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= psy8716
         (141 letters)

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

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



>pdb|1RQG|A Chain A, Methionyl-Trna Synthetase From Pyrococcus Abyssi
          Length = 722

 Score = 27.3 bits (59), Expect = 3.1,   Method: Composition-based stats.
 Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 5/39 (12%)

Query: 47  CPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASC 85
           CPYC       + +KG  C VC  P   + L++   A C
Sbjct: 143 CPYCG-----AEDQKGDQCEVCGRPLTPEILINPRCAIC 176


>pdb|1VDD|A Chain A, Crystal Structure Of Recombinational Repair Protein Recr
 pdb|1VDD|B Chain B, Crystal Structure Of Recombinational Repair Protein Recr
 pdb|1VDD|C Chain C, Crystal Structure Of Recombinational Repair Protein Recr
 pdb|1VDD|D Chain D, Crystal Structure Of Recombinational Repair Protein Recr
          Length = 228

 Score = 26.9 bits (58), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 11/73 (15%)

Query: 8  SFSPLAATGKAMSQEL-----KCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG 62
            S L   G   +Q L     + P +D E L  ++    +   +CP C+N     D +K 
Sbjct: 13 ELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFN---ITDAEK- 68

Query: 63 SGCNVCTHPTCGQ 75
            C+VC  P+  Q
Sbjct: 69 --CDVCADPSRDQ 79


>pdb|2V1C|A Chain A, Crystal Structure And Mutational Study Of Recor Provide
          Insight Into Its Role In Dna Repair
 pdb|2V1C|B Chain B, Crystal Structure And Mutational Study Of Recor Provide
          Insight Into Its Role In Dna Repair
          Length = 220

 Score = 26.9 bits (58), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 11/73 (15%)

Query: 8  SFSPLAATGKAMSQEL-----KCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG 62
            S L   G   +Q L     + P +D E L  ++    +   +CP C+N     D +K 
Sbjct: 13 ELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFN---ITDAEK- 68

Query: 63 SGCNVCTHPTCGQ 75
            C+VC  P+  Q
Sbjct: 69 --CDVCADPSRDQ 79


  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
   0.323    0.137    0.465 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,521,851
Number of Sequences: 62578
Number of extensions: 181252
Number of successful extensions: 345
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 341
Number of HSP's gapped (non-prelim): 13
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
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: 46 (22.3 bits)