BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy11423
(655 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OWO|A Chain A, Last Stop On The Road To Repair: Structure Of E.Coli Dna
Ligase Bound To Nicked Dna-Adenylate
Length = 671
Score = 508 bits (1308), Expect = e-144, Method: Compositional matrix adjust.
Identities = 260/664 (39%), Positives = 392/664 (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 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
G L A+TRGD PL 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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW----------LNNP-------- 598
L +P +G F + +R +IS+L G++W +++P
Sbjct: 546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVL 605
Query: 599 ----------NTK------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
+ K G KV +SK T+ ++ G+ G KL KA +L I+++DE
Sbjct: 606 TGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAEM 665
Query: 643 VKIV 646
++++
Sbjct: 666 LRLL 669
>pdb|4GLX|A Chain A, Dna Ligase A In Complex With Inhibitor
Length = 586
Score = 489 bits (1259), Expect = e-138, Method: Compositional matrix adjust.
Identities = 242/578 (41%), Positives = 357/578 (61%), Gaps = 1/578 (0%)
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 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
G L A+TRGD PL 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 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW 594
L +P +G F + +R +IS+L G++W
Sbjct: 546 LQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHW 583
>pdb|1DGS|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
pdb|1DGS|B Chain B, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
Length = 667
Score = 375 bits (962), Expect = e-104, Method: Compositional matrix adjust.
Identities = 241/665 (36%), Positives = 373/665 (56%), Gaps = 48/665 (7%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
R+ EL+ + HN YY+ +P ISD +YD+LL ELK++EE++PE + DS T+ VG
Sbjct: 9 RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARP 68
Query: 77 GENS-KYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY 135
E + + V H +M SLDN F+ E+V+ F +R+ E + Y E K DG++V L Y
Sbjct: 69 LEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAEAPSL--YTVEHKVDGLSV-LYY 125
Query: 136 EYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
E G S GD P +K P+ LEVR EV + + F++LN
Sbjct: 126 EEGVWSTGS--GDGEVGEEVTQNLLTIPTIPR--RLKGVPDRLEVRGEVYMPIEAFLRLN 181
Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILH--FFAHGVG---ELRGMNMPSSHS 250
+ G K F NPRNAAAG LRQ +P++ + L F+A G+G E G+ S
Sbjct: 182 EELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLK---SQY 238
Query: 251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKL 310
ELL W ++ G + Y G + E Y++ +R LP+E DGVV K++ L+ +L
Sbjct: 239 ELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGEL 298
Query: 311 GFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHN 370
G+T+RAPRFALAYKF ++E T++ + Q+GRTG +TPV +L+PV I+G ++R TLHN
Sbjct: 299 GYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHN 358
Query: 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIES 430
ES I +I+IGD V+VH++G VIP++ + R + + P CP C +++ +
Sbjct: 359 ESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLV--KE 416
Query: 431 NLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINF 490
+ RC C A+R ++H++SRKAM+I GLG+K+IE+L+ +V DLY +
Sbjct: 417 GKVHRCPNPL--CPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRK 474
Query: 491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF 550
++LL L+R+ K A N+L I++SK R +YALG+ VGE A+ LA F ++ +
Sbjct: 475 EDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLL 534
Query: 551 KATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW---------------- 594
+A+ E+L+ + ++G T +A ++ + P R L+ +L++ G+
Sbjct: 535 EASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESKEEVSDLLSGLTFV 594
Query: 595 ----LNNPNTK--------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
L+ P + G KV + +S+ T+YLV G+ PG KLEKA L + +L E+ F
Sbjct: 595 LTGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTEEEF 654
Query: 643 VKIVK 647
+ +K
Sbjct: 655 WRFLK 659
>pdb|1V9P|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase
pdb|1V9P|B Chain B, Crystal Structure Of Nad+-Dependent Dna Ligase
Length = 584
Score = 373 bits (957), Expect = e-103, Method: Compositional matrix adjust.
Identities = 222/580 (38%), Positives = 344/580 (59%), Gaps = 13/580 (2%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
R+ EL+ + HN YY+ +P ISD +YD+LL ELK++EE++PE + DS T+ VG
Sbjct: 9 RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARP 68
Query: 77 GENS-KYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY 135
E + + V H +M SLDN F+ E+V+ F +R+ L + Y E K DG++VNL Y
Sbjct: 69 LEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLERALGRKRPFLYTVEHKVDGLSVNLYY 128
Query: 136 EYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
E G L +TRGD P +K P+ LEVR EV + + F++LN
Sbjct: 129 EEGVLVFGATRGDGEVGEEVTQNLLTIPTIPR--RLKGVPDRLEVRGEVYMPIEAFLRLN 186
Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILH--FFAHGVG-ELRGMNMPSSHSEL 252
+ G K F NPRNAAAG LRQ +P++ + L F+A G+G E G+ S EL
Sbjct: 187 EELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLEESGLK---SQYEL 243
Query: 253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGF 312
L W ++ G + Y G + E Y++ +R LP+E DGVV K++ L+ ++LG+
Sbjct: 244 LLWLKEKGFPVEHGYEKALGAEGVEEVYRRFLAQRHALPFEADGVVVKLDDLALWRELGY 303
Query: 313 TSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNES 372
T+RAPRFALAYKF ++E T++ + Q+GRTG +TPV +L+PV I+G ++R TLHNES
Sbjct: 304 TARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNES 363
Query: 373 EIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNL 432
I +I+IGD V+VH++G VIP++ + R + + + P CP C ++ ++
Sbjct: 364 YIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGEERPIRWPETCPECGHRL--VKEGK 421
Query: 433 IARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKN 492
+ RC C A+R ++H++SRKAM+I GLG+K+IE+L+ +V DLY + ++
Sbjct: 422 VHRCPNPL--CPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKED 479
Query: 493 LLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA 552
LL L+R+ K A N+L I++SK R +YALG+ VGE A+ LA F ++ + +A
Sbjct: 480 LLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEA 539
Query: 553 TEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGI 592
+ E+LL + ++G T +A ++ + P R L+ +L++ G+
Sbjct: 540 SLEELLEVEEVGELTARAILETLKDPAFRDLVRRLKEAGV 579
>pdb|3SGI|A Chain A, Crystal Structure Of Dna Ligase A Brct Domain Deleted
Mutant Of Mycobacterium Tuberculosis
Length = 615
Score = 372 bits (955), Expect = e-103, Method: Compositional matrix adjust.
Identities = 210/591 (35%), Positives = 322/591 (54%), Gaps = 21/591 (3%)
Query: 21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG-GEN 79
L +E+ H YY+ D PIISD ++D+LL L+ +EE++PEL T DS TQ VG G +
Sbjct: 20 LAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATD 79
Query: 80 SKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGY 139
+ V H +M+SLDN F+ +++ + RI E+ + Y+ ELK DG+A++L Y G
Sbjct: 80 FEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAH--YLCELKIDGVALSLVYREGR 137
Query: 140 LKQASTRGDXXXXXXXXXXXXXXXXXP--LVLNIKYP-PELLEVRCEVLIYKKDFIKLNK 196
L +ASTRGD P L YP PE+LEVR EV DF LN
Sbjct: 138 LTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNA 197
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
G F NPRN+AAG LRQ +P + + L HG+G + G + H L
Sbjct: 198 SLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLA-L 256
Query: 257 QKIGLSICGEYSV---LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFT 313
+ GL + ++ L+GV + I+++ + R + +EIDGVV K++ ++ Q++LG T
Sbjct: 257 RAWGLPVSEHTTLATDLAGVRERIDYWGE---HRHEVDHEIDGVVVKVDEVALQRRLGST 313
Query: 314 SRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESE 373
SRAPR+A+AYK+ +EA TK+ I + +GRTG ITP A + PV + G T+ +ATLHN SE
Sbjct: 314 SRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASE 373
Query: 374 IYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII-YIESNL 432
I RK + IGDTVV+ ++G+VIP++ ++ LR + F +P CP C S + E +
Sbjct: 374 IKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKEGDA 433
Query: 433 IARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKN 492
RC + C Q + + H +SR ++I LG + L+ A ++ +L+ + ++
Sbjct: 434 DIRCPNA-RGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALTERD 492
Query: 493 LLRLDRVSNKLAN------NILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNL 546
LLR D K +L+ + K+K R + AL IRHVG T A+ LA F +L
Sbjct: 493 LLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSL 552
Query: 547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN 597
+ + A+ +QL + +G T A ++ HR ++ + R G+ ++
Sbjct: 553 DAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVDE 603
>pdb|3UQ8|A Chain A, Structure Of Adenylation Domain Of Haemophilus Influenzae
Dna Ligases Bound To Nad+ In Adenylated State
Length = 322
Score = 241 bits (614), Expect = 1e-63, Method: Compositional matrix adjust.
Identities = 128/317 (40%), Positives = 184/317 (58%), 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 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNEL-KLTKNIEYIAELKFDGIAVNLRY 135
+ H M+SLDN FSD + F RI + L L + + E K DG+AV++ Y
Sbjct: 65 LSGFSQIRHEIPMLSLDNAFSDAEFNAFVARIEDRLILLPAPLTFCCEPKLDGLAVSILY 124
Query: 136 EYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
G L QA+TRGD 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
>pdb|3PN1|A Chain A, Novel Bacterial Nad+-Dependent Dna Ligase Inhibitors With
Broad Spectrum Potency And Antibacterial Efficacy In
Vivo
Length = 318
Score = 239 bits (611), Expect = 3e-63, Method: Compositional matrix adjust.
Identities = 127/316 (40%), Positives = 183/316 (57%), Gaps = 1/316 (0%)
Query: 11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQ 70
+ + ++ L+K L ++ Y++ DNP + D++YD+L +LK +E ++PE LT DS TQ
Sbjct: 1 MTNIQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQ 60
Query: 71 HVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNEL-KLTKNIEYIAELKFDGI 129
VG + H M+SLDN FSD + F KRI + L L K + + E K DG+
Sbjct: 61 RVGAKPLSGFSQIRHEIPMLSLDNAFSDAEFNAFVKRIEDRLILLPKPLTFCCEPKLDGL 120
Query: 130 AVNLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKK 189
AV++ Y G L QA+TRGD PL L PP LEVR EV +
Sbjct: 121 AVSILYVNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHA 180
Query: 190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249
F +LNKY K F NPRNAAAG LRQL+P I + L A+G+G G+++P++H
Sbjct: 181 GFERLNKYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTH 240
Query: 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKK 309
L W + IG+ + E + +G ++++ FY+ I KR +L Y+IDG V KIN ++ Q +
Sbjct: 241 YARLQWLKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNE 300
Query: 310 LGFTSRAPRFALAYKF 325
LGF S+APR+A+AYKF
Sbjct: 301 LGFISKAPRWAIAYKF 316
>pdb|1B04|A Chain A, Structure Of The Adenylation Domain Of An Nad+ Dependent
Ligase
pdb|1B04|B Chain B, Structure Of The Adenylation Domain Of An Nad+ Dependent
Ligase
Length = 318
Score = 239 bits (611), Expect = 3e-63, Method: Compositional matrix adjust.
Identities = 124/316 (39%), Positives = 186/316 (58%), 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 LEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEV---GEAAYVCELAIDGLAVSVRYE 125
Query: 137 YGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
GY Q +TRGD 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 ERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALGI-ASHSEALDYL 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
>pdb|3JSL|A Chain A, Crystal Structure Of The Adenylation Domain Of Nad+-
Dependent Dna Ligase From Staphylococcus Aureus
pdb|3JSL|B Chain B, Crystal Structure Of The Adenylation Domain Of Nad+-
Dependent Dna Ligase From Staphylococcus Aureus
pdb|3JSN|A Chain A, Crystal Structure Of The Adenylation Domain Of Nad+-
Dependent Dna Ligase From Staphylococcus Aureus
Length = 318
Score = 214 bits (544), Expect = 1e-55, Method: Compositional matrix adjust.
Identities = 120/319 (37%), Positives = 188/319 (58%), Gaps = 7/319 (2%)
Query: 11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQ 70
+ LS RV EL L++++ YY+ DNP + D++YD+LL EL KIEE++PE T DS T
Sbjct: 1 MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTV 60
Query: 71 HVGLVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIA 130
VG + V+H M+SL N F+++D+ F++RI ++ N+EY+ ELK DG+A
Sbjct: 61 RVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQI---GNVEYMCELKIDGLA 117
Query: 131 VNLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKD 190
V+L+Y GY Q TRGD PL + P +EVR E + ++
Sbjct: 118 VSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMK---EPLNVEVRGEAYMPRRS 174
Query: 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHS 250
F++LN+ + + F NPRNAAAG LRQL+ K+ + L F + V + N S S
Sbjct: 175 FLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNA-RSQS 233
Query: 251 ELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKL 310
E L+ K+G + + ++ ++ ++E+ +K +R +LPY+IDG+V K+N L Q ++
Sbjct: 234 EALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEM 293
Query: 311 GFTSRAPRFALAYKFLSKE 329
GFT ++PR+A+AYKF ++E
Sbjct: 294 GFTQKSPRWAIAYKFPAEE 312
>pdb|1TA8|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
Length = 332
Score = 209 bits (532), Expect = 4e-54, Method: Compositional matrix adjust.
Identities = 122/332 (36%), Positives = 184/332 (55%), Gaps = 12/332 (3%)
Query: 6 KKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTK 65
++ + + + R EL+K+L++++ YY+ D P + D YD+L EL IE ++P+L+T
Sbjct: 3 QQPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITP 62
Query: 66 DSLTQHVG---LVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIA 122
DS TQ VG L G E + H M SL++GFS ED+ F++R+ + K + Y
Sbjct: 63 DSPTQRVGGKVLSGFEKAP---HDIPMYSLNDGFSKEDIFAFDERVRK--AIGKPVAYCC 117
Query: 123 ELKFDGIAVNLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRC 182
ELK DG+A++LRYE G + +TRGD P+ L P +EVR
Sbjct: 118 ELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLT---EPISVEVRG 174
Query: 183 EVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG 242
E + K+ F+ LN+ R G F NPRNAAAG LRQL+ KI + L+ F + V +
Sbjct: 175 ECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGP 234
Query: 243 MNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN 302
M + E L IG E + ++++ + ++ + KR LPYEIDG+V K+N
Sbjct: 235 MKA-KTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVN 293
Query: 303 CLSTQKKLGFTSRAPRFALAYKFLSKEALTKI 334
+ Q +LGFT +APR+A+AYKF +EA T +
Sbjct: 294 EFALQDELGFTVKAPRWAIAYKFPPEEAETVV 325
>pdb|1TAE|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
pdb|1TAE|B Chain B, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
pdb|1TAE|C Chain C, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
pdb|1TAE|D Chain D, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
pdb|3BA8|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+
Dependent Dna Ligase
pdb|3BA9|A Chain A, Structural Basis For Inhbition Of Nad-Dependent Ligase
pdb|3BAA|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+
Dependent Dna Ligase
pdb|3BAB|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+
Dependent Dna Ligase
Length = 332
Score = 209 bits (531), Expect = 6e-54, Method: Compositional matrix adjust.
Identities = 122/330 (36%), Positives = 183/330 (55%), Gaps = 12/330 (3%)
Query: 6 KKKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTK 65
++ + + + R EL+K+L++++ YY+ D P + D YD+L EL IE ++P+L+T
Sbjct: 3 QQPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITP 62
Query: 66 DSLTQHVG---LVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIA 122
DS TQ VG L G E + H M SL++GFS ED+ F++R+ + K + Y
Sbjct: 63 DSPTQRVGGKVLSGFEKAP---HDIPMYSLNDGFSKEDIFAFDERVRK--AIGKPVAYCC 117
Query: 123 ELKFDGIAVNLRYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRC 182
ELK DG+A++LRYE G + +TRGD P+ L P +EVR
Sbjct: 118 ELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLT---EPISVEVRG 174
Query: 183 EVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG 242
E + K+ F+ LN+ R G F NPRNAAAG LRQL+ KI + L+ F + V +
Sbjct: 175 ECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGP 234
Query: 243 MNMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN 302
M + E L IG E + ++++ + ++ + KR LPYEIDG+V K+N
Sbjct: 235 MKA-KTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVN 293
Query: 303 CLSTQKKLGFTSRAPRFALAYKFLSKEALT 332
+ Q +LGFT +APR+A+AYKF +EA T
Sbjct: 294 EFALQDELGFTVKAPRWAIAYKFPPEEAET 323
>pdb|1ZAU|A Chain A, Adenylation Domain Of Nad+ Dependent Dna Ligase From
M.Tuberculosis
Length = 328
Score = 205 bits (521), Expect = 8e-53, Method: Compositional matrix adjust.
Identities = 119/312 (38%), Positives = 174/312 (55%), Gaps = 13/312 (4%)
Query: 21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG-GEN 79
L +E+ H YY+ D PIISD ++D+LL L+ +EE++PEL T DS TQ VG G +
Sbjct: 20 LAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATD 79
Query: 80 SKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGY 139
+ V H +M+SLDN F+ +++ + RI E+ + Y+ ELK DG+A++L Y G
Sbjct: 80 FEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAH--YLCELKIDGVALSLVYREGR 137
Query: 140 LKQASTRGDXXXXXXXXXXXXXXXXXP--LVLNIKYP-PELLEVRCEVLIYKKDFIKLNK 196
L +ASTRGD P L YP PE+LEVR EV DF LN
Sbjct: 138 LTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNA 197
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
G F NPRN+AAG LRQ +P + + L HG+G + G + H L
Sbjct: 198 SLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLA-L 256
Query: 257 QKIGLSICGEYSV---LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFT 313
+ GL + ++ L+GV + I+++ + R + +EIDGVV K++ ++ Q++LG T
Sbjct: 257 RAWGLPVSEHTTLATDLAGVRERIDYWGE---HRHEVDHEIDGVVVKVDEVALQRRLGST 313
Query: 314 SRAPRFALAYKF 325
SRAPR+A+AYK+
Sbjct: 314 SRAPRWAIAYKY 325
>pdb|3BAC|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+
Dependent Dna Ligase
Length = 270
Score = 199 bits (506), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 106/251 (42%), Positives = 147/251 (58%), Gaps = 1/251 (0%)
Query: 83 VHHTFKMMSLDNGFSDEDVIIFNKRITNEL-KLTKNIEYIAELKFDGIAVNLRYEYGYLK 141
+ H M+SLDN FSD + F KRI + L L K + + E K DG+AV++ Y G L
Sbjct: 10 IRHEIPMLSLDNAFSDAEFNAFVKRIEDRLILLPKPLTFCCEPKLDGLAVSILYVNGELT 69
Query: 142 QASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHL 201
QA+TRGD PL L PP LEVR EV + F +LNKY
Sbjct: 70 QAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYALEH 129
Query: 202 GLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGL 261
K F NPRNAAAG LRQL+P I + L A+G+G G+ +P++H L W + IG+
Sbjct: 130 NEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVGLPTTHYARLQWLKSIGI 189
Query: 262 SICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFAL 321
+ E + +G +++++FY+ I KR +L Y+IDG V KIN ++ Q +LGF S+APR+A+
Sbjct: 190 PVNPEIRLCNGADEVLDFYQDIQNKRSSLGYDIDGTVLKINDIALQNELGFISKAPRWAI 249
Query: 322 AYKFLSKEALT 332
AYKF ++E LT
Sbjct: 250 AYKFPAQEELT 260
>pdb|4GLW|A Chain A, Dna Ligase A In Complex With Inhibitor
pdb|4GLW|B Chain B, Dna Ligase A In Complex With Inhibitor
Length = 305
Score = 181 bits (460), Expect = 8e-46, Method: Compositional matrix adjust.
Identities = 113/313 (36%), Positives = 175/313 (55%), Gaps = 17/313 (5%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVG--- 73
R+ EL L+R+ YY DNP +SD++YD+L EL ++E YPE + DS T VG
Sbjct: 4 RMNELVALLNRYATEYYTSDNPSVSDSEYDRLYRELVELETAYPEQVLADSPTHRVGGKV 63
Query: 74 LVGGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNL 133
L G E KY H + + SL + FS E++ F+ R+ E+ + YI ELK DG++++L
Sbjct: 64 LDGFE--KYSHQ-YPLYSLQDAFSREELDAFDARVRKEVA---HPTYICELKIDGLSISL 117
Query: 134 RYEYGYLKQASTRGDXXXXXXXXXXXXXXXXXPLVLNIKYPPEL-LEVRCEVLIYKKDFI 192
YE G L TRGD PL L P EL + VR E + + F
Sbjct: 118 TYEKGILVAGVTRGDGSIGENITENLKRVKDIPLTL----PEELDITVRGECYMPRASFD 173
Query: 193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSEL 252
++N+ R G +F NPRNAAAG LRQL+ + + L F + + + S +
Sbjct: 174 QVNQARQENGEPEFANPRNAAAGTLRQLDTAVVAKRNLATFLY---QEASPSTRDSQEKG 230
Query: 253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGF 312
L + +++G + + + ++++ F +++ +R NLPY+IDGVV K+N L++Q++LGF
Sbjct: 231 LKYLEQLGFVVNPKRILAENIDEIWNFIQEVGQERENLPYDIDGVVIKVNDLASQEELGF 290
Query: 313 TSRAPRFALAYKF 325
T +AP++A+AYKF
Sbjct: 291 TVKAPKWAVAYKF 303
>pdb|1L7B|A Chain A, Solution Nmr Structure Of Brct Domain Of T. Thermophilus:
Northeast Structural Genomics Consortium Target Wr64tt
Length = 92
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
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
>pdb|2EBU|A Chain A, Solution Structure Of The Brct Domain From Human
Replication Factor C Large Subunit 1
Length = 112
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 602 GGKVVNFISKNTNYLVKGQKPGK-KLEKAIKLNIKILDEKNFVKIVK 647
GGKV +SK TNYLV G+ G+ K +KA L KI+DE + +++
Sbjct: 50 GGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 96
>pdb|2K7F|A Chain A, Haddock Calculated Model Of The Complex Between The Brct
Region Of Rfc P140 And Dsdna
pdb|2K6G|A Chain A, Solution Structure Of The Dna Binding Brct Domain From The
Large Subunit Of Human Replication Factor C
Length = 109
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 602 GGKVVNFISKNTNYLVKGQKPGK-KLEKAIKLNIKILDEKNFVKIVK 647
GGKV +SK TNYLV G+ G+ K +KA L KI+DE + +++
Sbjct: 60 GGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 106
>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
Length = 720
Score = 33.5 bits (75), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 531 VGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577
VG A+ L N F+++E + +A E+LL I IG TV+A KF+ +
Sbjct: 654 VGRRRARALYNSGFRSIEDISQARPEELLKIEGIGVKTVEAIFKFLGK 701
>pdb|2CWL|A Chain A, Crystal Structure Of Manganese-Free Form Of Pseudocatalase
From Thermus Thermophilus Hb8
pdb|2CWL|B Chain B, Crystal Structure Of Manganese-Free Form Of Pseudocatalase
From Thermus Thermophilus Hb8
Length = 302
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 540 ANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLI----SQLRDVGIYWL 595
A Y K LE + ++L IPKI ++ + K+++ HR L RD+G+ W
Sbjct: 190 AAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWK 249
Query: 596 NNPNTKGGKVV 606
G +VV
Sbjct: 250 GASPEDGTEVV 260
>pdb|2V8T|A Chain A, Crystal Structure Of Mn Catalase From Thermus Thermophilus
Complexed With Chloride
pdb|2V8T|B Chain B, Crystal Structure Of Mn Catalase From Thermus Thermophilus
Complexed With Chloride
pdb|2V8U|A Chain A, Atomic Resolution Structure Of Mn Catalase From Thermus
Thermophilus
pdb|2V8U|B Chain B, Atomic Resolution Structure Of Mn Catalase From Thermus
Thermophilus
Length = 302
Score = 33.1 bits (74), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 540 ANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLI----SQLRDVGIYWL 595
A Y K LE + ++L IPKI ++ + K+++ HR L RD+G+ W
Sbjct: 190 AAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWK 249
Query: 596 NNPNTKGGKVV 606
G +VV
Sbjct: 250 GASPEDGTEVV 260
>pdb|3CAI|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Rv3778c
Protein
pdb|3CAI|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Rv3778c
Protein
Length = 406
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLEC 548
DRV +LA+N +LAI T SR + LG+ VG LA+Y E
Sbjct: 348 DRVVQRLADNGILAIAN----TGSRVLDVLGVNDVGGAVTVGLAHYSTMAEV 395
>pdb|1QEZ|A Chain A, Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An
Archael Pyrophosphatase.
pdb|1QEZ|B Chain B, Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An
Archael Pyrophosphatase.
pdb|1QEZ|C Chain C, Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An
Archael Pyrophosphatase.
pdb|1QEZ|D Chain D, Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An
Archael Pyrophosphatase.
pdb|1QEZ|E Chain E, Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An
Archael Pyrophosphatase.
pdb|1QEZ|F Chain F, Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An
Archael Pyrophosphatase
Length = 173
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 173 YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHF 232
YP ++EVR ++Y KD + + K T+P + + L P+ KNKI+HF
Sbjct: 77 YPGSVIEVRPIGILYMKDE-EGEDAKIVAVPKDKTDPSFSNIKDINDL-PQATKNKIVHF 134
Query: 233 FAH 235
F H
Sbjct: 135 FEH 137
>pdb|3IJI|A Chain A, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Ala-D-Glu;
Nonproductive Substrate Binding.
pdb|3IJI|B Chain B, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Ala-D-Glu;
Nonproductive Substrate Binding.
pdb|3IJL|A Chain A, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Pro-D-Glu;
Nonproductive Substrate Binding.
pdb|3IJL|B Chain B, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Pro-D-Glu;
Nonproductive Substrate Binding.
pdb|3IJQ|A Chain A, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Ala-D-Glu; Productive
Substrate Binding.
pdb|3IJQ|B Chain B, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Ala-D-Glu; Productive
Substrate Binding
Length = 338
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 9/33 (27%), Positives = 24/33 (72%)
Query: 273 VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLS 305
V ++ F KK+N+++F+ P++++ ++ ++ LS
Sbjct: 54 VESVMNFLKKVNLEQFSDPFQLEDILSYVDSLS 86
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.138 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,168,161
Number of Sequences: 62578
Number of extensions: 748550
Number of successful extensions: 2109
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2038
Number of HSP's gapped (non-prelim): 34
length of query: 655
length of database: 14,973,337
effective HSP length: 105
effective length of query: 550
effective length of database: 8,402,647
effective search space: 4621455850
effective search space used: 4621455850
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)