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= 009231
         (539 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 45/203 (22%), Positives = 76/203 (37%), Gaps = 32/203 (15%)

Query: 17  RTLPFIIANEAFERMATVG----FTPNMI--LYLCREYNMETTAATNIIFIWTAATNFLP 70
           R +P+IIA+EA ER +  G     TP ++  L L     +    A ++   +     F P
Sbjct: 12  RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFP 71

Query: 71  IVGALLADSYVGRYRMIGFGCFTCLLGMVLLWSTTILPGAKPPACDQLRNGCESATWSQL 130
           ++G  +AD + G+Y  I             LW + I        C  + +   +     +
Sbjct: 72  LLGGWIADRFFGKYNTI-------------LWLSLIY-------C--VGHAFLAIFEHSV 109

Query: 131 MPLYFAFXXXXXXXXXXXXXXXAFGAEQLDKGDGTKSKGALQSYFSWYYVFVSASSIVAV 190
              Y                  +F  +Q D+ +    K   Q  F  +Y  ++  S  A 
Sbjct: 110 QGFYTGLFLIALGSGGIKPLVSSFMGDQFDQSN----KSLAQKAFDMFYFTINFGSFFAS 165

Query: 191 TCIVYIQDNLGWKVGFGVPAVIM 213
             +  +  N G  V FG+P V+M
Sbjct: 166 LSMPLLLKNFGAAVAFGIPGVLM 188


  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    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,704,340
Number of Sequences: 62578
Number of extensions: 530358
Number of successful extensions: 911
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 908
Number of HSP's gapped (non-prelim): 3
length of query: 539
length of database: 14,973,337
effective HSP length: 104
effective length of query: 435
effective length of database: 8,465,225
effective search space: 3682372875
effective search space used: 3682372875
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)