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= 001083
(1160 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 = 158 bits (399), Expect = 2e-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 (350), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 138/509 (27%), Positives = 236/509 (46%), Gaps = 76/509 (14%)
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 QLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLD-HSEYGHA-- 283
LA R+ + +K+ G +V + K+DG+R QIHK +I FSR + S+Y
Sbjct: 256 MLAERLSNPEEILKKMGGNAIV-DYKYDGERAQIHKKEDKIFIFSRRLENITSQYPDVVD 314
Query: 284 -MSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAAR--DGLSSDRQV-LCY 339
+SK IE I++GE++ D F QE+ R D + ++ +
Sbjct: 315 YVSKYIEGK----EFIIEGEIVAIDPESGEMRPF---QELMHRKRKSDIYEAIKEYPVNV 367
Query: 340 FAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLV 399
F FD++Y D + L+ R +LL+ +VKP N +V+ +
Sbjct: 368 FLFDLMYYEDVDYTTKPLEARRKLLESIVKP--------------NDYVK----IAHHIQ 409
Query: 400 AHNVDEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEYIRAGSD-LDVL 456
A+NV++++ FF I EG+++K +G + ++ G R W+KLK +Y +D +D++
Sbjct: 410 ANNVEDLKSFFYRAISEGGEGVMVKAIGKDAIYQAGARGWLWIKLKRDYQSEMADTVDLV 469
Query: 457 IIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPY 516
++ +++ L+A A P D+ F S C+V +G SDE+LD + KL
Sbjct: 470 VVGGFYGKGKRGGKISSLLMA-AYNPKTDS----FESVCKVASGFSDEQLDELQKKLMEI 524
Query: 517 FRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILS---ITSDIRTIRSEVFS--AP 571
R ++P+ NSK PD+W+E + I+ S + T +V A
Sbjct: 525 KRDVKHPR----------VNSKMEPDIWVEPVYVAEIIGSEITISPLHTCCQDVVEKDAG 574
Query: 572 YSLRFPRIDRVRYDKPWHDCLDVQSFVEL 600
S+RFPR R R DK D +E+
Sbjct: 575 LSIRFPRFIRWRDDKSPEDATTTDEILEM 603
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic
Switching Between Two Dna Bound States
Length = 579
Score = 129 bits (325), Expect = 8e-30, Method: Compositional matrix adjust.
Identities = 130/497 (26%), Positives = 216/497 (43%), Gaps = 52/497 (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 VLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTS 351
ILD E+L+ D + FG+ KAA + +C F FD +Y D S
Sbjct: 296 PGGHSMILDSEVLLIDNKTGKPLPFGTLGVHKKAAFQDAN-----VCLFVFDCIYFNDVS 350
Query: 352 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFK 411
++ + L ER + L + +P+ + S ++ V +D +
Sbjct: 351 LMDRPLCERRKFLHDNM--------VEIPNRIMFSEMK--------RVTKALD-LADMIT 393
Query: 412 ETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGS---DLDVLIIXXXXXXXXXX 468
I+ EG+VLKD+ +EPG R WLK+K +Y+ G+ D++++
Sbjct: 394 RVIQEGLEGLVLKDVKGTYEPGKRH--WLKVKKDYLNEGAMADTADLVVLGAFYGQGSKG 451
Query: 469 XEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP 528
++ FL+ D +++ + + G D L + +L K P
Sbjct: 452 GMMSIFLMGCY-----DPGSQKWCTVTKCAGGHDDATLARLQNELD--MVKISKDPSKIP 504
Query: 529 SFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-PYSLRFPRIDRVRYDKP 587
S+ +V N PD + P+K+ + IT +SE +A S+RFPR R+R DK
Sbjct: 505 SWLKV--NKIYYPDFIVPDPKKAAVWEITG-AEFSKSEAHTADGISIRFPRCTRIRDDKD 561
Query: 588 WHDCLDVQSFVELVHSS 604
W ++ EL S
Sbjct: 562 WKSATNLPQLKELYQLS 578
>pdb|3RR5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sp. 1519
Length = 570
Score = 127 bits (319), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 129/509 (25%), Positives = 225/509 (44%), Gaps = 70/509 (13%)
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 DHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQ 335
+ + + + ++ ++ + I++GE++ + R F Q + + R + D
Sbjct: 284 NVTRSIPEIVEAVKASLKPSKVIVEGELVAVGEN-GRPRPF---QYVLRRFRRKYNIDEM 339
Query: 336 V----LCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQ 391
+ L FD+LYV S+I ER + L++ V+ S+ +
Sbjct: 340 IEKIPLELNLFDILYVDGESLIDTEFVERRKRLEESVEESE------------------K 381
Query: 392 GEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGS 451
+ LV V+E E F+K +E EG++ K L S +EPG+R KWLK+KP
Sbjct: 382 IKIAEQLVTKKVEEAEAFYKRALELGHEGLMAKRLDSVYEPGNRGKKWLKIKPTM----E 437
Query: 452 DLDVLIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVT 511
+LD++II + FLVA + PD+ F+ +VG+G +DE+L
Sbjct: 438 NLDLVIIGAEWGEGRRAHLLGSFLVAAYD---PDS--GEFLPVGKVGSGFTDEDLVEFTK 492
Query: 512 KLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAP 571
LKP + E F ++ P V IE + I +S + +
Sbjct: 493 MLKPLILREE------GKFVEI------EPKVVIEVTYQEI----------QKSPKYRSG 530
Query: 572 YSLRFPRIDRVRYDKPWHDCLDVQSFVEL 600
++LRFPR +R DK + ++ +L
Sbjct: 531 FALRFPRYVALREDKSPEEADTIERIAQL 559
>pdb|2CFM|A Chain A, Atp-Dependent Dna Ligase From Pyrococcus Furiosus
Length = 561
Score = 127 bits (318), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 121/497 (24%), Positives = 217/497 (43%), Gaps = 79/497 (15%)
Query: 124 LTIKELNDLLDRLASSENRA---EKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEK- 179
LTIK + L ++A + +K+ L+ L E K++ IL + G++E
Sbjct: 111 LTIKRVYQTLVKVAETTGEGSQDKKVKYLADLFXDAEPLEAKYLARTILGTXRTGVAEGL 170
Query: 180 ---SIFHEFHPDAEDL---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 ASIRDALLE-XGGEAEFEIKYDGARVQVHKDGSKIIVYSRRLENVTRAIPEIVEALKEAI 289
Query: 293 LVDRCILDGEM---------LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFD 343
+ ++ I++GE+ L + L RF + +E ++ L FD
Sbjct: 290 IPEKAIVEGELVAIGENGRPLPFQYVLRRFRRKHNIEE---------XXEKIPLELNLFD 340
Query: 344 VLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNV 403
VLYV S+I +R L++++K N ++ +L+ V
Sbjct: 341 VLYVDGQSLIDTKFIDRRRTLEEIIKQ--------------NEKIKV----AENLITKKV 382
Query: 404 DEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIXXXXX 463
+E E F+K +E EG+ K L + +EPG+R KWLK+KP +LD++II
Sbjct: 383 EEAEAFYKRALEXGHEGLXAKRLDAVYEPGNRGKKWLKIKP----TXENLDLVIIGAEWG 438
Query: 464 XXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYP 523
F++ A D F+ +VG+G +D++L LKP K E
Sbjct: 439 EGRRAHLFGSFILG-----AYDPETGEFLEVGKVGSGFTDDDLVEFTKXLKPLIIKEEGK 493
Query: 524 KRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 583
+ VW++ K +I +I+ +S + + ++LRFPR +R
Sbjct: 494 R------------------VWLQP--KVVIEVTYQEIQ--KSPKYRSGFALRFPRFVALR 531
Query: 584 YDKPWHDCLDVQSFVEL 600
DK D ++ +L
Sbjct: 532 DDKGPEDADTIERIAQL 548
>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus
Length = 571
Score = 124 bits (312), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 131/556 (23%), Positives = 249/556 (44%), Gaps = 85/556 (15%)
Query: 64 GLKESVLANCLIDALGM-SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ--GMI 120
G+ E +L + A G+ S++ ++VR + G+ A L +R+
Sbjct: 71 GIGEKLLIKAVSMATGINSEEIENSVR-----------DTGDLGESIALALNKRKQKSFF 119
Query: 121 SGGLTIKELNDLLDRLASSENRA---EKISVLSTLIKKTNAQEMKWIIMIILKDLKLGIS 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 EQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQV----LCYFAFDV 344
++ + ++ I++GE++ + + R F Q + + R + + + L FD+
Sbjct: 298 KEALKPEKVIVEGELVAVEET-GRPRPF---QYVLRRFRRKYNIEEMIEKIPLELNLFDI 353
Query: 345 LYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVD 404
LYV ++I ER ++L+ VV N ++ +L+ + +
Sbjct: 354 LYVDGQNMIDTPFMERRKVLESVVNS--------------NEWIKS----AENLITKSPE 395
Query: 405 EVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIXXXXXX 464
E E F+ + ++ EG++ K L S +EPG+R KWLK+KP +LD++++
Sbjct: 396 EAEAFYHKALDLGHEGLMAKRLDSTYEPGNRGKKWLKIKPTM----ENLDLVVLGAEWGE 451
Query: 465 XXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPK 524
++ FL+ A D F+ +VG+G +DE+L LKP +K
Sbjct: 452 GRRSGVLSSFLLG-----AYDPVKGDFVPVGKVGSGFTDEDLVEFTKMLKPLIKK----- 501
Query: 525 RAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRY 584
+ KE +E K +I +I+ +S + + ++LRFPR +R
Sbjct: 502 ----------EHGKE-----VELEPKVVIEVAYQEIQ--KSPKYESGFALRFPRYIALRE 544
Query: 585 DKPWHDCLDVQSFVEL 600
DK D VQ EL
Sbjct: 545 DKGPEDADTVQRLAEL 560
>pdb|1X9N|A Chain A, Crystal Structure Of Human Dna Ligase I Bound To
5'-Adenylated, Nicked Dna
Length = 688
Score = 110 bits (276), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 136/548 (24%), Positives = 227/548 (41%), Gaps = 101/548 (18%)
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 Q + R
Sbjct: 358 RNQEDNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPF---QVLTTRKRKE 414
Query: 330 L-SSDRQV-LCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSH 387
+ +S+ QV +C +AFD++Y+ S++ + L R +LL++ +
Sbjct: 415 VDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRE-------------------NF 455
Query: 388 VRPQGEPCW--SLVAHNVDEVEKFFKETIENRDEGIVLK--DLGSKWEPGDRSGKWLKLK 443
V +GE + SL +++++ +F ++++++ EG+ +K D+ + +E RS WLKLK
Sbjct: 456 VETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLXVKTLDVDATYEIAKRSHNWLKLK 515
Query: 444 PEYIRA-GSDLDVLIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLS 502
+Y+ G LD+++I FL+A + D + C++GTG S
Sbjct: 516 KDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLA-----SYDEDSEELQAICKLGTGFS 570
Query: 503 DEELDAVVTKLK----PYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPE----KSIIL 554
DEEL+ LK P R Y V + PD W++ K L
Sbjct: 571 DEELEEHHQSLKALVLPSPRPY------------VRIDGAVIPDHWLDPSAVWEVKCADL 618
Query: 555 SITSDIRTIRSEVFS-APYSLRFPRIDRVRYDK-PWHDCLDVQSFVELVHSSNGTTQKGK 612
S++ R V S SLRFPR RVR DK P Q S Q+G+
Sbjct: 619 SLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGE 678
Query: 613 EYGGLQDD 620
+ G +D
Sbjct: 679 DSGSDPED 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 = 1e-19, Method: Compositional matrix adjust.
Identities = 122/512 (23%), Positives = 220/512 (42%), Gaps = 97/512 (18%)
Query: 103 GNFPMVAAEVLQRRQ--GMISGGLTIKELNDLLDRLASSENRA---EKISVLSTLIKKTN 157
G+ +VA +++++++ + LT++++ + D +AS KI +L+ L
Sbjct: 92 GDLGLVAEQLIKKKKMTTLAFEELTVRKVRETFDEIASLTGEGSMKRKIMLLTGLYGLAT 151
Query: 158 AQEMKWIIMIILKDLKLGISEK----SIFHEFHPDAEDL---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---NALPDIVEEIKKSVKPGVILDGEVIAVKEGKPMPFQHVLRRFRR---K 323
Query: 320 QEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLV 379
++AK ++ L FD+LY D I L+ER +LL+ V S+
Sbjct: 324 HDVAKMV------EKIPLEAHFFDILY-HDGECIDLPLRERRKLLESAVNESE------- 369
Query: 380 PDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKW 439
+ + +V +VDEV K + E I EG+++K S + PG R W
Sbjct: 370 -----------KIKLAKQIVTDSVDEVRKMYDEAISAGHEGVMIKLPSSPYIPGKRGKNW 418
Query: 440 LKLKPEYIRAGSDLDVLIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGT 499
LK+K LD++++ ++ F +A D + + RV T
Sbjct: 419 LKVKA----IMETLDLVVVGGEWGEGKRSHWLSSFELACL-----DPVTGKLLKVGRVAT 469
Query: 500 GLSDEELDAVVTKLKPYF-----RKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 554
G ++E+L+ + +P +K E+ P ++V ++ SP+
Sbjct: 470 GFTEEDLEELTEMFRPLIVSQQGKKVEF---IPKYVFEVAYQEIQK------SPK----- 515
Query: 555 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 586
+ + Y+LRFPR R+R DK
Sbjct: 516 -------------YESGYALRFPRFVRLRDDK 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 = 82.0 bits (201), Expect = 2e-15, Method: Composition-based stats.
Identities = 47/138 (34%), Positives = 79/138 (57%), Gaps = 12/138 (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 GEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKER 360
GEM+ ++ + F + G+ +I + D SD Q CY FDVL V + + H++L++R
Sbjct: 63 GEMMAYNPNTQTFMQKGTKFDIKRMVED---SDLQT-CYCVFDVLMVNNKKLGHETLRKR 118
Query: 361 HELLQKVVKPSKGRLETL 378
+E+L + P GR+E +
Sbjct: 119 YEILSSIFTPIPGRIEIV 136
>pdb|3II6|X Chain X, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv.
pdb|3II6|Y Chain Y, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv
Length = 263
Score = 62.4 bits (150), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 60/267 (22%), Positives = 109/267 (40%), Gaps = 25/267 (9%)
Query: 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYE--AA 712
++IF D+ F ++ + L + E GG N T+CV A ++ ++ +
Sbjct: 8 SNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPD-TYCVIAGSENIRVKNIIL 66
Query: 713 KRRGDVIHYSWVLDCCSXXXXXXXXXXYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADI 772
+ DV+ +W+L+C + +H+ S+K+ E D + D YF D DL +
Sbjct: 67 SNKHDVVKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQL 126
Query: 773 KQLLSNVDRSED--PKTIDYYKKKYCPQDKWSC-----FHGCCIYF--YHSTEPLSPDWE 823
K++ S + S + P+ + + W C F +Y Y LS E
Sbjct: 127 KEVFSGIKNSNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVINDLSTKNE 186
Query: 824 VXXXXXXXXXXXEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLW 882
E+ FHG KV + LA +HV++ +F + +F
Sbjct: 187 ---GTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTF--------- 234
Query: 883 NKKLHVVRSQWLEDCLAKEQKSEEYEY 909
+K +++ W+ D + K + EE +Y
Sbjct: 235 KRKFKILKESWVTDSIDKCELQEENQY 261
>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 = 47.4 bits (111), Expect = 5e-05, Method: Composition-based stats.
Identities = 64/284 (22%), Positives = 110/284 (38%), Gaps = 55/284 (19%)
Query: 236 HAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLD-HSEYGHAMSKIIEQNVLV 294
H L + E +DG R+ + + + SRS D +EY + + +++
Sbjct: 16 HGTVAGLKASQWAFEGXWDGYRLLVEADHGAVRLRSRSGRDVTAEYPQL--RALAEDLAD 73
Query: 295 DRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIH 354
+LDGE +V D+S F Q + R + ++AFD+LY+ +++
Sbjct: 74 HHVVLDGEAVVLDSS--GVPSFSQXQNRGRDTR---------VEFWAFDLLYLDGRALLG 122
Query: 355 QSLKERHELLQKVVKPSKGRLETLVPDHGLNSHV--RPQGEPCWSLVAHNVDEVEKFFKE 412
++R +LL+ + + + L+P G + R G W
Sbjct: 123 TRYQDRRKLLETLANATSLTVPELLPGDGAQAFACSRKHG---W---------------- 163
Query: 413 TIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIXXXXXXXXXXXEVA 472
EG++ K S+++PG R W+K K + +V+I V
Sbjct: 164 ------EGVIAKRRDSRYQPGRRCASWVKDK-----HWNTQEVVIGGWRAGEGGRSSGVG 212
Query: 473 QFLVALAERPAPDTYPRRFISFC-RVGTGLSDEELDAVVTKLKP 515
L + P P + F RVGTGLS+ EL + L P
Sbjct: 213 SLLXGI---PGPGG-----LQFAGRVGTGLSERELANLKEXLAP 248
>pdb|2E2W|A Chain A, Solution Structure Of The First Brct Domain Of Human Dna
Ligase Iv
Length = 113
Score = 35.0 bits (79), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 23/105 (21%), Positives = 46/105 (43%), Gaps = 3/105 (2%)
Query: 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYE--AA 712
++IF D+ F ++ + L + E GG N T+CV A ++ ++ +
Sbjct: 10 SNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPD-TYCVIAGSENIRVKNIIL 68
Query: 713 KRRGDVIHYSWVLDCCSXXXXXXXXXXYYLHLSDSSKKKLQEEVD 757
+ DV+ +W+L+C + +H+ S+K+ E D
Sbjct: 69 SNKHDVVKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYD 113
>pdb|1Z56|C Chain C, Co-Crystal Structure Of Lif1p-Lig4p
Length = 264
Score = 34.3 bits (77), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 28/133 (21%), Positives = 53/133 (39%), Gaps = 29/133 (21%)
Query: 655 TSIFSDMVFYFV------NVPPAYSLDSLHKMVVENGGTFSMNL--------------NN 694
++IF+ ++FY + + + L K +VE+GG N+
Sbjct: 3 SNIFAGLLFYVLSDYVTEDTGIRITRAELEKTIVEHGGKLIYNVILKRHSIGDVRLISCK 62
Query: 695 SVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSXXXXXXXXXXYYLHLSDSSKKKLQE 754
+ T C A ++G D++H +WVLDC + Y ++S + ++
Sbjct: 63 TTTECKALIDRGY---------DILHPNWVLDCIAYKRLILIEPNYCFNVSQKMRAVAEK 113
Query: 755 EVDEFSDLYFWDL 767
VD D + D+
Sbjct: 114 RVDCLGDSFENDI 126
>pdb|2XNK|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|B Chain B, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|C Chain C, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|D Chain D, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 292
Score = 33.1 bits (74), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 677 LHKMVVENGGTFSMNLN-NSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLD 726
+ ++ V++GG + L N TH + + KG KYE AKR + W D
Sbjct: 220 VQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFD 271
Score = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 675 DSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKY-EAAKRRGDVIHYSWV 724
+ +HK V GG +LN SVTH +A + KY AA + ++ SW+
Sbjct: 124 EEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWI 174
>pdb|3OLC|X Chain X, Crystal Structure Of The N-Terminal Region Of Topbp1
Length = 298
Score = 33.1 bits (74), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 677 LHKMVVENGGTFSMNLN-NSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLD 726
+ ++ V++GG + L N TH + + KG KYE AKR + W D
Sbjct: 218 VQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFD 269
Score = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 675 DSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKY-EAAKRRGDVIHYSWV 724
+ +HK V GG +LN SVTH +A + KY AA + ++ SW+
Sbjct: 122 EEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWI 172
>pdb|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 287
Score = 33.1 bits (74), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 677 LHKMVVENGGTFSMNLN-NSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLD 726
+ ++ V++GG + L N TH + + KG KYE AKR + W D
Sbjct: 218 VQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFD 269
Score = 32.0 bits (71), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 675 DSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKY-EAAKRRGDVIHYSWV 724
+ +HK V GG +LN SVTH +A + KY AA + ++ SW+
Sbjct: 122 EEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWI 172
>pdb|1WF6|A Chain A, The Third Brca1 C-Terminus (Brct) Domain Of Similar To
S.Pombe Rad4+CUT5+ PRODUCT
Length = 132
Score = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 35/86 (40%), Gaps = 4/86 (4%)
Query: 647 DVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD-NK 705
DVS + + Y LD L +++ GG LN VTH + D +
Sbjct: 30 DVSAFQAPEDLLDGCRIYLCGFS-GRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYDD 88
Query: 706 GLK--YEAAKRRGDVIHYSWVLDCCS 729
LK + + R V+ W+L+C S
Sbjct: 89 ELKQFWNKSAHRPHVVGAKWLLECFS 114
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 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,985,688
Number of Sequences: 62578
Number of extensions: 1277119
Number of successful extensions: 2939
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2873
Number of HSP's gapped (non-prelim): 34
length of query: 1160
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1051
effective length of database: 8,152,335
effective search space: 8568104085
effective search space used: 8568104085
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: 57 (26.6 bits)