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= 008719
         (556 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 = 63.2 bits (152), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 51/214 (23%), Positives = 92/214 (42%), Gaps = 36/214 (16%)

Query: 3   ERMAYFGLSVNMVTFMFYVMHKSFAD------SSNAVNNFLGISQASSVLGGFLADAYLG 56
           ER +++G+   +  F+   +  S  +      + +  ++F+       +LGG++AD + G
Sbjct: 24  ERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGGWIADRFFG 83

Query: 57  RYWTIAIFTTIYLAGLTGITLCATMKVFMPNQDNCDRISQLLGSCEPAKSWQMLYLYTVL 116
           +Y TI   + IY  G       A + +F  +                         YT L
Sbjct: 84  KYNTILWLSLIYCVG------HAFLAIFEHSVQG---------------------FYTGL 116

Query: 117 YITGFGAAGIRPCVSSFGADQFDERSKDYKTHLDRFFNFFYLSVTVGAIVAFTLVVYIQM 176
           ++   G+ GI+P VSSF  DQFD+ +K       + F+ FY ++  G+  A   +  +  
Sbjct: 117 FLIALGSGGIKPLVSSFMGDQFDQSNKSLA---QKAFDMFYFTINFGSFFASLSMPLLLK 173

Query: 177 EHGWGSAFGALAIAMGISNMLFFIGTPLYRHRLP 210
             G   AFG   + M ++ + F++G   Y H  P
Sbjct: 174 NFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPP 207



 Score = 36.6 bits (83), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 14/83 (16%)

Query: 376 SQLQRVGIGLAVSILSVIWAGIFERYRRNYAISHGYEFSFLTAMPDLSAYWLLIQYCLIG 435
           + L+++G G+A++ LS I  G  +                +     LS +W ++ Y L+ 
Sbjct: 371 TALRKMGAGIAITGLSWIVVGTIQL--------------MMDGGSALSIFWQILPYALLT 416

Query: 436 IAEVFCIVGLLEFLYEEAPDAMK 458
             EV      LEF Y +AP AMK
Sbjct: 417 FGEVLVSATGLEFAYSQAPKAMK 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 = 40.8 bits (94), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 50/206 (24%), Positives = 87/206 (42%), Gaps = 37/206 (17%)

Query: 1   MAERMAYFGLSVNMVTFMFYV-----MHKSFADSSNAVNNFLGISQASSVLGGFLADAYL 55
           M ER +Y+G+   ++ +M+++     +H + A +++ +  +  +   S  +GGF+AD  +
Sbjct: 23  MWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRII 82

Query: 56  GRYWTIAIFTTIYLAGLTGITLCATMKVFMPNQDNCDRISQLLGSCEPAKSWQMLYLYTV 115
           G     A+F    L  L  I L                 S L GS              +
Sbjct: 83  GA--RPAVFWGGVLIMLGHIVLALPFGA-----------SALFGSI-------------I 116

Query: 116 LYITGFGAAGIRPCVSSFGADQFDERSKDYKTHLDRFFNFFYLSVTVGAIVAFTLVVYIQ 175
           L I G G   ++P VS+     +DE  +      D  F+ F   + +GA +A  +V   Q
Sbjct: 117 LIIIGTGF--LKPNVSTLVGTLYDEHDR----RRDAGFSIFVFGINLGAFIAPLIVGAAQ 170

Query: 176 MEHGWGSAFGALAIAMGISNMLFFIG 201
              G+  AF   AI M I  ++++ G
Sbjct: 171 EAAGYHVAFSLAAIGMFIGLLVYYFG 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    0.139    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,086,778
Number of Sequences: 62578
Number of extensions: 578768
Number of successful extensions: 1199
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1193
Number of HSP's gapped (non-prelim): 8
length of query: 556
length of database: 14,973,337
effective HSP length: 104
effective length of query: 452
effective length of database: 8,465,225
effective search space: 3826281700
effective search space used: 3826281700
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)