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= 011716
         (479 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 = 71.6 bits (174), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 82/353 (23%), Positives = 144/353 (40%), Gaps = 40/353 (11%)

Query: 97  YTGLYAMATGVGGVKAALPAHGADQLDHSNRRLISAFFNWFFFSLCAGGLVAATVMVWIE 156
           YTGL+ +A G GG+K  + +   DQ D SN+ L    F+ F+F++  G   A+  M  + 
Sbjct: 113 YTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKAFDMFYFTINFGSFFASLSMPLLL 172

Query: 157 ENRGWNCSFKISAVALGLALCIFTIGFPIYRYKRPSGSPITRIFKVIASAIRNRKASRSE 216
           +N G   +F I  V + +A   F +G   Y +  P          VI SA+  +   +  
Sbjct: 173 KNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKVEGKGN 232

Query: 217 MTEQIASPGATRSN-----------------DMFRV-----------LDKALFDDTITAA 248
           +   +A  G   +                   M  V           L++A    +   A
Sbjct: 233 IGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERA--RKSHPDA 290

Query: 249 QVEETKTFLGLLPIFASTIMMNCCLAQLQTFSVQQGIIMNRTINNFKIPTQSLTVFPLTI 308
            V+  ++ L +L +FA          Q  +  + Q   M +    +  P     + PL +
Sbjct: 291 AVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDMVKP--QWFEPAMMQALNPLLV 348

Query: 309 MLASIPLYERSVHIFERKISAKYNIFRPLKRIGLGLALASGSMAVAAVVESTRRAAAENH 368
           ML  IP     ++    ++  K      L+++G G+A+      ++ +V  T +   +  
Sbjct: 349 MLL-IPFNNFVLYPAIERMGVKLT---ALRKMGAGIAIT----GLSWIVVGTIQLMMDGG 400

Query: 369 VTLSVFWLVWQYLLLGVSDMLTLGGMLEFFYSEAPHSMRSISTALSWCSTSMG 421
             LS+FW +  Y LL   ++L     LEF YS+AP +M+    +    S ++G
Sbjct: 401 SALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVG 453


>pdb|1VD0|A Chain A, Capsid Stabilizing Protein Gpd, Nmr, 20 Structures
          Length = 109

 Score = 30.4 bits (67), Expect = 2.2,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 12/55 (21%)

Query: 77  YSRLQPAMNRRPSHTQAAILYTGLYAMATGVGGVKAALPAHGADQLDHSNRRLIS 131
           ++  QP  N  P+HT            AT  GG+ A  PA     LD S+R+L++
Sbjct: 6   FTHYQPQGNSDPAHT------------ATAPGGLSAKAPAMTPLMLDTSSRKLVA 48


>pdb|2VBI|A Chain A, Holostructure Of Pyruvate Decarboxylase From Acetobacter
           Pasteurianus
 pdb|2VBI|B Chain B, Holostructure Of Pyruvate Decarboxylase From Acetobacter
           Pasteurianus
 pdb|2VBI|C Chain C, Holostructure Of Pyruvate Decarboxylase From Acetobacter
           Pasteurianus
 pdb|2VBI|D Chain D, Holostructure Of Pyruvate Decarboxylase From Acetobacter
           Pasteurianus
 pdb|2VBI|E Chain E, Holostructure Of Pyruvate Decarboxylase From Acetobacter
           Pasteurianus
 pdb|2VBI|F Chain F, Holostructure Of Pyruvate Decarboxylase From Acetobacter
           Pasteurianus
 pdb|2VBI|G Chain G, Holostructure Of Pyruvate Decarboxylase From Acetobacter
           Pasteurianus
 pdb|2VBI|H Chain H, Holostructure Of Pyruvate Decarboxylase From Acetobacter
           Pasteurianus
          Length = 566

 Score = 29.6 bits (65), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 198 RIFKVIASAIRNRKASRSEMTEQIASPGATRSNDMFRVLDKALFDDTITAAQVEETKTFL 257
           +I  VI +A+R RK +  ++   IAS    R   +  +L +   D T   A V+ T   +
Sbjct: 147 KIDHVIRTALRERKPAYLDIACNIASEPCVRPGPVSSLLSEPEIDHTSLKAAVDAT---V 203

Query: 258 GLLPIFASTIMM 269
            LL   AS +M+
Sbjct: 204 ALLEKSASPVML 215


  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
   0.327    0.136    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,292,425
Number of Sequences: 62578
Number of extensions: 395986
Number of successful extensions: 1267
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1263
Number of HSP's gapped (non-prelim): 7
length of query: 479
length of database: 14,973,337
effective HSP length: 103
effective length of query: 376
effective length of database: 8,527,803
effective search space: 3206453928
effective search space used: 3206453928
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)