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= 045410
         (589 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 = 40.0 bits (92), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 79/358 (22%), Positives = 144/358 (40%), Gaps = 41/358 (11%)

Query: 158 RPCNIAFGADQFDTTTPKGKSQLESFFNWWYFSFXXXXXXXXXXXXYIQTNVSWILGFAI 217
           +P   +F  DQFD +    KS  +  F+ +YF+              +  N    + F I
Sbjct: 127 KPLVSSFMGDQFDQSN---KSLAQKAFDMFYFTINFGSFFASLSMPLLLKNFGAAVAFGI 183

Query: 218 PTGCFFLSIVVFLIGYHTYII-----KNPQGSVFVDMAKVITASCRKRKVNL------GQ 266
           P    F++ V F +G   YI      K+P G + V  + ++T    K  + L      G 
Sbjct: 184 PGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKVEGKGNIGLVLALIGGV 243

Query: 267 ASGNSLYDPPLTQSETESKTTKLPHTNRFRCLDKAAVIVDSSELDDDGKAKNGWRLCSLL 326
           ++  +L + P T          +     F     A++ ++ +       A +G R  S+L
Sbjct: 244 SAAYALVNIP-TLGIVAGLCCAMVLVMGFVG-AGASLQLERARKSHPDAAVDGVR--SVL 299

Query: 327 QVEQLKLLVAMFPVWITGIFCFLAMDQQNTIGILQAIQTNKRFGSFNVPPGWMGLISMLT 386
           ++  L  LV   P W          DQ+ +  ILQA   N         P  M  ++ L 
Sbjct: 300 RILVLFALVT--PFWSL-------FDQKASTWILQA---NDMVKPQWFEPAMMQALNPLL 347

Query: 387 LSTWIFFYERVFVPLSQKMTGKKIRLTMRQRITIGILMAILSLLVAGFVERKRRLSALQH 446
           +   I F   V  P  ++M    ++LT  +++  GI +  LS +V G ++       +  
Sbjct: 348 VMLLIPFNNFVLYPAIERM---GVKLTALRKMGAGIAITGLSWIVVGTIQL------MMD 398

Query: 447 GSFESPISILVLVPQFSFSGLTEGFAAVAVMEFLTTQLPESMRTVSGAVFFLSLSISS 504
           G   S +SI   +  ++     E   +   +EF  +Q P++M+    + + LS+++ +
Sbjct: 399 GG--SALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGN 454


  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    0.137    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,054,963
Number of Sequences: 62578
Number of extensions: 556169
Number of successful extensions: 1272
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1270
Number of HSP's gapped (non-prelim): 3
length of query: 589
length of database: 14,973,337
effective HSP length: 104
effective length of query: 485
effective length of database: 8,465,225
effective search space: 4105634125
effective search space used: 4105634125
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)