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= 036230
         (267 letters)

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

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



>pdb|4GL8|A Chain A, X-Ray Crystal Structure Of A Periplasmic
           Oligopeptide-Binding ProteinOLIGOPEPTIDE ABC
           TRANSPORTER(OPPAIV) FROM BORRELIA Burgdorferi
 pdb|4GL8|B Chain B, X-Ray Crystal Structure Of A Periplasmic
           Oligopeptide-Binding ProteinOLIGOPEPTIDE ABC
           TRANSPORTER(OPPAIV) FROM BORRELIA Burgdorferi
          Length = 529

 Score = 27.3 bits (59), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 13/64 (20%)

Query: 21  LDSSVIFHVINDVAGFVLYMHQQI--------PSILQDISLEFDAL-----QTEFKELDM 67
           LDS + F   N +  + +Y++ ++        P +L+D+ L  D        T F  L+M
Sbjct: 236 LDSIIFFVTDNSITAYNMYLNDELDAIFKNVPPDLLKDLKLRDDYYSMGINSTSFYSLNM 295

Query: 68  DLRP 71
            ++P
Sbjct: 296 KVKP 299


  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
   0.321    0.136    0.387 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,168,481
Number of Sequences: 62578
Number of extensions: 267213
Number of successful extensions: 647
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 646
Number of HSP's gapped (non-prelim): 5
length of query: 267
length of database: 14,973,337
effective HSP length: 97
effective length of query: 170
effective length of database: 8,903,271
effective search space: 1513556070
effective search space used: 1513556070
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: 50 (23.9 bits)