RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11423
(655 letters)
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 826 bits (2137), Expect = 0.0
Identities = 266/664 (40%), Positives = 397/664 (59%), Gaps = 35/664 (5%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
++TEL+ L H Y++ D P I D +YD+L+ EL+++E K+PEL+T DS TQ VG
Sbjct: 7 QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAP 66
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
+ H M+SLDN F +E + FNKR+ + LK + + + ELK DG+AV++ YE
Sbjct: 67 LAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYE 126
Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
G L A+TRGDG GE+IT+N+ I IPL L+ + P LEVR EV + + F K+N+
Sbjct: 127 NGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVFLPQAGFEKINE 186
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
G K F NPRNAAAG LRQL+P+I + L FF +GVG L G +P +H L +
Sbjct: 187 DARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQF 246
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
+K GL + ++ +++ FY K+ R L ++IDGVV K+N L+ Q++LGF +RA
Sbjct: 247 KKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARA 306
Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
PR+A+A+KF ++E +T ++ + Q+GRTG ITPVA L+PV + G+ ++ ATLHN EI R
Sbjct: 307 PRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIER 366
Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
++IGD VV+ R+G+VIP++ + +LS RP D++ P CP+C S + +E +ARC
Sbjct: 367 LGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFPTHCPVCGSDVERVEGEAVARC 426
Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
+G I C AQRK L+HF SR+AM++ G+G K+I++LV V T DL+K+ L L
Sbjct: 427 TGGLI-CGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGL 485
Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
+R+ K A N++ A++K+K TTF+RF+YALGIR VGE TA LA YF LE + A+ E+
Sbjct: 486 ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEE 545
Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK--------------- 601
L +P +G F + +R +IS+L G++W
Sbjct: 546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVL 605
Query: 602 -------------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
G KV +SK T+ ++ G+ G KL KA +L I+++DE
Sbjct: 606 TGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAEM 665
Query: 643 VKIV 646
++++
Sbjct: 666 LRLL 669
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A
{Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2
PDB: 1v9p_A*
Length = 667
Score = 787 bits (2036), Expect = 0.0
Identities = 241/665 (36%), Positives = 373/665 (56%), Gaps = 46/665 (6%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
R+ EL+ + HN YY+ +P ISD +YD+LL ELK++EE++PE + DS T+ VG
Sbjct: 9 RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVG--A 66
Query: 77 GENSKY---VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNL 133
V H +M SLDN F+ E+V+ F +R+ E + Y E K DG++V L
Sbjct: 67 RPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAE--APSLYTVEHKVDGLSV-L 123
Query: 134 RYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIK 193
YE G ++ GDG +GE +T N+ I IP L K P+ LEVR EV + + F++
Sbjct: 124 YYEEGVW--STGSGDGEVGEEVTQNLLTIPTIPRRL--KGVPDRLEVRGEVYMPIEAFLR 179
Query: 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMN--MPSSHSE 251
LN+ G K F NPRNAAAG LRQ +P++ + L + +G G+ S E
Sbjct: 180 LNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYE 239
Query: 252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLG 311
LL W ++ G + Y G + E Y++ +R LP+E DGVV K++ L+ +LG
Sbjct: 240 LLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELG 299
Query: 312 FTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNE 371
+T+RAPRFALAYKF ++E T++ + Q+GRTG +TPV +L+PV I+G ++R TLHNE
Sbjct: 300 YTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNE 359
Query: 372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESN 431
S I +I+IGD V+VH++G VIP++ + R + + P CP C +++
Sbjct: 360 SYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGK- 418
Query: 432 LIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK 491
+ RC C A+R ++H++SRKAM+I GLG+K+IE+L+ +V DLY + +
Sbjct: 419 -VHRCPNP--LCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKE 475
Query: 492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK 551
+LL L+R+ K A N+L I++SK R +YALG+ VGE A+ LA F ++ + +
Sbjct: 476 DLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLE 535
Query: 552 ATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK---------- 601
A+ E+L+ + ++G T +A ++ + P R L+ +L++ G+ +
Sbjct: 536 ASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESKEEVSDLLSGLTFVL 595
Query: 602 ------------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFV 643
G KV + +S+ T+YLV G+ PG KLEKA L + +L E+ F
Sbjct: 596 TGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTEEEFW 655
Query: 644 KIVKG 648
+ +K
Sbjct: 656 RFLKE 660
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 757 bits (1957), Expect = 0.0
Identities = 210/591 (35%), Positives = 322/591 (54%), Gaps = 19/591 (3%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
+ L +E+ H YY+ D PIISD ++D+LL L+ +EE++PEL T DS TQ VG G
Sbjct: 16 QWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVG--G 73
Query: 77 GENSKY---VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNL 133
+ V H +M+SLDN F+ +++ + RI E+ Y+ ELK DG+A++L
Sbjct: 74 AGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEV--GDAAHYLCELKIDGVALSL 131
Query: 134 RYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL---NIKYPPELLEVRCEVLIYKKD 190
Y G L +ASTRGDG GE++T N I +P L + PE+LEVR EV D
Sbjct: 132 VYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDD 191
Query: 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS 250
F LN G F NPRN+AAG LRQ +P + + L HG+G + G P++
Sbjct: 192 FQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFR-PATLH 250
Query: 251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKL 310
+ + GL + ++ + + + E R + +EIDGVV K++ ++ Q++L
Sbjct: 251 QAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRL 310
Query: 311 GFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHN 370
G TSRAPR+A+AYK+ +EA TK+ I + +GRTG ITP A + PV + G T+ +ATLHN
Sbjct: 311 GSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHN 370
Query: 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIY-IE 429
SEI RK + IGDTVV+ ++G+VIP++ ++ LR + F +P CP C S + E
Sbjct: 371 ASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKE 430
Query: 430 SNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489
+ RC + C Q + + H +SR ++I LG + L+ A ++ +L+ +
Sbjct: 431 GDADIRCPNARG-CPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALT 489
Query: 490 FKNLLRLDRVSNKLA------NNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543
++LLR D K +L+ + K+K R + AL IRHVG T A+ LA F
Sbjct: 490 ERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEF 549
Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW 594
+L+ + A+ +QL + +G T A ++ HR ++ + R G+
Sbjct: 550 GSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM 600
>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold,
adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus
influenzae} PDB: 3pn1_A* 3bac_A*
Length = 322
Score = 432 bits (1113), Expect = e-148
Identities = 136/317 (42%), Positives = 194/317 (61%), Gaps = 1/317 (0%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
++ L+K L ++ Y++ DNP + D++YD+L +LK +E ++PE LT DS TQ VG
Sbjct: 5 QLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQRVGAKP 64
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLT-KNIEYIAELKFDGIAVNLRY 135
+ H M+SLDN FSD + F RI + L L + + E K DG+AV++ Y
Sbjct: 65 LSGFSQIRHEIPMLSLDNAFSDAEFNAFVARIEDRLILLPAPLTFCCEPKLDGLAVSILY 124
Query: 136 EYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
G L QA+TRGDG GE+IT NI I +PL L PP LEVR EV + F +LN
Sbjct: 125 VNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLN 184
Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNW 255
KY K F NPRNAAAG LRQL+P I + L A+G+G G+++P++H L W
Sbjct: 185 KYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQW 244
Query: 256 YQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSR 315
+ IG+ + E + +G ++++ FY+ I KR +L Y+IDG V KIN ++ Q +LGF S+
Sbjct: 245 LKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELGFISK 304
Query: 316 APRFALAYKFLSKEALT 332
APR+A+AYKF ++E LT
Sbjct: 305 APRWAIAYKFPAQEELT 321
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA
NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB:
3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*
Length = 332
Score = 423 bits (1091), Expect = e-145
Identities = 126/336 (37%), Positives = 194/336 (57%), Gaps = 6/336 (1%)
Query: 5 AKKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLT 64
++ + + + R EL+K+L++++ YY+ D P + D YD+L EL IE ++P+L+T
Sbjct: 2 EQQPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLIT 61
Query: 65 KDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAEL 124
DS TQ VG + H M SL++GFS ED+ F++R+ + K + Y EL
Sbjct: 62 PDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIG--KPVAYCCEL 119
Query: 125 KFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEV 184
K DG+A++LRYE G + +TRGDG +GENIT N+ + +P+ L P +EVR E
Sbjct: 120 KIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLT---EPISVEVRGEC 176
Query: 185 LIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMN 244
+ K+ F+ LN+ R G F NPRNAAAG LRQL+ KI + L+ F + V + M
Sbjct: 177 YMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMK 236
Query: 245 MPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCL 304
+ E L IG E + ++++ + ++ + KR LPYEIDG+V K+N
Sbjct: 237 -AKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEF 295
Query: 305 STQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQ 340
+ Q +LGFT +APR+A+AYKF +EA T ++ +
Sbjct: 296 ALQDELGFTVKAPRWAIAYKFPPEEAETVVZHHHHH 331
>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA
replication, magnesium, manganese, metal-binding, NAD,
zinc; HET: DNA; 1.80A {Staphylococcus aureus} PDB:
3jsn_A*
Length = 318
Score = 420 bits (1083), Expect = e-144
Identities = 127/318 (39%), Positives = 196/318 (61%), Gaps = 7/318 (2%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
RV EL L++++ YY+ DNP + D++YD+LL EL KIEE++PE T DS T VG
Sbjct: 7 RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEA 66
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
+ V+H M+SL N F+++D+ F++RI ++ N+EY+ ELK DG+AV+L+Y
Sbjct: 67 QASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIG---NVEYMCELKIDGLAVSLKYV 123
Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
GY Q TRGDG GE+IT N+ IH IPL + P +EVR E + ++ F++LN+
Sbjct: 124 DGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMK---EPLNVEVRGEAYMPRRSFLRLNE 180
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
+ + F NPRNAAAG LRQL+ K+ + L F + V + N S SE L+
Sbjct: 181 EKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFN-ARSQSEALDEL 239
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
K+G + + ++ ++ ++E+ +K +R +LPY+IDG+V K+N L Q ++GFT ++
Sbjct: 240 DKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKS 299
Query: 317 PRFALAYKFLSKEALTKI 334
PR+A+AYKF ++E
Sbjct: 300 PRWAIAYKFPAEEHHHHH 317
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus
stearothermophilus} SCOP: d.142.2.2
Length = 318
Score = 417 bits (1074), Expect = e-143
Identities = 131/316 (41%), Positives = 195/316 (61%), Gaps = 7/316 (2%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
R EL++ L+R+ YY+ D P + D +YD+L+ EL IEE+YPEL T DS TQ +G
Sbjct: 9 RAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPP 68
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
E + V H MMSL N F + D+ F++R+ E+ Y+ EL DG+AV++RYE
Sbjct: 69 LEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEVG---EAAYVCELAIDGLAVSVRYE 125
Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
GY Q +TRGDG GE+IT N+ I +PL L P LE R E + K F++LN+
Sbjct: 126 DGYFVQGATRGDGTTGEDITENLKTIRSLPLRLK---EPVSLEARGEAFMPKASFLRLNE 182
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
R G + F NPRNAAAG LRQL+PK+ ++ L F +G+ + + +SHSE L++
Sbjct: 183 ERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALG-IASHSEALDYL 241
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
Q +G + E + ++++I F + + KR LPYEIDG+V K++ + Q+ LG T+++
Sbjct: 242 QALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKS 301
Query: 317 PRFALAYKFLSKEALT 332
PR+A+AYKF ++E +T
Sbjct: 302 PRWAIAYKFPAEEVVT 317
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}
Length = 328
Score = 413 bits (1065), Expect = e-141
Identities = 119/315 (37%), Positives = 176/315 (55%), Gaps = 11/315 (3%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
+ L +E+ H YY+ D PIISD ++D+LL L+ +EE++PEL T DS TQ VG G
Sbjct: 16 QWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVG--G 73
Query: 77 GENSKY---VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNL 133
+ V H +M+SLDN F+ +++ + RI E+ Y+ ELK DG+A++L
Sbjct: 74 AGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEV--GDAAHYLCELKIDGVALSL 131
Query: 134 RYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL---NIKYPPELLEVRCEVLIYKKD 190
Y G L +ASTRGDG GE++T N I +P L + PE+LEVR EV D
Sbjct: 132 VYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDD 191
Query: 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS 250
F LN G F NPRN+AAG LRQ +P + + L HG+G + G P++
Sbjct: 192 FQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFR-PATLH 250
Query: 251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKL 310
+ + GL + ++ + + + E R + +EIDGVV K++ ++ Q++L
Sbjct: 251 QAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRL 310
Query: 311 GFTSRAPRFALAYKF 325
G TSRAPR+A+AYK+
Sbjct: 311 GSTSRAPRWAIAYKY 325
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA
repair, endonuclease, helix-hairpin-helix, DNA binding
protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
Length = 91
Score = 68.3 bits (167), Expect = 2e-14
Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 501 NKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLN 559
A+ ++ +K + SR L ++ V +T ++ L F +LE + A+ E L
Sbjct: 12 QDPADLLM---EKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLAL 68
Query: 560 IPKIGSTTVKAFIKFINQPLHRL 582
P +G + +++P ++
Sbjct: 69 CPGLGPQKARRLFDVLHEPFLKV 91
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase;
HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Length = 89
Score = 67.2 bits (164), Expect = 5e-14
Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 4/80 (5%)
Query: 503 LANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIP 561
+A+ ++ +K + SR L ++ V +T ++ L F +LE + A+ E L P
Sbjct: 1 MADLLM---EKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCP 57
Query: 562 KIGSTTVKAFIKFINQPLHR 581
+G + +++P +
Sbjct: 58 GLGPQKARRLFDVLHEPFLK 77
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
domain, homodimer, hydrolase; 1.45A {Pyrococcus
furiosus} SCOP: a.60.2.5
Length = 75
Score = 65.0 bits (159), Expect = 2e-13
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 511 IQKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK 569
++K LT R + G+ HV T A+ L +F ++E +F A+ +L+ + IG K
Sbjct: 1 MEKKALTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAK 60
Query: 570 AFIKFINQPLHR 581
+ I P
Sbjct: 61 EIRRVITAPYIE 72
>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI,
protein structure initiative, northeast structural
genomics consortium; HET: DNA; NMR {Thermus
thermophilus} SCOP: c.15.1.2
Length = 92
Score = 64.6 bits (158), Expect = 3e-13
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 602 GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG 648
G KV + +S+ T+YLV G+ PG KLEKA L + L E+ ++++
Sbjct: 34 GAKVTDSVSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEA 80
>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 = 71.0 bits (173), Expect = 7e-13
Identities = 99/670 (14%), Positives = 201/670 (30%), Gaps = 192/670 (28%)
Query: 26 HRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHH 85
H H++ D + + ++ K I + + + + V
Sbjct: 3 HHHHM-----------DFETGEHQYQYKDILSVFEDAFVDNFDCKDV-------QDMPKS 44
Query: 86 TFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQAST 145
+D+ +D + R+ L L+K E + + + + LR Y +L
Sbjct: 45 ILSKEEIDHIIMSKDAVSGTLRLFWTL-LSKQ-EEMVQKFVEEV---LRINYKFLMSP-- 97
Query: 146 RGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKD--------FIKLNKY 197
I + P ++ Y I ++D F K N
Sbjct: 98 -------------IKTEQRQPSMMTRMY------------IEQRDRLYNDNQVFAKYNVS 132
Query: 198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGE-------LRG-------- 242
R L+ + R A L +L P KN ++ G G+
Sbjct: 133 R----LQPYLKLRQA----LLELRP--AKNVLIDGVL-GSGKTWVALDVCLSYKVQCKMD 181
Query: 243 -----MNMPSSHSE------LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRF--N 289
+N+ + +S L +I + S + I + ++R +
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA-ELRRLLKS 240
Query: 290 LPYE-----IDGV-------VYKINCLSTQKKLGFTSRAPRFA-----LAYKFLS----K 328
PYE + V + ++C K L T+R + +S
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSC----KIL-LTTRFKQVTDFLSAATTTHISLDHHS 295
Query: 329 EALTKIKAINIQIGRTGIIT---PVALLK--PVLIDGITITRATLHNE---SEIYRKNIQ 380
LT + ++ + P +L P + I ++ + + ++
Sbjct: 296 MTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIA---ESIRDGLATWDNWKHV-- 350
Query: 381 IGDTVVVHRSGNVIPKITSSILSLRPNDSK-------IF----KIP-NICPICNSKIIYI 428
+ I SS+ L P + + +F IP + + +I
Sbjct: 351 --------NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402
Query: 429 ESNLIAR--CSGSWIECIAQRKA------GLQHFSSRKAMNIIGLGKKMIE------KLV 474
+ ++ S +E Q K + K N L + +++
Sbjct: 403 DVMVVVNKLHKYSLVEK--QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460
Query: 475 NANIVVTAVDLYKINF-----KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIR 529
+ +++ +D Y + KN+ +R++ L + L F RF+ IR
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPERMT--LFRMVFL--------DF-RFLEQ-KIR 508
Query: 530 HVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRD 589
H TA + N K + + + V A + F+ + L+ S+ D
Sbjct: 509 HDS--TAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTD 566
Query: 590 VGIYWLNNPN 599
+ L +
Sbjct: 567 LLRIALMAED 576
Score = 61.4 bits (148), Expect = 6e-10
Identities = 68/438 (15%), Positives = 133/438 (30%), Gaps = 144/438 (32%)
Query: 268 SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF---ALA-- 322
S+LS E I + G + L ++++ +F L
Sbjct: 44 SILSK-----EEIDHI----IMSKDAVSGTLRLFWTLLSKQE----EMVQKFVEEVLRIN 90
Query: 323 YKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITI-TRATLHNESEIYRK-NIQ 380
YKFL ++ IK Q P ++ + I R L+N+++++ K N+
Sbjct: 91 YKFL----MSPIKTEQRQ--------------PSMMTRMYIEQRDRLYNDNQVFAKYNVS 132
Query: 381 IGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNIC--------------PICNS--- 423
+ K+ ++L LRP N+ +C S
Sbjct: 133 RLQPYL---------KLRQALLELRPA-------KNVLIDGVLGSGKTWVALDVCLSYKV 176
Query: 424 ------KIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNAN 477
KI ++ + C+ S + LQ + N + +
Sbjct: 177 QCKMDFKIFWLN---LKNCN-SPETVLEM----LQKLLYQIDPNWTSRSDHSSNIKLRIH 228
Query: 478 IVVTAVD--LYKINFKN-LLRLDRVSNKLANNILLA--IQ-KSKLTTFSRFIYALGIRHV 531
+ + L ++N LL L V N A + K LTT RF
Sbjct: 229 SIQAELRRLLKSKPYENCLLVLLNVQNA---KAWNAFNLSCKILLTT--RFKQVTDFLSA 283
Query: 532 GETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL----------HR 581
TT L ++ L T +++ ++ +K+++ +
Sbjct: 284 ATTTHISLDHHSMTL------TPDEVKSL----------LLKYLDCRPQDLPREVLTTNP 327
Query: 582 LLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDE-- 639
+S + + + ++ N+ KL I+ ++ +L+
Sbjct: 328 RRLSII--------------AESIRDGLATWDNWK---HVNCDKLTTIIESSLNVLEPAE 370
Query: 640 --KNFVKIVKGFSTETKI 655
K F ++ F I
Sbjct: 371 YRKMFDRLSV-FPPSAHI 387
Score = 35.6 bits (81), Expect = 0.068
Identities = 30/203 (14%), Positives = 66/203 (32%), Gaps = 68/203 (33%)
Query: 14 LSFRVT-ELKKELHRHNIAYYL----YDNPIISDNKYDQLLFELKKIEEKYPELLTKDSL 68
L +V E + LHR + +Y +D+ + DQ +
Sbjct: 433 LELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY------------------ 474
Query: 69 TQHVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYI-AELKFD 127
H+G HH + ++++ E + +F + + ++ +++ D
Sbjct: 475 -SHIG----------HH---LKNIEH---PERMTLFR-------MVFLDFRFLEQKIRHD 510
Query: 128 GIAVN-----------LRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYP-P 175
A N L++ Y+ D + + + KI L I
Sbjct: 511 STAWNASGSILNTLQQLKFYKPYI----CDNDPKYERLVNAILDFLPKIEENL-ICSKYT 565
Query: 176 ELLEVRCEVLIYKKDFIKLNKYR 198
+LL + L+ + + I ++
Sbjct: 566 DLLRI---ALMAEDEAIFEEAHK 585
>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel
beta-sheet, DNA replication, clamp loader, RFC1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 112
Score = 61.3 bits (149), Expect = 1e-11
Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 602 GGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVK 647
GGKV +SK TNYLV G+ G K +KA L KI+DE + +++
Sbjct: 50 GGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 96
>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding,
activator, alternative splicing, ATP-binding, DNA
replication, DNA- binding; NMR {Homo sapiens} PDB:
2k7f_A
Length = 109
Score = 59.7 bits (145), Expect = 3e-11
Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 602 GGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVK 647
GGKV +SK TNYLV G+ G K +KA L KI+DE + +++
Sbjct: 60 GGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 106
>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 = 55.1 bits (132), Expect = 6e-08
Identities = 40/253 (15%), Positives = 80/253 (31%), Gaps = 69/253 (27%)
Query: 427 YIESNLIARCSGSWIECIAQRKAGLQHFSSR--KAMNI----IGLGKKMIEKLVNANIVV 480
Y+ S + G + + + L F + + +I L ++ LV ++
Sbjct: 67 YVSSLVEPSKVGQFDQVL---NLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELI 123
Query: 481 TAVDLYKINFKNLLRLDRVSNKLANNILL-AIQKSKLTTFSRFIYALGIRHVGETTAKEL 539
Y + R +K +N+ L A+ + + F G G+ +
Sbjct: 124 KN---Y---ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF----G----GQGNTDD- 168
Query: 540 ANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIY------ 593
YF EE L ++ + V IKF + L L+ + L ++
Sbjct: 169 --YF----------EE-LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNI 215
Query: 594 --WLNNPNTKGGK----------VVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKN 641
WL NP+ K + + + +Y+V + G
Sbjct: 216 LEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLG-------------FTPGE 262
Query: 642 FVKIVKGFSTETK 654
+KG + ++
Sbjct: 263 LRSYLKGATGHSQ 275
Score = 52.7 bits (126), Expect = 4e-07
Identities = 70/385 (18%), Positives = 111/385 (28%), Gaps = 168/385 (43%)
Query: 70 QHVGLVGG----ENSKYVHHTF----KMMSLDNGFSDEDVIIFN-KRITNELKLTKNIEY 120
Q G+ G + SK + GFS D++I N +T
Sbjct: 1627 QEQGM--GMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLT----------- 1673
Query: 121 IAELKFDGI-AVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLE 179
+ F G +R Y + + DG + K E+ E
Sbjct: 1674 ---IHFGGEKGKRIRENYSAMIFETIV-DGKLKTE-----------------KIFKEINE 1712
Query: 180 VRCEVLIYKKDFIKLNKYRYH-----LGLKKFTNPRNAAAG--ILRQLNPK--INKNKIL 230
Y + L +FT P L K I +
Sbjct: 1713 -------------HSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADA-- 1757
Query: 231 HFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEYSVL---SGVNKLIEFYKKINIKR 287
FA G HS L GEY+ L + V
Sbjct: 1758 -TFA-------G------HS----------L---GEYAALASLADV-------------- 1776
Query: 288 FNLPYEIDGV--VYK----INCLSTQKKLGFTSRA-----P-RFALAYKFLSKEALTKIK 335
+ E V V+ + + +LG ++ P R A + S+EAL +
Sbjct: 1777 --MSIE-SLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAAS---FSQEALQYVV 1830
Query: 336 AINIQIG-RTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNV- 393
++G RTG L++ V N Y N++ V +G++
Sbjct: 1831 E---RVGKRTG-----WLVEIV-------------N----Y--NVE-NQQYVA--AGDLR 1860
Query: 394 -IPKITSSILSLRPNDSKIFKIPNI 417
+ +T ++L N K+ KI I
Sbjct: 1861 ALDTVT-NVL----NFIKLQKIDII 1880
Score = 51.6 bits (123), Expect = 8e-07
Identities = 75/520 (14%), Positives = 143/520 (27%), Gaps = 187/520 (35%)
Query: 28 HNIAYYLY---DNPIISDNK-----YDQLLFELKKIEEKYPELLTKDSLTQHVGLV---- 75
H +A L D ++ + + + ++K L + + LV
Sbjct: 102 HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFG 161
Query: 76 G-GENSKY------VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDG 128
G G Y ++ T+ ++ D+I K L EL
Sbjct: 162 GQGNTDDYFEELRDLYQTYHVLV-------GDLI---KFSAETLS---------ELIRTT 202
Query: 129 IAVNLRYEYGY-----LKQASTRGDGN-----------IGENITTNIH--IIHKIPLVLN 170
+ + G L+ S D + IG + H + K +L
Sbjct: 203 LDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIG--VIQLAHYVVTAK---LLG 257
Query: 171 IKYPPELLEVRCEVLIYKKD---------------FIKLN----KYRYHLGLK-KFTNPR 210
P EL + + F + +G++ P
Sbjct: 258 FT-PGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPN 316
Query: 211 NAAAGILRQLNPKINKNKILHFFAHGVGE------LRGMNMPS--SHSELLNWY----QK 258
+ L P I ++ + + G + + + N + ++
Sbjct: 317 TS-------LPPSILEDSL----ENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
Query: 259 IGLS---------ICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKK 309
+ +S + G L G+N + K P +D Q +
Sbjct: 366 VEISLVNGAKNLVVSGPPQSLYGLNLTLR-----KAKA---PSGLD-----------QSR 406
Query: 310 LGFTSRAPRFALAYKFL-------S---KEALTKIKAINIQIGRTGI-ITPVALLKPVL- 357
+ F+ R +F + +FL S A I + + + + PV
Sbjct: 407 IPFSERKLKF--SNRFLPVASPFHSHLLVPASDLINK---DLVKNNVSFNAKDIQIPVYD 461
Query: 358 -IDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPN--DSKIFKI 414
DG +++ SG++ +I I+ L + FK
Sbjct: 462 TFDG----------------SDLR-------VLSGSISERIVDCIIRLPVKWETTTQFKA 498
Query: 415 PNIC---PICNSKIIYIESNLIAR-CSGSWIECIAQRKAG 450
+I P S + L R G+ + I AG
Sbjct: 499 THILDFGPGGASGL----GVLTHRNKDGTGVRVIV---AG 531
Score = 50.4 bits (120), Expect = 2e-06
Identities = 102/618 (16%), Positives = 183/618 (29%), Gaps = 219/618 (35%)
Query: 111 ELKLTKNIEYIAEL-------KFDGIAVNL--RYEYGYLKQASTRGDGNIGENITTNIHI 161
EL + K + Y++ L +FD + +E YL+ GN +IH
Sbjct: 59 EL-VGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLE-------GN-------DIH- 102
Query: 162 IHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR-YHLGLKKFTNPRNAAAGILRQL 220
L +LL+ L+ K+ IK N + + F N+A + R +
Sbjct: 103 ----ALAA------KLLQENDTTLVKTKELIK-NYITARIMAKRPFDKKSNSA--LFRAV 149
Query: 221 NPKINKNKILHFFAHGVG-------ELRGMNMPSSHSELLNWYQKIGLSICGEYSVLSGV 273
+++ F G G ELR +L YQ Y VL V
Sbjct: 150 G--EGNAQLVAIFG-GQGNTDDYFEELR---------DL---YQ--------TYHVL--V 184
Query: 274 NKLIE-------------------FYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTS 314
LI+ F + +NI + L S
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW---------------------LENPS 223
Query: 315 RAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGIT------ITRATL 368
P K+ L I P++ P LI G+ +T L
Sbjct: 224 NTP---------DKDYLLSI--------------PISC--P-LI-GVIQLAHYVVTAKLL 256
Query: 369 HNESEIYRKNIQIGDTVVVHRSGNVIPKITS---SILSLRPNDSKIFKIPNICPICNSKI 425
R ++ H G V + S S + K + +
Sbjct: 257 GFTPGELRSYLK---GATGHSQGLVTAVAIAETDSWESFFVSVRKAITV----------L 303
Query: 426 IYI--ESNLIARCSGSWIECIAQRKAGLQHFSSRKAM-NIIGLGKKMIEK---------- 472
+I + + + S M +I L ++ ++
Sbjct: 304 FFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS--PMLSISNLTQEQVQDYVNKTNSHLP 361
Query: 473 --------LVNA--NIVVT--AVDLYKINFKNLLRLDRVSNKLA-NNILLAIQKSKLTTF 519
LVN N+VV+ LY LR + + L + I + +K K +
Sbjct: 362 AGKQVEISLVNGAKNLVVSGPPQSLY--GLNLTLRKAKAPSGLDQSRIPFSERKLKFSN- 418
Query: 520 SRF--IYA------LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAF 571
RF + + L + + F A + + IP + T +
Sbjct: 419 -RFLPVASPFHSHLL------VPASDLINKDLVKNNVSFNAKD---IQIP-VYDTFDGSD 467
Query: 572 IKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNF-------ISKNTNYLVKGQKPGK 624
++ ++ + ++ + + + W K +++F + T+ G G
Sbjct: 468 LRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGT--GV 525
Query: 625 KLEKAIKLNIKILDEKNF 642
++ A L+I D+ F
Sbjct: 526 RVIVAGTLDINPDDDYGF 543
Score = 50.4 bits (120), Expect = 2e-06
Identities = 55/312 (17%), Positives = 91/312 (29%), Gaps = 117/312 (37%)
Query: 34 LYDN-PIISD--NKYDQLL-----FELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHH 85
LY D N+ D F + I P +LT H G GE K +
Sbjct: 1635 LYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPV-----NLTIHFG---GEKGKRIRE 1686
Query: 86 TFKMMSLDNGFSDEDVI---IF---NKRITN--------ELKLTKN-------IEY--IA 122
+ M + D + IF N+ T+ L T+ +E
Sbjct: 1687 NYSAMIFET-IVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFE 1745
Query: 123 ELKFDGIAVNLRY-------EYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPP 175
+LK G+ EY L AS V++I+
Sbjct: 1746 DLKSKGLIPADATFAGHSLGEYAAL--ASLAD--------------------VMSIE--- 1780
Query: 176 ELLEVRCEVLIYKKDFIKLNKYRYHLG-LKKFTNPRNAAA----GILRQLNP-KINKN-- 227
+++ YR G + PR+ G++ +NP ++ +
Sbjct: 1781 --------------SLVEVVFYR---GMTMQVAVPRDELGRSNYGMIA-INPGRVAASFS 1822
Query: 228 -KILHFFAHGVGELRGM-------NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEF 279
+ L + VG+ G N+ + Q + G+ L V ++ F
Sbjct: 1823 QEALQYVVERVGKRTGWLVEIVNYNVENQ--------QYV---AAGDLRALDTVTNVLNF 1871
Query: 280 YKKINIKRFNLP 291
K I L
Sbjct: 1872 IKLQKIDIIELQ 1883
Score = 37.3 bits (86), Expect = 0.016
Identities = 45/253 (17%), Positives = 69/253 (27%), Gaps = 91/253 (35%)
Query: 453 HFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKL---ANNILL 509
HF G K I + +A I T VD K ++ S + LL
Sbjct: 1675 HFG--------GEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL 1726
Query: 510 AIQKSKLTTF--------SRFIYAL----GIR--------H-VGETTAKEL---ANYFKN 545
T F + + G+ H +GE A L A+
Sbjct: 1727 -----SATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAA--LASLADVMS- 1778
Query: 546 LECMFKATEEQLLNIPKI-GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNT---- 600
E L+ + G T A P L S + I NP
Sbjct: 1779 ----I----ESLVEVVFYRGMTMQVAV------PRDELGRSNYGMIAI----NPGRVAAS 1820
Query: 601 ----------------KGGKV--VNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
G V VN+ +N Y+ G L+ + + + +
Sbjct: 1821 FSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRA--LDTVTNV-LNFIKLQK- 1876
Query: 643 VKIVK---GFSTE 652
+ I++ S E
Sbjct: 1877 IDIIELQKSLSLE 1889
>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural
genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A
Length = 113
Score = 49.9 bits (119), Expect = 1e-07
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 602 GGKVVNFISKNTNYLVKG---QKPGKKLEKAIKLNIKILDEKNFVKIVKG 648
GGK+ +K + + +K KK+E+ + NI+++ E +
Sbjct: 37 GGKLTGTANKASLCISTKKEVEKMNKKMEEVKEANIRVVSEDFLQDVSAS 86
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease,
nucleotide excision repair; 2.8A {Aeropyrum pernix}
SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A
Length = 219
Score = 43.3 bits (101), Expect = 9e-05
Identities = 12/66 (18%), Positives = 25/66 (37%)
Query: 513 KSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFI 572
+ + +G TA+ + F +LE F A++ ++ + IG +
Sbjct: 152 RLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIK 211
Query: 573 KFINQP 578
K + P
Sbjct: 212 KILMTP 217
>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair,
DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A
{Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*
Length = 377
Score = 37.5 bits (87), Expect = 0.012
Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 5/99 (5%)
Query: 485 LYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAKELANYF 543
L + +S L ++ A Q + +R L + + + + F
Sbjct: 276 LQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKTVARIPLSIGYNVVRMF 335
Query: 544 KNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRL 582
K L+ + KA+ E L + IG +A I++ + L
Sbjct: 336 KTLDQISKASVEDLKKVEGIGEKRARA----ISESISSL 370
>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III,
poly(ADP-ribose) polymerase-1, DNA polymerase beta,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 129
Score = 33.7 bits (77), Expect = 0.048
Identities = 6/35 (17%), Positives = 15/35 (42%)
Query: 602 GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKI 636
G K ++++ +L+ K + + L +I
Sbjct: 49 GAKYRPDWTRDSTHLICAFANTPKYSQVLGLGGRI 83
>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo
sapiens} PDB: 3ktf_A* 2wt8_A*
Length = 107
Score = 33.0 bits (75), Expect = 0.069
Identities = 8/35 (22%), Positives = 15/35 (42%)
Query: 602 GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKI 636
G KV +K +++ +KA K +K+
Sbjct: 38 GAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKL 72
>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 = 31.6 bits (71), Expect = 0.56
Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 18/51 (35%)
Query: 403 SLRPNDSKIFKIPN-----ICPICNS---KIIYIESN--LIARCSGSWIEC 443
S+ + + PN CP C KI+ S ++ C+ C
Sbjct: 6 SIDKRAGR--RGPNLNIVLTCPECKVYPPKIVERFSEGDVV--CA----LC 48
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin
helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB:
2nrv_A 2nrw_A 2nrx_A 2nrz_A
Length = 220
Score = 31.3 bits (72), Expect = 0.68
Identities = 8/40 (20%), Positives = 18/40 (45%)
Query: 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGST 566
+ +G K+L +F +LE + A+ E++ +
Sbjct: 172 NVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGSTEI 211
>3rhg_A Putative phophotriesterase; hydrolase, amidohydrolase, zinc binding
site, enzyme functio initiative, EFI; HET: SO4; 1.53A
{Proteus mirabilis}
Length = 365
Score = 30.9 bits (69), Expect = 1.2
Identities = 12/75 (16%), Positives = 24/75 (32%), Gaps = 5/75 (6%)
Query: 30 IAYYLYDNPIISDNKYDQLLFELKKIEEKYPE--LLTKDSLTQHVGL-VGGENSKYVHHT 86
+ + S + + L IE Y +L+ D + + GG +V +
Sbjct: 258 DISFPKEGAAPSVMDTVEAVATL--IERGYGNQIVLSHDVFLKQMWAKNGGNGWGFVPNV 315
Query: 87 FKMMSLDNGFSDEDV 101
F + G +
Sbjct: 316 FLSLLAQRGIDKTII 330
>1nd9_A Translation initiation factor IF-2; NMR {Escherichia coli} SCOP:
a.6.1.6
Length = 49
Score = 27.3 bits (61), Expect = 1.7
Identities = 8/27 (29%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 566 TTVKAFIKFINQPLHRLLISQLRDVGI 592
T+K + RL+ Q D GI
Sbjct: 3 VTIKTLAAERQTSVERLV-QQFADAGI 28
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric
ring, heptamer, ring, oligomer, RAD51 polymerizat motif;
HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1
c.37.1.11
Length = 349
Score = 30.0 bits (67), Expect = 2.2
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513
G+G EKL A T + + L + +S A I+ A +K
Sbjct: 42 GVGPATAEKLREAGY-DTLEAIAVASPIELKEVAGISEGTALKIIQAARK 90
>3tem_A Ribosyldihydronicotinamide dehydrogenase [quinone;
oxidoreductase-oxidoreductase inhibitor complex; HET:
FAD 6A1 IMD; 1.45A {Homo sapiens} PDB: 3te7_A* 3tzb_A*
3fw1_A* 2qwx_A* 1zx1_A* 3g5m_A* 3gam_A* 3ovm_A* 3owh_A*
3owx_A* 3ox1_A* 3ox2_A* 3ox3_A* 1sg0_A* 1qr2_A* 1xi2_A*
2qmy_A* 2qmz_A* 2qr2_A* 2qx4_A* ...
Length = 228
Score = 29.5 bits (66), Expect = 3.0
Identities = 13/66 (19%), Positives = 24/66 (36%)
Query: 465 LGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIY 524
L +++L VT DLY +NF+ ++ L+N + + +
Sbjct: 20 LKNVAVDELSRQGCTVTVSDLYAMNFEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSL 79
Query: 525 ALGIRH 530
A I
Sbjct: 80 ASDITD 85
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain,
DNA-binding domain, DNA binding protein; NMR
{Escherichia coli} SCOP: a.60.2.3
Length = 78
Score = 27.5 bits (62), Expect = 3.1
Identities = 10/44 (22%), Positives = 18/44 (40%)
Query: 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKA 570
I VG + L Y L+ + A+ E++ +P I +
Sbjct: 28 TIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEK 71
>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 = 28.8 bits (63), Expect = 3.1
Identities = 5/9 (55%), Positives = 8/9 (88%)
Query: 624 KKLEKAIKL 632
KKL+ ++KL
Sbjct: 23 KKLQASLKL 31
Score = 28.0 bits (61), Expect = 5.9
Identities = 8/34 (23%), Positives = 12/34 (35%), Gaps = 12/34 (35%)
Query: 106 KRITNELKLTKNIEYIAELKFD---GIAVNLRYE 136
K++ LKL Y D +A+ E
Sbjct: 23 KKLQASLKL-----YAD----DSAPALAIKATME 47
Score = 28.0 bits (61), Expect = 5.9
Identities = 7/26 (26%), Positives = 12/26 (46%), Gaps = 8/26 (30%)
Query: 51 ELKKIE---EKY-----PELLTKDSL 68
LKK++ + Y P L K ++
Sbjct: 21 ALKKLQASLKLYADDSAPALAIKATM 46
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 29.8 bits (67), Expect = 3.2
Identities = 9/49 (18%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNIL 508
M + +G++ L N+ + D+ + + LL+++ + K I
Sbjct: 649 MQLPLVGRRRARALYNSGF-RSIEDISQARPEELLKIEGIGVKTVEAIF 696
>3pr9_A FKBP-type peptidyl-prolyl CIS-trans isomerase; FKBP protein,
chaperone; 1.95A {Methanocaldococcus jannaschii} PDB:
3pra_A
Length = 157
Score = 28.9 bits (65), Expect = 3.6
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 359 DGITI--TRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIP 415
DG T L + IY + G + G V+P + +IL + + + +P
Sbjct: 17 DGKLFDTTNEELAKKEGIYNPAMIYGPVAIFAGEGQVLPGLDEAILEMDVGEEREVVLP 75
>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP
complex, calcium stimulation, RECA, DMC1; HET: DNA ANP;
1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11
PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A*
3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A*
3etl_A* 4dc9_A* 2gdj_A*
Length = 322
Score = 29.2 bits (65), Expect = 4.2
Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK 515
++ G+G EKLV A + + + L ++ +S K A +++ +
Sbjct: 2 GDNLTDLPGVGPSTAEKLVEAGY-IDFMKIATATVGELTDIEGISEKAAAKMIMGARDLC 60
Query: 516 LTTF 519
F
Sbjct: 61 DLGF 64
>1ix5_A FKBP; ppiase, isomerase; NMR
{Methanothermococcusthermolithotrophicus} SCOP: d.26.1.1
Length = 151
Score = 28.1 bits (63), Expect = 5.0
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 2/59 (3%)
Query: 359 DGITI--TRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIP 415
G + + E+ IY + + V G +I ++L + D K KIP
Sbjct: 18 SGDVFDTSIEEVAKEAGIYAPDREYEPLEFVVGEGQLIQGFEEAVLDMEVGDEKTVKIP 76
>3l3u_A POL polyprotein; DNA integration, AIDS, integrase, endonuclease,
polynucleotidyl transferase, DNA binding, viral protein;
1.40A {Human immunodeficiency virus 1} PDB: 3ao1_A
3l3v_A* 3ovn_A* 3ao2_A* 3ao3_A* 3ao4_A* 3ao5_A* 2itg_A
1biz_A 1biu_A 1b9d_A 4dmn_A* 2b4j_A 1itg_A 1b92_A 1bl3_A
1bi4_A 1bis_A 1b9f_A 1bi4_B ...
Length = 163
Score = 28.2 bits (63), Expect = 5.4
Identities = 15/56 (26%), Positives = 19/56 (33%), Gaps = 3/56 (5%)
Query: 518 TFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIK 573
S +I A I T +E A + L + N STTVKA
Sbjct: 30 VASGYIEAEVIPA---ETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACD 82
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision
repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA
excision; 1.90A {Bacillus stearothermophilus}
Length = 226
Score = 28.2 bits (64), Expect = 7.0
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577
I VGE K L NYF +++ M +AT E+L I + + +++
Sbjct: 177 DIPGVGEKRKKALLNYFGSVKKMKEATVEELQRA-NIPRAVAEKIYEKLHE 226
>1pmh_X Cscbm27-1, beta-1,4-mannanase; jellyroll beta-sandwich, hydrolase;
HET: MAN BMA; 1.06A {Caldicellulosiruptor
saccharolyticus} SCOP: b.18.1.18 PDB: 1pmj_X
Length = 185
Score = 28.0 bits (61), Expect = 7.4
Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 1/78 (1%)
Query: 96 FSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENI 155
F D V+ F + + LK K + +L+ G LR + + + G++G I
Sbjct: 11 FEDGTVMSFGEAWGDSLKCIKKVSVSQDLQRPGNKYALRLDVEF-NPNNGWDQGDLGTWI 69
Query: 156 TTNIHIIHKIPLVLNIKY 173
+ ++++
Sbjct: 70 GGVVEGQFDFTGYKSVEF 87
>3prb_A FKBP-type peptidyl-prolyl CIS-trans isomerase; chaperone; 2.20A
{Methanocaldococcus jannaschii} PDB: 3prd_A
Length = 231
Score = 28.2 bits (63), Expect = 7.6
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 359 DGITI--TRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIP 415
DG T L + IY + G + G V+P + +IL + + + +P
Sbjct: 17 DGKLFDTTNEELAKKEGIYNPAMIYGPVAIFAGEGQVLPGLDEAILEMDVGEEREVVLP 75
>1d4a_A DT-diaphorase, quinone reductase; flavoprotein, rossman fold,
oxidoreductase; HET: FAD; 1.70A {Homo sapiens} SCOP:
c.23.5.3 PDB: 1dxo_A* 1gg5_A* 1kbo_A* 1kbq_A* 2f1o_A*
3jsx_A* 1h69_A* 1h66_A* 1qbg_A* 1dxq_A* 1qrd_A*
Length = 273
Score = 28.4 bits (63), Expect = 7.7
Identities = 10/61 (16%), Positives = 19/61 (31%)
Query: 470 IEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIR 529
L V DLY +NF ++ ++ KL + + + + I
Sbjct: 26 AAALKKKGWEVVESDLYAMNFNPIISRKDITGKLKDPANFQYPAESVLAYKEGHLSPDIV 85
Query: 530 H 530
Sbjct: 86 A 86
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 0.139 0.397
Gapped
Lambda K H
0.267 0.0847 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,032,544
Number of extensions: 628426
Number of successful extensions: 1748
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1691
Number of HSP's successfully gapped: 68
Length of query: 655
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 555
Effective length of database: 3,909,693
Effective search space: 2169879615
Effective search space used: 2169879615
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 (26.7 bits)