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= 026638
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 1.2, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 134 LRIKVVNLGSSSVNLKVSVDGLGPNSIK--LSGSTKTQLTSTNLKDENSFMEPNKVV--P 189
LR+K V++ +++N+ + S+K ++ STK LT L + N+F E NK++
Sbjct: 102 LRVKFVDIDINTLNIDIE-------SLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGR 154
Query: 190 SLTLLENAAKDMDVVISPYSFTSFDLL 216
+ 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 = 1.3, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 134 LRIKVVNLGSSSVNLKVSVDGLGPNSIK--LSGSTKTQLTSTNLKDENSFMEPNKVV--P 189
LR+K V++ +++N+ + S+K ++ STK LT L + N+F E NK++
Sbjct: 102 LRVKFVDIDINTLNIDIE-------SLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGR 154
Query: 190 SLTLLENAAKDMDVVISPYSFTSFDLL 216
+ 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 = 1.3, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 134 LRIKVVNLGSSSVNLKVSVDGLGPNSIK--LSGSTKTQLTSTNLKDENSFMEPNKVV--P 189
LR+K V++ +++N+ + S+K ++ STK LT L + N+F E NK++
Sbjct: 102 LRVKFVDIDINTLNIDIE-------SLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGR 154
Query: 190 SLTLLENAAKDMDVVISPYSFTSFDLL 216
+ LLE+ + M + +F L+
Sbjct: 155 DIILLEDNCESMGATFNNKCAGTFGLM 181
>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 = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 134 LRIKVVNLGSSSVNLKVSVDGLGPNSIK--LSGSTKTQLTSTNLKDENSFMEPNKVV--P 189
LR+K V++ +++N+ + S+K ++ STK LT L + N+F E NK++
Sbjct: 102 LRVKFVDIDINTLNIDIE-------SLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGR 154
Query: 190 SLTLLENAAKDMDVVISPYSFTSFDLL 216
+ 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 = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 138 VVNLGSSSVNLKVSVDGLGPNSIKLSGSTKTQLTSTNLKDENSFMEPNKVVPSLTLLENA 197
VV+LG S L + DG+ + ++ G+ + S + + +P P+ T ++ A
Sbjct: 150 VVDLGGGSTELVIGGDGVSAPTTQVQGAFSXNIGSVRXTERHLTNDP----PTQTQIDEA 205
Query: 198 AKDMD 202
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
0.313 0.128 0.360
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,881,994
Number of Sequences: 62578
Number of extensions: 206359
Number of successful extensions: 461
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 460
Number of HSP's gapped (non-prelim): 12
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
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: 50 (23.9 bits)