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= 038771
         (242 letters)

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

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



>pdb|2V5R|A Chain A, Structural Basis For Dscam Isoform Specificity
 pdb|2V5R|B Chain B, Structural Basis For Dscam Isoform Specificity
          Length = 391

 Score = 28.5 bits (62), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 6/46 (13%)

Query: 83  VPLQLPINRTLSLSLPRACNMGGVPVQCKASGTPLPAPGCLPSFGT 128
           V L+ P NR +  S     N  G  ++CKASG P+P    + S GT
Sbjct: 5   VFLKEPTNR-IDFS-----NSTGAEIECKASGNPMPEIIWIRSDGT 44


>pdb|2V5M|A Chain A, Structural Basis For Dscam Isoform Specificity
          Length = 388

 Score = 28.1 bits (61), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 6/46 (13%)

Query: 83  VPLQLPINRTLSLSLPRACNMGGVPVQCKASGTPLPAPGCLPSFGT 128
           V L+ P NR +  S     N  G  ++CKASG P+P    + S GT
Sbjct: 5   VFLKEPTNR-IDFS-----NSTGAEIECKASGNPMPEIIWIRSDGT 44


>pdb|2V5S|A Chain A, Structural Basis For Dscam Isoform Specificity
 pdb|2V5S|B Chain B, Structural Basis For Dscam Isoform Specificity
          Length = 394

 Score = 28.1 bits (61), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 6/46 (13%)

Query: 83  VPLQLPINRTLSLSLPRACNMGGVPVQCKASGTPLPAPGCLPSFGT 128
           V L+ P NR +  S     N  G  ++CKASG P+P    + S GT
Sbjct: 11  VFLKEPTNR-IDFS-----NSTGAEIECKASGNPMPEIIWIRSDGT 50


>pdb|3DMK|A Chain A, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
           (Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
 pdb|3DMK|B Chain B, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
           (Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
 pdb|3DMK|C Chain C, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
           (Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
          Length = 816

 Score = 27.3 bits (59), Expect = 8.8,   Method: Composition-based stats.
 Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 15/64 (23%)

Query: 74  CACLVITANVP---------LQLPINRTLSLSLPRACNMGGVPVQCKASGTPLPAPGCLP 124
           C    + AN P         L+ P NR +  S     N  G  ++CKASG P+P    + 
Sbjct: 22  CGSQTLAANPPDADQKGPVFLKEPTNR-IDFS-----NSTGAEIECKASGNPMPEIIWIR 75

Query: 125 SFGT 128
           S GT
Sbjct: 76  SDGT 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
   0.318    0.132    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,118,258
Number of Sequences: 62578
Number of extensions: 151503
Number of successful extensions: 358
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 354
Number of HSP's gapped (non-prelim): 5
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)