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= psy5801
         (176 letters)

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

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



>pdb|3LND|A Chain A, Crystal Structure Of Cadherin-6 Ec12 W4a
 pdb|3LND|B Chain B, Crystal Structure Of Cadherin-6 Ec12 W4a
 pdb|3LND|C Chain C, Crystal Structure Of Cadherin-6 Ec12 W4a
 pdb|3LND|D Chain D, Crystal Structure Of Cadherin-6 Ec12 W4a
          Length = 207

 Score = 28.9 bits (63), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 25/49 (51%)

Query: 26  AVYKLDSGAKFKAMKRGMSLQEMTGLSVSPGSDQLVVIHNNKGNDLVFT 74
           A  +LD   K   + R  ++   TG  V P S+ ++ IH+   N+ +FT
Sbjct: 59  ATKRLDREEKPVYILRAQAVNRRTGRPVEPESEFIIKIHDINDNEPIFT 107



 Score = 28.9 bits (63), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 25/49 (51%)

Query: 108 AVYKLDSGAKFKAMKRGMSLQEMTGLSVSPGSDQLVVIHNNKGNDLVFT 156
           A  +LD   K   + R  ++   TG  V P S+ ++ IH+   N+ +FT
Sbjct: 59  ATKRLDREEKPVYILRAQAVNRRTGRPVEPESEFIIKIHDINDNEPIFT 107


  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
   0.321    0.134    0.375 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,694,919
Number of Sequences: 62578
Number of extensions: 166069
Number of successful extensions: 279
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 277
Number of HSP's gapped (non-prelim): 2
length of query: 176
length of database: 14,973,337
effective HSP length: 92
effective length of query: 84
effective length of database: 9,216,161
effective search space: 774157524
effective search space used: 774157524
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)