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= 003386
(824 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 77.4 bits (189), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 61/209 (29%), Positives = 102/209 (48%), Gaps = 23/209 (11%)
Query: 64 AHNVDEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEYIRAGSD-LDVL 120
A+NV++++ FF I EG+++K +G + ++ G R W+KLK +Y +D +D++
Sbjct: 410 ANNVEDLKSFFYRAISEGGEGVMVKAIGKDAIYQAGARGWLWIKLKRDYQSEMADTVDLV 469
Query: 121 IIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPY 180
++ +++ L+A A P D+ F S C+V +G SDE+LD + KL
Sbjct: 470 VVGGFYGKGKRGGKISSLLMA-AYNPKTDS----FESVCKVASGFSDEQLDELQKKLMEI 524
Query: 181 FRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILS---ITSDIRTIRSEVFS--AP 235
R ++P+ NSK PD+W+E + I+ S + T +V A
Sbjct: 525 KRDVKHPR----------VNSKMEPDIWVEPVYVAEIIGSEITISPLHTCCQDVVEKDAG 574
Query: 236 YSLRFPRIDRVRYDKPWHDCLDVQSFVEL 264
S+RFPR R R DK D +E+
Sbjct: 575 LSIRFPRFIRWRDDKSPEDATTTDEILEM 603
>pdb|3RR5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sp. 1519
Length = 570
Score = 73.6 bits (179), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 60/203 (29%), Positives = 93/203 (45%), Gaps = 31/203 (15%)
Query: 62 LVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLI 121
LV V+E E F+K +E EG++ K L S +EPG+R KWLK+KP +LD++I
Sbjct: 388 LVTKKVEEAEAFYKRALELGHEGLMAKRLDSVYEPGNRGKKWLKIKPTM----ENLDLVI 443
Query: 122 IXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYF 181
I + FLVA + PD+ F+ +VG+G +DE+L LKP
Sbjct: 444 IGAEWGEGRRAHLLGSFLVAAYD---PDS--GEFLPVGKVGSGFTDEDLVEFTKMLKPLI 498
Query: 182 RKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFP 241
+ E F ++ P V IE + I +S + + ++LRFP
Sbjct: 499 LREE------GKFVEI------EPKVVIEVTYQEI----------QKSPKYRSGFALRFP 536
Query: 242 RIDRVRYDKPWHDCLDVQSFVEL 264
R +R DK + ++ +L
Sbjct: 537 RYVALREDKSPEEADTIERIAQL 559
>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus
Length = 571
Score = 70.9 bits (172), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 56/204 (27%), Positives = 94/204 (46%), Gaps = 31/204 (15%)
Query: 61 SLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVL 120
+L+ + +E E F+ + ++ EG++ K L S +EPG+R KWLK+KP +LD++
Sbjct: 388 NLITKSPEEAEAFYHKALDLGHEGLMAKRLDSTYEPGNRGKKWLKIKPTM----ENLDLV 443
Query: 121 IIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPY 180
++ ++ FL+ A D F+ +VG+G +DE+L LKP
Sbjct: 444 VLGAEWGEGRRSGVLSSFLLG-----AYDPVKGDFVPVGKVGSGFTDEDLVEFTKMLKPL 498
Query: 181 FRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRF 240
+K + KE +E K +I +I+ +S + + ++LRF
Sbjct: 499 IKK---------------EHGKE-----VELEPKVVIEVAYQEIQ--KSPKYESGFALRF 536
Query: 241 PRIDRVRYDKPWHDCLDVQSFVEL 264
PR +R DK D VQ EL
Sbjct: 537 PRYIALREDKGPEDADTVQRLAEL 560
>pdb|2CFM|A Chain A, Atp-Dependent Dna Ligase From Pyrococcus Furiosus
Length = 561
Score = 70.9 bits (172), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 56/217 (25%), Positives = 97/217 (44%), Gaps = 31/217 (14%)
Query: 48 QIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 107
+I+ ++ + +L+ V+E E F+K +E EG+ K L + +EPG+R KWLK+K
Sbjct: 363 EIIKQNEKIKVAENLITKKVEEAEAFYKRALEXGHEGLXAKRLDAVYEPGNRGKKWLKIK 422
Query: 108 PEYIRAGSDLDVLIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSD 167
P +LD++II F++ A D F+ +VG+G +D
Sbjct: 423 P----TXENLDLVIIGAEWGEGRRAHLFGSFILG-----AYDPETGEFLEVGKVGSGFTD 473
Query: 168 EELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTI 227
++L LKP K E + VW++ K +I +I+
Sbjct: 474 DDLVEFTKXLKPLIIKEEGKR------------------VWLQP--KVVIEVTYQEIQ-- 511
Query: 228 RSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVEL 264
+S + + ++LRFPR +R DK D ++ +L
Sbjct: 512 KSPKYRSGFALRFPRFVALRDDKGPEDADTIERIAQL 548
>pdb|1X9N|A Chain A, Crystal Structure Of Human Dna Ligase I Bound To
5'-Adenylated, Nicked Dna
Length = 688
Score = 62.8 bits (151), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 64/233 (27%), Positives = 101/233 (43%), Gaps = 22/233 (9%)
Query: 61 SLVAHNVDEVEKFFKETIENRDEGIVLK--DLGSKWEPGDRSGKWLKLKPEYIRA-GSDL 117
SL +++++ +F ++++++ EG+ +K D+ + +E RS WLKLK +Y+ G L
Sbjct: 467 SLDTKDIEQIAEFLEQSVKDSCEGLXVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTL 526
Query: 118 DVLIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKL 177
D+++I FL+A + D + C++GTG SDEEL+ L
Sbjct: 527 DLVVIGAYLGRGKRAGRYGGFLLA-----SYDEDSEELQAICKLGTGFSDEELEEHHQSL 581
Query: 178 KPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPE----KSIILSITSDIRTIRSEVFS 233
K P V + PD W++ K LS++ R V S
Sbjct: 582 KALVLPSPRP--------YVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDS 633
Query: 234 -APYSLRFPRIDRVRYDK-PWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDD 284
SLRFPR RVR DK P Q S Q+G++ G +D
Sbjct: 634 DKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGEDSGSDPED 686
>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 = 62.8 bits (151), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 60/267 (22%), Positives = 109/267 (40%), Gaps = 25/267 (9%)
Query: 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYE--AA 376
++IF D+ F ++ + L + E GG N T+CV A ++ ++ +
Sbjct: 8 SNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPD-TYCVIAGSENIRVKNIIL 66
Query: 377 KRRGDVIHYSWVLDCCSXXXXXXXXXXYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADI 436
+ DV+ +W+L+C + +H+ S+K+ E D + D YF D DL +
Sbjct: 67 SNKHDVVKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQL 126
Query: 437 KQLLSNVDRSED--PKTIDYYKKKYCPQDKWSC-----FHGCCIYF--YHSTEPLSPDWE 487
K++ S + S + P+ + + W C F +Y Y LS E
Sbjct: 127 KEVFSGIKNSNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVINDLSTKNE 186
Query: 488 VXXXXXXXXXXXEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLW 546
E+ FHG KV + LA +HV++ +F + +F
Sbjct: 187 ---GTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTF--------- 234
Query: 547 NKKLHVVRSQWLEDCLAKEQKSEEYEY 573
+K +++ W+ D + K + EE +Y
Sbjct: 235 KRKFKILKESWVTDSIDKCELQEENQY 261
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic
Switching Between Two Dna Bound States
Length = 579
Score = 56.2 bits (134), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 52/196 (26%), Positives = 86/196 (43%), Gaps = 16/196 (8%)
Query: 77 TIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGS---DLDVLIIXXXXXXXXXXX 133
I+ EG+VLKD+ +EPG R WLK+K +Y+ G+ D++++
Sbjct: 395 VIQEGLEGLVLKDVKGTYEPGKRH--WLKVKKDYLNEGAMADTADLVVLGAFYGQGSKGG 452
Query: 134 EVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 193
++ FL+ D +++ + + G D L + +L K PS
Sbjct: 453 MMSIFLMGCY-----DPGSQKWCTVTKCAGGHDDATLARLQNELD--MVKISKDPSKIPS 505
Query: 194 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-PYSLRFPRIDRVRYDKPW 252
+ +V N PD + P+K+ + IT +SE +A S+RFPR R+R DK W
Sbjct: 506 WLKV--NKIYYPDFIVPDPKKAAVWEITG-AEFSKSEAHTADGISIRFPRCTRIRDDKDW 562
Query: 253 HDCLDVQSFVELVHSS 268
++ EL S
Sbjct: 563 KSATNLPQLKELYQLS 578
>pdb|3GDE|A Chain A, The Closed Conformation Of Atp-Dependent Dna Ligase From
Archaeoglobus Fulgidus
Length = 558
Score = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 51/229 (22%), Positives = 93/229 (40%), Gaps = 41/229 (17%)
Query: 27 VAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 86
+ +DG C+ + + +L + + + +V +VDEV K + E I EG++
Sbjct: 342 ILYHDGECIDLPLRERRKLLESAVNESEKIKLAKQIVTDSVDEVRKMYDEAISAGHEGVM 401
Query: 87 LKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIXXXXXXXXXXXEVAQFLVALAERP 146
+K S + PG R WLK+K LD++++ ++ F E
Sbjct: 402 IKLPSSPYIPGKRGKNWLKVKA----IMETLDLVVVGGEWGEGKRSHWLSSF-----ELA 452
Query: 147 APDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYF-----RKYEYPKRAPPSFYQVTNNS 201
D + + RV TG ++E+L+ + +P +K E+ P ++V
Sbjct: 453 CLDPVTGKLLKVGRVATGFTEEDLEELTEMFRPLIVSQQGKKVEF---IPKYVFEVAYQE 509
Query: 202 KERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 250
++ SP+ + + Y+LRFPR R+R DK
Sbjct: 510 IQK------SPK------------------YESGYALRFPRFVRLRDDK 534
>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 = 0.19, Method: Compositional matrix adjust.
Identities = 23/105 (21%), Positives = 46/105 (43%), Gaps = 3/105 (2%)
Query: 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYE--AA 376
++IF D+ F ++ + L + E GG N T+CV A ++ ++ +
Sbjct: 10 SNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPD-TYCVIAGSENIRVKNIIL 68
Query: 377 KRRGDVIHYSWVLDCCSXXXXXXXXXXYYLHLSDSSKKKLQEEVD 421
+ 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 = 34.7 bits (78), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 28/133 (21%), Positives = 53/133 (39%), Gaps = 29/133 (21%)
Query: 319 TSIFSDMVFYFV------NVPPAYSLDSLHKMVVENGGTFSMNL--------------NN 358
++IF+ ++FY + + + L K +VE+GG N+
Sbjct: 3 SNIFAGLLFYVLSDYVTEDTGIRITRAELEKTIVEHGGKLIYNVILKRHSIGDVRLISCK 62
Query: 359 SVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSXXXXXXXXXXYYLHLSDSSKKKLQE 418
+ T C A ++G D++H +WVLDC + Y ++S + ++
Sbjct: 63 TTTECKALIDRGY---------DILHPNWVLDCIAYKRLILIEPNYCFNVSQKMRAVAEK 113
Query: 419 EVDEFSDLYFWDL 431
VD D + D+
Sbjct: 114 RVDCLGDSFENDI 126
>pdb|3OLC|X Chain X, Crystal Structure Of The N-Terminal Region Of Topbp1
Length = 298
Score = 33.1 bits (74), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 341 LHKMVVENGGTFSMNLN-NSVTHCVAADNKGLKYEAAKR 378
+ ++ V++GG + L N TH + + KG KYE AKR
Sbjct: 218 VQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKR 256
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 339 DSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKY-EAAKRRGDVIHYSWV 388
+ +HK V GG +LN SVTH +A + KY AA + ++ SW+
Sbjct: 122 EEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWI 172
>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 = 32.7 bits (73), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 341 LHKMVVENGGTFSMNLN-NSVTHCVAADNKGLKYEAAKR 378
+ ++ V++GG + L N TH + + KG KYE AKR
Sbjct: 220 VQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKR 258
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 339 DSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKY-EAAKRRGDVIHYSWV 388
+ +HK V GG +LN SVTH +A + KY AA + ++ SW+
Sbjct: 124 EEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWI 174
>pdb|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 287
Score = 32.7 bits (73), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 341 LHKMVVENGGTFSMNLN-NSVTHCVAADNKGLKYEAAKR 378
+ ++ V++GG + L N TH + + KG KYE AKR
Sbjct: 218 VQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKR 256
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 339 DSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKY-EAAKRRGDVIHYSWV 388
+ +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 = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 35/86 (40%), Gaps = 4/86 (4%)
Query: 311 DVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD-NK 369
DVS + + Y LD L +++ GG LN VTH + D +
Sbjct: 30 DVSAFQAPEDLLDGCRIYLCGFS-GRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYDD 88
Query: 370 GLK--YEAAKRRGDVIHYSWVLDCCS 393
LK + + R V+ W+L+C S
Sbjct: 89 ELKQFWNKSAHRPHVVGAKWLLECFS 114
>pdb|4ID3|A Chain A, Crystal Structure Of The Brct Domain Of S. Cerevisiae Rev1
pdb|4ID3|B Chain B, Crystal Structure Of The Brct Domain Of S. Cerevisiae Rev1
Length = 92
Score = 29.3 bits (64), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN--SVTHCVAADNKGLKYEAA 376
+ IF + V Y L LH+M+V +GG F L++ +VTH VA+ N LK
Sbjct: 5 SKIFKNCVIYINGYTKPGRLQ-LHEMIVLHGGKFLHYLSSKKTVTHIVAS-NLPLKKRIE 62
Query: 377 KRRGDVIHYSWVLD 390
V+ W++D
Sbjct: 63 FANYKVVSPDWIVD 76
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
0.316 0.132 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,929,803
Number of Sequences: 62578
Number of extensions: 845982
Number of successful extensions: 1778
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1737
Number of HSP's gapped (non-prelim): 30
length of query: 824
length of database: 14,973,337
effective HSP length: 107
effective length of query: 717
effective length of database: 8,277,491
effective search space: 5934961047
effective search space used: 5934961047
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: 56 (26.2 bits)