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= 030320
(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 = 33.5 bits (75), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 11/87 (12%)
Query: 78 LRIKVVNLRSNSVNLKVSVDGLGPNSIK--LSGSTKTQLTSSNLKDENSFTEPNKVVPS- 134
LR+K V++ N++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 = 33.1 bits (74), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 11/87 (12%)
Query: 78 LRIKVVNLRSNSVNLKVSVDGLGPNSIK--LSGSTKTQLTSSNLKDENSFTEPNKVVPS- 134
LR+K V++ N++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 = 33.1 bits (74), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 11/87 (12%)
Query: 78 LRIKVVNLRSNSVNLKVSVDGLGPNSIK--LSGSTKTQLTSSNLKDENSFTEPNKVVPS- 134
LR+K V++ N++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 = 33.1 bits (74), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 11/87 (12%)
Query: 78 LRIKVVNLRSNSVNLKVSVDGLGPNSIK--LSGSTKTQLTSSNLKDENSFTEPNKVVPS- 134
LR+K V++ N++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|2VRK|A Chain A, Structure Of A Seleno-Methionyl Derivative Of Wild Type
Arabinofuranosidase From Thermobacillus Xylanilyticus
pdb|2VRK|B Chain B, Structure Of A Seleno-Methionyl Derivative Of Wild Type
Arabinofuranosidase From Thermobacillus Xylanilyticus
pdb|2VRK|C Chain C, Structure Of A Seleno-Methionyl Derivative Of Wild Type
Arabinofuranosidase From Thermobacillus Xylanilyticus
Length = 496
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 109 STKTQLTSSNLKDENSFTEPNKVVPS-LTLLENAAKDMDVVISPYSFTSFDL 159
+T T LTS + N+F EP +V P+ + ++ + P S T +L
Sbjct: 442 ATGTTLTSGRIDGHNTFDEPERVKPAPFRDFKLEGGHLNASLPPXSVTVLEL 493
>pdb|2VRQ|A Chain A, Structure Of An Inactive Mutant Of Arabinofuranosidase
From Thermobacillus Xylanilyticus In Complex With A
Pentasaccharide
pdb|2VRQ|B Chain B, Structure Of An Inactive Mutant Of Arabinofuranosidase
From Thermobacillus Xylanilyticus In Complex With A
Pentasaccharide
pdb|2VRQ|C Chain C, Structure Of An Inactive Mutant Of Arabinofuranosidase
From Thermobacillus Xylanilyticus In Complex With A
Pentasaccharide
Length = 496
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 109 STKTQLTSSNLKDENSFTEPNKVVPS-LTLLENAAKDMDVVISPYSFTSFDL 159
+T T LTS + N+F EP +V P+ + ++ + P S T +L
Sbjct: 442 ATGTTLTSGRIDGHNTFDEPERVKPAPFRDFKLEGGHLNASLPPMSVTVLEL 493
>pdb|1FA2|A Chain A, Crystal Structure Of Beta-Amylase From Sweet Potato
Length = 498
Score = 26.9 bits (58), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 82 VVNLRSNSVNLKVSVDGLGPNSIKLSGSTKTQLTSSNLKDEN 123
++ LR N VNL GP +K+SG T +L+ L+ +N
Sbjct: 397 LLKLRPNGVNLN------GPPKLKMSGLTYLRLSDDLLQTDN 432
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 0.127 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,074,982
Number of Sequences: 62578
Number of extensions: 126042
Number of successful extensions: 246
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 244
Number of HSP's gapped (non-prelim): 8
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 (22.0 bits)
S2: 48 (23.1 bits)