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= 008623
         (559 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 =  155 bits (392), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 142/526 (26%), Positives = 241/526 (45%), Gaps = 82/526 (15%)

Query: 19  NPADKTKTGTW-KACPFILGNECCERLAYYGMSTNLVRYFKHQL-----DQSSSTASKNV 72
           +P D  K   W +  P+I+ +E CER ++YGM   L  +    L     ++     +K+V
Sbjct: 3   SPVDAPK---WPRQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDV 59

Query: 73  L-DWSGTCYITPLIGAFLADAYLGRYWTIAIFSIIYVIGMTFLTVTASVSGLKPVCHGPR 131
              +    Y  PL+G ++AD + G+Y TI   S+IY +G  FL +               
Sbjct: 60  FHSFVIGVYFFPLLGGWIADRFFGKYNTILWLSLIYCVGHAFLAIF-------------- 105

Query: 132 GEETCQVTDAQSATFFVALYLIALGTGGIKPCVSSYGADQFDDADEAEKKHKSSFFNWFY 191
            E + Q        F+  L+LIALG+GGIKP VSS+  DQFD ++++  +     F+ FY
Sbjct: 106 -EHSVQ-------GFYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFY 154

Query: 192 FSINIGALIASSVLVWIQDNEGWGWGFGIPAVAMAIAVVSFFSGTRLFRNQKPGGSPLTR 251
           F+IN G+  AS  +  +  N G    FGIP V M +A V F+ G + + +  P       
Sbjct: 155 FTINFGSFFASLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHG 214

Query: 252 ICQVVAASIRKHKVELPADKSLLYETADAESNITGSRKLDHTKDFSF------------- 298
              V+ +++   KVE   +  L+         ++ +  L +                   
Sbjct: 215 FLPVIRSALLT-KVEGKGNIGLVLALI---GGVSAAYALVNIPTLGIVAGLCCAMVLVMG 270

Query: 299 FDKAAVEIQSDNIKESVNPWRLCTVTQVEELKAIVRLLPIWATGIIFSAVYSQMSSLFVL 358
           F  A   +Q +  ++S +P        V+ +++++R+L ++A    F +++ Q +S ++L
Sbjct: 271 FVGAGASLQLERARKS-HP-----DAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWIL 324

Query: 359 QGERMDTHVGNSSFKIPPASLSIFDTLSVIFWVPIYDRFIVPVTRKFTGHKNGLTQLQRM 418
           Q   M   V    F+  PA +   + L V+  +P  +  + P   +  G K  LT L++M
Sbjct: 325 QANDM---VKPQWFE--PAMMQALNPLLVMLLIPFNNFVLYPAIER-MGVK--LTALRKM 376

Query: 419 GIGLFISILSMIAAAVLELIRLRMVREHNYYDLPEMPMSIMWQVPQYFLIGCAEVFTFIG 478
           G G+ I+ LS I    ++L    M+   +        +SI WQ+  Y L+   EV     
Sbjct: 377 GAGIAITGLSWIVVGTIQL----MMDGGS-------ALSIFWQILPYALLTFGEVLVSAT 425

Query: 479 QLEFFYEQAPDAMRSLCSALSLTTVALGNYLSSLLVTIVTSISTKN 524
            LEF Y QAP AM+    +    +V +GN     L  ++ ++S K+
Sbjct: 426 GLEFAYSQAPKAMKGTIMSFWTLSVTVGN-----LWVLLANVSVKS 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 = 63.5 bits (153), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 98/223 (43%), Gaps = 34/223 (15%)

Query: 22  DKTKT--GTWKACPFILGNECCERLAYYGMSTNLVRYF-----KHQLDQSSSTASKNVLD 74
           DK KT  G       +   E  ER +YYGM   L+ Y         L  + +TA+  +  
Sbjct: 3   DKGKTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAI 62

Query: 75  WSGTCYITPLIGAFLADAYLGRYWTIAIFSIIYVIGMTFLTVTASVSGLKPVCHGPRGEE 134
           ++   Y++  IG F+AD  +G    +    ++ ++G   L +    S L           
Sbjct: 63  YASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASAL----------- 111

Query: 135 TCQVTDAQSATFFVALYLIALGTGGIKPCVSSYGADQFDDADEAEKKHKSSFFNWFYFSI 194
                       F ++ LI +GTG +KP VS+     +D+ D    + + + F+ F F I
Sbjct: 112 ------------FGSIILIIIGTGFLKPNVSTLVGTLYDEHD----RRRDAGFSIFVFGI 155

Query: 195 NIGALIASSVLVWIQDNEGWGWGFGIPAVAMAIAVVSFFSGTR 237
           N+GA IA  ++   Q+  G+   F + A+ M I ++ ++ G +
Sbjct: 156 NLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGK 198


  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    0.428 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,575,761
Number of Sequences: 62578
Number of extensions: 660620
Number of successful extensions: 1269
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1260
Number of HSP's gapped (non-prelim): 4
length of query: 559
length of database: 14,973,337
effective HSP length: 104
effective length of query: 455
effective length of database: 8,465,225
effective search space: 3851677375
effective search space used: 3851677375
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)