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= 003961
         (783 letters)

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

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



>pdb|3MSU|A Chain A, Crystal Structure Of Citrate Synthase From Francisella
           Tular
 pdb|3MSU|B Chain B, Crystal Structure Of Citrate Synthase From Francisella
           Tular
          Length = 427

 Score = 30.4 bits (67), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 21/40 (52%), Gaps = 3/40 (7%)

Query: 533 KNADQRAEVSRSEKEEILVKLSHSEKMLAEGKGRANKLEE 572
           KN D RA   +   EEIL KL HS+  L      A KLEE
Sbjct: 314 KNTDPRATAMKKNCEEILAKLGHSDNPLLT---VAKKLEE 350


>pdb|2C5J|A Chain A, N-Terminal Domain Of Tlg1, Domain-Swapped Dimer
 pdb|2C5J|B Chain B, N-Terminal Domain Of Tlg1, Domain-Swapped Dimer
 pdb|2C5K|T Chain T, N-Terminal Domain Of Tlg1 Complexed With N-Terminus Of
           Vps51
          Length = 95

 Score = 30.0 bits (66), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 12/56 (21%), Positives = 33/56 (58%)

Query: 349 EKIFPDASEYPSRLDGMVSSESFPGKEEMEQSLQKLEKDLKETCSERDKALQELTR 404
           +++  D  E  +R++  ++  +  G ++ E+ +Q + KD++ET  + D+++  + R
Sbjct: 9   QQVVKDTKEQLNRINNYITRHNTAGDDDQEEEIQDILKDVEETIVDLDRSIIVMKR 64


>pdb|2C5I|T Chain T, N-Terminal Domain Of Tlg1 Complexed With N-Terminus Of
           Vps51 In Distorted Conformation
          Length = 101

 Score = 29.6 bits (65), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 11/51 (21%), Positives = 31/51 (60%)

Query: 349 EKIFPDASEYPSRLDGMVSSESFPGKEEMEQSLQKLEKDLKETCSERDKAL 399
           +++  D  E  +R++  ++  +  G ++ E+ +Q + KD++ET  + D+++
Sbjct: 9   QQVVKDTKEQLNRINNYITRHNTAGDDDQEEEIQDILKDVEETIVDLDRSI 59


  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
   0.309    0.125    0.329 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,265,094
Number of Sequences: 62578
Number of extensions: 596498
Number of successful extensions: 2030
Number of sequences better than 100.0: 94
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 83
Number of HSP's that attempted gapping in prelim test: 1908
Number of HSP's gapped (non-prelim): 169
length of query: 783
length of database: 14,973,337
effective HSP length: 106
effective length of query: 677
effective length of database: 8,340,069
effective search space: 5646226713
effective search space used: 5646226713
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 55 (25.8 bits)