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= 012670
         (458 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 = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 95/377 (25%), Positives = 165/377 (43%), Gaps = 47/377 (12%)

Query: 18  CVGALCPSATPAQYAVFFFGLYLIALGTGGIKPCVSSFGADQFDDTDSNERVKKGSFFNW 77
           CVG    +        F+ GL+LIALG+GGIKP VSSF  DQFD ++ +   K    F+ 
Sbjct: 96  CVGHAFLAIFEHSVQGFYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDM 152

Query: 78  FYFSINIGALISSSLIVWIQDNAGWGLGFGIPALFMGFAIASFFSGTSLYRFQRP----- 132
           FYF+IN G+  +S  +  +  N G  + FGIP + M  A   F+ G   Y    P     
Sbjct: 153 FYFTINFGSFFASLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDP 212

Query: 133 -GGSPITRMCQVLVASFRKWNLEVPNDSTLLYETQDKASAIEGSRKIEHSDELRCLDKAA 191
            G  P+ R   +         +E   +  L+       SA      I     +  L  A 
Sbjct: 213 HGFLPVIRSALLT-------KVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAM 265

Query: 192 VV--------SDAEIKSGDFSNPWILCTVTQVEELKILIRMFPIWATGIVFSAVYAQMST 243
           V+        +  +++    S+P        V+ ++ ++R+  ++A    F +++ Q ++
Sbjct: 266 VLVMGFVGAGASLQLERARKSHP-----DAAVDGVRSVLRILVLFALVTPFWSLFDQKAS 320

Query: 244 LFVEQGMVMDTSIGSFTIPPASLSSFDVISVIFWVPIYDKIIVPIARKFTGKERGFSELQ 303
            ++ Q    +  +      PA + + + + V+  +P  + ++ P   +   K    + L+
Sbjct: 321 TWILQA---NDMVKPQWFEPAMMQALNPLLVMLLIPFNNFVLYPAIERMGVK---LTALR 374

Query: 304 RMGIGLFLSVLCMSAAAVVEINRLRLARELELVDQNVSVPISIFWQIPQYFLLGAAEVCT 363
           +MG G+ ++ L       +++          ++D   +  +SIFWQI  Y LL   EV  
Sbjct: 375 KMGAGIAITGLSWIVVGTIQL----------MMDGGSA--LSIFWQILPYALLTFGEVLV 422

Query: 364 FIGQLEFFYDQSPDAMR 380
               LEF Y Q+P AM+
Sbjct: 423 SATGLEFAYSQAPKAMK 439


>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 = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 52/98 (53%), Gaps = 4/98 (4%)

Query: 26  ATPAQYAVFFFGLYLIALGTGGIKPCVSSFGADQFDDTDSNERVKKGSFFNWFYFSINIG 85
           A P   +  F  + LI +GTG +KP VS+     +D+ D     ++ + F+ F F IN+G
Sbjct: 103 ALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDR----RRDAGFSIFVFGINLG 158

Query: 86  ALISSSLIVWIQDNAGWGLGFGIPALFMGFAIASFFSG 123
           A I+  ++   Q+ AG+ + F + A+ M   +  ++ G
Sbjct: 159 AFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFG 196


>pdb|3O7Q|A Chain A, Crystal Structure Of A Major Facilitator Superfamily (Mfs)
           Transporter, Fucp, In The Outward Conformation
          Length = 438

 Score = 28.5 bits (62), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 15/55 (27%), Positives = 26/55 (47%)

Query: 24  PSATPAQYAVFFFGLYLIALGTGGIKPCVSSFGADQFDDTDSNERVKKGSFFNWF 78
           P+A    Y +F  GL++IA G G ++   + F      ++  + R+     FN F
Sbjct: 110 PAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSF 164


  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
   0.325    0.139    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,978,756
Number of Sequences: 62578
Number of extensions: 521600
Number of successful extensions: 1223
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1217
Number of HSP's gapped (non-prelim): 4
length of query: 458
length of database: 14,973,337
effective HSP length: 102
effective length of query: 356
effective length of database: 8,590,381
effective search space: 3058175636
effective search space used: 3058175636
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)