BLASTP 2.3.0+


Reference:
Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer,
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
composition-based statistics:
Alejandro A. Schäffer, L. Aravind, Thomas L. Madden, Sergei
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST
protein database searches with composition-based statistics and
other refinements", Nucleic Acids Res. 29:2994-3005.



Database: PDB protein database
           83,265 sequences; 20,561,802 total letters



Query= gi|33862495|ref|NP_894055.1| Amino acid permease:Permease for amino
acids and related comp... [Prochlorococcus marinus str. MIT 9313]

Length=615
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

pdb|3UNV|A  Chain A, Pantoea Agglomerans Phenylalanine Aminomutase    31.6    2.6  
pdb|2DQ0|A  Chain A, Crystal Structure Of Seryl-Trna Synthetase F...  30.4    5.3  



Query_1  73   AIVVLSYRQAIEAYPKGGGSYVVARDNLGRNVGLIAAAALLIDYTLTAGVSLMAGTQALS  132
3UNV_A   138  ..SIVNFKKL..I.NQ.IVPCIPEKGS..XDL.PL..I..VCTGQWK.RYEQ.S.AM..E  199
                                                                \         
                                                                |         
                                                               QG
2DQ0_A   144                                                         E.SQG  148

Query_1  133  SLVPSMLDHEVSLALLLLALIGWANLRGLKETGRLFSLPTYAFVVMVALLILAGLKDLIF  192
3UNV_A   200  KIS.ME.SFKEG...ITS.MV.LGV.L-YD.VK...D--..---LT.TS.SIE..-----  252
               \              \                                           
               |              |                                           
              AG             NG
2DQ0_A   149  KMEYEI.EWKPK.HVD..EIL.G.DF.AA.VS.SR.YYLLNEI.ILDLA..RFA.-.RLI  208
                                        \                                 
                                        |                                 
                                        A

Query_1  193  EHGFVPDMPPAVQAVQPLGWFLILRAFSSGCSAMTGIESI  232
3UNV_A   253  -..KTKPFE...HRMK.                         268
2DQ0_A   209  .K..T.VI..----------YMVR.FVEE.STSFEDF.DV  238


Lambda      K        H
   0.326    0.140    0.423 

Gapped
Lambda      K        H
   0.267   0.0410    0.140 

Effective search space used: 5919443076


  Database: PDB protein database
    Posted date:  Apr 23, 2016  10:52 AM
  Number of letters in database: 20,561,802
  Number of sequences in database:  83,265



Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40