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= 008106
         (577 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 = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 66/362 (18%), Positives = 141/362 (38%), Gaps = 46/362 (12%)

Query: 148 LFAGLYIVALGVGGIKGSLAPHGAEQYDETTQ-LGRKQRSAFFNYYVFCLSCGALIAVTF 206
            + GL+++ALG GGIK  ++    +Q+D++ + L +K     F+ + F ++ G+  A   
Sbjct: 112 FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA----FDMFYFTINFGSFFASLS 167

Query: 207 VVWIEDNKGWQWGFGISTATILLSIPIFLLGSPFYRNKIPTGSPLTTIFKVLTAAIFNTC 266
           +  +  N G    FGI    + ++   F LG   Y +  P          V+ +A+    
Sbjct: 168 MPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKV 227

Query: 267 KSKNS-------SNAVTEVHSSPTCSNESRDEGNSNVKEKVPSQKPTEDIKFLNRALRNN 319
           + K +          V+  ++           G       V           L RA +++
Sbjct: 228 EGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERARKSH 287

Query: 320 PAYPIVQCTXXXXXXXXXXXXXFPIFMSTIMLNCCLAQLSTFSVQQAATMNTKLGSLKVP 379
           P   +                     +  ++L   +    +   Q+A+T   +   +  P
Sbjct: 288 PDAAVDGVRSV---------------LRILVLFALVTPFWSLFDQKASTWILQANDMVKP 332

Query: 380 ----PASLPVFPVIFILILAPVYNHVIIPFARKVTKTEMGITHLQRIGTGLILSIVAMAV 435
               PA +     + +++L P  N V+ P    + +  + +T L+++G G+ ++ ++  V
Sbjct: 333 QWFEPAMMQALNPLLVMLLIPFNNFVLYP---AIERMGVKLTALRKMGAGIAITGLSWIV 389

Query: 436 AALVEIKRKRVAVNSGLVNSSEPLPITFLWVALQYLFLGSADLFTLAGMMEFFFTDAPLS 495
              +++          +++    L I   W  L Y  L   ++   A  +EF ++ AP +
Sbjct: 390 VGTIQL----------MMDGGSALSI--FWQILPYALLTFGEVLVSATGLEFAYSQAPKA 437

Query: 496 MR 497
           M+
Sbjct: 438 MK 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 = 21/90 (23%), Positives = 45/90 (50%), Gaps = 4/90 (4%)

Query: 148 LFAGLYIVALGVGGIKGSLAPHGAEQYDETTQLGRKQRSAFFNYYVFCLSCGALIAVTFV 207
           LF  + ++ +G G +K +++      YDE      ++R A F+ +VF ++ GA IA   V
Sbjct: 111 LFGSIILIIIGTGFLKPNVSTLVGTLYDEH----DRRRDAGFSIFVFGINLGAFIAPLIV 166

Query: 208 VWIEDNKGWQWGFGISTATILLSIPIFLLG 237
              ++  G+   F ++   + + + ++  G
Sbjct: 167 GAAQEAAGYHVAFSLAAIGMFIGLLVYYFG 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
   0.325    0.138    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,918,736
Number of Sequences: 62578
Number of extensions: 544113
Number of successful extensions: 1287
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1285
Number of HSP's gapped (non-prelim): 4
length of query: 577
length of database: 14,973,337
effective HSP length: 104
effective length of query: 473
effective length of database: 8,465,225
effective search space: 4004051425
effective search space used: 4004051425
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: 54 (25.4 bits)