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= 043156
         (578 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 = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 46/93 (49%), Gaps = 3/93 (3%)

Query: 130 FVALYLIATGTAGIKAALPPYGADQFDEKDPIEARQMSSFFNLLFLAVCIGGAISVTLIV 189
           +  L+LIA G+ GIK  +  +  DQFD+ +   A++    F++ +  +  G   +   + 
Sbjct: 113 YTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFASLSMP 169

Query: 190 WIQDNKGWDRGFGLSSVAVFLATIIFAAGLPLY 222
            +  N G    FG+  V +F+AT+ F  G   Y
Sbjct: 170 LLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRY 202



 Score = 31.6 bits (70), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 28/124 (22%), Positives = 55/124 (44%), Gaps = 19/124 (15%)

Query: 398 ITHLQRVGVGLVLSCISMAIAAIFEVIRKDVARDHNMLDAIPVVQPLPISTFWLSIQFFI 457
           +T L+++G G+ ++ +S  +    ++          M+D         +S FW  + + +
Sbjct: 370 LTALRKMGAGIAITGLSWIVVGTIQL----------MMDGGSA-----LSIFWQILPYAL 414

Query: 458 FGIADMFTYVGLLEFFYSEAPKGIKSLSTCFLWCSMALGYFFSTILVNI---VNSATRGI 514
               ++      LEF YS+APK +K     F   S+ +G  +  +L N+     + T  I
Sbjct: 415 LTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGNLW-VLLANVSVKSPTVTEQI 473

Query: 515 TQSG 518
            Q+G
Sbjct: 474 VQTG 477


>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 = 37.7 bits (86), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 37/165 (22%), Positives = 69/165 (41%), Gaps = 14/165 (8%)

Query: 54  NGVLHLDLAEAANQVTNYMGTSYILSIVVALLADAFIGRFKAVLISGSVEFLPPPCNVFD 113
            G LH+  A AA+ +  Y    Y+   +   +AD  IG   AV   G +  L        
Sbjct: 46  TGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALP 105

Query: 114 PTAGCKKIEGSDAALLFVALYLIATGTAGIKAALPPYGADQFDEKDPIEARQMSSFFNLL 173
                       A+ LF ++ LI  GT  +K  +       +DE D    R+  + F++ 
Sbjct: 106 ----------FGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHD----RRRDAGFSIF 151

Query: 174 FLAVCIGGAISVTLIVWIQDNKGWDRGFGLSSVAVFLATIIFAAG 218
              + +G  I+  ++   Q+  G+   F L+++ +F+  +++  G
Sbjct: 152 VFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFG 196


  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
   0.326    0.140    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,365,840
Number of Sequences: 62578
Number of extensions: 587493
Number of successful extensions: 1289
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1285
Number of HSP's gapped (non-prelim): 11
length of query: 578
length of database: 14,973,337
effective HSP length: 104
effective length of query: 474
effective length of database: 8,465,225
effective search space: 4012516650
effective search space used: 4012516650
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)