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= psy11734
(817 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3O7Q|A Chain A, Crystal Structure Of A Major Facilitator Superfamily (Mfs)
Transporter, Fucp, In The Outward Conformation
Length = 438
Score = 33.5 bits (75), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 20/39 (51%)
Query: 513 DAKFDWDERTQGVILSAFYYGYILTHIPGGILSQKFGGK 551
F G+I SAFY+GY + IP GIL +K K
Sbjct: 53 QQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYK 91
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 113 DAKFDWDERTQGVILSSFYYGYTLTHIPGGILSQKFGGK 151
F G+I S+FY+GY + IP GIL +K K
Sbjct: 53 QQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYK 91
>pdb|3O7P|A Chain A, Crystal Structure Of The E.Coli Fucose:proton Symporter,
Fucp (N162a)
Length = 438
Score = 33.5 bits (75), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 20/39 (51%)
Query: 513 DAKFDWDERTQGVILSAFYYGYILTHIPGGILSQKFGGK 551
F G+I SAFY+GY + IP GIL +K K
Sbjct: 53 QQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYK 91
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 113 DAKFDWDERTQGVILSSFYYGYTLTHIPGGILSQKFGGK 151
F G+I S+FY+GY + IP GIL +K K
Sbjct: 53 QQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYK 91
>pdb|1T3I|A Chain A, Structure Of Slr0077SUFS, THE ESSENTIAL CYSTEINE
Desulfurase From Synechocystis Pcc 6803
pdb|1T3I|B Chain B, Structure Of Slr0077SUFS, THE ESSENTIAL CYSTEINE
Desulfurase From Synechocystis Pcc 6803
Length = 420
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 28/113 (24%), Positives = 51/113 (45%), Gaps = 4/113 (3%)
Query: 338 TIMALSNGLGCVSGMVAPLTVGFLTQNIISINPIDLSPNFSGTIMALSNGLGCVSG--MV 395
T++ +SN LGCV+ + + ++ +P++ + + SG M
Sbjct: 174 TVVHISNTLGCVNPAEEIAQLAHQAGAKVLVDACQSAPHYPLDVQLIDCDWLVASGHKMC 233
Query: 396 APLTVGFLTQNKTLSEWRVVFWIMFLALVISNVFFVLFGSGEVQYWNESILPA 448
AP +GFL + + E F+ +I+ VFF F +GE+ + E+ PA
Sbjct: 234 APTGIGFLYGKEEILEAMPPFFGG--GEMIAEVFFDHFTTGELPHKFEAGTPA 284
>pdb|1F3D|H Chain H, Catalytic Antibody 4b2 In Complex With Its Amidinium
Hapten.
pdb|1F3D|K Chain K, Catalytic Antibody 4b2 In Complex With Its Amidinium
Hapten
Length = 217
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 496 PNANGNHTVVSKTYTTLDAKFDWDERTQGVILSAFYYGYILTHIPGGILSQKFGGKHTLG 555
P A+ + + Y+ +D W +++ G L + GYI+ + G +QKF GK TL
Sbjct: 14 PGASVKVSCKASGYSFIDYNIHWVKQSHGKSLE--WIGYIVPYSGGTTFNQKFKGKATLT 71
Query: 556 LGFLSTAIFTLLTPL 570
+ S+ F L L
Sbjct: 72 VDKSSSTAFMHLNSL 86
>pdb|1JAX|A Chain A, Structure Of Coenzyme F420h2:nadp+ Oxidoreductase (Fno)
pdb|1JAX|B Chain B, Structure Of Coenzyme F420h2:nadp+ Oxidoreductase (Fno)
pdb|1JAY|A Chain A, Structure Of Coenzyme F420h2:nadp+ Oxidoreductase (Fno)
With Its Substrates Bound
pdb|1JAY|B Chain B, Structure Of Coenzyme F420h2:nadp+ Oxidoreductase (Fno)
With Its Substrates Bound
Length = 212
Score = 30.4 bits (67), Expect = 4.2, Method: Composition-based stats.
Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 31/97 (31%)
Query: 502 HTVVSKTYTTLDAKFDW-------DERTQGVILSAFYYGYILTHIPGGILSQKFGGKHTL 554
HT+ + + LD KFDW D+ ++ V++S L + G L
Sbjct: 133 HTIPAARFANLDEKFDWDVPVCGDDDESKKVVMS---------------LISEIDGLRPL 177
Query: 555 GLGFLSTA-IFTLLTPLIAHSGPVSMTVLRFLEGVGE 590
G LS + + LTPLI + ++RF G+GE
Sbjct: 178 DAGPLSNSRLVESLTPLI-------LNIMRF-NGMGE 206
>pdb|3IY1|B Chain B, Variable Domains Of The Wam Of Fab B Fitted Into The
Cryoem Reconstruction Of The Virus-Fab B Complex
Length = 109
Score = 29.3 bits (64), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 509 YTTLDAKFDWDERTQGVILSAFYYGYILTHIPGGILSQKFGGKHTLGLGFLSTAIFTLLT 568
YT + W ++T G L Y GYI T G ++KF GK TL + S+ F L+
Sbjct: 21 YTFTNYYISWIKQTTGQGLE--YVGYISTGSGGTNYNEKFKGKATLTVDKSSSTTFMQLS 78
Query: 569 PLIAHSGPV 577
L V
Sbjct: 79 SLTPDDSAV 87
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
0.325 0.139 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,856,373
Number of Sequences: 62578
Number of extensions: 839116
Number of successful extensions: 1908
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1894
Number of HSP's gapped (non-prelim): 21
length of query: 817
length of database: 14,973,337
effective HSP length: 107
effective length of query: 710
effective length of database: 8,277,491
effective search space: 5877018610
effective search space used: 5877018610
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (26.2 bits)