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= 007604
         (596 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 = 41/183 (22%), Positives = 79/183 (43%), Gaps = 38/183 (20%)

Query: 33  RACSFVVVYEVFERMAYHG--------ISSNLVMYLTDKLHHGTVKSANNVTNWGGTIWV 84
           R   +++  E  ER +++G        + + L++ + ++L     K   +    G  ++ 
Sbjct: 12  RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIG--VYF 69

Query: 85  TPIFGAGVAEAYLGRYWTFVIAFFFYLMGMIVLAL-SVSLSGLKPPPCNDINSQDCRKAS 143
            P+ G  +A+ + G+Y T +     Y +G   LA+   S+ G                  
Sbjct: 70  FPLLGGWIADRFFGKYNTILWLSLIYCVGHAFLAIFEHSVQG------------------ 111

Query: 144 TLQLGTFFAALYTLAVGTGGTKPNILTIAADQFDEFEPKEKAHKLSFFNWWMFSIFFGTL 203
                 F+  L+ +A+G+GG KP + +   DQFD+   K  A K   F+ + F+I FG+ 
Sbjct: 112 ------FYTGLFLIALGSGGIKPLVSSFMGDQFDQ-SNKSLAQKA--FDMFYFTINFGSF 162

Query: 204 LGN 206
             +
Sbjct: 163 FAS 165



 Score = 31.6 bits (70), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 16/52 (30%), Positives = 28/52 (53%)

Query: 454 LTIFIMLPQFVLMGTADAFLEVAKIEFFYDQAPESMKSLGTSYSMTTLGVGN 505
           L+IF  +  + L+   +  +    +EF Y QAP++MK    S+   ++ VGN
Sbjct: 403 LSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGN 454


>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 = 41.2 bits (95), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 44/174 (25%), Positives = 75/174 (43%), Gaps = 47/174 (27%)

Query: 42  EVFERMAYHGISSNLVMYL-----TDKLHHGTVKSANNVTNWGGTIWVTPIFGAGVAEAY 96
           E++ER +Y+G+ + L+ Y+     T  LH     +A+ +  +   ++++   G  VA+  
Sbjct: 22  EMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRI 81

Query: 97  LGR----YWTFVIAFFFYLMGMIVLALSVSLSGLKPPPCNDINSQDCRKASTLQLGTFFA 152
           +G     +W  V+     ++G IVLAL    S L                        F 
Sbjct: 82  IGARPAVFWGGVLI----MLGHIVLALPFGASAL------------------------FG 113

Query: 153 ALYTLAVGTGGTKPNILTIAADQFDEFEPKEKAHKLSFFNWWMFSIF-FGTLLG 205
           ++  + +GTG  KPN+ T+    +DE + +  A          FSIF FG  LG
Sbjct: 114 SIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAG---------FSIFVFGINLG 158


  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    0.137    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,934,982
Number of Sequences: 62578
Number of extensions: 592319
Number of successful extensions: 1024
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1018
Number of HSP's gapped (non-prelim): 4
length of query: 596
length of database: 14,973,337
effective HSP length: 104
effective length of query: 492
effective length of database: 8,465,225
effective search space: 4164890700
effective search space used: 4164890700
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: 54 (25.4 bits)