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= 033188
         (125 letters)

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

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



>pdb|3JUX|A Chain A, Structure Of The Translocation Atpase Seca From Thermotoga
           Maritima
          Length = 822

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 13/29 (44%), Positives = 15/29 (51%)

Query: 78  TMIGAYLCDTYFGRYNTLGFATVASFLVL 106
           T   AYLCD  +G  N  GF  +   LVL
Sbjct: 208 TRKEAYLCDVTYGTNNEFGFDYLRDNLVL 236


>pdb|3DIN|A Chain A, Crystal Structure Of The Protein-Translocation Complex
           Formed By The Secy Channel And The Seca Atpase
 pdb|3DIN|B Chain B, Crystal Structure Of The Protein-Translocation Complex
           Formed By The Secy Channel And The Seca Atpase
          Length = 871

 Score = 26.9 bits (58), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/25 (48%), Positives = 14/25 (56%)

Query: 82  AYLCDTYFGRYNTLGFATVASFLVL 106
           AYLCD  +G  N  GF  +   LVL
Sbjct: 212 AYLCDVTYGTNNEFGFDYLRDNLVL 236


>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 = 26.6 bits (57), Expect = 4.0,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 12/88 (13%)

Query: 15 DEPKINYRGW-KAMPFIIGNETFEKLGAVGTLANLLIYLTSVF------NMKXXXXXXXX 67
          D PK     W + +P+II +E  E+    G    L  +L +         ++        
Sbjct: 6  DAPK-----WPRQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVF 60

Query: 68 XXXXXXXXXXTMIGAYLCDTYFGRYNTL 95
                     ++G ++ D +FG+YNT+
Sbjct: 61 HSFVIGVYFFPLLGGWIADRFFGKYNTI 88


  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    0.140    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,854,611
Number of Sequences: 62578
Number of extensions: 80864
Number of successful extensions: 170
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 167
Number of HSP's gapped (non-prelim): 3
length of query: 125
length of database: 14,973,337
effective HSP length: 86
effective length of query: 39
effective length of database: 9,591,629
effective search space: 374073531
effective search space used: 374073531
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: 45 (21.9 bits)