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= 038672
(148 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J2R|A Chain A, Crystal Structure Of Escherichia Coli Gene Product Yecd At
1.3 A Resolution
pdb|1J2R|B Chain B, Crystal Structure Of Escherichia Coli Gene Product Yecd At
1.3 A Resolution
pdb|1J2R|C Chain C, Crystal Structure Of Escherichia Coli Gene Product Yecd At
1.3 A Resolution
pdb|1J2R|D Chain D, Crystal Structure Of Escherichia Coli Gene Product Yecd At
1.3 A Resolution
Length = 199
Score = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 26/55 (47%)
Query: 88 STDEALNRHMKFCEQFRSSSPPARPAADDLISAMKHILRRSLDSPRKSKSPPTSF 142
+ DE +NR K +FR+S P + L++ +D+P +K P ++
Sbjct: 40 TADEVVNRAGKLAAKFRASGQPVFLVRVGWSADYAEALKQPVDAPSPAKVLPENW 94
>pdb|2Y6E|A Chain A, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|B Chain B, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|C Chain C, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|D Chain D, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|E Chain E, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|F Chain F, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
Length = 367
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 26 KDQSEVEFARCECCGLTEECTAAYVSRVKERYGGR 60
KD+ E E R G+ E AY +K+ + GR
Sbjct: 39 KDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGR 73
>pdb|2C5E|A Chain A, Gdp-Mannose-3', 5' -Epimerase (Arabidopsis Thaliana),
K217a, With Gdp-Alpha-D-Mannose Bound In The Active
Site.
pdb|2C5E|B Chain B, Gdp-Mannose-3', 5' -Epimerase (Arabidopsis Thaliana),
K217a, With Gdp-Alpha-D-Mannose Bound In The Active Site
Length = 379
Score = 26.2 bits (56), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 76 CRSKKRENHMMISTDEALNRHMK---FCEQFR 104
R K E H +I++D N HM FC++F
Sbjct: 46 ARRLKHEGHYVIASDWKKNEHMTEDMFCDEFH 77
>pdb|2C59|A Chain A, Gdp-Mannose-3', 5' -Epimerase (Arabidopsis Thaliana), With
Gdp-Alpha-D-Mannose And Gdp-Beta-L-Galactose Bound In
The Active Site.
pdb|2C59|B Chain B, Gdp-Mannose-3', 5' -Epimerase (Arabidopsis Thaliana), With
Gdp-Alpha-D-Mannose And Gdp-Beta-L-Galactose Bound In
The Active Site
Length = 379
Score = 26.2 bits (56), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 76 CRSKKRENHMMISTDEALNRHMK---FCEQFR 104
R K E H +I++D N HM FC++F
Sbjct: 46 ARRLKHEGHYVIASDWKKNEHMTEDMFCDEFH 77
>pdb|2C54|A Chain A, Gdp-Mannose-3', 5' -Epimerase (Arabidopsis Thaliana),
K178r, With Gdp-Beta-L-Gulose And
Gdp-4-Keto-Beta-L-Gulose Bound In Active Site.
pdb|2C54|B Chain B, Gdp-Mannose-3', 5' -Epimerase (Arabidopsis Thaliana),
K178r, With Gdp-Beta-L-Gulose And
Gdp-4-Keto-Beta-L-Gulose Bound In Active Site
Length = 379
Score = 26.2 bits (56), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 76 CRSKKRENHMMISTDEALNRHMK---FCEQF 103
R K E H +I++D N HM FC++F
Sbjct: 46 ARRLKHEGHYVIASDWKKNEHMTEDMFCDEF 76
>pdb|2C5A|A Chain A, Gdp-Mannose-3', 5' -Epimerase (Arabidopsis Thaliana),
Y174f, With Gdp-Beta-L-Galactose Bound In The Active
Site
pdb|2C5A|B Chain B, Gdp-Mannose-3', 5' -Epimerase (Arabidopsis Thaliana),
Y174f, With Gdp-Beta-L-Galactose Bound In The Active
Site
Length = 379
Score = 26.2 bits (56), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 76 CRSKKRENHMMISTDEALNRHMK---FCEQFR 104
R K E H +I++D N HM FC++F
Sbjct: 46 ARRLKHEGHYVIASDWKKNEHMTEDMFCDEFH 77
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
0.318 0.128 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,344,266
Number of Sequences: 62578
Number of extensions: 107578
Number of successful extensions: 260
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 258
Number of HSP's gapped (non-prelim): 9
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
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: 47 (22.7 bits)