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= psy5226
(582 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FNR|A Chain A, Crystal Structure Of Putative Arginyl T-Rna Synthetase
From Campylobacter Jejuni
Length = 464
Score = 209 bits (533), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 141/461 (30%), Positives = 224/461 (48%), Gaps = 37/461 (8%)
Query: 123 KKILIEFVSANPTGPLHIGHGRQCAIGDILSSLFISQGYKVTREFYYNDTGVQITNLALS 182
+ L+E+VSANPTGPLHIGH R GD L+ L GYK E+Y ND G QI L LS
Sbjct: 30 ESFLLEYVSANPTGPLHIGHARGAVFGDTLTRLARHLGYKFNTEYYVNDAGNQIYLLGLS 89
Query: 183 VQARAKAIFLGKST-WPDTAYNGEYITDXXXXXXXXXXXXXXXXXXXXXANGKINDLKAI 241
+ K L ++ +P+ Y GEYI D ++ ++
Sbjct: 90 ILLSVKESILHENVEYPEQYYKGEYIVDLAKEAFEKFGKEFFSE----------ENIPSL 139
Query: 242 RDFSVAYLRREQDIDLKIFGVKFDNYCLESSLYKTGKVSLVTKLLIQSGKTYYKDGALWL 301
D++ + +L+ +K D+Y E S Y +L + L + Y ++G +WL
Sbjct: 140 ADWAKDKMLVLIKQNLEQAKIKIDSYVSERSYYDALNATLES--LKEHKGIYEQEGKIWL 197
Query: 302 RTTDYGDDKDRVVRKSNGDFTYFVSDIAYHIFKWERGFIQAINIQGDDHQGTITRVKAGL 361
++ GD+KDRV+ + +G TY +DI YH K RG+ + INI G DH G I R+KA +
Sbjct: 198 ASSQKGDEKDRVIIREDGRGTYLAADIVYHKDKMSRGYGKCINIWGADHHGYIPRMKAAM 257
Query: 362 QAINIGIPNDYPNYILHKMVTVIKNGKEVKISKRSGSYITIRNLIKWLSKTESKNDSIEF 421
+ +G ++ IL +MV+++K+G+ K+SKR+G++I + +++ D I
Sbjct: 258 EF--LGFDSNNLEIILAQMVSLLKDGEPYKMSKRAGNFILMSDVV----------DEI-- 303
Query: 422 REDLIRGRDLMRFFLISRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWGGX 481
G D +R+ +S+K DT FDI K NPVYYI YAHARI + + G
Sbjct: 304 ------GSDALRYIFLSKKCDTHLEFDISDLQKEDSSNPVYYINYAHARIHQVFAKAGKK 357
Query: 482 XXXXXXXXXXXXXNTEKELSLLVKLSNYPEVLVNSVKDLCPHYVAFYLRDLAKELHGYYN 541
+ ++LL + N VL ++ + + YL++LA H +YN
Sbjct: 358 IDDVMKADLQSL--NQDGVNLLFEALNLKAVLNDAFEARALQKIPDYLKNLAANFHKFYN 415
Query: 542 TERILVKNITIKMARLALIYSIGQVLNNGLKLIGISAPTKM 582
+++ + +L + ++ + L+GI A KM
Sbjct: 416 ENKVVGSANENDLLKLFSLVALS--IKTAFSLMGIEAKNKM 454
>pdb|2ZUE|A Chain A, Crystal Structure Of Pyrococcus Horikoshii Arginyl-Trna
Synthetase Complexed With Trna(Arg) And An Atp Analog
(Anp)
pdb|2ZUF|A Chain A, Crystal Structure Of Pyrococcus Horikoshii Arginyl-Trna
Synthetase Complexed With Trna(Arg)
Length = 629
Score = 132 bits (331), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 151/608 (24%), Positives = 250/608 (41%), Gaps = 83/608 (13%)
Query: 41 GDISCNISMQISKKLQINSYKLA-KIIAKNLIQQKNYIKLIQSIEIIKPGFINLXXX-XX 98
GD I+ +++K L+ ++A KI+ K + IK ++++ G+IN+
Sbjct: 39 GDFGTPIAFKLAKLLKRPPIEIAEKIVEKLKLNLPEGIKDVKAVN----GYINVFIDYPH 94
Query: 99 XXXXXXXXXXXXGIKFGQSNIGSNKKILIEFVSANPTGPLHIGHGRQCAIGDILSSLFIS 158
G +FG S IG KK+++E S NPT PLH+GH R +GD+++ +
Sbjct: 95 FARILINDILAKGDRFGSSEIGKGKKVIVEHTSVNPTKPLHMGHARNAILGDVMARILRF 154
Query: 159 QGYKVTREFYYNDTGVQITNLA---LSVQARAKAIF-----LGKSTWP-DTAYNGEYITD 209
GY+V + Y +D G+Q + L ++ + I G P D A Y+
Sbjct: 155 LGYEVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIMNELRERGLKDNPIDHALGLLYVEV 214
Query: 210 XXXXXXXXXXXXXXXXXXXXXANGKINDLKAIRDFSVAYLRREQDIDLKIFGVKFDNYCL 269
+G++ K + + R Q + GVK+D
Sbjct: 215 NRRLEDNPELENEIRDIMKKLESGELYGRKLAEE-----VVRAQMVTTYKLGVKYDLLVW 269
Query: 270 ESSLYKTGKVSLVTKLL-------IQSGKTYYKDGALWLRTTDYGDDKDR--VVRKSNGD 320
ES + + + +LL I S Y + LR + D K+ V+R+S+G
Sbjct: 270 ESDIVRRKLFEIALELLSKNENFYIPSDGKYRGAFVMDLRKL-FPDMKNPILVLRRSDGT 328
Query: 321 FTYFVSDIAYHIFK------------WE--------------RGFIQA---INIQGDDHQ 351
TY DIAYH++K W+ F A IN+ G + +
Sbjct: 329 ATYTGKDIAYHLWKFGKIDVDLLYKEWDSTTWTTAPDGKSMPNKFGNANIVINVIGAEQK 388
Query: 352 GTITRVKAGLQAINIGIPNDYPNYILHKMVTVIKNGKEVKISKRSGSYITI--------- 402
+K LQ + D + H ++ E K S R G+++
Sbjct: 389 HPQLAIKYALQLLGF---EDAAANLYHLAYEHVER-PEGKFSGRKGTWVGFTVDEVIQEA 444
Query: 403 ----RNLIKWLSKTESKNDSIEFREDLIRGRDLMRFFLISRKSDTDFIFDIDLALKRSDE 458
R LI+ + S + E E + G +R+ LI D IF + L E
Sbjct: 445 VKRARELIEEKNPALSDEEKAEVAEKV--GIGAIRYNLIKYSPDKKIIFRWEDVLNFEGE 502
Query: 459 NPVYYIQYAHARIFSLLNQWGGXXXXXXXXXXXXXXN----TEKELSLLVKLSNYPEVLV 514
+ YIQYAHAR S+L + + +E+E L++ LS +P ++
Sbjct: 503 S-APYIQYAHARCSSILRKAEEEGIKVDPETLFKNADFTKLSERERELVIMLSKFPRIVE 561
Query: 515 NSVKDLCPHYVAFYLRDLAKELHGYYNTERILVKNITIKMARLALIYSIGQVLNNGLKLI 574
+ KD+ PH +A++ +LA + +Y +L ++ ARL L+ ++ QVL N L L+
Sbjct: 562 QAGKDVKPHLIAWFANELASLFNKFYMDHPVLKAEEGVREARLLLVMAVEQVLKNALYLM 621
Query: 575 GISAPTKM 582
GI AP +M
Sbjct: 622 GIEAPERM 629
>pdb|1BS2|A Chain A, Yeast Arginyl-Trna Synthetase
pdb|1F7U|A Chain A, Crystal Structure Of The Arginyl-trna Synthetase Complexed
With The Trna(arg) And L-arg
pdb|1F7V|A Chain A, Crystal Structure Of Yeast Arginyl-Trna Synthetase
Complexed With The Trnaarg
Length = 607
Score = 97.1 bits (240), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 120/508 (23%), Positives = 200/508 (39%), Gaps = 73/508 (14%)
Query: 114 FGQSNIGSNKKILIEFVSANPTGPLHIGHGRQCAIGDILSSLFISQGYKVTREFYYNDTG 173
+G + NKK++IEF S N P H GH R IG L++L+ G++V R Y D G
Sbjct: 134 YGSCKLVENKKVIIEFSSPNIAKPFHAGHLRSTIIGGFLANLYEKLGWEVIRMNYLGDWG 193
Query: 174 VQITNLALSVQARAKAIFLGKSTWPDTAYNGEYITDXXXXXXXXXXXXXXXXXXXXXANG 233
Q LA+ + L K ++ D NG
Sbjct: 194 KQFGLLAVGFERYGNEEALVKDPI-------HHLFDVYVRINKDIEEEGDSIPLEQSTNG 246
Query: 234 KIND-LKAIRDFSVAYLR-----REQDIDLKI-----FGVKFDNYCLESSLYKTGKVSLV 282
K + K + D L+ RE I+ I +K+D Y ES + K + +
Sbjct: 247 KAREYFKRMEDGDEEALKIWKRFREFSIEKYIDTYARLNIKYDVYSGESQVSKESMLKAI 306
Query: 283 TKLLIQSGKTYYKDGALWLRTTDYGDDKDR-VVRKSNGDFTYFVSDIAYHIFKWER---- 337
L + G T+ GA+ + T + + +V+KS+G Y D+ + ++E+
Sbjct: 307 D-LFKEKGLTHEDKGAVLIDLTKFNKKLGKAIVQKSDGTTLYLTRDVGAAMDRYEKYHFD 365
Query: 338 GFIQAINIQGDDHQGTITRV--------KAGLQAINIGIPNDYPNYILHKMVTVIKNGKE 389
I I Q D H + LQ +N G+
Sbjct: 366 KMIYVIASQQDLHAAQFFEILKQMGFEWAKDLQHVNFGMVQG------------------ 407
Query: 390 VKISKRSGSYITIRNLIKW--------LSKTESKNDSIEFREDLIRGRDLMRFFLI---- 437
+S R G+ + + N+++ + K E+K IE E++ DL+ +
Sbjct: 408 --MSTRKGTVVFLDNILEETKEKMHEVMKKNENKYAQIEHPEEVA---DLVGISAVMIQD 462
Query: 438 ---SRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWGGXXXXXXXXXXXXXX 494
R ++ +F ++ L+ + D P Y+QYAH+R+ S+ G
Sbjct: 463 MQGKRINNYEFKWERMLSFE-GDTGP--YLQYAHSRLRSVERNASGITQEKWINADFSLL 519
Query: 495 NTEKELSLLVKLSNYPEVLVNSVKDLCPHYVAFYLRDLAKELHGYYNTERILVKNITIKM 554
L+ L YP+VL N++K P V YL L ++ Y+ + + +
Sbjct: 520 KEPAAKLLIRLLGQYPDVLRNAIKTHEPTTVVTYLFKLTHQVSSCYDVLWVAGQTEELAT 579
Query: 555 ARLALIYSIGQVLNNGLKLIGISAPTKM 582
ARLAL + QVL NG++L+G++ +M
Sbjct: 580 ARLALYGAARQVLYNGMRLLGLTPVERM 607
>pdb|1IQ0|A Chain A, Thermus Thermophilus Arginyl-Trna Synthetase
Length = 592
Score = 90.1 bits (222), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 113/512 (22%), Positives = 202/512 (39%), Gaps = 78/512 (15%)
Query: 125 ILIEFVSANPTGPLHIGHGRQCAIGDILSSLFISQGYKVTREFYYNDTGVQITNLALSVQ 184
+L+E S NP LH+GH R A+GD ++ + G +V Y +DTG Q +++
Sbjct: 105 VLVEHTSVNPNKELHVGHLRNIALGDAIARILAYAGREVLVLNYIDDTGRQAAETLFALR 164
Query: 185 ARAKAIFLGKSTWPDTAYNGEYITDXXXXXXXXXXXXXXXXXXXXXANGKINDLKAIRDF 244
+ GK + + G G++ +
Sbjct: 165 -HYGLTWDGKEKY--DHFAGRAYVRLHQDPEYERLQPAIEEVLHALERGELRE------- 214
Query: 245 SVAYLRREQDIDLKIFGVKFDNYCLESSLYKTGKVSLVTKLLIQSGKTYYK-----DGAL 299
V + Q + ++D ES + + G + LL QS + GAL
Sbjct: 215 EVNRILLAQMATMHALNARYDLLVWESDIVRAGLLQKALALLEQSPHVFRPREGKYAGAL 274
Query: 300 WLRTTDY---GDDKDRVVRKSNGDFTYFVSDIAYHIFK-----------WERGFIQAINI 345
+ + +D V+ +SNG TY+ DIA+ +K +E + +
Sbjct: 275 VMDASPVIPGLEDPFFVLLRSNGTATYYAKDIAFQFWKMGILEGLRFRPYENPYYPGLRT 334
Query: 346 QGDDHQGTITRVKAGLQAINIGIPND------------YPNYI--LHKMV--TVIKNGKE 389
+ + + + + +++ + YP H + TV+ G++
Sbjct: 335 SAPEGEAYTPKAEETINVVDVRQSHPQALVRAALALAGYPALAEKAHHLAYETVLLEGRQ 394
Query: 390 VKISKRSGSYITIRNLIKWLSK-----TESKNDSIEFREDLIRGRDL--MRFFLI--SRK 440
+S R G +++ +++ ++ E KN +E+ R L +RF ++ K
Sbjct: 395 --MSGRKGLAVSVDEVLEEATRRARAIVEEKNPDHPDKEEAARMVALGAIRFSMVKTEPK 452
Query: 441 SDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLL---NQWGGXXXXXXXXXXXXXXNTE 497
DF + L+ + D P Y+QYAHAR S+L +WG T
Sbjct: 453 KQIDFRYQEALSFE-GDTGP--YVQYAHARAHSILRKAGEWGAPDLSQA---------TP 500
Query: 498 KELSLLVKLSNYPEVLVNSVKDLCPHYVAFYLRDLAKELHGYYNTER-------ILVKNI 550
E +L + L ++ E ++ + ++ PH +A YL DLA + YYN +L
Sbjct: 501 YERALALDLLDFEEAVLEAAEERTPHVLAQYLLDLAASWNAYYNARENGQPATPVLTAPE 560
Query: 551 TIKMARLALIYSIGQVLNNGLKLIGISAPTKM 582
++ RL+L+ S+ + L GL L+GI AP M
Sbjct: 561 GLRELRLSLVQSLQRTLATGLDLLGIPAPEVM 592
>pdb|1OBH|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Pre-Transfer Editing Substrate Analogue In Both
Synthetic Active Site And Editing Site
pdb|2BTE|A Chain A, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
With A Trnaleu Transcript In The Post-Editing
Conformation And A Post-Transfer Editing Substrate
Analogue
pdb|2BTE|D Chain D, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
With A Trnaleu Transcript In The Post-Editing
Conformation And A Post-Transfer Editing Substrate
Analogue
pdb|2BYT|A Chain A, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
A Trnaleu Transcript In The Post-Editing Conformation
pdb|2BYT|D Chain D, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
A Trnaleu Transcript In The Post-Editing Conformation
pdb|1H3N|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Sulphamoyl Analogue Of Leucyl-Adenylate
pdb|1OBC|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Post-Transfer Editing Substrate Analogue
pdb|2V0G|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Trna(Leu) Transcript With 5-Fluoro-1,3-Dihydro-1-
Hydroxy-2,1-Benzoxaborole (An2690) Forming An Adduct To
The Ribose Of Adenosine-76 In The Enzyme Editing Site.
pdb|2V0G|D Chain D, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Trna(Leu) Transcript With 5-Fluoro-1,3-Dihydro-1-
Hydroxy-2,1-Benzoxaborole (An2690) Forming An Adduct To
The Ribose Of Adenosine-76 In The Enzyme Editing Site
Length = 878
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 134 PTGPLHIGHGRQCAIGDILSSLFISQGYKVTREFYYNDTGVQITNLALSVQARAK 188
P+G LH+GH + +GD+L+ QGY+V ++ G+ N AL K
Sbjct: 44 PSGDLHMGHLKNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPK 98
>pdb|2V0C|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Sulphamoyl Analogue Of Leucyl-Adenylate In The
Synthetic Site And An Adduct Of Amp With 5-Fluoro-1,3-
Dihydro-1-Hydroxy-2,1-Benzoxaborole (An2690) In The
Editing Site
Length = 878
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 134 PTGPLHIGHGRQCAIGDILSSLFISQGYKVTREFYYNDTGVQITNLALSVQARAK 188
P+G LH+GH + +GD+L+ QGY+V ++ G+ N AL K
Sbjct: 44 PSGDLHMGHLKNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPK 98
>pdb|1WZ2|A Chain A, The Crystal Structure Of Leucyl-Trna Synthetase And
Trna(Leucine) Complex
pdb|1WZ2|B Chain B, The Crystal Structure Of Leucyl-Trna Synthetase And
Trna(Leucine) Complex
Length = 967
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 135 TGPLHIGHGRQCAIGDILSSLFISQGYKVTREFYYNDTGVQITNLALSVQAR 186
+G LH+GH R I D+++ QGY V ++ TG I +A ++ R
Sbjct: 46 SGHLHVGHARTYTIPDVIARFKRMQGYNVLFPMAWHITGSPIVGIAERIKNR 97
>pdb|1WKB|A Chain A, Crystal Structure Of Leucyl-Trna Synthetase From The
Archaeon Pyrococcus Horikoshii Reveals A Novel Editing
Domain Orientation
Length = 810
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 30/65 (46%)
Query: 122 NKKILIEFVSANPTGPLHIGHGRQCAIGDILSSLFISQGYKVTREFYYNDTGVQITNLAL 181
KK I +G LH+GH R I D+++ QGY V ++ TG I +A
Sbjct: 33 EKKFYITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQGYNVLFPMAWHITGSPIVGIAE 92
Query: 182 SVQAR 186
++ R
Sbjct: 93 RIKNR 97
>pdb|3U0T|D Chain D, Fab-Antibody Complex
pdb|3U0T|B Chain B, Fab-Antibody Complex
Length = 217
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 45/102 (44%), Gaps = 10/102 (9%)
Query: 383 VIKNGKEVKISKRSGSYITIRNLIKWLSKTESKNDSIEFREDLIRGRD-----LMRFFLI 437
V K G VK+S ++ Y T I W+ + + R D G L +
Sbjct: 11 VKKPGASVKVSCKASGYYTEAYYIHWVRQAPGQGLEWMGRIDPATGNTKYAPRLQDRVTM 70
Query: 438 SRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWG 479
+R + T ++ ++L+ RS++ VYY A ++SL WG
Sbjct: 71 TRDTSTSTVY-MELSSLRSEDTAVYYC----ASLYSLPVYWG 107
>pdb|3EO0|B Chain B, Structure Of The Transforming Growth Factor-Beta
Neutralizing Antibody Gc-1008
pdb|3EO0|D Chain D, Structure Of The Transforming Growth Factor-Beta
Neutralizing Antibody Gc-1008
Length = 225
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/111 (20%), Positives = 47/111 (42%), Gaps = 10/111 (9%)
Query: 376 ILHKMVTVIKNGKEVKISKRSGSYITIRNLIKWLSKTESKNDSIEFREDLIRGRDLMRF- 434
++ V K G VK+S ++ Y N+I W+ ++ +E+ +I D+ +
Sbjct: 4 LVQSGAEVKKPGSSVKVSCKASGYTFSSNVISWVR--QAPGQGLEWMGGVIPIVDIANYA 61
Query: 435 ------FLISRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWG 479
I+ T + ++L+ RS++ VYY + ++ WG
Sbjct: 62 QRFKGRVTITADESTSTTY-MELSSLRSEDTAVYYCASTLGLVLDAMDYWG 111
>pdb|3EO1|B Chain B, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|E Chain E, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|H Chain H, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|K Chain K, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
Length = 225
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 23/111 (20%), Positives = 47/111 (42%), Gaps = 10/111 (9%)
Query: 376 ILHKMVTVIKNGKEVKISKRSGSYITIRNLIKWLSKTESKNDSIEFREDLIRGRDLMRF- 434
++ V K G VK+S ++ Y N+I W+ ++ +E+ +I D+ +
Sbjct: 4 LVQSGAEVKKPGSSVKVSCKASGYTFSSNVISWVR--QAPGQGLEWMGGVIPIVDIANYA 61
Query: 435 ------FLISRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWG 479
I+ T + ++L+ RS++ VYY + ++ WG
Sbjct: 62 QRFKGRVTITADESTSTTY-MELSSLRSEDTAVYYCASTLGLVLDAMDYWG 111
>pdb|4DW2|H Chain H, The Crystal Structure Of Upa In Complex With The Fab
Fragment Of Mab- 112
Length = 212
Score = 33.1 bits (74), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 17/106 (16%)
Query: 383 VIKNGKEVKISKRSGSYITIRNLIKWLSKTESK---------NDSIEFREDLIRGRDLMR 433
++K G +K+S + + R + W+ +T K N + D ++GR
Sbjct: 11 LVKPGGSLKLSCSASGFTFSRYAMSWVRQTPEKRLEWVASITNGGSTYYSDSVKGR---- 66
Query: 434 FFLISRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWG 479
F+ISR + + I + ++ RS++ +YY + + ++ WG
Sbjct: 67 -FIISRDNARN-ILSLQMSSLRSEDTAMYYCE--RGELTYAMDYWG 108
>pdb|1IGF|H Chain H, Crystal Structures Of An Antibody To A Peptide And Its
Complex With Peptide Antigen At 2.8 Angstroms
pdb|2IGF|H Chain H, Crystal Structures Of An Antibody To A Peptide And Its
Complex With Peptide Antigen At 2.8 Angstroms
pdb|1IGF|J Chain J, Crystal Structures Of An Antibody To A Peptide And Its
Complex With Peptide Antigen At 2.8 Angstroms
Length = 221
Score = 33.1 bits (74), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 17/107 (15%)
Query: 383 VIKNGKEVKISKRSGSYITIRNLIKWLSKTESK----------NDSIEFREDLIRGRDLM 432
++K G +K+S + + R + W+ +T K S F D ++GR
Sbjct: 11 LVKPGGSLKLSCAASGFTFSRCAMSWVRQTPEKRLEWVAGISSGGSYTFYPDTVKGR--- 67
Query: 433 RFFLISRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWG 479
F+ISR + + + ++ RS++ +YY + F + WG
Sbjct: 68 --FIISRNNARN-TLSLQMSSLRSEDTAIYYCTRYSSDPF-YFDYWG 110
>pdb|4DVB|A Chain A, The Crystal Structure Of The Fab Fragment Of Pro-upa
Antibody Mab-112
pdb|4DVB|H Chain H, The Crystal Structure Of The Fab Fragment Of Pro-upa
Antibody Mab-112
Length = 213
Score = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 17/106 (16%)
Query: 383 VIKNGKEVKISKRSGSYITIRNLIKWLSKTESK---------NDSIEFREDLIRGRDLMR 433
++K G +K+S + + R + W+ +T K N + D ++GR
Sbjct: 11 LVKPGGSLKLSCSASGFTFSRYAMSWVRQTPEKRLEWVASITNGGSTYYSDSVKGR---- 66
Query: 434 FFLISRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWG 479
F+ISR + + I + ++ RS++ +YY + + ++ WG
Sbjct: 67 -FIISRDNARN-ILSLQMSSLRSEDTAMYYCE--RGELTYAMDYWG 108
>pdb|1XFO|A Chain A, Crystal Structure Of An Archaeal Aminopeptidase
pdb|1XFO|B Chain B, Crystal Structure Of An Archaeal Aminopeptidase
pdb|1XFO|C Chain C, Crystal Structure Of An Archaeal Aminopeptidase
pdb|1XFO|D Chain D, Crystal Structure Of An Archaeal Aminopeptidase
Length = 357
Score = 32.7 bits (73), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 363 AINIGIPNDYPNYILHKMVTVIKNGKEVKISKRSGSYITIRNLIKWLSKTESKND 417
AI++ I D P HK VT + G +KI R S I +++WL + K++
Sbjct: 237 AIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDR--SVICHPTIVRWLEELAKKHE 289
>pdb|1Y0R|A Chain A, Crystal Structure Of The Tetrahedral Aminopeptidase From
P. Horikoshii
pdb|1Y0Y|A Chain A, Crystal Structure Of Tetrahedral Aminopeptidase From P.
Horikoshii In Complex With Amastatin
Length = 353
Score = 32.7 bits (73), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 363 AINIGIPNDYPNYILHKMVTVIKNGKEVKISKRSGSYITIRNLIKWLSKTESKND 417
AI++ I D P HK VT + G +KI R S I +++WL + K++
Sbjct: 233 AIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDR--SVICHPTIVRWLEELAKKHE 285
>pdb|3AII|A Chain A, Archaeal Non-Discriminating Glutamyl-Trna Synthetase From
Methanothermobacter Thermautotrophicus
Length = 553
Score = 32.0 bits (71), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 120 GSNKKILIEFVSANPTGPLHIGHGRQC 146
G ++++ F + NP+GPLHIGH R
Sbjct: 92 GVKGEVVLRF-APNPSGPLHIGHARAA 117
>pdb|1NL0|H Chain H, Crystal Structure Of Human Factor Ix Gla Domain In Complex
Of An Inhibitory Antibody, 10c12
pdb|3D69|H Chain H, Crystal Structure Of The Fab Fragment Of An Anti-Factor Ix
Antibody 10c12
pdb|3D69|B Chain B, Crystal Structure Of The Fab Fragment Of An Anti-Factor Ix
Antibody 10c12
Length = 224
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/107 (19%), Positives = 48/107 (44%), Gaps = 16/107 (14%)
Query: 383 VIKNGKEVKISKRSGSYITIRNLIKWLSKTESK----------NDSIEFREDLIRGRDLM 432
V++ G+ +++S + + + W+ + K + S ++ D ++GR
Sbjct: 11 VVQPGRSLRLSCAASGFTFSTYAMHWVRQAPGKGLEWVAIISYDGSKKYYADSVKGR--- 67
Query: 433 RFFLISRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWG 479
F ISR + + ++ + + R+++ VYY A +L+ WG
Sbjct: 68 --FTISRDNSKNTLY-LQMNSLRAEDTAVYYCARASIAAARVLDYWG 111
>pdb|1PG7|X Chain X, Murine 6a6 Fab In Complex With Humanized Anti-Tissue
Factor D3h44 Fab
pdb|1PG7|Z Chain Z, Murine 6a6 Fab In Complex With Humanized Anti-Tissue
Factor D3h44 Fab
Length = 220
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 25/108 (23%), Positives = 45/108 (41%), Gaps = 18/108 (16%)
Query: 383 VIKNGKEVKISKRSGSYITIRNLIKWLSKTESK-----------NDSIEFREDLIRGRDL 431
++K G VKIS ++ Y +L+ W+ ++ K N +I + + L
Sbjct: 11 LVKPGASVKISCKASGYSFTGHLLNWVKQSHGKNLEWIGLVHPHNGAITYNQKFKDKATL 70
Query: 432 MRFFLISRKSDTDFIFDIDLALKRSDENPVYYIQYAHARIFSLLNQWG 479
+ R S T + I+L S+++ VYY R ++ WG
Sbjct: 71 T----VDRSSTTAY---IELVRLTSNDSAVYYCAREDFRYHYSMDYWG 111
>pdb|1GGL|A Chain A, Human Cellular Retinol Binding Protein Iii
pdb|1GGL|B Chain B, Human Cellular Retinol Binding Protein Iii
Length = 134
Score = 30.0 bits (66), Expect = 3.7, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 12/71 (16%)
Query: 361 LQAINIGIPNDYPNYILHKMVTVIKNGKEVKISKRSGSYITIRNLIKWLSKTESKNDSIE 420
LQA+NI + + K+ ++K KE++ G+++T+R L + + T + +E
Sbjct: 20 LQALNISLA-------VRKIALLLKPDKEIE---HQGNHMTVRTLSTFRNYTVQFDVGVE 69
Query: 421 FREDL--IRGR 429
F EDL + GR
Sbjct: 70 FEEDLRSVDGR 80
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 0.139 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,408,669
Number of Sequences: 62578
Number of extensions: 594074
Number of successful extensions: 1367
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1337
Number of HSP's gapped (non-prelim): 36
length of query: 582
length of database: 14,973,337
effective HSP length: 104
effective length of query: 478
effective length of database: 8,465,225
effective search space: 4046377550
effective search space used: 4046377550
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: 54 (25.4 bits)