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= 018971
(348 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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 60/131 (45%), Gaps = 12/131 (9%)
Query: 209 DGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREETEWFIEGDFDLY 268
DG CLFRAVA V +++ + +R D +K + ++ DF Y
Sbjct: 54 DGACLFRAVA-----------DQVYGDQDMHEVVRKHCMDYLMKNADYFSNYVTEDFTTY 102
Query: 269 VSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEY-GQEYGKEKPIRVLY 327
+++ RK + G E+ + + P+ VY + + I + G +++PIRV Y
Sbjct: 103 INRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSY 162
Query: 328 HGFGHYDALQN 338
H HY+++ N
Sbjct: 163 HRNIHYNSVVN 173
>pdb|3TMO|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba
Length = 184
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 56/131 (42%), Gaps = 12/131 (9%)
Query: 209 DGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREETEWFIEGDFDLY 268
DG CLFRAVA V ++ + +R D K + ++ DF Y
Sbjct: 54 DGACLFRAVA-----------DQVYGDQDXHEVVRKHCXDYLXKNADYFSNYVTEDFTTY 102
Query: 269 VSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEY-GQEYGKEKPIRVLY 327
+++ RK + G E + P+ VY + + I + G +++PIRV Y
Sbjct: 103 INRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSY 162
Query: 328 HGFGHYDALQN 338
H HY+++ N
Sbjct: 163 HRNIHYNSVVN 173
>pdb|3PFY|A Chain A, The Catalytic Domain Of Human Otud5
Length = 185
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 55/130 (42%), Gaps = 15/130 (11%)
Query: 209 DGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREETEWFIEGDFDLY 268
DG CLFRAVA + + R+ D K AD F ++ DF Y
Sbjct: 67 DGACLFRAVAD----QVYGDQDXHEVVRKHCXDYLXKNADYFSN-------YVTEDFTTY 115
Query: 269 VSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEYGQEYGKEKPIRVLYH 328
+++ RK + G E + P+ VY + + +G +++PIRV YH
Sbjct: 116 INRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTEPINTF----HGIHQNEDEPIRVSYH 171
Query: 329 GFGHYDALQN 338
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 = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 35/136 (25%), Positives = 62/136 (45%), Gaps = 20/136 (14%)
Query: 202 SVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKR-REETEWF 260
SV + D CLF A+A+G +++ DLR V+ E + + +
Sbjct: 21 SVHPVLDDNSCLFHAIAYGI------------FKQDSVRDLREXVSKEVLNNPVKFNDAI 68
Query: 261 IEGDFDLYVSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEYGQEYGKE 320
++ Y I K WGG E+ + S L + +Y+ D DA + I ++ ++ +
Sbjct: 69 LDKPNKDYAQWILKXESWGGAIEIGIISDAL--AVAIYVVDIDA---VKIEKFNED-KFD 122
Query: 321 KPIRVLYHGFGHYDAL 336
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 = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 35/136 (25%), Positives = 62/136 (45%), Gaps = 20/136 (14%)
Query: 202 SVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKR-REETEWF 260
SV + D CLF A+A+G +++ DLR V+ E + + +
Sbjct: 21 SVHPVLDDNSCLFHAIAYGI------------FKQDSVRDLREMVSKEVLNNPVKFNDAI 68
Query: 261 IEGDFDLYVSQIRKPHVWGGEPELLMASHVLRMPITVYMHDKDAGGLISIAEYGQEYGKE 320
++ Y I K WGG E+ + S L + +Y+ D DA + I ++ ++ +
Sbjct: 69 LDKPNKDYAQWILKMESWGGAIEIGIISDAL--AVAIYVVDIDA---VKIEKFNED-KFD 122
Query: 321 KPIRVLYHGFGHYDAL 336
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 = 0.19, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 286 MASHVLRMPITVYMHDKDAGGLISIAEYGQEYGKEKPIRVLYHGFG 331
M + + R P+ VY D DAGG++ A Y Y + + + +H F
Sbjct: 3 MNTTLFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFS 48
>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 = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 309 SIAEYGQEYGKEKPIRVLYHGFGHY 333
+++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 = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 17/77 (22%)
Query: 88 LTKPR-CNLRPLTIRSFIGSRGSQKRHIEISLACRSMKMRLLVPSQGVLPKLKLNAGPID 146
+T+P C LR LT RH E +A S+++ +P+ +KL P
Sbjct: 328 ITEPAVCALRHLT-----------SRHPEAEMAQNSVRLNYGIPA-----IVKLLNQPNQ 371
Query: 147 WPKGCASAGLICGLLVC 163
WP A+ GLI L +C
Sbjct: 372 WPLVKATIGLIRNLALC 388
>pdb|2OYO|A Chain A, Crystal Structure Of Uncharacterized Peroxidase-Related
Protein (Yp_604910.1) From Deinococcus Geothermalis Dsm
11300 At 1.51 A Resolution
pdb|2OYO|B Chain B, Crystal Structure Of Uncharacterized Peroxidase-Related
Protein (Yp_604910.1) From Deinococcus Geothermalis Dsm
11300 At 1.51 A Resolution
Length = 196
Score = 27.7 bits (60), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 204 IGIPGDGRCLFRAVAHGACLRA--GKP--APSVSIQRELAD 240
+ + G RCL+ AV+HGA LR G P A +V++ AD
Sbjct: 83 VVVSGVNRCLYCAVSHGAALREFLGDPQKADAVAVNWRHAD 123
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 0.138 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,049,459
Number of Sequences: 62578
Number of extensions: 394075
Number of successful extensions: 815
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 806
Number of HSP's gapped (non-prelim): 14
length of query: 348
length of database: 14,973,337
effective HSP length: 100
effective length of query: 248
effective length of database: 8,715,537
effective search space: 2161453176
effective search space used: 2161453176
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)