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= 009413
         (535 letters)

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

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



>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 98.6 bits (244), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 118/470 (25%), Positives = 200/470 (42%), Gaps = 60/470 (12%)

Query: 17  ERFAFKGVASNLVTYLTDVVKMS-----NSSAAKTV-NSWCGFTSMLPLVLAPLADSYWD 70
           ERF+F G+ + L  +L   + +S       + AK V +S+       PL+   +AD ++ 
Sbjct: 24  ERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGGWIADRFFG 83

Query: 71  RYSTILAFSFIYVVGLVALXXXXXXXXXXXXNKISSSSAFLFWSLCLISLGQGGYNPSLQ 130
           +Y+TIL  S IY VG   L                 S    +  L LI+LG GG  P + 
Sbjct: 84  KYNTILWLSLIYCVGHAFLAI------------FEHSVQGFYTGLFLIALGSGGIKPLVS 131

Query: 131 AFGADQLDSDDELPTTTDNQKSDKKSLFFKWWYFGVCSGSLLGVTVMSYIQDTFGWVLGF 190
           +F  DQ D  ++    +  QK+      F  +YF +  GS      M  +   FG  + F
Sbjct: 132 SFMGDQFDQSNK----SLAQKA------FDMFYFTINFGSFFASLSMPLLLKNFGAAVAF 181

Query: 191 AIPTIAMVTSTAFFSFGSQIYRYKSDETLKCTVSLINIVQAIKAAASKLKNSKIVLPIDN 250
            IP + M  +T FF  G + Y +   E       L  I  A+        N  +VL +  
Sbjct: 182 GIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKVEGKGNIGLVLALIG 241

Query: 251 SDTVELELQE------QKPLC-------GNKKLGSSKELD--EDEYPKSGNHLVKNAKVV 295
             +    L           LC       G    G+S +L+     +P +    V   + V
Sbjct: 242 GVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERARKSHPDAA---VDGVRSV 298

Query: 296 LKLFPIWTMLLMFAVIFQQPATFFTKQGMTMKRNIGSNFKIPPATLQSAITVSIILLMPL 355
           L++  ++ ++  F  +F Q A+ +  Q   M +     F+  PA +Q+   + ++LL+P 
Sbjct: 299 LRILVLFALVTPFWSLFDQKASTWILQANDMVKP--QWFE--PAMMQALNPLLVMLLIPF 354

Query: 356 YDKILIPFIHIIIRCEKGITVMQRMGIGMFLSIIAMIIAAIVETKRLEMNQQYSETVPLS 415
            + +L P I    R    +T +++MG G+ ++ ++ I   +V T +L M+   +    LS
Sbjct: 355 NNFVLYPAIE---RMGVKLTALRKMGAGIAITGLSWI---VVGTIQLMMDGGSA----LS 404

Query: 416 IFWLLPQYILLGISDIFTVIGMQEFFYNEVPVRMRTMGFALYTSVFGVGS 465
           IFW +  Y LL   ++       EF Y++ P  M+    + +T    VG+
Sbjct: 405 IFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGN 454


  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
   0.324    0.137    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,518,328
Number of Sequences: 62578
Number of extensions: 501088
Number of successful extensions: 1224
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1216
Number of HSP's gapped (non-prelim): 11
length of query: 535
length of database: 14,973,337
effective HSP length: 103
effective length of query: 432
effective length of database: 8,527,803
effective search space: 3684010896
effective search space used: 3684010896
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)