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= 018549
(354 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
Length = 130
Score = 108 bits (269), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 52/95 (54%), Positives = 64/95 (67%), Gaps = 7/95 (7%)
Query: 165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 224
LF+K +TPSDVGKLNRLVIPK +A K+FP S V V L F D + K+W+
Sbjct: 13 LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVS-------VKGVLLNFEDVNGKVWR 65
Query: 225 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
FRY YW SSQS+V T+GW+RFVKE L+A D + F
Sbjct: 66 FRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSF 100
>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 = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 3/58 (5%)
Query: 45 FKGVVPQQNGHWGAQIY---ANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFP 99
++GV + G + A+I N R+WLGTF++ +DAA+AYD AA R+RG + NFP
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 = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 3/58 (5%)
Query: 45 FKGVVPQQNGHWGAQIY---ANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFP 99
++GV + G + A+I N R+WLGTF++ +DAA+AYD AA R+RG + NFP
Sbjct: 6 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63
>pdb|4I1K|A Chain A, Crystal Structure Of Vrn1 (residues 208-341)
pdb|4I1K|B Chain B, Crystal Structure Of Vrn1 (residues 208-341)
Length = 146
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 31/110 (28%), Positives = 46/110 (41%), Gaps = 17/110 (15%)
Query: 165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 224
F+ L PS + + + +P +A KY IS ++ VQL + K W
Sbjct: 48 FFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIK----------VQL-----AEKQWP 92
Query: 225 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTF 274
R C +K+ ++ F++GW F EN L D F L RD F
Sbjct: 93 VR-CLYKAGRA-KFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAF 140
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 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,404,926
Number of Sequences: 62578
Number of extensions: 427913
Number of successful extensions: 1048
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1043
Number of HSP's gapped (non-prelim): 6
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
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: 52 (24.6 bits)