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= 007159
(615 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 = 0.11, 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 = 35.4 bits (80), Expect = 0.11, 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|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
From E.Coli
Length = 451
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 44/203 (21%), Positives = 80/203 (39%), Gaps = 18/203 (8%)
Query: 418 KLILSKAPVWALIISHFCHNWGTFILLTWMPTYYNQVLKFNLTESGLFCVLPWLTMAVFA 477
+ +L +W + I++ + +L W PTY +V F L +S L
Sbjct: 246 QYVLPNKLLWYIAIANVFVYLLRYGILDWSPTYLKEVKHFALDKSSWAYFLYEYAGIPGT 305
Query: 478 NMGGWIADTLV-----SKGLSITAVRKIMQSIGFLGPAFFLTQLSHVRTPAMAVLCMACS 532
+ GW++D + + G+ + I + ++ PA P + ++CM
Sbjct: 306 LLCGWMSDKVFRGNRGATGVFFMTLVTIATIVYWMNPA---------GNPTVDMICMIVI 356
Query: 533 QGSDAFSQSGLYSNHQ-DIGP-RYAGVLLGLSNTAGVLAG-VFGTAATGYILQRGSWDDV 589
G + L H ++ P + AG G + G L G V +A GY + WD
Sbjct: 357 -GFLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSVAASAIVGYTVDFFGWDGG 415
Query: 590 FKVAVVLYIIGTLVWNLFATGER 612
F V + I+ ++ + GE+
Sbjct: 416 FMVMIGGSILAVILLIVVMIGEK 438
>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 = 30.4 bits (67), Expect = 2.9, 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 = 5.0, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 260 IVGGIWADKFGGKPVLGFGVIWWSVATVLTPVAARIGLPF 299
I G+W + G LGFG++ W+ A+ A GLP+
Sbjct: 48 INPGLWQNLDEGNTSLGFGLVQWTPASNYINWANSQGLPY 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 = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 5/91 (5%)
Query: 258 TQIVGGIWADKFGGKPVLGFGVIWWSVATVLTPVAARIGLPFL----LIMRAFMGIGEGV 313
+ I G+W + G LGFG++ W+ A+ A GLP+ + R +
Sbjct: 46 STINPGLWQNLDEGNTSLGFGLVQWTPASNYINWANSQGLPYKNMDSELKRIIWEVNNNA 105
Query: 314 AMPAMNNM-LSKWIPVSERSRSLAFVYSGMY 343
+ +M ++I ++ R LA ++ Y
Sbjct: 106 QWINLRDMTFKEYIKSTKTPRELAMIFLASY 136
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 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,803,795
Number of Sequences: 62578
Number of extensions: 793809
Number of successful extensions: 1522
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1514
Number of HSP's gapped (non-prelim): 11
length of query: 615
length of database: 14,973,337
effective HSP length: 105
effective length of query: 510
effective length of database: 8,402,647
effective search space: 4285349970
effective search space used: 4285349970
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)