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= 016728
         (384 letters)

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

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



>pdb|3AL8|B Chain B, Plexin A2  SEMAPHORIN 6A COMPLEX
 pdb|3AL9|A Chain A, Mouse Plexin A2 Extracellular Domain
 pdb|3AL9|B Chain B, Mouse Plexin A2 Extracellular Domain
          Length = 539

 Score = 30.8 bits (68), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 23/115 (20%), Positives = 45/115 (39%), Gaps = 12/115 (10%)

Query: 87  IIGITYYFIAKSSFSYIPGYYLSGFHRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQY 146
           + G+T Y  ++   + +  Y  +G+      +G   G    +       G V+ E VS +
Sbjct: 389 VEGLTLYTTSRDRLTSVASYVYNGYS--VVFVGTKSGKLKKIRADGPPHGGVQYEMVSVF 446

Query: 147 QSAYPY---------DNIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHCGW 192
           +   P             +Y   E    ++P  +  ++ + C  C++  D HCGW
Sbjct: 447 KDGSPILRDMAFSINQLYLYVMSERQVTRVPVESCEQY-TTCGECLSSGDPHCGW 500


>pdb|3OKT|A Chain A, Mouse Plexin A2, Extracellular Domains 1-4
 pdb|3OKY|A Chain A, Plexin A2 In Complex With Semaphorin 6a
 pdb|4GZA|A Chain A, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|B Chain B, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|C Chain C, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|D Chain D, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|E Chain E, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|F Chain F, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
          Length = 681

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 23/115 (20%), Positives = 45/115 (39%), Gaps = 12/115 (10%)

Query: 87  IIGITYYFIAKSSFSYIPGYYLSGFHRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQY 146
           + G+T Y  ++   + +  Y  +G+      +G   G    +       G V+ E VS +
Sbjct: 388 VEGLTLYTTSRDRLTSVASYVYNGYS--VVFVGTKSGKLKKIRADGPPHGGVQYEMVSVF 445

Query: 147 QSAYPY---------DNIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHCGW 192
           +   P             +Y   E    ++P  +  ++ + C  C++  D HCGW
Sbjct: 446 KDGSPILRDMAFSINQLYLYVMSERQVTRVPVESCEQY-TTCGECLSSGDPHCGW 499


>pdb|3T2L|A Chain A, Crystal Structure Of A Putative Cell Adhesion Protein
           (Bf1858) From Bacteroides Fragilis Nctc 9343 At 2.33 A
           Resolution
          Length = 308

 Score = 28.9 bits (63), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 324 SSERKPPDSKWKTFFRRSPLEDSGAVVKNNI 354
           S +R+  D +WK    R PL+ S AV+K  +
Sbjct: 2   SDDREXDDGRWKASALRVPLQVSSAVIKQEV 32


  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
   0.326    0.141    0.461 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,806,493
Number of Sequences: 62578
Number of extensions: 409188
Number of successful extensions: 964
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 963
Number of HSP's gapped (non-prelim): 4
length of query: 384
length of database: 14,973,337
effective HSP length: 101
effective length of query: 283
effective length of database: 8,652,959
effective search space: 2448787397
effective search space used: 2448787397
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)