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= 008070
(579 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
From E.Coli
Length = 451
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 44/203 (21%), Positives = 80/203 (39%), Gaps = 18/203 (8%)
Query: 382 KLILSKAPVWALIISHFCHNWGTFILLTWMPTYYNQVLKFNLTESGLFCVLPWLTMAVFA 441
+ +L +W + I++ + +L W PTY +V F L +S L
Sbjct: 246 QYVLPNKLLWYIAIANVFVYLLRYGILDWSPTYLKEVKHFALDKSSWAYFLYEYAGIPGT 305
Query: 442 NMGGWIADTLV-----SKGLSITAVRKIMQSIGFLGPAFFLTQLSHVRTPAMAVLCMACS 496
+ GW++D + + G+ + I + ++ PA P + ++CM
Sbjct: 306 LLCGWMSDKVFRGNRGATGVFFMTLVTIATIVYWMNPA---------GNPTVDMICMIVI 356
Query: 497 QGSDAFSQSGLYSNHQ-DIGP-RYAGVLLGLSNTAGVLAG-VFGTAATGYILQRGSWDDV 553
G + L H ++ P + AG G + G L G V +A GY + WD
Sbjct: 357 -GFLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSVAASAIVGYTVDFFGWDGG 415
Query: 554 FKVAVVLYIIGTLVWNLFATGER 576
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 = 2.7, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 401 NWGTFILLTWMPTYYNQVLKFNLTESGLFCVLPWLTMAVFANMGGWIADTLVSKGLSITA 460
N G +L P+Y+ N+++ GLF W + AVF+ +G D LV S+T
Sbjct: 96 NAGARNILLAPPSYFK-----NVSDDGLFA---WFS-AVFSKIGKDARDILVYNIPSVTM 146
Query: 461 VRKIMQSIGFLGPAF 475
V ++ +G L AF
Sbjct: 147 VTLSVELVGRLKAAF 161
>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 = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 5/107 (4%)
Query: 206 WVVVLLCFSAFLLCNMDRIVGGIWADKFGGKPVLGFGVIWWSVATVLTPVAARIGLPFL- 264
W +C + + I G+W + G LGFG++ W+ A+ A GLP+
Sbjct: 30 WTKQAICGMLGNMQSESTINPGLWQNLDEGNTSLGFGLVQWTPASNYINWANSQGLPYKN 89
Query: 265 ---LIMRAFMGIGEGVAMPAMNNM-LSKWIPVSERSRSLAFVYSGMY 307
+ R + + +M ++I ++ R LA ++ Y
Sbjct: 90 MDSELKRIIWEVNNNAQWINLRDMTFKEYIKSTKTPRELAMIFLASY 136
>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 = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 26/58 (44%)
Query: 206 WVVVLLCFSAFLLCNMDRIVGGIWADKFGGKPVLGFGVIWWSVATVLTPVAARIGLPF 263
W +C + + I G+W + G LGFG++ W+ A+ A GLP+
Sbjct: 30 WTKQAICGMLGNMQSESTINPGLWQNLDEGNTSLGFGLVQWTPASNYINWANSQGLPY 87
>pdb|2P3X|A Chain A, Crystal Structure Of Grenache (Vitis Vinifera) Polyphenol
Oxidase
Length = 339
Score = 28.9 bits (63), Expect = 9.3, 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 0.445
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,882,863
Number of Sequences: 62578
Number of extensions: 762724
Number of successful extensions: 1444
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1438
Number of HSP's gapped (non-prelim): 8
length of query: 579
length of database: 14,973,337
effective HSP length: 104
effective length of query: 475
effective length of database: 8,465,225
effective search space: 4020981875
effective search space used: 4020981875
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)