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= 007736
         (591 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 = 40.4 bits (93), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 37  ILGGEACERLTTLGIAVNLVTYLTGTM------HLGNASAANTVTNFLGTSFMLCLLGGF 90
           I+  EACER +  G+   L  +L   +       L  A A +   +F+   +   LLGG+
Sbjct: 17  IIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGGW 76

Query: 91  IADTFLGRYLTIAIFATVQAAG 112
           IAD F G+Y TI   + +   G
Sbjct: 77  IADRFFGKYNTILWLSLIYCVG 98



 Score = 36.6 bits (83), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 40/168 (23%), Positives = 78/168 (46%), Gaps = 21/168 (12%)

Query: 333 VEEVKMVIRMLPIWATTIIFWTVYAQMTTFSVSQATTMNRHIGSFEIPGASLTFFFVGSI 392
           V+ V+ V+R+L ++A    FW+++ Q  +  + QA  M +    FE   A +       +
Sbjct: 292 VDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDMVKP-QWFE--PAMMQALNPLLV 348

Query: 393 LLTVPVYDRIIVP-IARKVFKTPQGLTPLQRIGVGLVLSIFAMVAAALCEIKRLRAARSH 451
           +L +P  + ++ P I R   K    LT L+++G G+ ++  + +     ++         
Sbjct: 349 MLLIPFNNFVLYPAIERMGVK----LTALRKMGAGIAITGLSWIVVGTIQL--------- 395

Query: 452 GLTNDPTAEIPLSVFWLVPQFFLVGAGEAFTYIGQLDFFLRECPKGMK 499
            + +  +A   LS+FW +  + L+  GE       L+F   + PK MK
Sbjct: 396 -MMDGGSA---LSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMK 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 = 33.5 bits (75), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 41 EACERLTTLGIAVNLVTYL-----TGTMHLGNASAANTVTNFLGTSFMLCLLGGFIADTF 95
          E  ER +  G+   L+ Y+     TG +H+  A+AA+ +  +    ++   +GGF+AD  
Sbjct: 22 EMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRI 81

Query: 96 LG 97
          +G
Sbjct: 82 IG 83


>pdb|3NQN|A Chain A, Crystal Structure Of A Protein With Unknown Function.
           (Dr_2006) From Deinococcus Radiodurans At 1.88 A
           Resolution
 pdb|3NQN|B Chain B, Crystal Structure Of A Protein With Unknown Function.
           (Dr_2006) From Deinococcus Radiodurans At 1.88 A
           Resolution
          Length = 158

 Score = 30.0 bits (66), Expect = 3.8,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 390 GSILLTVPVYDRIIVPIARKVFKTPQG--LTPLQRIGVGLVLSIFAMVAAA 438
           G +L+TVP+   + +P   ++ +TPQG  L PL   G    +++     AA
Sbjct: 50  GELLVTVPLLGEVDLPFRSEIVRTPQGAELRPLTLTGERAWVAVSGQATAA 100


  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    0.139    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,096,356
Number of Sequences: 62578
Number of extensions: 506043
Number of successful extensions: 983
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 975
Number of HSP's gapped (non-prelim): 9
length of query: 591
length of database: 14,973,337
effective HSP length: 104
effective length of query: 487
effective length of database: 8,465,225
effective search space: 4122564575
effective search space used: 4122564575
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)