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= 043236
(222 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FPX|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Q237n Mutant From Helicobacter Pylori
pdb|4FPX|B Chain B, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Q237n Mutant From Helicobacter Pylori
Length = 271
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 13 LAPAEYHLRSDYEDQAMSGGKLTLQHRRRCLQ 44
L P E H++S++ +SG +TL + R Q
Sbjct: 43 LLPLESHIKSEFLHLGLSGANVTLPFKERAFQ 74
>pdb|4FQ8|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Y210a Mutant From Helicobacter Pylori In Complex With
Shikimate
pdb|4FQ8|B Chain B, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Y210a Mutant From Helicobacter Pylori In Complex With
Shikimate
Length = 271
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 13 LAPAEYHLRSDYEDQAMSGGKLTLQHRRRCLQ 44
L P E H++S++ +SG +TL + R Q
Sbjct: 43 LLPLESHIKSEFLHLGLSGANVTLPFKERAFQ 74
>pdb|4FOS|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Q237a Mutant From Helicobacter Pylori In Complex With
Shikimate
Length = 271
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 13 LAPAEYHLRSDYEDQAMSGGKLTLQHRRRCLQ 44
L P E H++S++ +SG +TL + R Q
Sbjct: 43 LLPLESHIKSEFLHLGLSGANVTLPFKERAFQ 74
>pdb|4FR5|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Y210s Mutant From Helicobacter Pylori In Complex With
Shikimate
pdb|4FR5|B Chain B, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Y210s Mutant From Helicobacter Pylori In Complex With
Shikimate
Length = 271
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 13 LAPAEYHLRSDYEDQAMSGGKLTLQHRRRCLQ 44
L P E H++S++ +SG +TL + R Q
Sbjct: 43 LLPLESHIKSEFLHLGLSGANVTLPFKERAFQ 74
>pdb|3PHG|A Chain A, Crystal Structure Of The Shikimate 5-Dehydrogenase
(Aroe) From Helicobacter Pylori
pdb|3PHG|B Chain B, Crystal Structure Of The Shikimate 5-Dehydrogenase
(Aroe) From Helicobacter Pylori
pdb|3PHH|A Chain A, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter
Pylori In Complex With Shikimate
pdb|3PHI|A Chain A, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter
Pylori In Complex With Shikimate And Nadph
pdb|3PHI|B Chain B, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter
Pylori In Complex With Shikimate And Nadph
pdb|3PHJ|A Chain A, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter
Pylori In Complex With 3-Dehydroshikimate
pdb|3PHJ|B Chain B, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter
Pylori In Complex With 3-Dehydroshikimate
Length = 269
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 13 LAPAEYHLRSDYEDQAMSGGKLTLQHRRRCLQ 44
L P E H++S++ +SG +TL + R Q
Sbjct: 43 LLPLESHIKSEFLHLGLSGANVTLPFKERAFQ 74
>pdb|4FOO|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Q237k Mutant From Helicobacter Pylori
pdb|4FOO|B Chain B, Crystal Structure Of Shikimate Dehydrogenase (Aroe)
Q237k Mutant From Helicobacter Pylori
Length = 271
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 13 LAPAEYHLRSDYEDQAMSGGKLTLQHRRRCLQ 44
L P E H++S++ +SG +TL + R Q
Sbjct: 43 LLPLESHIKSEFLHLGLSGANVTLPFKERAFQ 74
>pdb|1XO8|A Chain A, Solution Structure Of At1g01470 From Arabidopsis Thaliana
Length = 151
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 98 ENVTLLADVSVKNPNYNSFKYGNTTTSIYYGGVVVGEGHIPQA---QAKARRTLRMNVTV 154
++V LA VSV NP +S + + + G +G+G IP +AK L + V V
Sbjct: 37 DSVEYLAKVSVTNPYSHSIPICEISFTFHSAGREIGKGKIPDPGSLKAKDMTALDIPVVV 96
>pdb|1AY0|A Chain A, Identification Of Catalytically Important Residues In
Yeast Transketolase
pdb|1AY0|B Chain B, Identification Of Catalytically Important Residues In
Yeast Transketolase
Length = 680
Score = 26.9 bits (58), Expect = 8.1, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 122 TTSIYYGGVVVGEGHIPQAQAKARRTLRMNVTVDLNPEKFLTVP 165
TT+I YG + G + A KA ++ NP+K VP
Sbjct: 247 TTTIGYGSLHAGSHSVAGAPLKADDVKQLKSKFGFNPDKSFVVP 290
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
0.316 0.130 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,198,941
Number of Sequences: 62578
Number of extensions: 169049
Number of successful extensions: 397
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 389
Number of HSP's gapped (non-prelim): 16
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)