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= 013609
         (439 letters)

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

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



>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
           From E.Coli
          Length = 451

 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 79/392 (20%), Positives = 152/392 (38%), Gaps = 33/392 (8%)

Query: 7   RYLIVILTFISTCVCYIERVGFSIAYTAAADAAGVNQSSKGTILSTFYYGYACSQVPGGW 66
           R+ I +  F      Y+ R  F++A     +  G ++   G  LS     Y  S+   G 
Sbjct: 26  RWQIFLGIFFGYAAYYLVRKNFALAMPYLVEQ-GFSRGDLGFALSGISIAYGFSKFIMGS 84

Query: 67  AAQKIGGRKVLLFSFVLWSSTCFWLKLDP---NNVFILVVARLLVGVSQGFIFPSIHTVL 123
            + +   R  L    +L ++   ++   P   +++ ++ V   L G  QG  +P     +
Sbjct: 85  VSDRSNPRVFLPAGLILAAAVMLFMGFVPWATSSIAVMFVLLFLCGWFQGMGWPPCGRTM 144

Query: 124 AQWVPPHERSRSVSLTTSGMYLGAAMG-MLFLPSLVKYNGPNSVFNAEAALGGMWSLLWF 182
             W    ER   VS+      +G  +  +LFL  +  +N  ++     A    + +L  F
Sbjct: 145 VHWWSQKERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFNDWHAALYMPAFCAILVALFAF 204

Query: 183 KYATDPPRSEHPKASAAGFGESLLPMRDQKVKV-----DNGGSAMKAAKIPWKRIVVNLP 237
               D P+S             L P+ + K        +     + A +I  + ++ N  
Sbjct: 205 AMMRDTPQSC-----------GLPPIEEYKNDYPDDYNEKAEQELTAKQIFMQYVLPNKL 253

Query: 238 VWAIVVNNFTFHYALYVLMNWLPTYFELGLQLSLQEMGSSKMMPYLNMFIFSNIGGVVAD 297
           +W I + N   +   Y +++W PTY +     +L +   +       ++ ++ I G +  
Sbjct: 254 LWYIAIANVFVYLLRYGILDWSPTYLKEVKHFALDKSSWAYF-----LYEYAGIPGTLLC 308

Query: 298 HLITKRILSVTR--TRKFLNTVGFMVASIALMALPIFRSSNGAIFCSSIALGFLALGRAG 355
             ++ ++    R  T  F  T+   +A+I     P    +   I    I +GFL  G   
Sbjct: 309 GWMSDKVFRGNRGATGVFFMTL-VTIATIVYWMNPAGNPTVDMI--CMIVIGFLIYGPVM 365

Query: 356 F-AVNHMDIAPRY-AGIVMGISNTAGTLAGIV 385
              ++ +++AP+  AG   G +   G L G V
Sbjct: 366 LIGLHALELAPKKAAGTAAGFTGLFGYLGGSV 397


>pdb|3QR0|A Chain A, Crystal Structure Of S. Officinalis Plc21
          Length = 816

 Score = 32.7 bits (73), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 27/100 (27%), Positives = 48/100 (48%), Gaps = 7/100 (7%)

Query: 183 KYATDPPRSEHPKASAAGFGESLLPMRDQKVKVDNGGSAMKAAKIPWKRIVVNLPVWAIV 242
           KYA  PP+ +  K +   FG S +P++D+ V + +G + +    + W  +V      A  
Sbjct: 77  KYAK-PPKDKKIKEAGTNFGSSNIPLQDKCVTICHGYNYI---DLEWTHLVAENSSVAKK 132

Query: 243 VNNFTFHYALYVL---MNWLPTYFELGLQLSLQEMGSSKM 279
            +   F YA  +L    N L  + +L  +L+  EM  +K+
Sbjct: 133 WSEEVFSYAYNLLSLNKNQLGEWEKLYFRLTTVEMEKNKI 172


>pdb|3O7P|A Chain A, Crystal Structure Of The E.Coli Fucose:proton Symporter,
           Fucp (N162a)
          Length = 438

 Score = 31.2 bits (69), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 25/121 (20%), Positives = 52/121 (42%), Gaps = 2/121 (1%)

Query: 47  GTILSTFYYGYACSQVPGGWAAQKIGGRKVLLFSFVLWS--STCFWLKLDPNNVFILVVA 104
           G I S FY+GY    +P G   +K+  +  ++    L++  +  FW   +  N  + +V 
Sbjct: 64  GLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVG 123

Query: 105 RLLVGVSQGFIFPSIHTVLAQWVPPHERSRSVSLTTSGMYLGAAMGMLFLPSLVKYNGPN 164
             ++    G +  + +  +    P       ++L  +    GA + ++F  SL+  N P+
Sbjct: 124 LFIIAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFASFGAIIAVVFGQSLILSNVPH 183

Query: 165 S 165
            
Sbjct: 184 Q 184


>pdb|3O7Q|A Chain A, Crystal Structure Of A Major Facilitator Superfamily (Mfs)
           Transporter, Fucp, In The Outward Conformation
          Length = 438

 Score = 30.8 bits (68), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 25/121 (20%), Positives = 52/121 (42%), Gaps = 2/121 (1%)

Query: 47  GTILSTFYYGYACSQVPGGWAAQKIGGRKVLLFSFVLWS--STCFWLKLDPNNVFILVVA 104
           G I S FY+GY    +P G   +K+  +  ++    L++  +  FW   +  N  + +V 
Sbjct: 64  GLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVG 123

Query: 105 RLLVGVSQGFIFPSIHTVLAQWVPPHERSRSVSLTTSGMYLGAAMGMLFLPSLVKYNGPN 164
             ++    G +  + +  +    P       ++L  +    GA + ++F  SL+  N P+
Sbjct: 124 LFIIAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPH 183

Query: 165 S 165
            
Sbjct: 184 Q 184


  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
   0.326    0.138    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,309,171
Number of Sequences: 62578
Number of extensions: 477784
Number of successful extensions: 1224
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1222
Number of HSP's gapped (non-prelim): 8
length of query: 439
length of database: 14,973,337
effective HSP length: 102
effective length of query: 337
effective length of database: 8,590,381
effective search space: 2894958397
effective search space used: 2894958397
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)