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= 008953
         (547 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 = 98/472 (20%), Positives = 199/472 (42%), Gaps = 68/472 (14%)

Query: 41  FVLGLQAFEIMAIAAVGNNLITYVINEMHFSLSN------SANIVTNFIGTVFLLALLGG 94
           +++  +A E  +   + N L  +++  +  S+        + ++  +F+  V+   LLGG
Sbjct: 16  YIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGG 75

Query: 95  YLSDSFLGSFWTMLIFGFVELSGFILLSVQAHLPQLKPPKCNMVTDSENCEEAKGFKASI 154
           +++D F G + T+L    +   G   L++  H                     +GF    
Sbjct: 76  WIADRFFGKYNTILWLSLIYCVGHAFLAIFEH-------------------SVQGF---- 112

Query: 155 FFLALYLVAIGSGCVKPNMIAHGADQFDQSNPKQSKKLSSYFNAAYFAFSTGELVALTVL 214
            +  L+L+A+GSG +KP + +   DQFDQSN   ++K    F+  YF  + G   A   +
Sbjct: 113 -YTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFASLSM 168

Query: 215 VWVQTHSGMDVGFGVSAAAMALGLFGVVSGTLYYRN-----KRPQGSIFTPIAQVFVAAM 269
             +  + G  V FG+    M +       G   Y +     K P G  F P+ +  +   
Sbjct: 169 PLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHG--FLPVIRSALLTK 226

Query: 270 LKRKQICPSNPQMLHGLNQN----NVPNDSGSVFLTQRFRFL-----DKACIKVEDGTNK 320
           ++ K        ++ G++      N+P       L      +       A +++E    +
Sbjct: 227 VEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERA--R 284

Query: 321 KESPWRLCTVTQVEQVKVLISVVPIFACTIIFNTILAQLQTFSVQQGSAMNNKLTKNFHV 380
           K  P        V+ V+ ++ ++ +FA    F ++  Q  +  + Q     N + K    
Sbjct: 285 KSHP-----DAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQA----NDMVKPQWF 335

Query: 381 PPASLQSIPYIMLVILVPLYDKFFVPFARKYTGHESGISPLQRIGFGLFLATFSMISAAL 440
            PA +Q++  +++++L+P ++ F +  A +  G +  ++ L+++G G+ +   S I    
Sbjct: 336 EPAMMQALNPLLVMLLIP-FNNFVLYPAIERMGVK--LTALRKMGAGIAITGLSWIVVGT 392

Query: 441 MEKKRRDSALDSGKTLSIFSITPQFLIFGLSEMFTAVGLIEFFYKQSLKGMQ 492
           ++       +D G  LSIF     + +    E+  +   +EF Y Q+ K M+
Sbjct: 393 IQLM-----MDGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMK 439


>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 = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 41/177 (23%), Positives = 80/177 (45%), Gaps = 37/177 (20%)

Query: 66  NEMHFSLSNSANIVTNFIGTVFLLALLGGYLSDSFLGS----FWTMLIFGFVELSGFILL 121
            ++H + + +A+I+  +   V+L   +GG+++D  +G+    FW     G + + G I+L
Sbjct: 47  GDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWG----GVLIMLGHIVL 102

Query: 122 SVQAHLPQLKPPKCNMVTDSENCEEAKGFKASIFFLALYLVAIGSGCVKPNMIAHGADQF 181
           +    LP                     F AS  F ++ L+ IG+G +KPN+       +
Sbjct: 103 A----LP---------------------FGASALFGSIILIIIGTGFLKPNVSTLVGTLY 137

Query: 182 DQSNPKQSKKLSSYFNAAYFAFSTGELVALTVLVWVQTHSGMDVGFGVSAAAMALGL 238
           D+ + ++    S +     F  + G  +A  ++   Q  +G  V F ++A  M +GL
Sbjct: 138 DEHDRRRDAGFSIFV----FGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGL 190


>pdb|4DVE|A Chain A, Crystal Structure At 2.1 A Of The S-Component For Biotin
           From An Ecf- Type Abc Transporter
 pdb|4DVE|B Chain B, Crystal Structure At 2.1 A Of The S-Component For Biotin
           From An Ecf- Type Abc Transporter
 pdb|4DVE|C Chain C, Crystal Structure At 2.1 A Of The S-Component For Biotin
           From An Ecf- Type Abc Transporter
          Length = 198

 Score = 30.0 bits (66), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 97  SDSFLGSFWTMLIFG--FVELSGFILLSVQAHLPQLKPPKCNMVTDSENCEEA 147
           S ++ G    +L+FG  FV+  G I LS Q+++P L     N+V    +C +A
Sbjct: 125 SQNWFGELIIVLLFGVIFVDFVGAIWLSFQSNIPLLTSLISNLVFIPGDCIKA 177


  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
   0.322    0.135    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,113,591
Number of Sequences: 62578
Number of extensions: 531956
Number of successful extensions: 948
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 942
Number of HSP's gapped (non-prelim): 5
length of query: 547
length of database: 14,973,337
effective HSP length: 104
effective length of query: 443
effective length of database: 8,465,225
effective search space: 3750094675
effective search space used: 3750094675
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)