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= 013138
         (449 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 =  114 bits (286), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 108/406 (26%), Positives = 187/406 (46%), Gaps = 50/406 (12%)

Query: 22  GEETCQVTDAQSATFFVALYLIALGTGGIKPCVSSYGADQFDDADEAEKKHKSSFFNWFY 81
           G     + +     F+  L+LIALG+GGIKP VSS+  DQFD ++++  +     F+ FY
Sbjct: 98  GHAFLAIFEHSVQGFYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFY 154

Query: 82  FSINIGALIASSVLVWIQDNEGWGWGFGIPAVAMAIAVVSFFSGTRLFRNQKPGGSPLTR 141
           F+IN G+  AS  +  +  N G    FGIP V M +A V F+ G + + +  P       
Sbjct: 155 FTINFGSFFASLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHG 214

Query: 142 ICQVVAASIRKHKVELPADKSLLYETADAESNITGSRKLDHTKDFSF------------- 188
              V+ +++   KVE   +  L+         ++ +  L +                   
Sbjct: 215 FLPVIRSALLT-KVEGKGNIGLVLALI---GGVSAAYALVNIPTLGIVAGLCCAMVLVMG 270

Query: 189 FDKAAVEIQSDNIKESVNPWRLCTVTQVEELKAIVRLLPIWATGIIFSAVYSQMSSLFVL 248
           F  A   +Q +  ++S +P        V+ +++++R+L ++A    F +++ Q +S ++L
Sbjct: 271 FVGAGASLQLERARKS-HP-----DAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWIL 324

Query: 249 QGERMDTHVGNSSFKIPPASLSIFDTLSVIFWVPIYDRFIVPVTRKFTGHKNGLTQLQRM 308
           Q   M   V    F+  PA +   + L V+  +P  +  + P   +  G K  LT L++M
Sbjct: 325 QANDM---VKPQWFE--PAMMQALNPLLVMLLIPFNNFVLYPAIER-MGVK--LTALRKM 376

Query: 309 GIGLFISILSMIAAAVLELIRLRMVREHNYYDLPEMPMSIMWQVPQYFLIGCAEVFTFIG 368
           G G+ I+ LS I    ++L    M+   +        +SI WQ+  Y L+   EV     
Sbjct: 377 GAGIAITGLSWIVVGTIQL----MMDGGS-------ALSIFWQILPYALLTFGEVLVSAT 425

Query: 369 QLEFFYEQAPDAMRSLCSALSLTTVALGNYLSSLLVTIVTSISTKN 414
            LEF Y QAP AM+    +    +V +GN     L  ++ ++S K+
Sbjct: 426 GLEFAYSQAPKAMKGTIMSFWTLSVTVGN-----LWVLLANVSVKS 466


>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation.
 pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation
          Length = 491

 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 53/95 (55%), Gaps = 4/95 (4%)

Query: 33  SATFFVALYLIALGTGGIKPCVSSYGADQFDDADEAEKKHKSSFFNWFYFSINIGALIAS 92
           ++  F ++ LI +GTG +KP VS+     +D+ D    + + + F+ F F IN+GA IA 
Sbjct: 108 ASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHD----RRRDAGFSIFVFGINLGAFIAP 163

Query: 93  SVLVWIQDNEGWGWGFGIPAVAMAIAVVSFFSGTR 127
            ++   Q+  G+   F + A+ M I ++ ++ G +
Sbjct: 164 LIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGK 198


  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    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,965,165
Number of Sequences: 62578
Number of extensions: 504943
Number of successful extensions: 1328
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1322
Number of HSP's gapped (non-prelim): 4
length of query: 449
length of database: 14,973,337
effective HSP length: 102
effective length of query: 347
effective length of database: 8,590,381
effective search space: 2980862207
effective search space used: 2980862207
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: 53 (25.0 bits)