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= psy6352
         (136 letters)

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

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



>pdb|4FOM|A Chain A, Crystal Structure Of Human Nectin-3 Full Ectodomain
           (D1-D3)
          Length = 308

 Score = 27.3 bits (59), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 15/33 (45%)

Query: 78  PHSVAAKFWPYPRFPVPGDRERLITCVDGHPRL 110
           P+  A     Y  FP    R R ITCV  HP L
Sbjct: 164 PNETATIISQYKLFPTRFARGRRITCVVKHPAL 196


>pdb|2ID3|A Chain A, Crystal Structure Of Transcriptional Regulator Sco5951
           From Streptomyces Coelicolor A3(2)
 pdb|2ID3|B Chain B, Crystal Structure Of Transcriptional Regulator Sco5951
           From Streptomyces Coelicolor A3(2)
          Length = 225

 Score = 25.8 bits (55), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 10/23 (43%), Positives = 13/23 (56%)

Query: 61  GCNSEAIVGFKCPDSVDPHSVAA 83
           GC  +A+   + PD  DPH V A
Sbjct: 162 GCVRDAVARGEVPDGTDPHGVVA 184


>pdb|1JR8|A Chain A, Crystal Structure Of Erv2p
 pdb|1JR8|B Chain B, Crystal Structure Of Erv2p
 pdb|1JRA|A Chain A, Crystal Structure Of Erv2p
 pdb|1JRA|B Chain B, Crystal Structure Of Erv2p
 pdb|1JRA|C Chain C, Crystal Structure Of Erv2p
 pdb|1JRA|D Chain D, Crystal Structure Of Erv2p
          Length = 117

 Score = 25.8 bits (55), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 3/37 (8%)

Query: 79  HSVAAKFWPYPRFPVPGDRERLITCVDGHPRLISCGD 115
           H++ A+F   P  P P +RE+L T +  +  L  CG+
Sbjct: 20  HTLLARF---PDEPTPEEREKLHTFIGLYAELYPCGE 53


  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
   0.320    0.143    0.492 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,080,569
Number of Sequences: 62578
Number of extensions: 216440
Number of successful extensions: 283
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: 280
Number of HSP's gapped (non-prelim): 5
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)