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= 004212
(768 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X9N|A Chain A, Crystal Structure Of Human Dna Ligase I Bound To
5'-Adenylated, Nicked Dna
Length = 688
Score = 559 bits (1440), Expect = e-159, Method: Compositional matrix adjust.
Identities = 272/567 (47%), Positives = 385/567 (67%), Gaps = 12/567 (2%)
Query: 177 FDPKMVACWEKGERVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVY 236
+ P ACW+ G++VP++ ++ F+ I + R+ + + N+LR+V+ +P DL+PV+Y
Sbjct: 42 YHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRXVETLSNLLRSVVALSPPDLLPVLY 101
Query: 237 LAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQSM 296
L+ N + P +GLELG+GD ++KA+A+A GR V+ + E GD+GLVA+ SRS+Q +
Sbjct: 102 LSLNHLGPPQQGLELGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRL 161
Query: 297 MRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRI 356
P PLT + VF FR IA+ G S KK + IK L VA E +++ R L +LR+
Sbjct: 162 XLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRL 221
Query: 357 GLAEQTLLAALGQAAVYNEQHSKPPPNI------------QSPLEEAAKIVKQVFSVLPV 404
GLAEQ++LAAL QA + PP ++ LEE I+KQ F +P
Sbjct: 222 GLAEQSVLAALSQAVSLTPPGQEFPPAXVDAGKGKTAEARKTWLEEQGXILKQTFCEVPD 281
Query: 405 YEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGE 464
++I+P LL G+ L C +PGIP+ P LA PT+G+SE++ +F++ FTCEYKYDG+
Sbjct: 282 LDRIIPVLLEHGLERLPEHCKLSPGIPLKPXLAHPTRGISEVLKRFEEAAFTCEYKYDGQ 341
Query: 465 RAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKI 524
RAQIH LE G V+I+SRN E NTGK+PD++ + ++K PSV SF+LD E VA+DREK++I
Sbjct: 342 RAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQI 401
Query: 525 LPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF 584
PFQ L+TR RK V S+I+V VC+YAFD++Y NG+ L++E L RR+ L ++F E G
Sbjct: 402 QPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGE 461
Query: 585 FQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIES 644
F FAT+L + D+++I +FL+ +V SCEGL +KT+D DATYE +KRS NWLKLKKDY++
Sbjct: 462 FVFATSLDTKDIEQIAEFLEQSVKDSCEGLXVKTLDVDATYEIAKRSHNWLKLKKDYLDG 521
Query: 645 IGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSL 704
+GD+LDLV I A+ GRGKR G YG FLLA YD ++EE Q+ICK+GTGFS+ LEE SL
Sbjct: 522 VGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSL 581
Query: 705 RSKVIPKPRPYYRFADTISPDVWFEPT 731
++ V+P PRPY R + PD W +P+
Sbjct: 582 KALVLPSPRPYVRIDGAVIPDHWLDPS 608
>pdb|2HIV|A Chain A, Atp-Dependent Dna Ligase From S. Solfataricus
pdb|2HIX|A Chain A, Atp Dependent Dna Ligase From S. Solfataricus Bound To Atp
Length = 621
Score = 256 bits (654), Expect = 3e-68, Method: Compositional matrix adjust.
Identities = 171/567 (30%), Positives = 293/567 (51%), Gaps = 35/567 (6%)
Query: 187 KGERVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAH 246
+G + F ++ FD + + R+ +T ++ ++L +T + VVY+ K+ P
Sbjct: 17 RGSHMEFKVIAEYFDKLEKISSRLQLTALLADLLSKSDKTIID---KVVYIIQGKLWPDF 73
Query: 247 EGL-ELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQSMM-------- 297
G ELGIG+ +IKA++ A E+ V+ Y+ +GDLG VA+ +S Q
Sbjct: 74 LGYPELGIGEKFLIKAISIATNTDENSVENLYKTIGDLGEVARRLKSKQQSTGILGFLGT 133
Query: 298 RKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRIG 357
+ LT+ +V+ T +A G+ S++ K + LL A E ++L+R ++ +LR+G
Sbjct: 134 TSKESLTVDEVYSTLSKVALTTGEGSRDLKIRLLAGLLKKADPLEAKFLVRFVEGRLRVG 193
Query: 358 LAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGV 417
+ + T+L A+ A + S A++I+++ +++ I ++ G+
Sbjct: 194 IGDATVLDAM--AIAFGGGQS------------ASEIIERAYNLRADLGNIAKIIVEKGI 239
Query: 418 WNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVE 477
L T GIPI PMLA+ EI+ K +YKYDGERAQIH ED +
Sbjct: 240 EAL-KTLKPQVGIPIRPMLAERLSNPEEILKKMGG-NAIVDYKYDGERAQIHKKED-KIF 296
Query: 478 IYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKN 537
I+SR E T ++PDVV VS+ + + F+++ EIVA D E ++ PFQ L R RK+
Sbjct: 297 IFSRRLENITSQYPDVVDYVSKYIEG--KEFIIEGEIVAIDPESGEMRPFQELMHRKRKS 354
Query: 538 VSLSDIK-VDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDL 596
IK V ++ FD++Y + L RR+ L +S + + + A + + ++
Sbjct: 355 DIYEAIKEYPVNVFLFDLMYYEDVDYTTKPLEARRK-LLESIVKPNDYVKIAHHIQANNV 413
Query: 597 DEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAA 656
++++ F A+ EG+++K + +DA Y+ R W+KLK+DY + D++DLV +
Sbjct: 414 EDLKSFFYRAISEGGEGVMVKAIGKDAIYQAGARGWLWIKLKRDYQSEMADTVDLVVVGG 473
Query: 657 FHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYY 716
F+G+GKR G + L+A Y+ + F+S+CK+ +GFS+ L+E L I + +
Sbjct: 474 FYGKGKRGGKISSLLMAAYNPKTDSFESVCKVASGFSDEQLDELQKKLME--IKRDVKHP 531
Query: 717 RFADTISPDVWFEPTERPETSNSPASI 743
R + PD+W EP E S +I
Sbjct: 532 RVNSKMEPDIWVEPVYVAEIIGSEITI 558
>pdb|3RR5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sp. 1519
Length = 570
Score = 206 bits (525), Expect = 3e-53, Method: Compositional matrix adjust.
Identities = 168/524 (32%), Positives = 268/524 (51%), Gaps = 46/524 (8%)
Query: 224 METTPEDLVPVV-YLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGD 282
++ TP++L+ VV YL K+ P + ELG+G+ +IKA++ A G E ++ ++ GD
Sbjct: 41 LKKTPDELLEVVPYLILGKVFPDWDERELGVGEKLLIKAVSMATGVPEKEIENSIKDTGD 100
Query: 283 LG---LVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAAT 339
LG +A R +S +P LTI +V+ TF +A+ +G+ SQ++K + L + A
Sbjct: 101 LGESVALALKKRKQKSFFSQP--LTIKRVYSTFVKVAEASGEGSQDRKMKYLANLFMDAQ 158
Query: 340 DCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVF 399
E +Y+ R + +R G+AE L A+ +A ++ L E A ++ F
Sbjct: 159 PEEGKYIARTVLGTMRTGVAEGILRDAIAEAF-----------RVKPELVERAYMLTSDF 207
Query: 400 SVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEY 459
+ K+ +G LS S G PI PMLA+ V E + + E E
Sbjct: 208 GYVAKVAKL------EGNEGLSK-VSIQIGKPIRPMLAQNAASVKEALIEMGG-EAAFEI 259
Query: 460 KYDGERAQIHYLEDGS-VEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYD 518
KYDG R Q+H DG V IYSR E T P++V AV KPS +++ E+VA
Sbjct: 260 KYDGARVQVH--RDGDRVIIYSRRLENVTRSIPEIVEAVKASLKPS--KVIVEGELVAVG 315
Query: 519 REKQKILPFQTLSTRARKNVSLSDI--KVDVCIYAFDILYRNGQPLLQEQLRVRREHLYD 576
E + PFQ + R R+ ++ ++ K+ + + FDILY +G+ L+ + RR+ L +
Sbjct: 316 -ENGRPRPFQYVLRRFRRKYNIDEMIEKIPLELNLFDILYVDGESLIDTEFVERRKRLEE 374
Query: 577 SFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLK 636
S EE + A L + ++E + F A++ EGL+ K +D + YEP R WLK
Sbjct: 375 SVEESEKI-KIAEQLVTKKVEEAEAFYKRALELGHEGLMAKRLD--SVYEPGNRGKKWLK 431
Query: 637 LKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAM 696
+K ++LDLV I A G G+R + G+FL+A YD ++ EF + K+G+GF++
Sbjct: 432 IKPTM-----ENLDLVIIGAEWGEGRRAHLLGSFLVAAYDPDSGEFLPVGKVGSGFTDED 486
Query: 697 LEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSP 740
L E + L+ ++ R +F + I P V E T + E SP
Sbjct: 487 LVEFTKMLKPLIL---REEGKFVE-IEPKVVIEVTYQ-EIQKSP 525
>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus
Length = 571
Score = 188 bits (478), Expect = 8e-48, Method: Compositional matrix adjust.
Identities = 158/498 (31%), Positives = 249/498 (50%), Gaps = 44/498 (8%)
Query: 215 IVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVK 274
V + L++V PE L + YL K+ P + ELGIG+ +IKA++ A G ++
Sbjct: 36 FVSDFLKSV--EKPELLEVIPYLILGKVFPDWDERELGIGEKLLIKAVSMATGINSEEIE 93
Query: 275 KQYQEMGDLG---LVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRI 331
++ GDLG +A R +S +P LTI +V++T IA+ +G SQ++K +
Sbjct: 94 NSVRDTGDLGESIALALNKRKQKSFFSQP--LTIERVYNTLVKIAEASGAGSQDRKLKYL 151
Query: 332 KALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEA 391
L + A+ E +YL R + +R G+AE L AL A ++ L E
Sbjct: 152 ANLFMDASPDEGKYLARTVLGIMRTGVAEGLLRDALADAF-----------KVRVELVER 200
Query: 392 AKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSE-IVNKF 450
A ++ F + K+ +G L+ G PI PMLA+ V E +V
Sbjct: 201 AYMLTSDFGFVAKVAKL------EGDEGLAK-VKIQVGKPIKPMLAQMAANVREALVEMG 253
Query: 451 QDMEFTCEYKYDGERAQIHYLEDGS-VEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509
+ EF E KYDG R Q+H ++G+ V IYSR E T P+VV V KP +
Sbjct: 254 GEAEF--EIKYDGARVQVH--KNGNKVLIYSRRLENVTKSIPEVVERVKEALKPE--KVI 307
Query: 510 LDCEIVAYDREKQKILPFQTLSTRARKNVSLSDI--KVDVCIYAFDILYRNGQPLLQEQL 567
++ E+VA + E + PFQ + R R+ ++ ++ K+ + + FDILY +GQ ++
Sbjct: 308 VEGELVAVE-ETGRPRPFQYVLRRFRRKYNIEEMIEKIPLELNLFDILYVDGQNMIDTPF 366
Query: 568 RVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEP 627
RR+ L +S + + A L + +E + F A+D EGL+ K +D +TYEP
Sbjct: 367 MERRKVL-ESVVNSNEWIKSAENLITKSPEEAEAFYHKALDLGHEGLMAKRLD--STYEP 423
Query: 628 SKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICK 687
R WLK+K ++LDLV + A G G+R+GV +FLL YD +F + K
Sbjct: 424 GNRGKKWLKIKPTM-----ENLDLVVLGAEWGEGRRSGVLSSFLLGAYDPVKGDFVPVGK 478
Query: 688 IGTGFSEAMLEERSSSLR 705
+G+GF++ L E + L+
Sbjct: 479 VGSGFTDEDLVEFTKMLK 496
>pdb|2CFM|A Chain A, Atp-Dependent Dna Ligase From Pyrococcus Furiosus
Length = 561
Score = 186 bits (473), Expect = 4e-47, Method: Compositional matrix adjust.
Identities = 155/544 (28%), Positives = 258/544 (47%), Gaps = 53/544 (9%)
Query: 193 FIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVV-YLAANKIAPAHEGLEL 251
++ L+ ++ + T +++ T +V + L+ V P+D + + YL ++ P + EL
Sbjct: 3 YLELAQLYQKLEKTTXKLIKTRLVADFLKKV----PDDHLEFIPYLILGEVFPEWDEREL 58
Query: 252 GIGDASIIKALAEACGRTESHVKKQYQEMGDLG-LVAKASRSSQSMMRKPDPLTITKVFD 310
G+G+ +IKA+A A G +++ ++ GDLG +A A + + PLTI +V+
Sbjct: 59 GVGEKLLIKAVAXATGIDAKEIEESVKDTGDLGESIALAVKKKKQKSFFSQPLTIKRVYQ 118
Query: 311 TFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQA 370
T +A+ G+ SQ+KK + L A E +YL R + R G+AE L A+ A
Sbjct: 119 TLVKVAETTGEGSQDKKVKYLADLFXDAEPLEAKYLARTILGTXRTGVAEGLLRDAIAXA 178
Query: 371 AVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGI 430
+ + + S AKI K +G L+ G
Sbjct: 179 FHVKVELVERAYXLTSDFGYVAKIAK-----------------LEGNEGLAK-VQVQLGK 220
Query: 431 PIGPMLAKPTKGVSE-IVNKFQDMEFTCEYKYDGERAQIHYLEDGS-VEIYSRNAERNTG 488
PI P LA+ + + ++ + EF E KYDG R Q+H +DGS + +YSR E T
Sbjct: 221 PIKPXLAQQAASIRDALLEXGGEAEF--EIKYDGARVQVH--KDGSKIIVYSRRLENVTR 276
Query: 489 KFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARK--NVSLSDIKVD 546
P++V A+ P +++ E+VA E + LPFQ + R R+ N+ K+
Sbjct: 277 AIPEIVEALKEAIIPE--KAIVEGELVAIG-ENGRPLPFQYVLRRFRRKHNIEEXXEKIP 333
Query: 547 VCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAA 606
+ + FD+LY +GQ L+ + RR L + ++ + A L + ++E + F A
Sbjct: 334 LELNLFDVLYVDGQSLIDTKFIDRRRTLEEIIKQNEKI-KVAENLITKKVEEAEAFYKRA 392
Query: 607 VDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGV 666
++ EGL K +D A YEP R WLK+K ++LDLV I A G G+R +
Sbjct: 393 LEXGHEGLXAKRLD--AVYEPGNRGKKWLKIK-----PTXENLDLVIIGAEWGEGRRAHL 445
Query: 667 YGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726
+G+F+L YD EF + K+G+GF++ L E + L+ +I + V
Sbjct: 446 FGSFILGAYDPETGEFLEVGKVGSGFTDDDLVEFTKXLKPLIIKEE----------GKRV 495
Query: 727 WFEP 730
W +P
Sbjct: 496 WLQP 499
>pdb|3GDE|A Chain A, The Closed Conformation Of Atp-Dependent Dna Ligase From
Archaeoglobus Fulgidus
Length = 558
Score = 180 bits (456), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 144/469 (30%), Positives = 232/469 (49%), Gaps = 40/469 (8%)
Query: 230 DLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKA 289
DL VV K+ P + ELG+G + +AL G S ++ +E GDLGLVA+
Sbjct: 41 DLYDVVLFITGKVYPPWDERELGVGIGLLYEALENVSGVKRSEIESMIREYGDLGLVAEQ 100
Query: 290 SRSSQSMMRKP-DPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIR 348
+ M + LT+ KV +TF IA G+ S ++K + L AT E +YL R
Sbjct: 101 LIKKKKMTTLAFEELTVRKVRETFDEIASLTGEGSMKRKIMLLTGLYGLATPLEARYLTR 160
Query: 349 LLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKI 408
L+ +++R+G+ E + A+ +A + + + I + L A + K+
Sbjct: 161 LILNEMRLGVGEGIMRDAIARAFRADPETVERAYMITNDLGRVAVVAKK----------- 209
Query: 409 VPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQI 468
+G L IP+ MLA+ + + V + + E+K+DG R Q+
Sbjct: 210 ------EGEEGLRK-MKIEIHIPVRMMLAQVAESLESAVREMRTA--AVEWKFDGSRVQV 260
Query: 469 HYLEDGS-VEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPF 527
H+ DGS V IYSR E T PD+V + + KP V +LD E++A ++ K +PF
Sbjct: 261 HW--DGSRVTIYSRRLENVTNALPDIVEEIKKSVKPGV---ILDGEVIAV--KEGKPMPF 313
Query: 528 QTLSTRARKNVSLSDI--KVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFF 585
Q + R R+ ++ + K+ + + FDILY +G+ + LR RR+ L +S E
Sbjct: 314 QHVLRRFRRKHDVAKMVEKIPLEAHFFDILYHDGE-CIDLPLRERRK-LLESAVNESEKI 371
Query: 586 QFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESI 645
+ A + + +DE++K D A+ A EG++IK + Y P KR NWLK+K +I
Sbjct: 372 KLAKQIVTDSVDEVRKMYDEAISAGHEGVMIKL--PSSPYIPGKRGKNWLKVK-----AI 424
Query: 646 GDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSE 694
++LDLV + G GKR+ +F LAC D + + ++ TGF+E
Sbjct: 425 METLDLVVVGGEWGEGKRSHWLSSFELACLDPVTGKLLKVGRVATGFTE 473
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic
Switching Between Two Dna Bound States
Length = 579
Score = 137 bits (345), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 89/280 (31%), Positives = 139/280 (49%), Gaps = 20/280 (7%)
Query: 431 PIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAE----RN 486
P+ PMLA+ K V + K + F+ E KYDGER Q+H D +SR+ +
Sbjct: 226 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHKNGD-HFSYFSRSLKPVLPHK 283
Query: 487 TGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVD 546
F D + P S +LD E++ D + K LPF TL K + D +
Sbjct: 284 VAHFKDYIPQAF----PGGHSMILDSEVLLIDNKTGKPLPFGTLGVH--KKAAFQD--AN 335
Query: 547 VCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAA 606
VC++ FD +Y N L+ L RR+ L+D+ E P F+ ++ +
Sbjct: 336 VCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRV 395
Query: 607 VDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIE--SIGDSLDLVPIAAFHGRGKRT 664
+ EGL++K D TYEP KR +WLK+KKDY+ ++ D+ DLV + AF+G+G +
Sbjct: 396 IQEGLEGLVLK--DVKGTYEPGKR--HWLKVKKDYLNEGAMADTADLVVLGAFYGQGSKG 451
Query: 665 GVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSL 704
G+ FL+ CYD ++++ ++ K G +A L + L
Sbjct: 452 GMMSIFLMGCYDPGSQKWCTVTKCAGGHDDATLARLQNEL 491
>pdb|1VS0|A Chain A, Crystal Structure Of The Ligase Domain From M.
Tuberculosis Ligd At 2.4a
pdb|1VS0|B Chain B, Crystal Structure Of The Ligase Domain From M.
Tuberculosis Ligd At 2.4a
Length = 310
Score = 62.0 bits (149), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 69/262 (26%), Positives = 109/262 (41%), Gaps = 36/262 (13%)
Query: 439 PTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVS 498
P V + ++ E +DG R + + G+V + SR+ T ++P +
Sbjct: 11 PXLATHGTVAGLKASQWAFEGXWDGYRLLVE-ADHGAVRLRSRSGRDVTAEYPQLRALAE 69
Query: 499 RLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRN 558
L V VLD E V D + F R R D +V+ +AFD+LY +
Sbjct: 70 DLADHHV---VLDGEAVVLD--SSGVPSFSQXQNRGR------DTRVE--FWAFDLLYLD 116
Query: 559 GQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDL---DEIQKFLDAAVDASCEGLI 615
G+ LL + + RR+ L AT+LT +L D Q F + EG+I
Sbjct: 117 GRALLGTRYQDRRKLLET--------LANATSLTVPELLPGDGAQAFA-CSRKHGWEGVI 167
Query: 616 IKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACY 675
K RD+ Y+P +R +W+K K ++ ++V G G R+ G+ L
Sbjct: 168 AKR--RDSRYQPGRRCASWVKDKH------WNTQEVVIGGWRAGEGGRSSGVGSLLXGIP 219
Query: 676 DSNNEEFQSICKIGTGFSEAML 697
+F ++GTG SE L
Sbjct: 220 GPGGLQFAG--RVGTGLSEREL 239
>pdb|3VNN|A Chain A, Crystal Structure Of A Sub-Domain Of The
Nucleotidyltransferase (Adenylation) Domain Of Human Dna
Ligase Iv
Length = 139
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 42/136 (30%), Positives = 60/136 (44%), Gaps = 12/136 (8%)
Query: 455 FTCEYKYDGERAQIHYLEDGSV-EIYSRNAERNTGKF------PDVVLAVSRLKKPSVRS 507
F E K DGER Q+H +DG V + +SRN T +F + + K ++
Sbjct: 1 FYIETKLDGERMQMH--KDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQI 58
Query: 508 FVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQL 567
+LD E++AY+ Q F T+ + D + C FD+L N + L E L
Sbjct: 59 CILDGEMMAYNPNTQT---FMQKGTKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGHETL 115
Query: 568 RVRREHLYDSFEEEPG 583
R R E L F PG
Sbjct: 116 RKRYEILSSIFTPIPG 131
>pdb|4HTO|A Chain A, Crystal Structure Of The Dbd Domain Of Human Dna Ligase Iv
Apo Form
pdb|4HTP|A Chain A, Crystal Structure Of The Dbd Domain Of Human Dna Ligase Iv
Bound To Artemis Peptide
pdb|4HTP|B Chain B, Crystal Structure Of The Dbd Domain Of Human Dna Ligase Iv
Bound To Artemis Peptide
Length = 240
Score = 34.3 bits (77), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 26/117 (22%), Positives = 55/117 (47%), Gaps = 9/117 (7%)
Query: 277 YQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLV 336
+ + GD ++A + + + LTI +V D IA ++ K + L+
Sbjct: 119 HGDAGDFAMIAYFVLKPRCLQK--GSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLIT 176
Query: 337 AATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAK 393
++ E ++LIR++ L++G+++QT+ + A E H N+ + LE+ +
Sbjct: 177 QSSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAA--ELH-----NVTTDLEKVCR 226
>pdb|3VR6|H Chain H, Crystal Structure Of Amp-pnp Bound Enterococcus Hirae
V1-atpase [bv1]
Length = 115
Score = 33.1 bits (74), Expect = 0.57, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 201 DMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIK 260
+M NE G I IT+ N++ +E L P + L P+H+G LGIG I
Sbjct: 39 EMAKNEYGVIYITEQCANLVPETIERYKGQLTPAIIL-----IPSHQG-TLGIGLEEIQN 92
Query: 261 ALAEACGR 268
++ +A G+
Sbjct: 93 SVEKAVGQ 100
>pdb|3AON|B Chain B, Crystal Structure Of The Central Axis (Ntpd-Ntpg) In The
Catalytic Portion Of Enterococcus Hirae V-Type Sodium
Atpase
pdb|3VR4|H Chain H, Crystal Structure Of Enterococcus Hirae V1-atpase [ev1]
pdb|3VR5|H Chain H, Crystal Structure Of Nucleotide-free Enterococcus Hirae
V1-atpase [ev1(l)]
Length = 115
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 205 NETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAE 264
NE G I IT+ N++ +E L P + L P+H+G LGIG I ++ +
Sbjct: 43 NEYGVIYITEQCANLVPETIERYKGQLTPAIIL-----IPSHQG-TLGIGLEEIQNSVEK 96
Query: 265 ACGR 268
A G+
Sbjct: 97 AVGQ 100
>pdb|3I44|A Chain A, Crystal Structure Of Aldehyde Dehydrogenase From
Bartonella Henselae At 2.0a Resolution
Length = 497
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 90 RTLDTQTPKTTNSVVGEKIQEVAEEPSNDLVKPISNQIDNPIDSEKESQPTPPSPKKRK 148
+T T +P V EKI E+ E+ S+D+ K IS ++ PID +Q S R
Sbjct: 77 QTWKTTSPHERLGFV-EKILEIYEKRSSDMAKTISMEMGAPIDMALNAQTATGSSHIRN 134
>pdb|2UUU|A Chain A, Alkyldihydroxyacetonephosphate Synthase In P212121
pdb|2UUU|B Chain B, Alkyldihydroxyacetonephosphate Synthase In P212121
pdb|2UUU|C Chain C, Alkyldihydroxyacetonephosphate Synthase In P212121
pdb|2UUU|D Chain D, Alkyldihydroxyacetonephosphate Synthase In P212121
pdb|2UUV|A Chain A, Alkyldihydroxyacetonephosphate Synthase In P1
pdb|2UUV|B Chain B, Alkyldihydroxyacetonephosphate Synthase In P1
pdb|2UUV|C Chain C, Alkyldihydroxyacetonephosphate Synthase In P1
pdb|2UUV|D Chain D, Alkyldihydroxyacetonephosphate Synthase In P1
Length = 584
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 13/87 (14%)
Query: 438 KPTKG-----VSEIVNKFQDMEFTCEYK--------YDGERAQIHYLEDGSVEIYSRNAE 484
KP+KG S +V K+ + ++K ++G + + + +I S+NA
Sbjct: 363 KPSKGAVSEFTSAMVKKYLHYIRSFDFKNVCLSIIGFEGPKKVVDFHRTSVFDILSKNAA 422
Query: 485 RNTGKFPDVVLAVSRLKKPSVRSFVLD 511
G P A R P +R F+LD
Sbjct: 423 FGLGSAPGKTWAEKRYDLPYIRDFLLD 449
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
0.317 0.133 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,896,253
Number of Sequences: 62578
Number of extensions: 837299
Number of successful extensions: 1976
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1923
Number of HSP's gapped (non-prelim): 16
length of query: 768
length of database: 14,973,337
effective HSP length: 106
effective length of query: 662
effective length of database: 8,340,069
effective search space: 5521125678
effective search space used: 5521125678
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)