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= 014301
         (427 letters)

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

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



>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
           From E.Coli
          Length = 451

 Score = 34.3 bits (77), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 62/169 (36%), Gaps = 25/169 (14%)

Query: 52  FSRLAMGPVCDLLGPRVASATLSLITAPIVLSASLVSSPQSFILVRFLVGFCLANFVANQ 111
           FS+  MG V D   PRV      ++ A ++L    V    S I V F++ F    F    
Sbjct: 77  FSKFIMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWATSSIAVMFVLLFLCGWFQGMG 136

Query: 112 F---------WMSSMFSGCVVGLANGVSAGWANMGAGVSQLLMPLIFTAITSLNVGTHTA 162
           +         W S    G +V + N       N+G G+     PL+F     L +     
Sbjct: 137 WPPCGRTMVHWWSQKERGGIVSVWNCAH----NVGGGIP----PLLFL----LGMAWFND 184

Query: 163 WRLAFIVPSTFQALTAIMVLIYGQDLPSG----NYKEFKKTKTESREEK 207
           W  A  +P+    L A+      +D P        +E+K    +   EK
Sbjct: 185 WHAALYMPAFCAILVALFAFAMMRDTPQSCGLPPIEEYKNDYPDDYNEK 233


>pdb|2QRY|A Chain A, Periplasmic Thiamin Binding Protein
 pdb|2QRY|B Chain B, Periplasmic Thiamin Binding Protein
 pdb|2QRY|C Chain C, Periplasmic Thiamin Binding Protein
 pdb|2QRY|D Chain D, Periplasmic Thiamin Binding Protein
          Length = 330

 Score = 31.2 bits (69), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 6/111 (5%)

Query: 157 VGTHTAWRLAFIVPSTFQALTAIMV---LIYGQDLPSGNYKEFKKTKTESREEKFVHVLF 213
           V +   WR+ +  P T      +++    +YG D P    K  KKT T ++     + LF
Sbjct: 148 VESDQNWRVIYQDPRTSTPGLGLLLWXQKVYGDDAPQAWQKLAKKTVTVTKGWSEAYGLF 207

Query: 214 NGLKNYRGWILGLTYGFCFGV-ELTTDNIIAQYFYDRFGVNLQVAGTIAAS 263
             LK     +L  T    + + E   DN  A  F +   + ++VA   AAS
Sbjct: 208 --LKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAAS 256


  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
   0.328    0.141    0.443 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,972,906
Number of Sequences: 62578
Number of extensions: 409014
Number of successful extensions: 881
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 879
Number of HSP's gapped (non-prelim): 6
length of query: 427
length of database: 14,973,337
effective HSP length: 102
effective length of query: 325
effective length of database: 8,590,381
effective search space: 2791873825
effective search space used: 2791873825
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)