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= 013611
         (439 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 = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 82/388 (21%), Positives = 145/388 (37%), Gaps = 65/388 (16%)

Query: 25  CSPHHFQIIV------FIFSLYLVAIGQGGHKPCTQAFGADQFDAQNPQERRAKSSFFNW 78
           C  H F  I       F   L+L+A+G GG KP   +F  DQFD  N   +      F+ 
Sbjct: 96  CVGHAFLAIFEHSVQGFYTGLFLIALGSGGIKPLVSSFMGDQFDQSN---KSLAQKAFDM 152

Query: 79  WYFGISFGANSTILVVIYIQDNLNWALGFGIPCXXXXXXXXXXXXGTKTYRFSIKSKQRN 138
           +YF I+FG+    L +  +  N   A+ FGIP             G K Y   +  + ++
Sbjct: 153 FYFTINFGSFFASLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRY-IHMPPEPKD 211

Query: 139 PFARIGRVFVVAIKTRKATLASEDEAQSSQQFKFLNK-----ALLATPDVSLEDGKLCTL 193
           P       F+  I++   T   E +         +       AL+  P + +  G  C +
Sbjct: 212 PHG-----FLPVIRSALLT-KVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAM 265

Query: 194 ------------------------EDVEEAKALLRLIPIWATCLVYAIVFAQYTTFFTKQ 229
                                     V+  +++LR++ ++A    +  +F Q  + +  Q
Sbjct: 266 VLVMGFVGAGASLQLERARKSHPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQ 325

Query: 230 GATMDRTITRSIKIPAASLQLXXXXXXXXXXXXYDCIFVPITRYFTQNPSGITMLQRIGA 289
              M +        PA    L               ++  I R   +    +T L+++GA
Sbjct: 326 ANDMVKPQWFE---PAMMQALNPLLVMLLIPFNNFVLYPAIERMGVK----LTALRKMGA 378

Query: 290 GMLLSSISMVVAALVEIKRLETAKEYGLIDKPNVTIPTSVWWLIPQYLLCGIADVFTIVG 349
           G+ ++ +S +V   +++          ++D  +     S++W I  Y L    +V     
Sbjct: 379 GIAITGLSWIVVGTIQL----------MMDGGSA---LSIFWQILPYALLTFGEVLVSAT 425

Query: 350 LQEFFYDQIPKELKSFGLSIYMSVLGVG 377
             EF Y Q PK +K   +S +   + VG
Sbjct: 426 GLEFAYSQAPKAMKGTIMSFWTLSVTVG 453


  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    0.138    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,761,740
Number of Sequences: 62578
Number of extensions: 387588
Number of successful extensions: 919
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 912
Number of HSP's gapped (non-prelim): 6
length of query: 439
length of database: 14,973,337
effective HSP length: 102
effective length of query: 337
effective length of database: 8,590,381
effective search space: 2894958397
effective search space used: 2894958397
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)