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= 045901
         (171 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 = 38.9 bits (89), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/166 (24%), Positives = 66/166 (39%), Gaps = 28/166 (16%)

Query: 6   LMPNMILYLCREYNMETTAATNVLFIWTAATNFVPILGAFLADSCMGRYPMIGFGCIISL 65
           LM  ++L +  E  +    A +V   +     F P+LG ++AD   G+Y  I +  +I  
Sbjct: 39  LMTALLLSIPEE--LRGAVAKDVFHSFVIGVYFFPLLGGWIADRFFGKYNTILWLSLIYC 96

Query: 66  LGMVLLWFTAIFPQEKPPVCDQMRSGCESATASQLMLLYSAFGLMSLGGGSIRASSLVFG 125
           +G     F AIF                      +   Y+   L++LG G I+     F 
Sbjct: 97  VGHA---FLAIFEHS-------------------VQGFYTGLFLIALGSGGIKPLVSSFM 134

Query: 126 ADQLDKGNGAKNAGALQSYFSWYYVSIAAGSMLSATFIVYIQDNLG 171
            DQ D+ N +      Q  F  +Y +I  GS  ++  +  +  N G
Sbjct: 135 GDQFDQSNKSLA----QKAFDMFYFTINFGSFFASLSMPLLLKNFG 176


>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation.
 pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation
          Length = 491

 Score = 27.3 bits (59), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 13  YLCREYNMETTAAT--NVLFIWTAATNFVPILGAFLADSCMGRYPMIGFGCIISLLGMVL 70
           +L    ++  T AT  +++ I+ +       +G F+AD  +G  P + +G ++ +LG ++
Sbjct: 42  FLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIV 101

Query: 71  L 71
           L
Sbjct: 102 L 102


  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
   0.325    0.137    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,438,249
Number of Sequences: 62578
Number of extensions: 152257
Number of successful extensions: 340
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 328
Number of HSP's gapped (non-prelim): 13
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)