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= 007910
         (585 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 = 71.2 bits (173), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 110/225 (48%), Gaps = 44/225 (19%)

Query: 18  RTMPFIIANEAFEKVAGVGLHANMIFYLILEYHMSGPEGANVLFLWGAISN--------- 68
           R +P+IIA+EA E+ +  G+   +  +L+    +S PE      L GA++          
Sbjct: 12  RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEE-----LRGAVAKDVFHSFVIG 66

Query: 69  --FLPIIGASISDSFLGRFRVIALGTFTALLGMILLWLTAIIPAARPPKCNPFIEICPAA 126
             F P++G  I+D F G++  I             LWL+ I         + F+ I   +
Sbjct: 67  VYFFPLLGGWIADRFFGKYNTI-------------LWLSLIYCVG-----HAFLAIFEHS 108

Query: 127 KPRQLGFLFSSFVLMSIGAGGIRPCSLAFGADQFHNPDNPNNERILQTFFNWYYASVGL- 185
                GF ++   L+++G+GGI+P   +F  DQF    + +N+ + Q  F+ +Y ++   
Sbjct: 109 VQ---GF-YTGLFLIALGSGGIKPLVSSFMGDQF----DQSNKSLAQKAFDMFYFTINFG 160

Query: 186 SYMASITLIVYIQDKAGWVVGFGVPVGLMLFSTVMFLLGSSLYIK 230
           S+ AS+++ + +++  G  V FG+P  LM  +TV F LG   YI 
Sbjct: 161 SFFASLSMPLLLKN-FGAAVAFGIPGVLMFVATVFFWLGRKRYIH 204



 Score = 35.4 bits (80), Expect = 0.089,   Method: Compositional matrix adjust.
 Identities = 25/99 (25%), Positives = 45/99 (45%), Gaps = 13/99 (13%)

Query: 398 LSYRQRIGIGLAISCVAMAVAALVERKRRSAAIREGLADNPEGVVALTAMWLVPQNCLIG 457
           L+  +++G G+AI+ ++  V   ++                +G  AL+  W +    L+ 
Sbjct: 370 LTALRKMGAGIAITGLSWIVVGTIQLMM-------------DGGSALSIFWQILPYALLT 416

Query: 458 LAEAFNAIGQIEFYYSQFPKTMSSIGVALLSLGMAVGNL 496
             E   +   +EF YSQ PK M    ++  +L + VGNL
Sbjct: 417 FGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGNL 455


>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 = 28.9 bits (63), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 40/222 (18%), Positives = 84/222 (37%), Gaps = 36/222 (16%)

Query: 16  GLRTMPFIIANEAFEKVAGVGLHANMIFYLIL-----EYHMSGPEGANVLFLWGAISNFL 70
           GL T+      E +E+ +  G+ A +++Y+       + H++    A+++ ++ ++    
Sbjct: 14  GLSTL---FMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLS 70

Query: 71  PIIGASISDSFLGRFRVIALGTFTALLGMILLWLTAIIPAARPPKCNPFIEICPAAKPRQ 130
             IG  ++D  +G    +  G    +LG I+L                       A P  
Sbjct: 71  GTIGGFVADRIIGARPAVFWGGVLIMLGHIVL-----------------------ALPFG 107

Query: 131 LGFLFSSFVLMSIGAGGIRPCSLAFGADQFHNPDNPNNERILQTFFNWYYASVGLSYMAS 190
              LF S +L+ IG G ++P         +   D   +       F+ +   + L    +
Sbjct: 108 ASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAG-----FSIFVFGINLGAFIA 162

Query: 191 ITLIVYIQDKAGWVVGFGVPVGLMLFSTVMFLLGSSLYIKPK 232
             ++   Q+ AG+ V F +    M    +++  G    + P 
Sbjct: 163 PLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPH 204


  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    0.139    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,624,355
Number of Sequences: 62578
Number of extensions: 732655
Number of successful extensions: 1727
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: 1721
Number of HSP's gapped (non-prelim): 5
length of query: 585
length of database: 14,973,337
effective HSP length: 104
effective length of query: 481
effective length of database: 8,465,225
effective search space: 4071773225
effective search space used: 4071773225
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: 54 (25.4 bits)