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= 037039
(505 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3N9I|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Yersinia Pestis Co92
pdb|3N9I|B Chain B, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Yersinia Pestis Co92
Length = 346
Score = 35.8 bits (81), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 3/105 (2%)
Query: 84 EDQRRQVMKQRSIGRKFRNFFGS--SNPIAFRFRMGHQIKKIRERFDEIAKLS-GEFNLI 140
EDQ++ + R I +F N +G P F + G ++ +++ +++K N+I
Sbjct: 160 EDQKQHLELSRDIASRFNNLYGDIFKIPEPFIPKAGARVMSLQDPTKKMSKSDDNRNNVI 219
Query: 141 ERLDDHRRVVHKEREATQPNVPPDIIGRDKDREKIIELLMQTSDG 185
E L+D + VV K + A + P +I D +++ + L+ G
Sbjct: 220 ELLEDPKSVVKKIKRAMTDSDEPALIRYDVEKKAGVSNLLDILSG 264
>pdb|2V1U|A Chain A, Structure Of The Aeropyrum Pernix Orc1 Protein In Complex
With Dna
Length = 387
Score = 32.3 bits (72), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 31/139 (22%), Positives = 69/139 (49%), Gaps = 8/139 (5%)
Query: 150 VHKEREATQPNVPPDIIG-RDKDREKIIELLMQTSDGKSETVSVVPIVGIGGLGKTAVAQ 208
+ ++R P+ PD++ R+ + ++ E+L G+ + ++ + G+ G GKTAVA+
Sbjct: 5 IFRKRWVLLPDYVPDVLPHREAELRRLAEVLAPALRGEKPSNAL--LYGLTGTGKTAVAR 62
Query: 209 LVYNDQRVKEHFELKIWIR-VFEDFGERQIMRKIMELIIEQIMTNYVFQGDLNTHRLQQI 267
LV + L + ++ ++ + R+ ++ I E + F G L+ + +
Sbjct: 63 LVLRRLEARAS-SLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTG-LSVGEVYER 120
Query: 268 LRDCLNGKR--YLLVMDDV 284
L L+ R Y++V+D++
Sbjct: 121 LVKRLSRLRGIYIIVLDEI 139
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 41/140 (29%), Positives = 64/140 (45%), Gaps = 20/140 (14%)
Query: 193 VPIVGIGGLGKTAVAQLVYNDQRVKEH-FELKI-WIRVFEDFGERQIMRK---IMELIIE 247
V I G+ G GK+ +A D + E F + W+ + + +M+ M L E
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 209
Query: 248 QIMTNYVFQGDLNTHRLQQILRDCLNGK--RYLLVMDDVWNEDPEAWRNLKSLLLGGANG 305
+ + + LN + LR + K R LL++DDVW DP W +L N
Sbjct: 210 ESFSQRL---PLNIEEAKDRLRVLMLRKHPRSLLILDDVW--DP--W-----VLKAFDNQ 257
Query: 306 SKILVTTRSRKVA-SIMGTR 324
+IL+TTR + V S+MG +
Sbjct: 258 CQILLTTRDKSVTDSVMGPK 277
>pdb|3QFL|A Chain A, Coiled-Coil Domain-Dependent Homodimerization Of
Intracellular Mla Immune Receptors Defines A Minimal
Functional Module For Triggering Cell Death
Length = 115
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 2/80 (2%)
Query: 7 PIEKLLEKLGSSAYEELLLFCGVKNDLHKLKEKLTTVKSVVLDAEEKQNHNRRLSD--WL 64
I L+ KLG EE L GVK ++ L ++L + + ++ E D W
Sbjct: 2 AISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESXNAALIKIGEVPREQLDSQDKLWA 61
Query: 65 GKLKDACYDAEDVLDEFEVE 84
++++ Y EDV+D+F V+
Sbjct: 62 DEVRELSYVIEDVVDKFLVQ 81
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 73/348 (20%), Positives = 134/348 (38%), Gaps = 76/348 (21%)
Query: 172 REKIIELLMQTSDGKSETVSVVPIVGIGGLGKTAVAQLVYNDQRVKEH-FELKI-WIRVF 229
R+K++ + Q V I G+ G GK+ +A D + E F + W+ V
Sbjct: 129 RKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVG 188
Query: 230 EDFGERQIMRKIMELIIEQIMTNYVFQG--DLNTHRLQQILRDCLNGK--RYLLVMDDVW 285
+ +M+ ++ + ++ + F LN + LR + K R LL++DDVW
Sbjct: 189 KQDKSGLLMK--LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVW 246
Query: 286 NEDPEAWRNLKSLLLGGANGSKILVTTRSRKVA-SIMGTR---------GGTTGYNL--- 332
+ +W +L + +IL+TTR + V S+MG + G G +
Sbjct: 247 D----SW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSL 297
Query: 333 ------QGLP------FEDCLSLFMKFRTLGSVLCGKTDKRDWEF------------VRD 368
LP ++C + +G++L ++ WE+ +R
Sbjct: 298 FVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNR--WEYYLKQLQNKQFKRIRK 355
Query: 369 NEIWQLEQMERGILPTLRLSYDQLSPHLKQCFAYCSIFPRDYQFYGDSLVQFWMAHGLLQ 428
+ + E ++ + +S + L +K + SI +D + L W
Sbjct: 356 SSSYDYEALDEA----MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILW------- 404
Query: 429 SHNKKEELEDIGMRYLKELLSRFFFQDLSFGMLGMETFSFKMHDLMHD 476
+ EE+EDI L F + L F ++F + +HDL D
Sbjct: 405 -DMETEEVEDI--------LQEFVNKSLLFCDRNGKSFRYYLHDLQVD 443
>pdb|2EL7|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Thermus Thermophilus
pdb|2EL7|B Chain B, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Thermus Thermophilus
Length = 337
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 53 KQNHNRRLSDWLGKLKDACYDAEDVL----DEFEV-EDQRRQVMKQRSIGRKFRNFFGSS 107
K +++ + W G L A D+L D V EDQ + + R I R+F + FG +
Sbjct: 113 KDKASKQETVWSGLLMYPVLQAADILIYKADTVPVGEDQVQHIELTREIARRFNHLFGET 172
Query: 108 NP 109
P
Sbjct: 173 FP 174
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 40/140 (28%), Positives = 63/140 (45%), Gaps = 20/140 (14%)
Query: 193 VPIVGIGGLGKTAVAQLVYNDQRVKEH-FELKI-WIRVFEDFGERQIMRK---IMELIIE 247
V I G+ G GK+ +A D + E F + W+ + + +M+ M L E
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 216
Query: 248 QIMTNYVFQGDLNTHRLQQILRDCLNGK--RYLLVMDDVWNEDPEAWRNLKSLLLGGANG 305
+ + + LN + LR + K R LL++DDVW DP W +L N
Sbjct: 217 ESFSQRL---PLNIEEAKDRLRVLMLRKHPRSLLILDDVW--DP--W-----VLKAFDNQ 264
Query: 306 SKILVTTRSRKVA-SIMGTR 324
+IL+TT + V S+MG +
Sbjct: 265 CQILLTTSDKSVTDSVMGPK 284
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 72/160 (45%), Gaps = 18/160 (11%)
Query: 172 REKIIELLMQTSDGKSETVSVVPIVGIGGLGKTAVAQLVYNDQRVKEH-FELKI-WIRVF 229
R+K++ + Q V I G+ G GK+ +A D + E F + W+ V
Sbjct: 135 RKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVG 194
Query: 230 EDFGERQIMRKIMELIIEQIMTNYVFQG--DLNTHRLQQILRDCLNGK--RYLLVMDDVW 285
+ +M+ ++ + ++ + F LN + LR + K R LL++DDVW
Sbjct: 195 KQDKSGLLMK--LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVW 252
Query: 286 NEDPEAWRNLKSLLLGGANGSKILVTTRSRKVA-SIMGTR 324
++W +L + +IL+TTR + V S+MG +
Sbjct: 253 ----DSW-----VLKAFDSQCQILLTTRDKSVTDSVMGPK 283
>pdb|2JE8|A Chain A, Structure Of A Beta-Mannosidase From Bacteroides
Thetaiotaomicron
pdb|2JE8|B Chain B, Structure Of A Beta-Mannosidase From Bacteroides
Thetaiotaomicron
Length = 848
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 207 AQLVYNDQRVKEHFELKIWIRVFEDFGERQIMRKIMELIIEQIMTNYVFQGDLNTHRLQQ 266
A+ VYN +R++ H L +W G +I+ + E+ T V+QG + H +
Sbjct: 416 AEAVYNIRRLRNHASLAMWC------GNNEILEALKYWGFEKKFTPEVYQGLM--HGYDK 467
Query: 267 ILRDCL 272
+ R+ L
Sbjct: 468 LFRELL 473
>pdb|2VJX|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VJX|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VL4|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VL4|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VMF|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VMF|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VO5|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VO5|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VOT|A Chain A, Structural And Biochemical Evidence For A Boat-like
Transition State In Beta-mannosidases
pdb|2VOT|B Chain B, Structural And Biochemical Evidence For A Boat-like
Transition State In Beta-mannosidases
pdb|2VQT|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VQT|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VR4|A Chain A, Transition-state Mimicry In Mannoside Hydrolysis:
Characterisation Of Twenty Six Inhibitors And Insight
Into Binding From Linear Free Energy Relationships And
3-d Structure
pdb|2VR4|B Chain B, Transition-state Mimicry In Mannoside Hydrolysis:
Characterisation Of Twenty Six Inhibitors And Insight
Into Binding From Linear Free Energy Relationships And
3-d Structure
Length = 846
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 207 AQLVYNDQRVKEHFELKIWIRVFEDFGERQIMRKIMELIIEQIMTNYVFQGDLNTHRLQQ 266
A+ VYN +R++ H L +W G +I+ + E+ T V+QG + H +
Sbjct: 414 AEAVYNIRRLRNHASLAMWC------GNNEILEALKYWGFEKKFTPEVYQGLM--HGYDK 465
Query: 267 ILRDCL 272
+ R+ L
Sbjct: 466 LFRELL 471
>pdb|2VQU|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VQU|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
Length = 846
Score = 29.3 bits (64), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 207 AQLVYNDQRVKEHFELKIWIRVFEDFGERQIMRKIMELIIEQIMTNYVFQGDLNTHRLQQ 266
A+ VYN +R++ H L +W G +I+ + E+ T V+QG + H +
Sbjct: 414 AEAVYNIRRLRNHASLAMWC------GNNEILEALKYWGFEKKFTPEVYQGLM--HGYDK 465
Query: 267 ILRDCL 272
+ R+ L
Sbjct: 466 LFRELL 471
>pdb|2WBK|A Chain A, Structure Of The Michaelis Complex Of Beta-Mannosidase,
Man2a, Provides Insight Into The Conformational
Itinerary Of Mannoside Hydrolysis
pdb|2WBK|B Chain B, Structure Of The Michaelis Complex Of Beta-Mannosidase,
Man2a, Provides Insight Into The Conformational
Itinerary Of Mannoside Hydrolysis
Length = 847
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 207 AQLVYNDQRVKEHFELKIWIRVFEDFGERQIMRKIMELIIEQIMTNYVFQGDLNTHRLQQ 266
A+ VYN +R++ H L +W G +I+ + E+ T V+QG + H +
Sbjct: 414 AEAVYNIRRLRNHASLAMWC------GNNEILEALKYWGFEKKFTPEVYQGLM--HGYDK 465
Query: 267 ILRDCL 272
+ R+ L
Sbjct: 466 LFRELL 471
>pdb|3GDE|A Chain A, The Closed Conformation Of Atp-Dependent Dna Ligase From
Archaeoglobus Fulgidus
Length = 558
Score = 28.9 bits (63), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 120 IKKIRERFDEIAKLSGEFNL 139
++K+RE FDEIA L+GE ++
Sbjct: 117 VRKVRETFDEIASLTGEGSM 136
>pdb|1C6V|A Chain A, Siv Integrase (Catalytic Domain + Dna Biding Domain
Comprising Residues 50-293) Mutant With Phe 185 Replaced
By His (F185h)
pdb|1C6V|B Chain B, Siv Integrase (Catalytic Domain + Dna Biding Domain
Comprising Residues 50-293) Mutant With Phe 185 Replaced
By His (F185h)
pdb|1C6V|C Chain C, Siv Integrase (Catalytic Domain + Dna Biding Domain
Comprising Residues 50-293) Mutant With Phe 185 Replaced
By His (F185h)
pdb|1C6V|D Chain D, Siv Integrase (Catalytic Domain + Dna Biding Domain
Comprising Residues 50-293) Mutant With Phe 185 Replaced
By His (F185h)
Length = 164
Score = 28.9 bits (63), Expect = 7.6, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 29 VKNDLHKLKEKLTTVKSVVLDAEEKQNHNRR 59
+KN + +++E+ +V+++VL A NH RR
Sbjct: 109 LKNQIDRIREQANSVETIVLMAVHCMNHKRR 139
>pdb|1JEQ|B Chain B, Crystal Structure Of The Ku Heterodimer
pdb|1JEY|B Chain B, Crystal Structure Of The Ku Heterodimer Bound To Dna
Length = 565
Score = 28.9 bits (63), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 91 MKQRSIGRKFRNF-FGSSNPIAFRFRMGHQIKKIRERFDEIAKLSGEFNLIERLDD 145
MK +S G+ F F S+ + RF MG+Q+ K+ D+ A +LI LDD
Sbjct: 331 MKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDD 386
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
0.323 0.140 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,036,951
Number of Sequences: 62578
Number of extensions: 635658
Number of successful extensions: 1647
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1636
Number of HSP's gapped (non-prelim): 26
length of query: 505
length of database: 14,973,337
effective HSP length: 103
effective length of query: 402
effective length of database: 8,527,803
effective search space: 3428176806
effective search space used: 3428176806
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)