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= psy408
         (132 letters)

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

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



>pdb|2AKH|Y Chain Y, Normal Mode-Based Flexible Fitted Coordinates Of A Non-
           Translocating Secyeg Protein-Conducting Channel Into The
           Cryo-Em Map Of A Secyeg-Nascent Chain-70s Ribosome
           Complex From E. Coli
 pdb|2AKH|B Chain B, Normal Mode-Based Flexible Fitted Coordinates Of A Non-
           Translocating Secyeg Protein-Conducting Channel Into The
           Cryo-Em Map Of A Secyeg-Nascent Chain-70s Ribosome
           Complex From E. Coli
 pdb|2AKI|Y Chain Y, Normal Mode-Based Flexible Fitted Coordinates Of A
           Translocating Secyeg Protein-Conducting Channel Into The
           Cryo-Em Map Of A Secyeg-Nascent Chain-70s Ribosome
           Complex From E. Coli
 pdb|2AKI|B Chain B, Normal Mode-Based Flexible Fitted Coordinates Of A
           Translocating Secyeg Protein-Conducting Channel Into The
           Cryo-Em Map Of A Secyeg-Nascent Chain-70s Ribosome
           Complex From E. Coli
          Length = 400

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 87  VPYYYFGESLL-VSVLTMNFFRYILTLNFTWAVNSA 121
           VP+Y+ G SLL V V+ M+F   + TL  +    SA
Sbjct: 361 VPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESA 396


>pdb|3J01|A Chain A, Structure Of The Ribosome-Secye Complex In The Membrane
           Environment
          Length = 435

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 87  VPYYYFGESLL-VSVLTMNFFRYILTLNFTWAVNSA 121
           VP+Y+ G SLL V V+ M+F   + TL  +    SA
Sbjct: 390 VPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESA 425


  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
   0.331    0.142    0.493 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,399,150
Number of Sequences: 62578
Number of extensions: 161011
Number of successful extensions: 298
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: 298
Number of HSP's gapped (non-prelim): 2
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 bits)