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= 030117
         (182 letters)

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

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



>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
           Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
 pdb|2DFY|C Chain C, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
           Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
          Length = 195

 Score = 26.6 bits (57), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 1/25 (4%)

Query: 95  TCGLCKRRLVPGRDIYMYRGDSAFC 119
           TC  C+ RLVPG D + Y   S FC
Sbjct: 97  TCSTCRNRLVPG-DRFHYINGSLFC 120


>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
           Domain
          Length = 188

 Score = 26.6 bits (57), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 1/25 (4%)

Query: 95  TCGLCKRRLVPGRDIYMYRGDSAFC 119
           TC  C+ RLVPG D + Y   S FC
Sbjct: 99  TCSTCRNRLVPG-DRFHYINGSLFC 122


  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    0.133    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,198,897
Number of Sequences: 62578
Number of extensions: 75486
Number of successful extensions: 73
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 73
Number of HSP's gapped (non-prelim): 3
length of query: 182
length of database: 14,973,337
effective HSP length: 93
effective length of query: 89
effective length of database: 9,153,583
effective search space: 814668887
effective search space used: 814668887
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)