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= 042337
         (236 letters)

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

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



>pdb|2NUD|C Chain C, The Structure Of The Type Iii Effector Avrb Complexed With
           A High-Affinity Rin4 Peptide
 pdb|2NUD|D Chain D, The Structure Of The Type Iii Effector Avrb Complexed With
           A High-Affinity Rin4 Peptide
          Length = 35

 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/34 (67%), Positives = 29/34 (85%)

Query: 164 DHTAAVPEFGDWDEPDPTSADGYTYIFNQVREER 197
           +    VP+FGDWDE +P+SADGYT+IFN+VREER
Sbjct: 2   EKVTVVPKFGDWDENNPSSADGYTHIFNKVREER 35


>pdb|4AQ1|C Chain C, Structure Of The Sbsb S-Layer Protein Of Geobacillus
           Stearothermophilus Pv72p2 In Complex With Nanobody Kb6
          Length = 892

 Score = 28.1 bits (61), Expect = 4.5,   Method: Composition-based stats.
 Identities = 16/38 (42%), Positives = 22/38 (57%)

Query: 54  NDTHENQNTISDNLASIKTSTFETETKSGAQNGREDGD 91
           N T+  QNT++ N A   TS F  ETK+ A    ++GD
Sbjct: 370 NLTNAPQNTVAFNKAEKVTSMFAGETKTVAMYDTKNGD 407


>pdb|2IIF|A Chain A, Single Chain Integration Host Factor Mutant Protein
           (Scihf2- K45ae) In Complex With Dna
          Length = 204

 Score = 27.7 bits (60), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 5/49 (10%)

Query: 91  DLR----RPTESPWYHHTVNIEVAINSLVHRPGRKMTTRQQNAGFDSRI 135
           DLR    RP  +P     + I  A   +  RPG+K+ +R +NAG   RI
Sbjct: 97  DLRDKNQRPGRNPKTGEDIPI-TARRVVTFRPGQKLKSRVENAGGGERI 144


>pdb|2IIE|A Chain A, Single Chain Integration Host Factor Protein (Scihf2) In
           Complex With Dna
          Length = 204

 Score = 27.7 bits (60), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 5/49 (10%)

Query: 91  DLR----RPTESPWYHHTVNIEVAINSLVHRPGRKMTTRQQNAGFDSRI 135
           DLR    RP  +P     + I  A   +  RPG+K+ +R +NAG   RI
Sbjct: 97  DLRDKNQRPGRNPKTGEDIPI-TARRVVTFRPGQKLKSRVENAGGGERI 144


  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
   0.315    0.130    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,717,429
Number of Sequences: 62578
Number of extensions: 315237
Number of successful extensions: 795
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 791
Number of HSP's gapped (non-prelim): 6
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)