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= 017035
(378 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 = 189 bits (481), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 90/109 (82%), Positives = 98/109 (89%), Gaps = 1/109 (0%)
Query: 204 DQLFEKAVTPSDVGKLNRLVIPKQHAEKHFPLQSGSTS-KGLLLNFEDVTGKVWRFRYSY 262
+ LFEKAVTPSDVGKLNRLVIPK HAEKHFPL S + S KG+LLNFEDV GKVWRFRYSY
Sbjct: 11 EALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSY 70
Query: 263 WNSSQSYVLTKGWSRFVKEKNLKAGDIVSFHRSTGGDRQLYIDWKARTG 311
WNSSQSYVLTKGWSRFVKEKNL+AGD+VSF RS G D+QLYI WK+R+G
Sbjct: 71 WNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSG 119
>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 = 52.0 bits (123), Expect = 6e-07, Method: Composition-based stats.
Identities = 28/57 (49%), Positives = 37/57 (64%), Gaps = 3/57 (5%)
Query: 71 YKGVVPQPNGRWGAQIYEKHQ---RVWLGTFNEEEEAARAYDIAAQRFRGRDAVTNF 124
Y+GV +P G++ A+I + + RVWLGTF E+AA AYD AA R RG A+ NF
Sbjct: 3 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 37/57 (64%), Gaps = 3/57 (5%)
Query: 71 YKGVVPQPNGRWGAQIYEKHQ---RVWLGTFNEEEEAARAYDIAAQRFRGRDAVTNF 124
Y+GV +P G++ A+I + + RVWLGTF E+AA AYD AA R RG A+ NF
Sbjct: 6 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62
>pdb|1YEL|A Chain A, Structure Of The Hypothetical Arabidopsis Thaliana Protein
At1g16640.1
Length = 104
Score = 31.6 bits (70), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 244 LLLNFEDVTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSFHRSTGGDRQLY 303
+ ++ D +G+ W R + LT GW FVK+ NL+ G + F DR Y
Sbjct: 40 ITVDLLDYSGRSWTVRMK--KRGEKVFLTVGWENFVKDNNLEDGKYLQFIYDR--DRTFY 95
Query: 304 I 304
+
Sbjct: 96 V 96
>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 = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 9/101 (8%)
Query: 193 AFGSDRVLKARDQLFEKAVTPSDVGKLNRLVIPKQHAEKHFPLQSGSTSKGLLLNFEDVT 252
A + + + + F + PS + + + +P AEK+ SG L
Sbjct: 35 AINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQL-------A 87
Query: 253 GKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSFH 293
K W R Y + ++GW F E NL GD+ F
Sbjct: 88 EKQWPVRCLYKAGRAKF--SQGWYEFTLENNLGEGDVCVFE 126
>pdb|3BGW|A Chain A, The Structure Of A Dnab-like Replicative Helicase And Its
Interactions With Primase
pdb|3BGW|B Chain B, The Structure Of A Dnab-like Replicative Helicase And Its
Interactions With Primase
pdb|3BGW|C Chain C, The Structure Of A Dnab-like Replicative Helicase And Its
Interactions With Primase
pdb|3BGW|D Chain D, The Structure Of A Dnab-like Replicative Helicase And Its
Interactions With Primase
pdb|3BGW|E Chain E, The Structure Of A Dnab-like Replicative Helicase And Its
Interactions With Primase
pdb|3BGW|F Chain F, The Structure Of A Dnab-like Replicative Helicase And Its
Interactions With Primase
Length = 444
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 118 RDAVTNFKQISCAGTSSDDGDIEMAFLSSHSKSEIVD 154
++AV+ +I +GT DDG I+ A ++ + + E D
Sbjct: 138 QEAVSELMEIEASGTDDDDGSIDEALVTVYEEIESAD 174
>pdb|3BH0|A Chain A, Atpase Domain Of G40p
Length = 315
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 118 RDAVTNFKQISCAGTSSDDGDIEMAFLSSHSKSEIVD 154
++AV+ +I +GT DDG I+ A ++ + + E D
Sbjct: 9 QEAVSELMEIEASGTDDDDGSIDEALVTVYEEIESAD 45
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 0.133 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,229,725
Number of Sequences: 62578
Number of extensions: 478943
Number of successful extensions: 1352
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1344
Number of HSP's gapped (non-prelim): 12
length of query: 378
length of database: 14,973,337
effective HSP length: 100
effective length of query: 278
effective length of database: 8,715,537
effective search space: 2422919286
effective search space used: 2422919286
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)