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= 041163
         (483 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 = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/100 (30%), Positives = 53/100 (53%), Gaps = 3/100 (3%)

Query: 37  AFFAALYTLAVGTGGTKPNILTIAADQFDDFEPKEKAHKFSFFNWWMFSIFFGTLLGNTA 96
            F+  L+ +A+G+GG KP + +   DQFD    K  A K   F+ + F+I FG+   + +
Sbjct: 111 GFYTGLFLIALGSGGIKPLVSSFMGDQFDQ-SNKSLAQKA--FDMFYFTINFGSFFASLS 167

Query: 97  LVYIQDDVGWALGYGLPTLGLAISIVIFLAGTPFYRHKKP 136
           +  +  + G A+ +G+P + + ++ V F  G   Y H  P
Sbjct: 168 MPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPP 207



 Score = 32.7 bits (73), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 342 LTIFILLPQFVLMGTADAFLEVAKIEFFYDQAPESMKSLGTSYSMTTLGVGNFLSSFLLS 401
           L+IF  +  + L+   +  +    +EF Y QAP++MK    S+   ++ VGN     LL+
Sbjct: 403 LSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGNLWV--LLA 460

Query: 402 TVSDKT 407
            VS K+
Sbjct: 461 NVSVKS 466


>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 = 38.5 bits (88), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 4/91 (4%)

Query: 37  AFFAALYTLAVGTGGTKPNILTIAADQFDDFEPKEKAHKFSFFNWWMFSIFFGTLLGNTA 96
           A F ++  + +GTG  KPN+ T+    +D+ + +  A  FS F   +F I  G  +    
Sbjct: 110 ALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDA-GFSIF---VFGINLGAFIAPLI 165

Query: 97  LVYIQDDVGWALGYGLPTLGLAISIVIFLAG 127
           +   Q+  G+ + + L  +G+ I ++++  G
Sbjct: 166 VGAAQEAAGYHVAFSLAAIGMFIGLLVYYFG 196


>pdb|3U1R|A Chain A, Structure Analysis Of A New Psychrophilic Marine Protease
          Length = 480

 Score = 29.3 bits (64), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 21/81 (25%), Positives = 31/81 (38%), Gaps = 15/81 (18%)

Query: 349 PQFVLMGTADAFLEVAKIEFFYDQAPESMKSLGTSYSMTTLGVGNFLSSFLLSTVSDKTK 408
           P F   GT+ AF +V     FYD+    +               N   SF +   +D+  
Sbjct: 14  PTFAANGTSSAFTQVDNFSHFYDRGNHLV---------------NGKPSFTVDQAADQLT 58

Query: 409 RHGHKGWILNNLNVSHLDYYY 429
           R G   + LN   V +L Y +
Sbjct: 59  RSGASWYDLNGDGVINLSYTF 79


  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    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,727,852
Number of Sequences: 62578
Number of extensions: 499897
Number of successful extensions: 1184
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1179
Number of HSP's gapped (non-prelim): 7
length of query: 483
length of database: 14,973,337
effective HSP length: 103
effective length of query: 380
effective length of database: 8,527,803
effective search space: 3240565140
effective search space used: 3240565140
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: 53 (25.0 bits)