DVQHSIISDL 529
+GR+ D + L + S++L +V+ L E K D + ++
Sbjct: 269 --------FAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDEI 320
Query: 530 Q 530
Sbjct: 321 D 321
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B
polymer alpha family polymerase, transferase; 2.10A
{Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A
2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A*
4ail_C* 3a2f_A* 2jgu_A* 1d5a_A
Length = 775
Score = 193 bits (491), Expect = 2e-53
Identities = 78/492 (15%), Positives = 123/492 (25%), Gaps = 213/492 (43%)
Query: 49 KPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGN 108
P++R+F G + F PY Y + + + +
Sbjct: 11 NGKPVIRVFKKE-NGEFKIEYDRTFEPYFYALLKDDSAIEDVKKVTAKRHGTV------- 62
Query: 109 KDEIQEAVLMVEIVQKQTVFGFWGEELENFLKIT----------ESVFPTFPTHTYKAFE 158
V E VQK+ F G + K+ P +E
Sbjct: 63 -----VKVKRAEKVQKK----FLGRPI-EVWKLYFNHPQDVPAIRDRIRAHPAV-VDIYE 111
Query: 159 SNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVS 218
+I F R+++D ++
Sbjct: 112 YDIPFAKRYLIDKGLIPMEG---------------------------------------- 131
Query: 219 HAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCI 278
EE+ + I + EGE PI+ I+
Sbjct: 132 --DEELTMLAFAIATLYHEGEE------------------------FGTGPILMIS---Y 162
Query: 279 SQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNV 338
+ G+ + T I V TE E+
Sbjct: 163 ADGSEARVI--------TWKKIDLPYVDVVSTEKEM------------------------ 190
Query: 339 FTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLG 398
+ ++ +RE DPD+ YN NFDF YL R + LG
Sbjct: 191 -----------------------IKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELG 227
Query: 399 VKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKD 458
+K LGR S + ++MG R
Sbjct: 228 IKF--TLGRDG--------SEPKIQRMGDR------------------------------ 247
Query: 459 IRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQK 518
+ +GR+ FDL V+ R L +YTL +V + K
Sbjct: 248 --------------------FAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGKPK 287
Query: 519 EDVQHSIISDLQ 530
E V I+
Sbjct: 288 EKVYAEEIAQAW 299
>1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding,
complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A
{Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A*
Length = 388
Score = 64.7 bits (156), Expect = 2e-11
Identities = 53/312 (16%), Positives = 90/312 (28%), Gaps = 79/312 (25%)
Query: 214 DDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQI 273
+DI A D I +R+ + DIE G K P I I
Sbjct: 74 EDIGLEALGMNDFKLAYISDTYGSEIVYDRKFVRVANCDIEVTGDKFPDPMKAEYEIDAI 133
Query: 274 ANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENI 333
+ +V ++ + + K + E D+ I
Sbjct: 134 THYDSIDD---RFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEIL---------- 180
Query: 334 FVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINR 393
V + E ++L ++ + P IFTG+NI+ FD PY++NR
Sbjct: 181 --DRVI------------YMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNR 226
Query: 394 AKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFL 453
K + + F+ +
Sbjct: 227 VKMILGERSMKR--------------------------------------------FSPI 242
Query: 454 GRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHF 513
GRVK G +E +I+ + + L+ L S++L SV+ H
Sbjct: 243 GRVKSKL--------LQNMYGSKEIYSIDGVSILDYLDLYKKFAFTNLPSFSLESVAQHE 294
Query: 514 LQEQKEDVQHSI 525
++ K I
Sbjct: 295 TKKGKLPYDGPI 306
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT;
1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A*
3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A*
3spz_A* 3ne6_A* 3nhg_A* 3si6_A* 3scx_A* 3sjj_A* 3snn_A*
3ngi_A* 3lzi_A* 3lzj_A* 3ndk_A* ...
Length = 903
Score = 63.4 bits (153), Expect = 1e-10
Identities = 33/192 (17%), Positives = 64/192 (33%), Gaps = 34/192 (17%)
Query: 245 PLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQ 304
+R+ +FDIE G FP+P I + + +V F L
Sbjct: 107 KIRVANFDIEVTSPDG-FPEP-SQAKHPIDAITHYDSIDDRFYV---FDLLNSPY----- 156
Query: 305 VICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDK 364
E + +A ++ G + + + + E ELL +
Sbjct: 157 ----GNVEEWSIEIAAKLQEQGGDEVPSEIIDKI------------IYMPFDNEKELLME 200
Query: 365 WSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQ 424
+ F ++ P I TG+N+++F PY+ NR K++ + + + + K
Sbjct: 201 YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGE--------STAKRLSPHRKTRVKV 252
Query: 425 MGKRENKTINFE 436
+
Sbjct: 253 IENMYGSREIIT 264
>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 = 59.1 bits (142), Expect = 3e-09
Identities = 77/577 (13%), Positives = 150/577 (25%), Gaps = 228/577 (39%)
Query: 47 QLKPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMR 106
+L+P V + GV G + + + C ++K
Sbjct: 146 ELRPAKNVLIDGVLGSGKTW----------VALDV--------CLSYK------------ 175
Query: 107 GNKDEIQEAVLMVEIVQKQTVFG-FW---G---------EELENFLKITESVFPTFPTHT 153
VQ + F FW E L+ L + + + H+
Sbjct: 176 ---------------VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS 220
Query: 154 YKA---FESNIDFDIRFMVDNDIVGC-----N-WIEIPPGKWQLRGQHKFSNTNRPCVSR 204
S R + C N F+
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN-----AKAWN---AFNL-------S 265
Query: 205 CQLEI---DVSTDDIVSHA---------------PEE--------IDVSTDDIVSHAPEG 238
C++ + D +S A P+E +D D+ P
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL----PR- 320
Query: 239 EWSKVAPLR---ILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASEN---------I 286
E P R I + + N D + I ++ +
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380
Query: 287 FVKNVFTLNTCAPIVGSQVIC---CKTETE-------------LLDKWSAFIRTMGQGAS 330
F + I + ++ L++K
Sbjct: 381 FPPSA-------HIP-TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK---------- 422
Query: 331 ENIFVKNVFTLNTCAPIVGSQVICCKTETE------LLDKWSAFIRELDPDIFTGYNIQN 384
++ ++ + + K E E ++D ++ + D D +
Sbjct: 423 -----ESTISIPSI-----YLELKVKLENEYALHRSIVDHYN-IPKTFDSDDLIPPYLDQ 471
Query: 385 FDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKD-SFIQSKQMGKRENKTINFEGNSDRRE 443
+ + ++ HL KN R+ R V D F++ K I + +
Sbjct: 472 YFYSHI---GHHL--KNIEHPERMTLFRMVFLDFRFLEQK---------IRHDSTA-WNA 516
Query: 444 TLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRS 503
+ + N L ++K + I D+ + K +E V +L
Sbjct: 517 SGSILN--TLQQLKFYKPYICDN----------DPK---YERLVN-AIL----------- 549
Query: 504 YTLNSVSYHFLQEQKEDVQHSIISDL-QIALLQPSDP 539
FL + +E++ S +DL +IAL+ +
Sbjct: 550 --------DFLPKIEENLICSKYTDLLRIALMAEDEA 578
Score = 44.8 bits (105), Expect = 6e-05
Identities = 61/445 (13%), Positives = 127/445 (28%), Gaps = 133/445 (29%)
Query: 208 EIDVSTDDIVSHAPEEI-------DVS-----------TDDIVSHAPEGEWSKVAPLRIL 249
E DI+S + DV D I+ V+ L
Sbjct: 13 EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHII-----MSKDAVSGTLRL 67
Query: 250 SFDIECAGRKGIFP-------DPNHDPII-QIANMCISQGASENIFVKNVFTL-NTCAPI 300
F + ++ + N+ ++ I ++++ L N
Sbjct: 68 -FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126
Query: 301 VGSQVICCKTETELLDKWSAFIRTMGQGA--SENIFV-------KNVFTLNTCAPIVGSQ 351
V + + K +R ++N+ + K L+ C +
Sbjct: 127 AKYNV----SRLQPYLK----LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS---YK 175
Query: 352 VIC-------------CKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKH-- 396
V C C + +L+ + ++DP+ +T + + + I+ +
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN-WTSRSDHSSNIKLRIHSIQAEL 234
Query: 397 ---LGVKNFT----FLGRVKDIRSVIKDSF-IQSK------------QMGKRENKTINFE 436
L K + L V++ ++ ++F + K + I+ +
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAW--NAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292
Query: 437 GNSD---RRETLGVKNF-TFLG-RVKDIR-----------SVI-------KDSFIQSKQM 473
+S E + +L R +D+ S+I ++ K +
Sbjct: 293 HHSMTLTPDEVKSL--LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV 350
Query: 474 G-KRENKTIN--------FEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHS 524
+ I E R FD L V + + L+ + + K DV
Sbjct: 351 NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI---WFDVIKSDVM-V 406
Query: 525 IISDLQIALLQPSDPKSNAAPLRYS 549
+++ L L PK S
Sbjct: 407 VVNKLHKYSLVEKQPK----ESTIS 427
Score = 28.3 bits (62), Expect = 7.8
Identities = 36/246 (14%), Positives = 75/246 (30%), Gaps = 68/246 (27%)
Query: 18 LNPKEDKIVFQQISI--EHYTGEPIPGMPGSQL-------KPVPIVRMFGVTMEGNSVC- 67
L P E + +F ++S+ IP + L V + + S+
Sbjct: 366 LEPAEYRKMFDRLSVFPPS---AHIP----TILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418
Query: 68 -------CHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVE 120
+ +Y+ + + + AL+R+I+ + I + +
Sbjct: 419 KQPKESTISIPS----IYLELKVKLEN------EYALHRSIV-----DHYNIPKTFDSDD 463
Query: 121 IVQKQTVFGFWGEELENFLKITESVFPTFPTHTYKAFESNIDFDIRFMVDNDI--VGCNW 178
++ + ++ + + LK E F + D RF+ + I W
Sbjct: 464 LI-PPYLDQYFYSHIGHHLKNIE------HPERMTLF-RMVFLDFRFL-EQKIRHDSTAW 514
Query: 179 IEIPPGKW-----QLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVS--HAPEEIDVSTD-- 229
G QL+ + N P R + I+ EE + +
Sbjct: 515 --NASGSILNTLQQLKFYKPYICDNDPKYER-------LVNAILDFLPKIEENLICSKYT 565
Query: 230 DIVSHA 235
D++ A
Sbjct: 566 DLLRIA 571
>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 = 41.6 bits (97), Expect = 8e-04
Identities = 40/236 (16%), Positives = 80/236 (33%), Gaps = 46/236 (19%)
Query: 179 IEIPPGKW----QLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVS----TDD 230
+ +P + QL+ Q F+ P + D D+ + P E+
Sbjct: 20 LLVPTASFFIASQLQEQ--FNKI-LPEPTE-GFAAD---DEPTT--PAELVGKFLGYVSS 70
Query: 231 IVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKN 290
+V + G++ +V L + F+ I H ++ + +KN
Sbjct: 71 LVEPSKVGQFDQVLNLCLTEFENCYLEGNDI-----HALAAKLLQENDTTLVKTKELIKN 125
Query: 291 VFTLNTCAPIVGSQVICCKTETELLDKWSA-FIRTM----GQGASENIF--VKNVFTLNT 343
T A I+ + K+ + L + + GQG +++ F +++++ T
Sbjct: 126 YIT----ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLY--QT 179
Query: 344 CAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNF--------DFPYLI 391
+VG K E L + + + G NI + D YL+
Sbjct: 180 YHVLVGD---LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLL 232
Score = 39.6 bits (92), Expect = 0.003
Identities = 62/390 (15%), Positives = 105/390 (26%), Gaps = 153/390 (39%)
Query: 19 NPKEDKIVFQQ-ISIEHYTGEPIPGMPGSQLK--PV--PIVRMFGVTMEGN-SVCCHVHG 72
+ + VF Q ++I + P L P+ P++ GV + V + G
Sbjct: 201 TTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI---GVIQLAHYVVTAKLLG 257
Query: 73 FSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFGFWG 132
F+ P E R+ + G+ + AV I + + W
Sbjct: 258 FT-------PGEL-------------RSYLKGATGHSQGLVTAVA---IAETDS----WE 290
Query: 133 EELENFLKITESVFPTFPTHTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQH 192
+ K +F +I G +R
Sbjct: 291 SFFVSVRKAITVLF-------------------------------FI----G---VRCYE 312
Query: 193 KFSNTN---------------RPC-------VSRCQLEIDVSTDDIVSHAPEEIDVS--- 227
+ NT+ P +++ Q++ V + SH P V
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV--NKTNSHLPAGKQVEISL 370
Query: 228 --TDD--IVSHAPEGEWSKVAPLRILS----FD---IECAGRKGIF-----P--DPNHDP 269
+VS P+ + LR D I + RK F P P H
Sbjct: 371 VNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSH 430
Query: 270 IIQIANMCISQGASENIF----------VKNVFT---L-NTCAPIVGS--QVICCK---- 309
++ A+ I++ +N V + F L I I
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKW 490
Query: 310 ------TETELLDKWSAFIRTMGQGASENI 333
T +LD F G G + +
Sbjct: 491 ETTTQFKATHILD----F----GPGGASGL 512
Score = 38.5 bits (89), Expect = 0.007
Identities = 46/336 (13%), Positives = 80/336 (23%), Gaps = 137/336 (40%)
Query: 71 HG-FSPYLYVSAPKEFNSTHCRA-FKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVF 128
HG L V F ++ + F + L + DE E+V K F
Sbjct: 13 HGSLEHVLLVPTASFFIASQLQEQFNKILPEP--TEGFAADDEPTTPA---ELVGK---F 64
Query: 129 -GFWGEELEN-----FLKITESVFPTFPTHTYKAFESNIDFDIRFMVDNDI--------- 173
G+ +E F ++ FE+ ++ NDI
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNLCL--------TEFENC------YLEGNDIHALAAKLLQ 110
Query: 174 -----------------VGCNWIEIPPGKWQ----LR--------------GQHKFSNTN 198
+ P K R GQ NT+
Sbjct: 111 ENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ---GNTD 167
Query: 199 -------------RPCVSRCQLEIDVSTDDIVSHAPEEIDVSTD-----DIVS------H 234
V I S + + +D +I+ +
Sbjct: 168 DYFEELRDLYQTYHVLVGDL---IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSN 224
Query: 235 APEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPII---QIAN---MCISQGASENIFV 288
P+ ++ P +S P+I Q+A+ G +
Sbjct: 225 TPDKDYLLSIP---ISC-----------------PLIGVIQLAHYVVTAKLLGFTPGELR 264
Query: 289 KNVFTLNTCAP-IVGSQVICCKTETELLDKWSAFIR 323
+ + +V + I D W +F
Sbjct: 265 SYLKGATGHSQGLVTAVAI------AETDSWESFFV 294
Score = 37.0 bits (85), Expect = 0.019
Identities = 23/104 (22%), Positives = 43/104 (41%), Gaps = 23/104 (22%)
Query: 420 IQSKQMGK--REN----KTINFEGNSDR--RETLGVKNFTFLGRVKD--IRSVIKDSFIQ 469
Q + MG + + + + +D ++T G F+ L V + + I +
Sbjct: 1626 SQEQGMGMDLYKTSKAAQDV-WN-RADNHFKDTYG---FSILDIVINNPVNLTIHFGGEK 1680
Query: 470 SKQMGKREN-KTINFE----GRVCFDLLFVLLREYKLRSYTLNS 508
K++ REN + FE G++ + +F + E SYT S
Sbjct: 1681 GKRI--RENYSAMIFETIVDGKLKTEKIFKEINE-HSTSYTFRS 1721
Score = 36.2 bits (83), Expect = 0.039
Identities = 28/146 (19%), Positives = 55/146 (37%), Gaps = 40/146 (27%)
Query: 413 SVIKDSFIQSKQMGKRENKTINFEGN---SDRRETLGVKNFTFLGRVKDIRSVIKDSFIQ 469
S +++ F + T F + + E +G FLG V S ++
Sbjct: 31 SQLQEQFNKI-----LPEPTEGFAADDEPTTPAELVG----KFLGYV--------SSLVE 73
Query: 470 SKQMGKRENKTINFEGRVCFDLLFVLLREYK---LRSYTLNSVSYHFLQEQKEDV--QHS 524
++G+ + +L + L E++ L +++++ LQE +
Sbjct: 74 PSKVGQFD------------QVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKE 121
Query: 525 IIS---DLQIALLQPSDPKSNAAPLR 547
+I +I +P D KSN+A R
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALFR 147
Score = 34.6 bits (79), Expect = 0.097
Identities = 39/286 (13%), Positives = 74/286 (25%), Gaps = 104/286 (36%)
Query: 155 KAFESNIDFDIRFMVDNDIVGCNWIEI---PPGKWQLRGQHKFSNTNRPCVSRCQLEIDV 211
F+ F I DIV N + + G+ +G+ N + + +
Sbjct: 1651 NHFKDTYGFSIL-----DIVINNPVNLTIHFGGE---KGKRIRENYSA-------MIFET 1695
Query: 212 STDDIVSHAP--EEIDVSTDDIVSHAPEGE-------------WSKVAPLRILSFDIECA 256
D + +EI+ + + +G A L
Sbjct: 1696 IVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME-KAAFEDLK------ 1748
Query: 257 GRKGIFPDPN----HDPIIQIANMCISQG------ASENIF-----VKNVF----TLNTC 297
KG+ P H S G + ++ V+ VF T+
Sbjct: 1749 -SKGLIPADATFAGH-----------SLGEYAALASLADVMSIESLVEVVFYRGMTMQVA 1796
Query: 298 AP-------------IVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTC 344
P I +V ++ L + +G+ + + N N
Sbjct: 1797 VPRDELGRSNYGMIAINPGRVAASFSQEAL----QYVVERVGKRTGWLVEIVN---YN-- 1847
Query: 345 APIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYL 390
Q + + LD + + + +Q D L
Sbjct: 1848 VE--NQQYVAAG-DLRALDTVTNVLNFI--------KLQKIDIIEL 1882
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline
type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus
musculus} PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A*
3b6p_A* 2o4i_A 2oa8_A
Length = 242
Score = 33.8 bits (77), Expect = 0.10
Identities = 24/154 (15%), Positives = 43/154 (27%), Gaps = 30/154 (19%)
Query: 251 FDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKT 310
D+E G + + ++ + + + A EN + P
Sbjct: 17 LDLEATGL-----PSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRP----------- 60
Query: 311 ETELLDKWSAFI---RTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367
++DK S I + GASE + + + L A
Sbjct: 61 -PRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQ---------RFDDNLAILLRA 110
Query: 368 FIRELDPDI-FTGYNIQNFDFPYLINRAKHLGVK 400
F++ +N +DFP L L
Sbjct: 111 FLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTP 144
>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 = 31.8 bits (71), Expect = 0.31
Identities = 8/42 (19%), Positives = 19/42 (45%), Gaps = 14/42 (33%)
Query: 123 QKQTVFGFWGEELENFLKI--TESVFPTFPTHTYKAFESNID 162
+KQ + ++L+ LK+ +S P A ++ ++
Sbjct: 18 EKQAL-----KKLQASLKLYADDSA-PAL------AIKATME 47
>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease,
homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus
musculus} PDB: 3u6f_B*
Length = 314
Score = 32.4 bits (73), Expect = 0.36
Identities = 24/154 (15%), Positives = 42/154 (27%), Gaps = 30/154 (19%)
Query: 251 FDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKT 310
D+E G + + ++ + + + A EN I
Sbjct: 17 LDLEATGL-----PSSRPEVTELCLLAVHRRALEN------------TSISQGHPPPVPR 59
Query: 311 ETELLDKWSAFI---RTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367
++DK S I + GASE + + + L A
Sbjct: 60 PPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQ---------RFDDNLAILLRA 110
Query: 368 FIRELDPDI-FTGYNIQNFDFPYLINRAKHLGVK 400
F++ +N +DFP L L
Sbjct: 111 FLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTP 144
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo
sapiens} SCOP: c.55.3.5
Length = 238
Score = 30.6 bits (69), Expect = 1.1
Identities = 24/158 (15%), Positives = 47/158 (29%), Gaps = 41/158 (25%)
Query: 251 FDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKT 310
D+E G I +++ + + + EN + +V +V+
Sbjct: 15 LDLEATGL-----PSVEPEIAELSLFAVHRSSLENP------EHDESGALVLPRVL---- 59
Query: 311 ETELLDKWSAFI---RTMGQGASE-----NIFVKNVFTLNTCAPIVGSQVICCKTETELL 362
DK + + R ASE + + +V L
Sbjct: 60 -----DKLTLCMCPERPFTAKASEITGLSSEGLARCRKAGFDGAVV-----------RTL 103
Query: 363 DKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
+ + P +N ++DFP L + LG +
Sbjct: 104 QAFLSRQA--GPICLVAHNGFDYDFPLLCAELRRLGAR 139
>1nm8_A Carnitine O-acetyltransferase; two equally sized domains,
anti-parallel beta-strand; 1.60A {Homo sapiens} SCOP:
c.43.1.3 c.43.1.3 PDB: 1s5o_A* 2h3u_A* 2h3p_A* 1t7q_A*
1t7n_A 1t7o_A* 1ndb_A 1ndf_A* 1ndi_A* 2h3w_A*
Length = 616
Score = 28.3 bits (62), Expect = 7.4
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 59 VTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMR 106
V +G VC + +SA T+ L +A + DMR
Sbjct: 548 VVPDGYGVCYNPMEAHINFSLSAYNSCAETNAARLAHYLEKA-LLDMR 594
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 0.418
Gapped
Lambda K H
0.267 0.0631 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,506,041
Number of extensions: 514303
Number of successful extensions: 1134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1088
Number of HSP's successfully gapped: 37
Length of query: 551
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 453
Effective length of database: 3,965,535
Effective search space: 1796387355
Effective search space used: 1796387355
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 (27.1 bits)