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= 012167
         (469 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 = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 66/362 (18%), Positives = 142/362 (39%), Gaps = 46/362 (12%)

Query: 40  LFAGLYIVALGVGGIKGSLAPHGAEQYDETTQ-LGRKQRSAFFNYYVFCLSCGALIAVTF 98
            + GL+++ALG GGIK  ++    +Q+D++ + L +K     F+ + F ++ G+  A   
Sbjct: 112 FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA----FDMFYFTINFGSFFASLS 167

Query: 99  VVWIEDNKGWQWGFGISTATILLSIPIFLLGSPFYRNKIPTGSPLTTIFKVLTAAIFNTC 158
           +  +  N G    FGI    + ++   F LG   Y +  P          V+ +A+    
Sbjct: 168 MPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKV 227

Query: 159 KSKNSSNAVTEVHSSPTCSNESRD-------EGNSNVKEKVPSQKPTEDIKFLNRALRNN 211
           + K +   V  +    + +    +        G       V           L RA +++
Sbjct: 228 EGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERARKSH 287

Query: 212 PAYPIVQCTXXXXXXXXXXXXXFPIFMSTIMLNCCLAQLSTFSVQQAATMNTKLGSLKVP 271
           P   +                     +  ++L   +    +   Q+A+T   +   +  P
Sbjct: 288 PDAAVDGVRSV---------------LRILVLFALVTPFWSLFDQKASTWILQANDMVKP 332

Query: 272 ----PASLPVFPVIFILILAPVYNHVIIPFARKVTKTEMGITHLQRIGTGLILSIVAMAV 327
               PA +     + +++L P  N V+ P    + +  + +T L+++G G+ ++ ++  V
Sbjct: 333 QWFEPAMMQALNPLLVMLLIPFNNFVLYP---AIERMGVKLTALRKMGAGIAITGLSWIV 389

Query: 328 AALVEIKRKRVAVNSGLVNSSEPLPITFLWVALQYLFLGSADLFTLAGMMEFFFTDAPLS 387
              +++          +++    L I   W  L Y  L   ++   A  +EF ++ AP +
Sbjct: 390 VGTIQL----------MMDGGSALSI--FWQILPYALLTFGEVLVSATGLEFAYSQAPKA 437

Query: 388 MR 389
           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 = 0.26,   Method: Compositional matrix adjust.
 Identities = 22/93 (23%), Positives = 46/93 (49%), Gaps = 4/93 (4%)

Query: 37  AVMLFAGLYIVALGVGGIKGSLAPHGAEQYDETTQLGRKQRSAFFNYYVFCLSCGALIAV 96
           A  LF  + ++ +G G +K +++      YDE      ++R A F+ +VF ++ GA IA 
Sbjct: 108 ASALFGSIILIIIGTGFLKPNVSTLVGTLYDEH----DRRRDAGFSIFVFGINLGAFIAP 163

Query: 97  TFVVWIEDNKGWQWGFGISTATILLSIPIFLLG 129
             V   ++  G+   F ++   + + + ++  G
Sbjct: 164 LIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFG 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
   0.324    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: 12,452,223
Number of Sequences: 62578
Number of extensions: 466542
Number of successful extensions: 1125
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: 1123
Number of HSP's gapped (non-prelim): 4
length of query: 469
length of database: 14,973,337
effective HSP length: 102
effective length of query: 367
effective length of database: 8,590,381
effective search space: 3152669827
effective search space used: 3152669827
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)