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= 024637
         (265 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 = 35.0 bits (79), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 45/204 (22%), Positives = 79/204 (38%), Gaps = 26/204 (12%)

Query: 23  NEESNLLRDTHMLSITRKITEKLKSGFSSFFMLFSRKLIRTTLLLWVLFFANVFSYYGAV 82
            E  N   D +     +++T K        FM    + +    LLW +  ANVF Y    
Sbjct: 220 EEYKNDYPDDYNEKAEQELTAK------QIFM----QYVLPNKLLWYIAIANVFVY---- 265

Query: 83  LLTSKLSSGDSKCGSKVLHVDKSKDNSLYVDVFIASLAELPGLILSAIIVDKIGRK---- 138
           LL   +         +V H    K +  Y   F+   A +PG +L   + DK+ R     
Sbjct: 266 LLRYGILDWSPTYLKEVKHFALDKSSWAY---FLYEYAGIPGTLLCGWMSDKVFRGNRGA 322

Query: 139 ---LSMVLMFVSACIFLLPLVFHQSAVVTTLLLFGVRMCVTGTITVATIYAPEIYPTPAR 195
                M L+ ++  ++ +    + +  +  +++ G    + G + +  ++A E+ P  A 
Sbjct: 323 TGVFFMTLVTIATIVYWMNPAGNPTVDMICMIVIG--FLIYGPVMLIGLHALELAPKKAA 380

Query: 196 TTGFGVASSLGKVGGMVCPLVAVG 219
            T  G     G +GG V     VG
Sbjct: 381 GTAAGFTGLFGYLGGSVAASAIVG 404


  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
   0.326    0.139    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,513,142
Number of Sequences: 62578
Number of extensions: 225413
Number of successful extensions: 552
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 552
Number of HSP's gapped (non-prelim): 3
length of query: 265
length of database: 14,973,337
effective HSP length: 97
effective length of query: 168
effective length of database: 8,903,271
effective search space: 1495749528
effective search space used: 1495749528
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)