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= 036655
(243 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
Structure
Length = 63
Score = 76.3 bits (186), Expect = 1e-14, Method: Composition-based stats.
Identities = 35/58 (60%), Positives = 46/58 (79%), Gaps = 1/58 (1%)
Query: 36 YKGVRQRTWGKWVAEIREPNR-GARLWLGTFDTSHEAAMAYDAAARKLYGPDAKLNLP 92
Y+GVRQR WGK+ AEIR+P + GAR+WLGTF+T+ +AA+AYD AA ++ G A LN P
Sbjct: 3 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60
>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
Minimized Mean Structure
pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
46 Structures
Length = 70
Score = 75.1 bits (183), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 35/58 (60%), Positives = 46/58 (79%), Gaps = 1/58 (1%)
Query: 36 YKGVRQRTWGKWVAEIREPNR-GARLWLGTFDTSHEAAMAYDAAARKLYGPDAKLNLP 92
Y+GVRQR WGK+ AEIR+P + GAR+WLGTF+T+ +AA+AYD AA ++ G A LN P
Sbjct: 6 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63
>pdb|4G29|A Chain A, Structure Of The Catalytic Domain Of The Salmonella
Virulence Factor Ssei
Length = 186
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 46 KWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKL 82
+WV + R R ++ F S AA AYDA R+L
Sbjct: 119 EWVCKYRXATRRKLIYYTDFSNSSIAANAYDALPREL 155
>pdb|4G2B|A Chain A, Structure Of The Catalytic Domain Of The Salmonella
Virulence Factor Ssei
pdb|4G2B|B Chain B, Structure Of The Catalytic Domain Of The Salmonella
Virulence Factor Ssei
Length = 186
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 46 KWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKL 82
+WV + R R ++ F S AA AYDA R+L
Sbjct: 119 EWVCKYRMATRRKLIYYTDFSNSSIAANAYDALPREL 155
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
0.315 0.130 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,463,092
Number of Sequences: 62578
Number of extensions: 284434
Number of successful extensions: 657
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 651
Number of HSP's gapped (non-prelim): 4
length of query: 243
length of database: 14,973,337
effective HSP length: 96
effective length of query: 147
effective length of database: 8,965,849
effective search space: 1317979803
effective search space used: 1317979803
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)