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= 046901
(172 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 = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 35/64 (54%), Positives = 41/64 (64%), Gaps = 2/64 (3%)
Query: 8 TKQSAFRGVRMRKWGKWVSEIRQPGTK-TRIWLGSYETPEMAAAAYDVAALHFRGRSGAH 66
K +RGVR R WGK+ +EIR P R+WLG++ET E AA AYD AA RG S A
Sbjct: 1 AKGKHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRG-SRAL 59
Query: 67 LNFP 70
LNFP
Sbjct: 60 LNFP 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 = 63.9 bits (154), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 34/59 (57%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 13 FRGVRMRKWGKWVSEIRQPGTK-TRIWLGSYETPEMAAAAYDVAALHFRGRSGAHLNFP 70
+RGVR R WGK+ +EIR P R+WLG++ET E AA AYD AA RG S A LNFP
Sbjct: 3 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRG-SRALLNFP 60
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 21/84 (25%)
Query: 56 ALHFRGRSGA---------HLNFPELADTLPRPASSKPEDVQLAAQEAALSFRKPIAENC 106
A+++ G SGA H++ P+ A+ L P SS P AA P E+C
Sbjct: 672 AVYYTGNSGAEAAMNWVMSHMDDPDFANPLILPGSSGPGSTSAAAD--------PPPEDC 723
Query: 107 SLGPVRIGLSPSQ----IQAINES 126
V +G S Q ++A N S
Sbjct: 724 VTTIVSMGFSRDQALKALRATNNS 747
>pdb|1GGB|H Chain H, Major Antigen-Induced Domain Rearrangements In An
Antibody
pdb|1GGC|H Chain H, Major Antigen-Induced Domain Rearrangements In An
Antibody
Length = 215
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 1 METNQVVTKQSAFRGVRMRKWGKWVSEIRQPGTKTRIWL 39
++ +Q ++ +F G + +G VS IRQP K WL
Sbjct: 12 LQPSQTLSLTCSFSGFSLSTYGMGVSWIRQPSGKGLEWL 50
>pdb|1GGI|H Chain H, Crystal Structure Of An Hiv-1 Neutralizing Antibody 50.1
In Complex With Its V3 Loop Peptide Antigen
pdb|1GGI|J Chain J, Crystal Structure Of An Hiv-1 Neutralizing Antibody 50.1
In Complex With Its V3 Loop Peptide Antigen
Length = 222
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 1 METNQVVTKQSAFRGVRMRKWGKWVSEIRQPGTKTRIWL 39
++ +Q ++ +F G + +G VS IRQP K WL
Sbjct: 12 LQPSQTLSLTCSFSGFSLSTYGMGVSWIRQPSGKGLEWL 50
>pdb|3IFO|H Chain H, X-Ray Structure Of Amyloid Beta Peptide:antibody
(Abeta1- 7:10d5) Complex
pdb|3IFO|A Chain A, X-Ray Structure Of Amyloid Beta Peptide:antibody
(Abeta1- 7:10d5) Complex
Length = 226
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 1 METNQVVTKQSAFRGVRMRKWGKWVSEIRQPGTKTRIWL 39
++++Q ++ +F G + G VS IRQP K WL
Sbjct: 12 LQSSQTLSLTCSFSGFSLSTSGMGVSWIRQPSGKGLEWL 50
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 0.131 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,349,449
Number of Sequences: 62578
Number of extensions: 207103
Number of successful extensions: 435
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 427
Number of HSP's gapped (non-prelim): 11
length of query: 172
length of database: 14,973,337
effective HSP length: 92
effective length of query: 80
effective length of database: 9,216,161
effective search space: 737292880
effective search space used: 737292880
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: 48 (23.1 bits)