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= 015208
         (411 letters)

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

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



>pdb|1OLZ|A Chain A, The Ligand-Binding Face Of The Semaphorins Revealed By The
           High Resolution Crystal Structure Of Sema4d
 pdb|1OLZ|B Chain B, The Ligand-Binding Face Of The Semaphorins Revealed By The
           High Resolution Crystal Structure Of Sema4d
 pdb|3OL2|A Chain A, Receptor-Ligand Structure Of Human Semaphorin 4d With
           Plexin B1
          Length = 663

 Score = 32.3 bits (72), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 38/161 (23%), Positives = 65/161 (40%), Gaps = 14/161 (8%)

Query: 52  DVSTDGKWCYIVFWVIGDSQTRW----GLLKKRLMGACPSCSSASVVLYYRAEMQAPKPS 107
           +V + GK  Y+    +  S T+W    G + K   GAC    S +    Y + +  P  +
Sbjct: 314 EVFSHGK--YMQSTTVEQSHTKWVRYNGPVPKPRPGAC--IDSEARAANYTSSLNLPDKT 369

Query: 108 DVFLLKLSCYDRKGLLYDVTAVLCELELTIEKVKISTTP--DGKVMDLFFVTDTRELLHT 165
             F+      D      D    L + ++   ++ +  T   DG V D+ FV+  R  LH 
Sbjct: 370 LQFVKDHPLMDDSVTPIDNRPRLIKKDVNYTQIVVDRTQALDGTVYDVMFVSTDRGALH- 428

Query: 166 RKRKEDTYEHLKTILGNAMISCDVEMVGTEITACSQASSFL 206
              K  + EH   I+    +  D E V T + +  + + F+
Sbjct: 429 ---KAISLEHAVHIIEETQLFQDFEPVQTLLLSSKKGNRFV 466


>pdb|3MTJ|A Chain A, The Crystal Structure Of A Homoserine Dehydrogenase From
           Thiobacillus Denitrificans To 2.15a
          Length = 444

 Score = 29.3 bits (64), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 10/30 (33%), Positives = 20/30 (66%)

Query: 109 VFLLKLSCYDRKGLLYDVTAVLCELELTIE 138
            + L+L  +DR G+L D+T +L +  ++I+
Sbjct: 359 AYYLRLRAFDRPGVLADITRILADSSISID 388


  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
   0.323    0.140    0.428 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,413,401
Number of Sequences: 62578
Number of extensions: 502681
Number of successful extensions: 1079
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1077
Number of HSP's gapped (non-prelim): 7
length of query: 411
length of database: 14,973,337
effective HSP length: 101
effective length of query: 310
effective length of database: 8,652,959
effective search space: 2682417290
effective search space used: 2682417290
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: 53 (25.0 bits)