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= 015223
         (411 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 = 58.5 bits (140), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 78/353 (22%), Positives = 153/353 (43%), Gaps = 38/353 (10%)

Query: 19  FFLALYLVAIGSGCVKPNMIAHGADQFDQSNPKQSKKLSSYFNAAYFAFSTGELVALTVL 78
           F+  L+L+A+GSG +KP + +   DQFDQSN   ++K    F+  YF  + G   A   +
Sbjct: 112 FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFASLSM 168

Query: 79  VWVQTHSGMDVGFGVSAAAMALGLFGVVSGTLYYRN-----KRPQGSIFTPIAQVFVAAM 133
             +  + G  V FG+    M +       G   Y +     K P G  F P+ +  +   
Sbjct: 169 PLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHG--FLPVIRSALLTK 226

Query: 134 LKRKQICPSNPQMLHGLNQN----NVPNDSGSVFLTQRFRFL-----DKACIKVEDGTNK 184
           ++ K        ++ G++      N+P       L      +       A +++E    +
Sbjct: 227 VEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERA--R 284

Query: 185 KESPWRLCTVTQVEQVKVLISVVPIFACTIIFNTILAQLQTFSVQQGSAMNNKLTKNFHV 244
           K  P        V+ V+ ++ ++ +FA    F ++  Q  +  + Q     N + K    
Sbjct: 285 KSHP-----DAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQA----NDMVKPQWF 335

Query: 245 PPASLQSIPYIMLVILVPLYDKFFVPFARKYTGHESGISPLQRIGFGLFLATFSMISAAL 304
            PA +Q++  +++++L+P ++ F +  A +  G +  ++ L+++G G+ +   S I    
Sbjct: 336 EPAMMQALNPLLVMLLIP-FNNFVLYPAIERMGVK--LTALRKMGAGIAITGLSWIVVGT 392

Query: 305 MEKKRRDSALDSGKTLSIFSITPQFLIFGLSEMFTAVGLIEFFYKQSLKGMQA 357
           ++       +D G  LSIF     + +    E+  +   +EF Y Q+ K M+ 
Sbjct: 393 IQLM-----MDGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKG 440


>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 = 37.4 bits (85), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 51/230 (22%), Positives = 95/230 (41%), Gaps = 35/230 (15%)

Query: 14  FKASIFFLALYLVAIGSGCVKPNMIAHGADQFDQSNPKQSKKLSSYFNAAYFAFSTGELV 73
           F AS  F ++ L+ IG+G +KPN+       +D+ + ++    S +     F  + G  +
Sbjct: 106 FGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFV----FGINLGAFI 161

Query: 74  ALTVLVWVQTHSGMDVGFGVSAAAMALGLFGVVSG---TLYYRNKRPQGSIFTPIAQVFV 130
           A  ++   Q  +G  V F ++A  M +GL     G   TL     RP      P+A   V
Sbjct: 162 APLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPT----DPLAPEEV 217

Query: 131 AAMLKRKQICPSN----PQMLHGLNQNNVPNDSGSVFLTQRFRFLDKACIKVEDGTNKKE 186
             +L +  +  +       +++ +  N++P              L    I +        
Sbjct: 218 KPLLVKVSLAVAGFIAIIVVMNLVGWNSLP---------AYINLLTIVAIAIP----VFY 264

Query: 187 SPWRLCT--VTQVEQVKVLISVVPIFACTIIFNTILAQ----LQTFSVQQ 230
             W + +  VT  E ++V +S +P+F   ++F  I  Q    L TF+ ++
Sbjct: 265 FAWMISSVKVTSTEHLRV-VSYIPLFIAAVLFWAIEEQGSVVLATFAAER 313


  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    0.135    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,291,026
Number of Sequences: 62578
Number of extensions: 376092
Number of successful extensions: 666
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: 663
Number of HSP's gapped (non-prelim): 4
length of query: 411
length of database: 14,973,337
effective HSP length: 101
effective length of query: 310
effective length of database: 8,652,959
effective search space: 2682417290
effective search space used: 2682417290
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)