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= 024129
         (272 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 = 0.74,   Method: Compositional matrix adjust.
 Identities = 33/166 (19%), Positives = 62/166 (37%), Gaps = 25/166 (15%)

Query: 58  GEKAINAILSVEYFCCDRPNPV------LQIIY-----LAIIGITYYFIAKSSFSYIPGY 106
           G   +N +L  +  C   P P+      L I         + G+T Y  ++   + +  Y
Sbjct: 349 GNLELNWLLGKDVQCTKAPVPIDDNFCGLDINQPLGGSTPVEGLTLYTTSRDRLTSVASY 408

Query: 107 YLSGFHRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQYQSAYPYDNI---------IY 157
             +G+      +G   G    +       G V+ E VS ++   P             +Y
Sbjct: 409 VYNGYS--VVFVGTKSGKLKKIRADGPPHGGVQYEMVSVFKDGSPILRDMAFSINQLYLY 466

Query: 158 TEKECSTCKIPKPARSKHCSICNRCVARFDHHCGW--MNNCIGERN 201
              E    ++P  +  ++ + C  C++  D HCGW  ++N    R+
Sbjct: 467 VMSERQVTRVPVESCEQY-TTCGECLSSGDPHCGWCALHNMCSRRD 511


>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 = 30.8 bits (68), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 31/155 (20%), Positives = 57/155 (36%), Gaps = 23/155 (14%)

Query: 58  GEKAINAILSVEYFCCDRPNPV------LQIIY-----LAIIGITYYFIAKSSFSYIPGY 106
           G   +N +L  +  C   P P+      L I         + G+T Y  ++   + +  Y
Sbjct: 348 GNLELNWLLGKDVQCTKAPVPIDDNFCGLDINQPLGGSTPVEGLTLYTTSRDRLTSVASY 407

Query: 107 YLSGFHRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQYQSAYPYDNI---------IY 157
             +G+      +G   G    +       G V+ E VS ++   P             +Y
Sbjct: 408 VYNGYS--VVFVGTKSGKLKKIRADGPPHGGVQYEMVSVFKDGSPILRDMAFSINQLYLY 465

Query: 158 TEKECSTCKIPKPARSKHCSICNRCVARFDHHCGW 192
              E    ++P  +  ++ + C  C++  D HCGW
Sbjct: 466 VMSERQVTRVPVESCEQY-TTCGECLSSGDPHCGW 499


>pdb|3S4E|A Chain A, Crystal Structrue Of A Novel Mitogen-Activated Protein
           Kinase Phosphatase, Skrp1
          Length = 144

 Score = 28.1 bits (61), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 11/20 (55%), Positives = 16/20 (80%)

Query: 231 LKELRVVYILTVYYGIENSF 250
           LK+ +V +IL V YG+EN+F
Sbjct: 25  LKKNKVTHILNVAYGVENAF 44


  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
   0.331    0.145    0.483 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,934,785
Number of Sequences: 62578
Number of extensions: 314342
Number of successful extensions: 838
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 837
Number of HSP's gapped (non-prelim): 7
length of query: 272
length of database: 14,973,337
effective HSP length: 97
effective length of query: 175
effective length of database: 8,903,271
effective search space: 1558072425
effective search space used: 1558072425
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (24.3 bits)