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= psy10535
         (591 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3TIJ|A Chain A, Crystal Structure Of A Concentrative Nucleoside
           Transporter From Vibrio Cholerae
          Length = 424

 Score =  219 bits (557), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 138/408 (33%), Positives = 227/408 (55%), Gaps = 14/408 (3%)

Query: 193 ISLLGFGVFILLGYVFSKYPNRVPWKIVIWGVIMQLAIGLVTIRLSLGRYVLECIGHHVQ 252
           +SL+G  V + +  + S     +  + V     +Q ++G   + +  G+ +L      V 
Sbjct: 11  MSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFSDAVS 70

Query: 253 TFLEFAYQGAAFVYG--------DEIVFVYHVFAFKVLSVIFFMSFIIQICFYYGWLQSI 304
             + +   G +F++G        +       +FAF+VL  + F S +I + +Y G +Q +
Sbjct: 71  NVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGVMQWV 130

Query: 305 FLKLGWLLQVSLGTTVAESVNTCASVFLGMTEAPLLIKPYLPDLTRSELTAVMLGGFSTV 364
              LG  LQ +LGT+ AES++  A++F+G TEAPL+++P++P +T+SEL AVM GG +++
Sbjct: 131 IRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGGLASI 190

Query: 365 AGTVFAAYTSLGVQAAHIITASIMTAPSALSYSKILYPETEISKTTISNIKKWKSDD--L 422
           AG V A Y S+GV+  +++ AS M AP  L ++K++ PETE  +    +I     DD   
Sbjct: 191 AGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDN-EDITLDGGDDKPA 249

Query: 423 NVIDAACKGAQIGTEMVLGIIANIIAFVSFVAFCNAMLIWFGSLVGVEDLTIEFIFGKIF 482
           NVIDAA  GA  G ++ L + A +IAF+  +A  N ML   G   G+ +L +E + G +F
Sbjct: 250 NVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLGWLF 309

Query: 483 IPLTWIMGVEPSQCEEVARLIGLKTVINEFVAYKELGRVKKLG---LLSPRSEAIATYSL 539
            PL +++GV  ++       IGLKTV NEFVAY +           +LS +++AI +++L
Sbjct: 310 APLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVVLSEKTKAIISFAL 369

Query: 540 CGFANPGSVGCLIATLNTLVPSQRRNTIDLAFRAFIGGCVVCLLTACI 587
           CGFAN  S+  L+  L +L P +R +   +  +A I G +  L+ A I
Sbjct: 370 CGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATI 417


  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
   0.331    0.145    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,921,925
Number of Sequences: 62578
Number of extensions: 603455
Number of successful extensions: 1322
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: 1316
Number of HSP's gapped (non-prelim): 5
length of query: 591
length of database: 14,973,337
effective HSP length: 104
effective length of query: 487
effective length of database: 8,465,225
effective search space: 4122564575
effective search space used: 4122564575
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 54 (25.4 bits)