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= psy13914
         (87 letters)

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

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



>pdb|3LHA|A Chain A, Crystal Structure Of Mouse Vps26b(R240sG241AE242S) IN
           SPACEGROUP P41 21 2
 pdb|3LHA|B Chain B, Crystal Structure Of Mouse Vps26b(R240sG241AE242S) IN
           SPACEGROUP P41 21 2
          Length = 340

 Score = 30.8 bits (68), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 30/71 (42%)

Query: 7   ELPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVFPRLFTCPT 66
           E+ IK +E+ +++ ET G       +   I   +I +G    G  IPI +        PT
Sbjct: 203 EIKIKHMEIDIIKRETTGTGPNVYHENDTIAKYEIMDGAPVRGSSIPIRLFLAGYELTPT 262

Query: 67  LITSNFKIGER 77
           +   N K   R
Sbjct: 263 MRDINKKFSVR 273


>pdb|3LH8|A Chain A, Crystal Structure Of Mouse Vps26b In Spacegroup P41 21 2
 pdb|3LH8|B Chain B, Crystal Structure Of Mouse Vps26b In Spacegroup P41 21 2
 pdb|3LH9|A Chain A, Crystal Structure Of Mouse Vps26b(L197sR199E) IN
           SPACEGROUP P41 21 2
 pdb|3LH9|B Chain B, Crystal Structure Of Mouse Vps26b(L197sR199E) IN
           SPACEGROUP P41 21 2
          Length = 340

 Score = 30.0 bits (66), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 30/71 (42%)

Query: 7   ELPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVFPRLFTCPT 66
           E+ IK +E+ +++ ET G       +   I   +I +G    G  IPI +        PT
Sbjct: 203 EIKIKHMEIDIIKRETTGTGPNVYHENDTIAKYEIMDGAPVRGESIPIRLFLAGYELTPT 262

Query: 67  LITSNFKIGER 77
           +   N K   R
Sbjct: 263 MRDINKKFSVR 273


>pdb|2FAU|A Chain A, Crystal Structure Of Human Vps26
          Length = 341

 Score = 29.6 bits (65), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 19/70 (27%), Positives = 30/70 (42%)

Query: 8   LPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVFPRLFTCPTL 67
           + I+ +ELQL++ E  G     + +   I   +I +G    G  IPI +        PT+
Sbjct: 204 IKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTM 263

Query: 68  ITSNFKIGER 77
              N K   R
Sbjct: 264 RDVNKKFSVR 273


>pdb|2R51|A Chain A, Crystal Structure Of Mouse Vps26b
          Length = 340

 Score = 26.9 bits (58), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 27/70 (38%)

Query: 8   LPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVFPRLFTCPTL 67
           + IK  E+ +++ ET G       +   I   +I +G    G  IPI +        PT 
Sbjct: 204 IKIKHXEIDIIKRETTGTGPNVYHENDTIAKYEIXDGAPVRGESIPIRLFLAGYELTPTX 263

Query: 68  ITSNFKIGER 77
              N K   R
Sbjct: 264 RDINKKFSVR 273


  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
   0.322    0.141    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,341,683
Number of Sequences: 62578
Number of extensions: 77178
Number of successful extensions: 100
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 96
Number of HSP's gapped (non-prelim): 4
length of query: 87
length of database: 14,973,337
effective HSP length: 55
effective length of query: 32
effective length of database: 11,531,547
effective search space: 369009504
effective search space used: 369009504
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)