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= 030307
(179 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GR9|A Chain A, Crystal Structure Of Cold H188k S187n
pdb|3GR9|B Chain B, Crystal Structure Of Cold H188k S187n
pdb|3GR9|C Chain C, Crystal Structure Of Cold H188k S187n
pdb|3GR9|D Chain D, Crystal Structure Of Cold H188k S187n
pdb|3GR9|E Chain E, Crystal Structure Of Cold H188k S187n
pdb|3GR9|F Chain F, Crystal Structure Of Cold H188k S187n
pdb|3GR9|G Chain G, Crystal Structure Of Cold H188k S187n
pdb|3GR9|H Chain H, Crystal Structure Of Cold H188k S187n
Length = 390
Score = 30.4 bits (67), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 78 LRIKVVNLGSSSVNLKVSVDGLGPNSIK--LSGSTKTQLTSTNLKDENSFMEPNKVVPS- 134
LR+K V++ +++N+ + S+K ++ STK LT L + N+F E NK++
Sbjct: 102 LRVKFVDIDINTLNIDIE-------SLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGR 154
Query: 135 -LTLLENAAKDMDVVISPYSFTSFDLL 160
+ LLE+ + M + +F L+
Sbjct: 155 DIILLEDNCESMGATFNNKCAGTFGLM 181
>pdb|2GMS|A Chain A, E Coli Gdp-4-Keto-6-Deoxy-D-Mannose-3-Dehydratase With
Bound Hydrated Plp
pdb|2GMS|B Chain B, E Coli Gdp-4-Keto-6-Deoxy-D-Mannose-3-Dehydratase With
Bound Hydrated Plp
pdb|2GMU|A Chain A, Crystal Structure Of E Coli
Gdp-4-Keto-6-Deoxy-D-Mannose-3- Dehydratase Complexed
With Plp-Glutamate Ketimine Intermediate
pdb|2GMU|B Chain B, Crystal Structure Of E Coli
Gdp-4-Keto-6-Deoxy-D-Mannose-3- Dehydratase Complexed
With Plp-Glutamate Ketimine Intermediate
Length = 390
Score = 30.0 bits (66), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 78 LRIKVVNLGSSSVNLKVSVDGLGPNSIK--LSGSTKTQLTSTNLKDENSFMEPNKVVPS- 134
LR+K V++ +++N+ + S+K ++ STK LT L + N+F E NK++
Sbjct: 102 LRVKFVDIDINTLNIDIE-------SLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGR 154
Query: 135 -LTLLENAAKDMDVVISPYSFTSFDLL 160
+ LLE+ + M + +F L+
Sbjct: 155 DIILLEDNCESMGATFNNKCAGTFGLM 181
>pdb|2R0T|A Chain A, Crystal Sructure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase With A Trapped
Plp-Glutamate Geminal Diamine
pdb|2R0T|B Chain B, Crystal Sructure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase With A Trapped
Plp-Glutamate Geminal Diamine
Length = 390
Score = 30.0 bits (66), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 78 LRIKVVNLGSSSVNLKVSVDGLGPNSIK--LSGSTKTQLTSTNLKDENSFMEPNKVVPS- 134
LR+K V++ +++N+ + S+K ++ STK LT L + N+F E NK++
Sbjct: 102 LRVKFVDIDINTLNIDIE-------SLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGR 154
Query: 135 -LTLLENAAKDMDVVISPYSFTSFDLL 160
+ LLE+ + M + +F L+
Sbjct: 155 DIILLEDNCESMGATFNNKCAGTFGLM 181
>pdb|3B8X|A Chain A, Crystal Structure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188n
Mutant With Bound Gdp-Perosamine
pdb|3B8X|B Chain B, Crystal Structure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188n
Mutant With Bound Gdp-Perosamine
Length = 390
Score = 30.0 bits (66), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 78 LRIKVVNLGSSSVNLKVSVDGLGPNSIK--LSGSTKTQLTSTNLKDENSFMEPNKVVPS- 134
LR+K V++ +++N+ + S+K ++ STK LT L + N+F E NK++
Sbjct: 102 LRVKFVDIDINTLNIDIE-------SLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGR 154
Query: 135 -LTLLENAAKDMDVVISPYSFTSFDLL 160
+ LLE+ + M + +F L+
Sbjct: 155 DIILLEDNCESMGATFNNKCAGTFGLM 181
>pdb|3CER|A Chain A, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
pdb|3CER|B Chain B, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
pdb|3CER|C Chain C, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
pdb|3CER|D Chain D, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
pdb|3CER|E Chain E, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
Length = 343
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 82 VVNLGSSSVNLKVSVDGLGPNSIKLSGSTKTQLTSTNLKDENSFMEPNKVVPSLTLLENA 141
VV+LG S L + DG+ + ++ G+ + S + + +P P+ T ++ A
Sbjct: 150 VVDLGGGSTELVIGGDGVSAPTTQVQGAFSXNIGSVRXTERHLTNDP----PTQTQIDEA 205
Query: 142 AKDMD 146
D+D
Sbjct: 206 VADVD 210
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
0.312 0.127 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,137,468
Number of Sequences: 62578
Number of extensions: 125840
Number of successful extensions: 271
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 270
Number of HSP's gapped (non-prelim): 7
length of query: 179
length of database: 14,973,337
effective HSP length: 93
effective length of query: 86
effective length of database: 9,153,583
effective search space: 787208138
effective search space used: 787208138
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)