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= 030591
(175 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 11 KHPSYRGIRCRN-SKWVSEIREPRK-STRIWLGTYPTPEMXXXXXXXXXXXLKGSDAVLN 68
K YRG+R R K+ +EIR+P K R+WLGT+ T E ++GS A+LN
Sbjct: 2 KGKHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLN 61
Query: 69 FP 70
FP
Sbjct: 62 FP 63
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 11 KHPSYRGIRCRN-SKWVSEIREPRK-STRIWLGTYPTPEMXXXXXXXXXXXLKGSDAVLN 68
KH YRG+R R K+ +EIR+P K R+WLGT+ T E ++GS A+LN
Sbjct: 1 KH--YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLN 58
Query: 69 FP 70
FP
Sbjct: 59 FP 60
>pdb|2LBP|A Chain A, Structure Of The L-Leucine-Binding Protein Refined At 2.4
Angstroms Resolution And Comparison With The Leu(Slash)
Ile(Slash)val-Binding Protein Structure
Length = 346
Score = 29.6 bits (65), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 109 PDENQRMEQSRSNDVIGEFVDEDALLN--MPNLLVDMAEGMMVSPPR 153
P+ Q + Q+RS + +F+ + + N + N+ D AEGM+V+ P+
Sbjct: 204 PEMGQMLRQARSVGLKTQFMGPEGVGNASLSNIAGDAAEGMLVTMPK 250
>pdb|1USG|A Chain A, L-Leucine-Binding Protein, Apo Form
pdb|1USK|A Chain A, L-Leucine-Binding Protein With Leucine Bound
pdb|1USK|B Chain B, L-Leucine-Binding Protein With Leucine Bound
pdb|1USK|C Chain C, L-Leucine-Binding Protein With Leucine Bound
pdb|1USK|D Chain D, L-Leucine-Binding Protein With Leucine Bound
pdb|1USI|A Chain A, L-Leucine-Binding Protein With Phenylalanine Bound
pdb|1USI|C Chain C, L-Leucine-Binding Protein With Phenylalanine Bound
Length = 346
Score = 29.6 bits (65), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 109 PDENQRMEQSRSNDVIGEFVDEDALLN--MPNLLVDMAEGMMVSPPR 153
P+ Q + Q+RS + +F+ + + N + N+ D AEGM+V+ P+
Sbjct: 204 PEMGQMLRQARSVGLKTQFMGPEGVGNASLSNIAGDAAEGMLVTMPK 250
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
0.314 0.129 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,153,059
Number of Sequences: 62578
Number of extensions: 123973
Number of successful extensions: 90
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 88
Number of HSP's gapped (non-prelim): 4
length of query: 175
length of database: 14,973,337
effective HSP length: 92
effective length of query: 83
effective length of database: 9,216,161
effective search space: 764941363
effective search space used: 764941363
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)