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= 017519
(370 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TMP|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|C Chain C, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|E Chain E, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|G Chain G, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
Length = 184
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 60/131 (45%), Gaps = 12/131 (9%)
Query: 231 DGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREETEWFIEGDFDLY 290
DG CLFRAVA V +++ + +R D +K + ++ DF Y
Sbjct: 54 DGACLFRAVA-----------DQVYGDQDMHEVVRKHCMDYLMKNADYFSNYVTEDFTTY 102
Query: 291 VSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEY-GQEYGKEKPIRVLY 349
+++ RK + G E+ + + P+ VY + + I + G +++PIRV Y
Sbjct: 103 INRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSY 162
Query: 350 HGFGHYDALQN 360
H HY+++ N
Sbjct: 163 HRNIHYNSVVN 173
>pdb|3TMO|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba
Length = 184
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 56/131 (42%), Gaps = 12/131 (9%)
Query: 231 DGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREETEWFIEGDFDLY 290
DG CLFRAVA V ++ + +R D K + ++ DF Y
Sbjct: 54 DGACLFRAVA-----------DQVYGDQDXHEVVRKHCXDYLXKNADYFSNYVTEDFTTY 102
Query: 291 VSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEY-GQEYGKEKPIRVLY 349
+++ RK + G E + P+ VY + + I + G +++PIRV Y
Sbjct: 103 INRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSY 162
Query: 350 HGFGHYDALQN 360
H HY+++ N
Sbjct: 163 HRNIHYNSVVN 173
>pdb|3PFY|A Chain A, The Catalytic Domain Of Human Otud5
Length = 185
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 55/130 (42%), Gaps = 15/130 (11%)
Query: 231 DGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREETEWFIEGDFDLY 290
DG CLFRAVA + + R+ D K AD F ++ DF Y
Sbjct: 67 DGACLFRAVA----DQVYGDQDXHEVVRKHCXDYLXKNADYFSN-------YVTEDFTTY 115
Query: 291 VSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEYGQEYGKEKPIRVLYH 350
+++ RK + G E + P+ VY + + +G +++PIRV YH
Sbjct: 116 INRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTEPINTF----HGIHQNEDEPIRVSYH 171
Query: 351 GFGHYDALQN 360
HY+++ N
Sbjct: 172 RNIHYNSVVN 181
>pdb|3C0R|A Chain A, Structure Of Ovarian Tumor (Otu) Domain In Complex With
Ubiquitin
pdb|3C0R|C Chain C, Structure Of Ovarian Tumor (Otu) Domain In Complex With
Ubiquitin
Length = 212
Score = 37.0 bits (84), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 35/136 (25%), Positives = 62/136 (45%), Gaps = 20/136 (14%)
Query: 224 SVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREE-TEWF 282
SV + D CLF A+A+G +++ DLR V+ E + + +
Sbjct: 21 SVHPVLDDNSCLFHAIAYGI------------FKQDSVRDLREXVSKEVLNNPVKFNDAI 68
Query: 283 IEGDFDLYVSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEYGQEYGKE 342
++ Y I K WGG E+ + S L + +Y+ D DA + I ++ ++ +
Sbjct: 69 LDKPNKDYAQWILKXESWGGAIEIGIISDAL--AVAIYVVDIDA---VKIEKFNEDKF-D 122
Query: 343 KPIRVLYHGFGHYDAL 358
I +L++G HYD+L
Sbjct: 123 NYILILFNGI-HYDSL 137
>pdb|3BY4|A Chain A, Structure Of Ovarian Tumor (Otu) Domain In Complex With
Ubiquitin
Length = 212
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 35/136 (25%), Positives = 62/136 (45%), Gaps = 20/136 (14%)
Query: 224 SVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREE-TEWF 282
SV + D CLF A+A+G +++ DLR V+ E + + +
Sbjct: 21 SVHPVLDDNSCLFHAIAYGI------------FKQDSVRDLREMVSKEVLNNPVKFNDAI 68
Query: 283 IEGDFDLYVSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEYGQEYGKE 342
++ Y I K WGG E+ + S L + +Y+ D DA + I ++ ++ +
Sbjct: 69 LDKPNKDYAQWILKMESWGGAIEIGIISDAL--AVAIYVVDIDA---VKIEKFNEDKF-D 122
Query: 343 KPIRVLYHGFGHYDAL 358
I +L++G HYD+L
Sbjct: 123 NYILILFNGI-HYDSL 137
>pdb|1S5U|A Chain A, Crystal Structure Of Hypothetical Protein Ec709 From
Escherichia Coli
pdb|1S5U|B Chain B, Crystal Structure Of Hypothetical Protein Ec709 From
Escherichia Coli
pdb|1S5U|C Chain C, Crystal Structure Of Hypothetical Protein Ec709 From
Escherichia Coli
pdb|1S5U|D Chain D, Crystal Structure Of Hypothetical Protein Ec709 From
Escherichia Coli
pdb|1S5U|E Chain E, Crystal Structure Of Hypothetical Protein Ec709 From
Escherichia Coli
pdb|1S5U|F Chain F, Crystal Structure Of Hypothetical Protein Ec709 From
Escherichia Coli
pdb|1S5U|G Chain G, Crystal Structure Of Hypothetical Protein Ec709 From
Escherichia Coli
pdb|1S5U|H Chain H, Crystal Structure Of Hypothetical Protein Ec709 From
Escherichia Coli
Length = 138
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 308 MASHVLRMPITVYMHDKDAGGLISIAEYGQEYGKEKPIRVLYHGFGH 354
M + + R P+ VY D DAGG++ A Y Y + + + +H F
Sbjct: 3 MNTTLFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQ 49
>pdb|2VGL|A Chain A, Ap2 Clathrin Adaptor Core
pdb|2XA7|A Chain A, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 621
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 16/79 (20%)
Query: 10 SVFYLLLLAVVA-GDIDGYANMIVSTSICA--CAKNVVNLGGRFQGQMGGNICGVTYRGP 66
V+Y ++ V+ D+ GYA V ++ A C +N+V +GG G+ G I G P
Sbjct: 460 EVWYRVIQIVINRDDVQGYAAKTVFEALQAPACHENLVKVGGYILGEFGNLIAG----DP 515
Query: 67 SSS---------CCFYLCS 76
SS F+LCS
Sbjct: 516 RSSPLIQFNLLHSKFHLCS 534
>pdb|2JKR|A Chain A, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKR|L Chain L, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKT|A Chain A, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2JKT|L Chain L, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
Length = 623
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 16/79 (20%)
Query: 10 SVFYLLLLAVVA-GDIDGYANMIVSTSICA--CAKNVVNLGGRFQGQMGGNICGVTYRGP 66
V+Y ++ V+ D+ GYA V ++ A C +N+V +GG G+ G I G P
Sbjct: 460 EVWYRVIQIVINRDDVQGYAAKTVFEALQAPACHENLVKVGGYILGEFGNLIAG----DP 515
Query: 67 SSS---------CCFYLCS 76
SS F+LCS
Sbjct: 516 RSSPLIQFNLLHSKFHLCS 534
>pdb|3K2I|A Chain A, Human Acyl-Coenzyme A Thioesterase 4
pdb|3K2I|B Chain B, Human Acyl-Coenzyme A Thioesterase 4
Length = 422
Score = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 331 SIAEYGQEYGKEKPIRVLYHGFGHY 355
+++E Q +GKEKP + Y G GHY
Sbjct: 338 TVSERLQAHGKEKPQIICYPGTGHY 362
>pdb|3IFQ|A Chain A, Interction Of Plakoglobin And Beta-Catenin With Desmosomal
Cadherins
pdb|3IFQ|B Chain B, Interction Of Plakoglobin And Beta-Catenin With Desmosomal
Cadherins
Length = 553
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 17/77 (22%)
Query: 110 LTKPR-CNLRPLTIRSFIGSRGSQKRHIEISLACRSMKMRLLVPSQGVLPKLKLNAGPID 168
+T+P C LR LT RH E +A S+++ +P+ +KL P
Sbjct: 328 ITEPAVCALRHLT-----------SRHPEAEMAQNSVRLNYGIPA-----IVKLLNQPNQ 371
Query: 169 WPKGCASAGLICGLLVC 185
WP A+ GLI L +C
Sbjct: 372 WPLVKATIGLIRNLALC 388
>pdb|4HXD|B Chain B, Diversity Of Ubiquitin And Isg15 Specificity Amongst
Nairoviruses Viral Ovarian Tumor Domain Proteases
pdb|4HXD|D Chain D, Diversity Of Ubiquitin And Isg15 Specificity Amongst
Nairoviruses Viral Ovarian Tumor Domain Proteases
Length = 174
Score = 27.7 bits (60), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 32/138 (23%), Positives = 58/138 (42%), Gaps = 11/138 (7%)
Query: 223 YSVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREETEWF 282
+ VI PGDG C + ++A P+ ++ L ++A E E
Sbjct: 28 FEVIRQPGDGNCFYHSIAE-LFFDVKTPSSFRKVKEHL------QLAAEVYYDTEPEAVG 80
Query: 283 IEGDFDLYVSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEYGQEYGK- 341
D Y+ K + WGG E M S L+ I +++ + +I ++G G+
Sbjct: 81 TGISKDEYIKVAMKDNEWGGSLEASMLSKHLQTTIILWVVNSTEQVTAAI-KFGP--GRV 137
Query: 342 EKPIRVLYHGFGHYDALQ 359
+ +++ G H+DAL+
Sbjct: 138 STALNLMHVGRTHFDALR 155
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 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,609,066
Number of Sequences: 62578
Number of extensions: 417391
Number of successful extensions: 863
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 854
Number of HSP's gapped (non-prelim): 15
length of query: 370
length of database: 14,973,337
effective HSP length: 100
effective length of query: 270
effective length of database: 8,715,537
effective search space: 2353194990
effective search space used: 2353194990
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)