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= 009469
(534 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3O7P|A Chain A, Crystal Structure Of The E.Coli Fucose:proton Symporter,
Fucp (N162a)
Length = 438
Score = 35.4 bits (80), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 2/122 (1%)
Query: 210 LLCFSAFLLCNMDRVNMSIAILPMSKEFNWNSTTVGLIQSSFFWGYLLTQIVGGIWADKF 269
LLC FL + +N I + + F + GLIQS+F++GY + I GI K
Sbjct: 30 LLCSLFFLWAVANNLN-DILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKL 88
Query: 270 GGKPVLGFGVIWWSVATVLT-PVAARIGLPFLLIMRAFMGIGEGVAMPAMNNMLSKWIPV 328
K + G+ +++ L P A + L+ + G G A N ++ P
Sbjct: 89 SYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLGPE 148
Query: 329 SE 330
S
Sbjct: 149 SS 150
>pdb|3O7Q|A Chain A, Crystal Structure Of A Major Facilitator Superfamily (Mfs)
Transporter, Fucp, In The Outward Conformation
Length = 438
Score = 35.0 bits (79), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 2/122 (1%)
Query: 210 LLCFSAFLLCNMDRVNMSIAILPMSKEFNWNSTTVGLIQSSFFWGYLLTQIVGGIWADKF 269
LLC FL + +N I + + F + GLIQS+F++GY + I GI K
Sbjct: 30 LLCSLFFLWAVANNLN-DILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKL 88
Query: 270 GGKPVLGFGVIWWSVATVLT-PVAARIGLPFLLIMRAFMGIGEGVAMPAMNNMLSKWIPV 328
K + G+ +++ L P A + L+ + G G A N ++ P
Sbjct: 89 SYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLGPE 148
Query: 329 SE 330
S
Sbjct: 149 SS 150
>pdb|3B4U|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase From
Agrobacterium Tumefaciens Str. C58
pdb|3B4U|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase From
Agrobacterium Tumefaciens Str. C58
Length = 294
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 437 NWGTFILLTWMPTYYNQVLKFNLTESGLFCVLPWLTMAVFANMGGWIADTLVSKGLSITA 496
N G +L P+Y+ N+++ GLF W + AVF+ +G D LV S+T
Sbjct: 96 NAGARNILLAPPSYFK-----NVSDDGLFA---WFS-AVFSKIGKDARDILVYNIPSVTM 146
Query: 497 VRKIMQSIGFLGPAF 511
V ++ +G L AF
Sbjct: 147 VTLSVELVGRLKAAF 161
>pdb|3CSR|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CSZ|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CT0|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CT1|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CT5|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
Length = 159
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 258 TQIVGGIWADKFGGKPVLGFGVIWWSVATVLTPVAARIGLPF 299
+ I G+W + G LGFG++ W+ A+ A GLP+
Sbjct: 46 STINPGLWQNLDEGNTSLGFGLVQWTPASNYINWANSQGLPY 87
>pdb|3CSQ|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CSQ|B Chain B, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CSQ|C Chain C, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CSQ|D Chain D, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
Length = 334
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 5/86 (5%)
Query: 263 GIWADKFGGKPVLGFGVIWWSVATVLTPVAARIGLPFL----LIMRAFMGIGEGVAMPAM 318
G+W + G LGFG++ W+ A+ A GLP+ + R + +
Sbjct: 51 GLWQNLDEGNTSLGFGLVQWTPASNYINWANSQGLPYKNMDSELKRIIWEVNNNAQWINL 110
Query: 319 NNM-LSKWIPVSERSRSLAFVYSGMY 343
+M ++I ++ R LA ++ Y
Sbjct: 111 RDMTFKEYIKSTKTPRELAMIFLASY 136
>pdb|2P3X|A Chain A, Crystal Structure Of Grenache (Vitis Vinifera) Polyphenol
Oxidase
Length = 339
Score = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 64 EHANRSMLHVWGNSDEKALKHIANCHTGKEHPLFLQCNEKFNRIYP-WKRTNNKCECYFS 122
EHA +++H W +K + + N +T P+F + +R++ WK K F+
Sbjct: 235 EHAPHNIVHKWTGLADKPSEDMGNFYTAGRDPIFFGHHANVDRMWNIWKTIGGKNRKDFT 294
Query: 123 SRHSLGGWF 131
L F
Sbjct: 295 DTDWLDATF 303
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
0.323 0.137 0.447
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,326,957
Number of Sequences: 62578
Number of extensions: 684186
Number of successful extensions: 1262
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1255
Number of HSP's gapped (non-prelim): 12
length of query: 534
length of database: 14,973,337
effective HSP length: 103
effective length of query: 431
effective length of database: 8,527,803
effective search space: 3675483093
effective search space used: 3675483093
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)