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= 029003
         (200 letters)

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

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



>pdb|2V3U|A Chain A, Structure Of The Ligand-binding Core Of The Ionotropic
           Glutamate Receptor-like Glurdelta2 In Complex With D-
           Serine
          Length = 265

 Score = 28.9 bits (63), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 8/59 (13%)

Query: 93  VMIAVNLFGKKLDYKGLRLAMIAIFDLLNTVLVSAGVNGAVYMAELGKYG--NSHARWN 149
           VM++ N+ GK   Y+G     I + D L+  L   G N  +Y+A   KYG       WN
Sbjct: 16  VMVSENVLGKPKKYQGFS---IDVLDALSNYL---GFNYEIYVAPDHKYGSPQEDGTWN 68


>pdb|3JRU|B Chain B, Crystal Structure Of Leucyl Aminopeptidase (Pepa) From
           Xoo0834, Xanthomonas Oryzae Pv. Oryzae Kacc10331
 pdb|3JRU|A Chain A, Crystal Structure Of Leucyl Aminopeptidase (Pepa) From
           Xoo0834, Xanthomonas Oryzae Pv. Oryzae Kacc10331
          Length = 490

 Score = 28.1 bits (61), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 43/111 (38%), Gaps = 1/111 (0%)

Query: 87  VSFHNVVMIAVNLFGKKLDYKGLRLAMIAIFDLLNTVLVSAGVNGAVYMAELGKYGNSHA 146
           VS H        L  KK+D  GL    IA  D     +  A   G  +  ELG    ++ 
Sbjct: 134 VSDHAAYRYTATLGKKKVDETGLTTLAIAGDDARALAVGVATAEGVEFARELGNLPPNYC 193

Query: 147 RWNKICDRFKTFCDHGGGAIIASFIGLALMIVISIISIVKLAKSKSNTPLL 197
               + D    F     GA  A  +  A M  + + S++ +A+  +N P L
Sbjct: 194 TPAYLADTAAAFAGKFPGA-EAEILDEAQMEALGMGSLLSVARGSANRPRL 243


  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    0.138    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,959,796
Number of Sequences: 62578
Number of extensions: 163814
Number of successful extensions: 296
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 296
Number of HSP's gapped (non-prelim): 3
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)