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= 011595
         (482 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 = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/99 (32%), Positives = 55/99 (55%), Gaps = 3/99 (3%)

Query: 37  FFAALYTLAVGTGGTKPNISTIGADQFDEFEPKEKAHKLSFFNWWMFSIFFGALFANTVL 96
           F+  L+ +A+G+GG KP +S+   DQFD+   K  A K   F+ + F+I FG+ FA+  +
Sbjct: 112 FYTGLFLIALGSGGIKPLVSSFMGDQFDQ-SNKSLAQKA--FDMFYFTINFGSFFASLSM 168

Query: 97  VYIQDNMGWTLGYGLPTLGLSISIAIFFAGTPFYRHKKP 135
             +  N G  + +G+P + + ++   F+ G   Y H  P
Sbjct: 169 PLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPP 207



 Score = 30.8 bits (68), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 341 LTIFVLLPQFVLMGTADAFLEVAKIEFFYDQAPENMKSLGTSYSMTTLGVGNFFSTFLLS 400
           L+IF  +  + L+   +  +    +EF Y QAP+ MK    S+   ++ VGN +   LL+
Sbjct: 403 LSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGNLW--VLLA 460

Query: 401 TVS 403
            VS
Sbjct: 461 NVS 463


>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 = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/89 (26%), Positives = 48/89 (53%), Gaps = 4/89 (4%)

Query: 38  FAALYTLAVGTGGTKPNISTIGADQFDEFEPKEKAHKLSFFNWWMFSIFFGALFANTVLV 97
           F ++  + +GTG  KPN+ST+    +DE + +  A     F+ ++F I  GA  A  ++ 
Sbjct: 112 FGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAG----FSIFVFGINLGAFIAPLIVG 167

Query: 98  YIQDNMGWTLGYGLPTLGLSISIAIFFAG 126
             Q+  G+ + + L  +G+ I + +++ G
Sbjct: 168 AAQEAAGYHVAFSLAAIGMFIGLLVYYFG 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
   0.323    0.136    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,517,383
Number of Sequences: 62578
Number of extensions: 476102
Number of successful extensions: 863
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 859
Number of HSP's gapped (non-prelim): 3
length of query: 482
length of database: 14,973,337
effective HSP length: 103
effective length of query: 379
effective length of database: 8,527,803
effective search space: 3232037337
effective search space used: 3232037337
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)