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= 040090
         (112 letters)

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

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



>pdb|2P4Q|A Chain A, Crystal Structure Analysis Of Gnd1 In Saccharomyces
           Cerevisiae
          Length = 497

 Score = 27.7 bits (60), Expect = 1.9,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 35/81 (43%), Gaps = 12/81 (14%)

Query: 14  ARQGETVVPGGTGGKSLEAQEHLAE-----GRSRGGQTRREQLGTEG---YQEMGHRGGQ 65
           AR G +++PGG    S EA  H+            G+   E +G  G   Y +M H G +
Sbjct: 142 ARYGPSLMPGG----SEEAWPHIKNIFQSISAKSDGEPCCEWVGPAGAGHYVKMVHNGIE 197

Query: 66  MRREQMGSEGYQEMGRKGGLS 86
               Q+  E Y  M R GG +
Sbjct: 198 YGDMQLICEAYDIMKRLGGFT 218


>pdb|3A58|B Chain B, Crystal Structure Of Sec3p - Rho1p Complex From
           Saccharomyces Cerevisiae
 pdb|3A58|D Chain D, Crystal Structure Of Sec3p - Rho1p Complex From
           Saccharomyces Cerevisiae
 pdb|3A58|F Chain F, Crystal Structure Of Sec3p - Rho1p Complex From
           Saccharomyces Cerevisiae
          Length = 188

 Score = 26.6 bits (57), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 20/36 (55%)

Query: 49  EQLGTEGYQEMGHRGGQMRREQMGSEGYQEMGRKGG 84
           EQL  EG Q +  + GQ   +Q+G+ GY E   K G
Sbjct: 134 EQLRQEGQQPVTSQEGQSVADQIGATGYYECSAKTG 169


  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
   0.306    0.126    0.343 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,083,269
Number of Sequences: 62578
Number of extensions: 114210
Number of successful extensions: 102
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 98
Number of HSP's gapped (non-prelim): 8
length of query: 112
length of database: 14,973,337
effective HSP length: 76
effective length of query: 36
effective length of database: 10,217,409
effective search space: 367826724
effective search space used: 367826724
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 45 (21.9 bits)