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= 009816
         (524 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 = 89.7 bits (221), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 112/509 (22%), Positives = 194/509 (38%), Gaps = 83/509 (16%)

Query: 2   GSLSEPAPQRSSRKPLGIRFLECIKGRNLSFKNHQAIVLIVTFFAYTSYHAARKTTSIVK 61
           GS+ +PAP ++      I         + +++  +  + +  FF Y +Y+  RK  ++  
Sbjct: 1   GSIFKPAPHKARLPAAEI---------DPTYRRLRWQIFLGIFFGYAAYYLVRKNFALA- 50

Query: 62  STLDPQSPDTSLKSLPWRISYLQEPAESRKLSWKLGDGWAPFNGSDGTALLGELDLAFLS 121
                             + YL E   SR              G  G AL G      +S
Sbjct: 51  ------------------MPYLVEQGFSR--------------GDLGFALSG------IS 72

Query: 122 I-YAGGMFFSGHLGDRLDLRIFLTVGMVGTGLFTSLYGIGYWGNVHSFYYYLVVQMLAGL 180
           I Y    F  G + DR + R+FL  G++         G   W    S     V+  L G 
Sbjct: 73  IAYGFSKFIMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWAT-SSIAVMFVLLFLCGW 131

Query: 181 FQSTGWPSVVAVVGNWFGKSKRGLIMGIWN-AHTSIGNITGSLVASALLTYG-WGWSFVV 238
           FQ  GWP     + +W+ + +RG I+ +WN AH   G I   L    +  +  W  +  +
Sbjct: 132 FQGMGWPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFNDWHAALYM 191

Query: 239 PGLIIAFVGLIVFLFLPVNPESVGTDTNEEDESLSPKKIGEGVTQPLLRRETKIE----E 294
           P      V L  F  +   P+S G    EE ++  P    E   Q L  ++  ++     
Sbjct: 192 PAFCAILVALFAFAMMRDTPQSCGLPPIEEYKNDYPDDYNEKAEQELTAKQIFMQYVLPN 251

Query: 295 KAVGFIEAWKIPGVAPFALCLFFAKLVAYTFLYWLPFYVSHTAVDGKYLSSEMAGNLSTL 354
           K + +I           A+   F  L+ Y  L W P Y+       K+ + + +     L
Sbjct: 252 KLLWYI-----------AIANVFVYLLRYGILDWSPTYLKEV----KHFALDKSSWAYFL 296

Query: 355 FDVGGVLGGILAGHISDRL--DARAITAASFMYCAIPALFFYRSYGHLSLALNIALMFIT 412
           ++  G+ G +L G +SD++    R  T   FM     A   Y      +  +++  M + 
Sbjct: 297 YEYAGIPGTLLCGWMSDKVFRGNRGATGVFFMTLVTIATIVYWMNPAGNPTVDMICMIVI 356

Query: 413 GMFVNGPYALITTAVSADLGTHSSLKGNSRALATVTAIIDGTGSVGAAIGP-LLTGY-IS 470
           G  + GP  LI        G H+      +A  T        G +G ++    + GY + 
Sbjct: 357 GFLIYGPVMLI--------GLHALELAPKKAAGTAAGFTGLFGYLGGSVAASAIVGYTVD 408

Query: 471 ATSWTAVFTMLMAAALISGLLLTRLVVAE 499
              W   F +++  ++++ +LL  +++ E
Sbjct: 409 FFGWDGGFMVMIGGSILAVILLIVVMIGE 437


  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    0.139    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,724,374
Number of Sequences: 62578
Number of extensions: 614648
Number of successful extensions: 1156
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1152
Number of HSP's gapped (non-prelim): 8
length of query: 524
length of database: 14,973,337
effective HSP length: 103
effective length of query: 421
effective length of database: 8,527,803
effective search space: 3590205063
effective search space used: 3590205063
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)