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= 040772
         (142 letters)

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

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



>pdb|4GL0|A Chain A, Putative SpermidinePUTRESCINE ABC TRANSPORTER FROM
           LISTERIA Monocytogenes
          Length = 333

 Score = 28.1 bits (61), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 10/24 (41%), Positives = 13/24 (54%)

Query: 105 WAAPYRWGTMVIAYQKSKFRKHNL 128
           ++ PY WGT+ I Y K  F   N 
Sbjct: 108 YSXPYFWGTLGIIYNKEXFPDKNF 131


>pdb|3SGG|A Chain A, Crystal Structure Of A Hypothetical Hydrolase (Bt_2193)
           From Bacteroides Thetaiotaomicron Vpi-5482 At 1.25 A
           Resolution
          Length = 536

 Score = 26.9 bits (58), Expect = 4.3,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 1   MNLCASIGGIFNNLSLP---FNKVKANSATYMAADLVSVGDSWLSFAIKERLIEPTAGAE 57
           +N+  S+ G+   +++P    +KVKA   T    D+ S  + WL    K++L +  A   
Sbjct: 139 INVATSLCGLLRGIAVPESLVDKVKAXGVTTELXDVRSYDEKWLYENYKDQLDKSLAADX 198

Query: 58  DQDWFKCL 65
             + F  L
Sbjct: 199 KPEIFHHL 206


  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
   0.322    0.135    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,933,143
Number of Sequences: 62578
Number of extensions: 125890
Number of successful extensions: 223
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 222
Number of HSP's gapped (non-prelim): 3
length of query: 142
length of database: 14,973,337
effective HSP length: 89
effective length of query: 53
effective length of database: 9,403,895
effective search space: 498406435
effective search space used: 498406435
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: 46 (22.3 bits)