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= 006003
(665 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 157 bits (398), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 92/213 (43%), Positives = 137/213 (64%), Gaps = 17/213 (7%)
Query: 12 LVSLFNWIQKTKPAAKKRSKFRKFLDT-----------YCDSVD-YFSALRLILPSLDRE 59
L S IQK+K A+K FR+FLD+ + D D ++ A+RLILP L+RE
Sbjct: 19 LCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKDVTDSFYPAMRLILPQLERE 78
Query: 60 RGSYGLKESVLANCLIDALGMSKDSADAVRLINWRK-GGAAPNAGNFPMVAAEVLQRRQG 118
R +YG+KE++LA I+ L + +D DA++L+N+R G +AG+F M+A VL+ R
Sbjct: 79 RMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTHGDAGDFAMIAYFVLKPR-C 137
Query: 119 MISGGLTIKELNDLLDRLASSENRAEKISV---LSTLIKKTNAQEMKWIIMIILKDLKLG 175
+ G LTI+++NDLLD +AS+ + K + L LI +++A E KW+I +I+KDLKLG
Sbjct: 138 LQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSSALEQKWLIRMIIKDLKLG 197
Query: 176 ISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKD 208
+S+++IF FH DA +L NVT DL+ VC +L D
Sbjct: 198 VSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHD 230
>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 = 139 bits (351), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 131/507 (25%), Positives = 231/507 (45%), Gaps = 69/507 (13%)
Query: 124 LTIKELNDLLDRLASSE---NRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKS 180
LT+ E+ L ++A + +R KI +L+ L+KK + E K+++ + L++GI + +
Sbjct: 139 LTVDEVYSTLSKVALTTGEGSRDLKIRLLAGLLKKADPLEAKFLVRFVEGRLRVGIGDAT 198
Query: 181 IFHEF----------HPDAEDLFNVTCDL----KLVCEKLKDRNQRHKRQDIEVGKAVRP 226
+ E +N+ DL K++ EK + + K Q VG +RP
Sbjct: 199 VLDAMAIAFGGGQSASEIIERAYNLRADLGNIAKIIVEKGIEALKTLKPQ---VGIPIRP 255
Query: 227 QLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSK 286
LA R+ + +K+ G +V + K+DG+R QIHK +I FSR + + +
Sbjct: 256 MLAERLSNPEEILKKMGGNAIV-DYKYDGERAQIHKKEDKIFIFSRRLENITSQYPDVVD 314
Query: 287 IIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDG----LSSDRQLCYFAFD 342
+ + + I++GE++ D F QE+ R + + F FD
Sbjct: 315 YVSKYIEGKEFIIEGEIVAIDPESGEMRPF---QELMHRKRKSDIYEAIKEYPVNVFLFD 371
Query: 343 VLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNV 402
++Y D + L+ R +LL+ +VKP N +V+ + A+NV
Sbjct: 372 LMYYEDVDYTTKPLEARRKLLESIVKP--------------NDYVK----IAHHIQANNV 413
Query: 403 DEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEYIRAGSD-LDVLIIXX 459
++++ FF I EG+++K +G + ++ G R W+KLK +Y +D +D++++
Sbjct: 414 EDLKSFFYRAISEGGEGVMVKAIGKDAIYQAGARGWLWIKLKRDYQSEMADTVDLVVVGG 473
Query: 460 XXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKY 519
+++ L+A A P D+ F S C+V +G SDE+LD + KL R
Sbjct: 474 FYGKGKRGGKISSLLMA-AYNPKTDS----FESVCKVASGFSDEQLDELQKKLMEIKRDV 528
Query: 520 EYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILS---ITSDIRTIRSEVFS--APYSLR 574
++P+ NSK PD+W+E + I+ S + T +V A S+R
Sbjct: 529 KHPRV----------NSKMEPDIWVEPVYVAEIIGSEITISPLHTCCQDVVEKDAGLSIR 578
Query: 575 FPRIDRVRYDKPWHDCLDVQSFVELVH 601
FPR R R DK D +E+ +
Sbjct: 579 FPRFIRWRDDKSPEDATTTDEILEMYN 605
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic
Switching Between Two Dna Bound States
Length = 579
Score = 133 bits (334), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 131/496 (26%), Positives = 216/496 (43%), Gaps = 51/496 (10%)
Query: 124 LTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFH 183
LTI+E+++ L RL+ E+ L + + A ++K II +I DLK+ K +
Sbjct: 118 LTIQEVDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLD 177
Query: 184 EFHPDAEDLFNVTCDLKLVCEKLKDRNQR-----HKRQDIEVGKA----VRPQLAMRIGD 234
P+A + F + +L+ V E++ Q +R+ + V + V+P LA
Sbjct: 178 ALDPNAYEAFKASRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKS 237
Query: 235 AHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSF---LDHSEYGHAMSKIIEQN 291
A +K + E K+DG+R+Q+HKNG YFSRS L H + H I +
Sbjct: 238 VEYAMKKCPNG-MFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPH-KVAHFKDYIPQAF 295
Query: 292 VLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSV 351
ILD E+L+ D + FG+ KAA D +C F FD +Y D S+
Sbjct: 296 PGGHSMILDSEVLLIDNKTGKPLPFGTLGVHKKAA----FQDANVCLFVFDCIYFNDVSL 351
Query: 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKE 411
+ + L ER + L + +P+ + S ++ V +D +
Sbjct: 352 MDRPLCERRKFLHDNM--------VEIPNRIMFSEMK--------RVTKALD-LADMITR 394
Query: 412 TIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGS---DLDVLIIXXXXXXXXXXX 468
I+ EG+VLKD+ +EPG R WLK+K +Y+ G+ D++++
Sbjct: 395 VIQEGLEGLVLKDVKGTYEPGKRH--WLKVKKDYLNEGAMADTADLVVLGAFYGQGSKGG 452
Query: 469 EVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528
++ FL+ D +++ + + G D L + +L K PS
Sbjct: 453 MMSIFLMGCY-----DPGSQKWCTVTKCAGGHDDATLARLQNELD--MVKISKDPSKIPS 505
Query: 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAP-YSLRFPRIDRVRYDKPW 587
+ +V N PD + P+K+ + IT +SE +A S+RFPR R+R DK W
Sbjct: 506 WLKV--NKIYYPDFIVPDPKKAAVWEITG-AEFSKSEAHTADGISIRFPRCTRIRDDKDW 562
Query: 588 HDCLDVQSFVELVHSS 603
++ EL S
Sbjct: 563 KSATNLPQLKELYQLS 578
>pdb|3RR5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sp. 1519
Length = 570
Score = 128 bits (322), Expect = 9e-30, Method: Compositional matrix adjust.
Identities = 128/505 (25%), Positives = 224/505 (44%), Gaps = 63/505 (12%)
Query: 108 VAAEVLQRRQ-GMISGGLTIKELNDLLDRLASSENRA---EKISVLSTLIKKTNAQEMKW 163
VA + +R+Q S LTIK + ++A + K+ L+ L +E K+
Sbjct: 105 VALALKKRKQKSFFSQPLTIKRVYSTFVKVAEASGEGSQDRKMKYLANLFMDAQPEEGKY 164
Query: 164 IIMIILKDLKLGISEK----SIFHEFH--PD-AEDLFNVTCDLKLVCEKLK-DRNQRHKR 215
I +L ++ G++E +I F P+ E + +T D V + K + N+ +
Sbjct: 165 IARTVLGTMRTGVAEGILRDAIAEAFRVKPELVERAYMLTSDFGYVAKVAKLEGNEGLSK 224
Query: 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFL 275
I++GK +RP LA A ++ G E E K+DG R+Q+H++G + +SR
Sbjct: 225 VSIQIGKPIRPMLAQNAASVKEALIEMGG-EAAFEIKYDGARVQVHRDGDRVIIYSRRLE 283
Query: 276 DHSEYGHAMSKIIEQNVLVDRCILDGEML-VWDTSLNRFAEFGSNQEIAKAARDGLSSDR 334
+ + + + ++ ++ + I++GE++ V + R ++ + K D +
Sbjct: 284 NVTRSIPEIVEAVKASLKPSKVIVEGELVAVGENGRPRPFQYVLRRFRRKYNIDEMIEKI 343
Query: 335 QLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPC 394
L FD+LYV S+I ER + L++ V+ S+ + +
Sbjct: 344 PLELNLFDILYVDGESLIDTEFVERRKRLEESVEESE------------------KIKIA 385
Query: 395 WSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDV 454
LV V+E E F+K +E EG++ K L S +EPG+R KWLK+KP +LD+
Sbjct: 386 EQLVTKKVEEAEAFYKRALELGHEGLMAKRLDSVYEPGNRGKKWLKIKPTM----ENLDL 441
Query: 455 LIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKP 514
+II + FLVA + PD+ F+ +VG+G +DE+L LKP
Sbjct: 442 VIIGAEWGEGRRAHLLGSFLVAAYD---PDS--GEFLPVGKVGSGFTDEDLVEFTKMLKP 496
Query: 515 YFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLR 574
+ E F ++ P V IE + I +S + + ++LR
Sbjct: 497 LILREE------GKFVEI------EPKVVIEVTYQEI----------QKSPKYRSGFALR 534
Query: 575 FPRIDRVRYDKPWHDCLDVQSFVEL 599
FPR +R DK + ++ +L
Sbjct: 535 FPRYVALREDKSPEEADTIERIAQL 559
>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus
Length = 571
Score = 127 bits (318), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 131/552 (23%), Positives = 248/552 (44%), Gaps = 78/552 (14%)
Query: 64 GLKESVLANCLIDALGM-SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ--GMI 120
G+ E +L + A G+ S++ ++VR + G+ A L +R+
Sbjct: 71 GIGEKLLIKAVSMATGINSEEIENSVR-----------DTGDLGESIALALNKRKQKSFF 119
Query: 121 SGGLTIKELNDLLDRLASSENRAE---KISVLSTLIKKTNAQEMKWIIMIILKDLKLGIS 177
S LTI+ + + L ++A + K+ L+ L + E K++ +L ++ G++
Sbjct: 120 SQPLTIERVYNTLVKIAEASGAGSQDRKLKYLANLFMDASPDEGKYLARTVLGIMRTGVA 179
Query: 178 EKSIFHEFHPDA--------EDLFNVTCDLKLVCEKLK-DRNQRHKRQDIEVGKAVRPQL 228
E + + DA E + +T D V + K + ++ + I+VGK ++P L
Sbjct: 180 E-GLLRDALADAFKVRVELVERAYMLTSDFGFVAKVAKLEGDEGLAKVKIQVGKPIKPML 238
Query: 229 AMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKII 288
A + A ++ G E E K+DG R+Q+HKNG+++ +SR + ++ + + +
Sbjct: 239 AQMAANVREALVEMGG-EAEFEIKYDGARVQVHKNGNKVLIYSRRLENVTKSIPEVVERV 297
Query: 289 EQNVLVDRCILDGEML-VWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVG 347
++ + ++ I++GE++ V +T R ++ + K + + L FD+LYV
Sbjct: 298 KEALKPEKVIVEGELVAVEETGRPRPFQYVLRRFRRKYNIEEMIEKIPLELNLFDILYVD 357
Query: 348 DTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEK 407
++I ER ++L+ VV N ++ +L+ + +E E
Sbjct: 358 GQNMIDTPFMERRKVLESVVNS--------------NEWIKS----AENLITKSPEEAEA 399
Query: 408 FFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIXXXXXXXXXX 467
F+ + ++ EG++ K L S +EPG+R KWLK+KP +LD++++
Sbjct: 400 FYHKALDLGHEGLMAKRLDSTYEPGNRGKKWLKIKPTM----ENLDLVVLGAEWGEGRRS 455
Query: 468 XEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP 527
++ FL+ A D F+ +VG+G +DE+L LKP +K
Sbjct: 456 GVLSSFLLG-----AYDPVKGDFVPVGKVGSGFTDEDLVEFTKMLKPLIKK--------- 501
Query: 528 SFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPW 587
+ KE +E K +I +I+ +S + + ++LRFPR +R DK
Sbjct: 502 ------EHGKE-----VELEPKVVIEVAYQEIQ--KSPKYESGFALRFPRYIALREDKGP 548
Query: 588 HDCLDVQSFVEL 599
D VQ EL
Sbjct: 549 EDADTVQRLAEL 560
>pdb|2CFM|A Chain A, Atp-Dependent Dna Ligase From Pyrococcus Furiosus
Length = 561
Score = 125 bits (315), Expect = 6e-29, Method: Compositional matrix adjust.
Identities = 121/496 (24%), Positives = 216/496 (43%), Gaps = 78/496 (15%)
Query: 124 LTIKELNDLLDRLASSENRA---EKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISE-- 178
LTIK + L ++A + +K+ L+ L E K++ IL + G++E
Sbjct: 111 LTIKRVYQTLVKVAETTGEGSQDKKVKYLADLFXDAEPLEAKYLARTILGTXRTGVAEGL 170
Query: 179 --KSIFHEFHPDAEDL---FNVTCDLKLVCEKLK-DRNQRHKRQDIEVGKAVRPQLAMRI 232
+I FH E + + +T D V + K + N+ + +++GK ++P LA +
Sbjct: 171 LRDAIAXAFHVKVELVERAYXLTSDFGYVAKIAKLEGNEGLAKVQVQLGKPIKPXLAQQA 230
Query: 233 GDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNV 292
A + G E E K+DG R+Q+HK+GS+I +SR + + + + +++ +
Sbjct: 231 ASIRDALLEXGG-EAEFEIKYDGARVQVHKDGSKIIVYSRRLENVTRAIPEIVEALKEAI 289
Query: 293 LVDRCILDGEM---------LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDV 343
+ ++ I++GE+ L + L RF + +E + L FDV
Sbjct: 290 IPEKAIVEGELVAIGENGRPLPFQYVLRRFRRKHNIEEXXEKI--------PLELNLFDV 341
Query: 344 LYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVD 403
LYV S+I +R L++++K N ++ +L+ V+
Sbjct: 342 LYVDGQSLIDTKFIDRRRTLEEIIKQ--------------NEKIKV----AENLITKKVE 383
Query: 404 EVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIXXXXXX 463
E E F+K +E EG+ K L + +EPG+R KWLK+KP +LD++II
Sbjct: 384 EAEAFYKRALEXGHEGLXAKRLDAVYEPGNRGKKWLKIKP----TXENLDLVIIGAEWGE 439
Query: 464 XXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPK 523
F++ A D F+ +VG+G +D++L LKP K E +
Sbjct: 440 GRRAHLFGSFILG-----AYDPETGEFLEVGKVGSGFTDDDLVEFTKXLKPLIIKEEGKR 494
Query: 524 RAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRY 583
VW++ K +I +I+ +S + + ++LRFPR +R
Sbjct: 495 ------------------VWLQP--KVVIEVTYQEIQ--KSPKYRSGFALRFPRFVALRD 532
Query: 584 DKPWHDCLDVQSFVEL 599
DK D ++ +L
Sbjct: 533 DKGPEDADTIERIAQL 548
>pdb|1X9N|A Chain A, Crystal Structure Of Human Dna Ligase I Bound To
5'-Adenylated, Nicked Dna
Length = 688
Score = 113 bits (283), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 133/545 (24%), Positives = 221/545 (40%), Gaps = 96/545 (17%)
Query: 133 LDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIF---------- 182
+ RL S + A+KI ++ L E ++I + L+LG++E+S+
Sbjct: 180 IARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLT 239
Query: 183 ---HEFHPDAED--------------------LFNVTCD-------LKLVCEKLKDRNQR 212
EF P D L C+ + ++ E +R
Sbjct: 240 PPGQEFPPAXVDAGKGKTAEARKTWLEEQGXILKQTFCEVPDLDRIIPVLLEHGLERLPE 299
Query: 213 HKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFS 271
H + + G ++P LA ++ E K+DG R QIH G E+ FS
Sbjct: 300 HCK--LSPGIPLKPXLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFS 357
Query: 272 RSFLDHS-EYGHAMSKIIEQNVL-VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDG 329
R+ D++ +Y +S+I + + V ILD E + WD + F + D
Sbjct: 358 RNQEDNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDA 417
Query: 330 LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRP 389
Q+C +AFD++Y+ S++ + L R +LL++ + V
Sbjct: 418 SEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRE-------------------NFVET 458
Query: 390 QGEPCW--SLVAHNVDEVEKFFKETIENRDEGIVLK--DLGSKWEPGDRSGKWLKLKPEY 445
+GE + SL +++++ +F ++++++ EG+ +K D+ + +E RS WLKLK +Y
Sbjct: 459 EGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLXVKTLDVDATYEIAKRSHNWLKLKKDY 518
Query: 446 IRA-GSDLDVLIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEE 504
+ G LD+++I FL+A + D + C++GTG SDEE
Sbjct: 519 LDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLA-----SYDEDSEELQAICKLGTGFSDEE 573
Query: 505 LDAVVTKLK----PYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPE----KSIILSIT 556
L+ LK P R Y V + PD W++ K LS++
Sbjct: 574 LEEHHQSLKALVLPSPRPY------------VRIDGAVIPDHWLDPSAVWEVKCADLSLS 621
Query: 557 SDIRTIRSEVFS-APYSLRFPRIDRVRYDK-PWHDCLDVQSFVELVHSSNGTTQKGKEYG 614
R V S SLRFPR RVR DK P Q S Q+G++ G
Sbjct: 622 PIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGEDSG 681
Query: 615 GLQDD 619
+D
Sbjct: 682 SDPED 686
>pdb|3GDE|A Chain A, The Closed Conformation Of Atp-Dependent Dna Ligase From
Archaeoglobus Fulgidus
Length = 558
Score = 95.9 bits (237), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 122/506 (24%), Positives = 219/506 (43%), Gaps = 86/506 (16%)
Query: 103 GNFPMVAAEVLQRRQ--GMISGGLTIKELNDLLDRLASSENRA---EKISVLSTLIKKTN 157
G+ +VA +++++++ + LT++++ + D +AS KI +L+ L
Sbjct: 92 GDLGLVAEQLIKKKKMTTLAFEELTVRKVRETFDEIASLTGEGSMKRKIMLLTGLYGLAT 151
Query: 158 AQEMKWIIMIILKDLKLGISE----KSIFHEFHPDAEDL---FNVTCDLKLVCEKLKDRN 210
E +++ +IL +++LG+ E +I F D E + + +T DL V K
Sbjct: 152 PLEARYLTRLILNEMRLGVGEGIMRDAIARAFRADPETVERAYMITNDLGRVAVVAKKEG 211
Query: 211 QRHKRQ-DIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHY 269
+ R+ IE+ VR LA +A R++ + +E KFDG R+Q+H +GS +
Sbjct: 212 EEGLRKMKIEIHIPVRMMLAQVAESLESAVREM--RTAAVEWKFDGSRVQVHWDGSRVTI 269
Query: 270 FSRSFLDHSEYGHAMSKIIEQ--NVLVDRCILDGEMLV--------WDTSLNRFAEFGSN 319
+SR + + +A+ I+E+ + ILDGE++ + L RF
Sbjct: 270 YSRRLENVT---NALPDIVEEIKKSVKPGVILDGEVIAVKEGKPMPFQHVLRRFR---RK 323
Query: 320 QEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP 379
++AK + L FD+LY D I L+ER +LL+ V S+
Sbjct: 324 HDVAK-----MVEKIPLEAHFFDILY-HDGECIDLPLRERRKLLESAVNESE-------- 369
Query: 380 DHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWL 439
+ + +V +VDEV K + E I EG+++K S + PG R WL
Sbjct: 370 ----------KIKLAKQIVTDSVDEVRKMYDEAISAGHEGVMIKLPSSPYIPGKRGKNWL 419
Query: 440 KLKPEYIRAGSDLDVLIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTG 499
K+K LD++++ ++ F +A D + + RV TG
Sbjct: 420 KVKA----IMETLDLVVVGGEWGEGKRSHWLSSFELACL-----DPVTGKLLKVGRVATG 470
Query: 500 LSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDI 559
++E+L+ + +P V+ K+ +E K + +I
Sbjct: 471 FTEEDLEELTEMFRPLI---------------VSQQGKK-----VEFIPKYVFEVAYQEI 510
Query: 560 RTIRSEVFSAPYSLRFPRIDRVRYDK 585
+ +S + + Y+LRFPR R+R DK
Sbjct: 511 Q--KSPKYESGYALRFPRFVRLRDDK 534
>pdb|3VNN|A Chain A, Crystal Structure Of A Sub-Domain Of The
Nucleotidyltransferase (Adenylation) Domain Of Human Dna
Ligase Iv
Length = 139
Score = 87.4 bits (215), Expect = 2e-17, Method: Composition-based stats.
Identities = 47/137 (34%), Positives = 79/137 (57%), Gaps = 11/137 (8%)
Query: 249 IECKFDGDRIQIHKNGSEIHYFSRSFLDHS-EYGHA-----MSKIIEQNVLVDR--CILD 300
IE K DG+R+Q+HK+G YFSR+ +++ ++G + ++ I D CILD
Sbjct: 3 IETKLDGERMQMHKDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQICILD 62
Query: 301 GEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERH 360
GEM+ ++ + F + G+ +I + D SD Q CY FDVL V + + H++L++R+
Sbjct: 63 GEMMAYNPNTQTFMQKGTKFDIKRMVED---SDLQTCYCVFDVLMVNNKKLGHETLRKRY 119
Query: 361 ELLQKVVKPSKGRLETL 377
E+L + P GR+E +
Sbjct: 120 EILSSIFTPIPGRIEIV 136
>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 = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 62/281 (22%), Positives = 112/281 (39%), Gaps = 50/281 (17%)
Query: 236 HAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLD-HSEYGHAMSKIIEQNVLV 294
H L + E +DG R+ + + + SRS D +EY + + +++
Sbjct: 16 HGTVAGLKASQWAFEGXWDGYRLLVEADHGAVRLRSRSGRDVTAEY--PQLRALAEDLAD 73
Query: 295 DRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQ 354
+LDGE +V D+S F Q + D ++ ++AFD+LY+ +++
Sbjct: 74 HHVVLDGEAVVLDSS--GVPSFSQXQNRGR--------DTRVEFWAFDLLYLDGRALLGT 123
Query: 355 SLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE 414
++R +LL+ + + + L+P G + F + +
Sbjct: 124 RYQDRRKLLETLANATSLTVPELLPGDGAQA-----------------------FACSRK 160
Query: 415 NRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIXXXXXXXXXXXEVAQFL 474
+ EG++ K S+++PG R W+K K + +V+I V L
Sbjct: 161 HGWEGVIAKRRDSRYQPGRRCASWVKDKHWNTQ-----EVVIGGWRAGEGGRSSGVGSLL 215
Query: 475 VALAERPAPDTYPRRFISFC-RVGTGLSDEELDAVVTKLKP 514
+ P P + F RVGTGLS+ EL + L P
Sbjct: 216 XGI---PGPGG-----LQFAGRVGTGLSERELANLKEXLAP 248
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
0.319 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,482,681
Number of Sequences: 62578
Number of extensions: 809668
Number of successful extensions: 1994
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1941
Number of HSP's gapped (non-prelim): 15
length of query: 665
length of database: 14,973,337
effective HSP length: 105
effective length of query: 560
effective length of database: 8,402,647
effective search space: 4705482320
effective search space used: 4705482320
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)