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= 018609
         (353 letters)

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

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



>pdb|3MKT|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKT|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKU|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKU|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
          Length = 460

 Score = 68.6 bits (166), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 79/334 (23%), Positives = 135/334 (40%), Gaps = 25/334 (7%)

Query: 6   INRLERQDPEIATEACNFSISLI---PALLAFAVLRPLIHNLQSQSLILPLFLSACATLC 62
           I R    +  +AT+   +  ++I   PA L F  LR     +   SL  P  +     L 
Sbjct: 115 IIRFMDVEEAMATKTVGYMHAVIFAVPAYLLFQALRSFTDGM---SLTKPAMVIGFIGLL 171

Query: 63  FHILLCWYLVFKA----NFRIVGAALAIGLSYCLNAVILALYMRYSSSCEKTRVFIFSDI 118
            +I L W  V+          VG  +A  + Y +  ++L  Y+  S      +VF   + 
Sbjct: 172 LNIPLNWIFVYGKFGAPELGGVGCGVATAIVYWIMLLLLLFYIVTSKRLAHVKVF---ET 228

Query: 119 FSCIK-----EFFSFALPTVVMFCLEWWSFEILILLSGLLPNSKLETSVLSICLTISSTH 173
           F   +       F    P       E   F ++ LL  + P      +   + L  SS  
Sbjct: 229 FHKPQPKELIRLFRLGFPVAAALFFEVTLFAVVALL--VAPLGSTVVAAHQVALNFSSLV 286

Query: 174 YFIPYGIGAAASTRVSNELGAGNPQAAQLAACVVMVLAVTEAVIVGTILFCCRYVLAYAF 233
           +  P  IGAA S RV ++LG  + + A +AA V ++  +  A I   +    R  +A  +
Sbjct: 287 FMFPMSIGAAVSIRVGHKLGEQDTKGAAIAANVGLMTGLATACITALLTVLFREQIALLY 346

Query: 234 NSDKDVVNYVSELVPLLSFSIIMDSLQSVLSGVARGTGWQHIGAYVNLGAYYIVGIPLAS 293
             ++ VV    +L+   +    MD++Q V +G  RG        +    +Y+++G+P   
Sbjct: 347 TENQVVVALAMQLLLFAAIYQCMDAVQVVAAGSLRGYKDMTAIFHRTFISYWVLGLPTGY 406

Query: 294 VLCFV-----LNLRGKGLWIGIMTGSAVQAIVLA 322
           +L          L  KG W+G + G +  A++L 
Sbjct: 407 ILGMTNWLTEQPLGAKGFWLGFIIGLSAAALMLG 440


>pdb|4HUK|A Chain A, Mate Transporter Norm-ng In Complex With Tpp And Monobody
 pdb|4HUL|A Chain A, Mate Transporter Norm-ng In Complex With Cs+ And Monobody
 pdb|4HUM|A Chain A, Mate Transporter Norm-ng In Complex With Ethidium And
           Monobody
 pdb|4HUN|A Chain A, Mate Transporter Norm-ng In Complex With R6g And Monobody
          Length = 459

 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 42/203 (20%), Positives = 86/203 (42%), Gaps = 2/203 (0%)

Query: 119 FSCIKEFFSFALPTVVMFCLEWWSFEILILLSGLLPNSKLETSVLSICLTISSTHYFIPY 178
           ++  K+ +    P  + + LE  +F  ++ L  + P  +   +   + +++S   Y IP 
Sbjct: 237 WAVFKQIWKIGAPIGLSYFLEASAFSFIVFL--IAPFGEDYVAAQQVGISLSGILYMIPQ 294

Query: 179 GIGAAASTRVSNELGAGNPQAAQLAACVVMVLAVTEAVIVGTILFCCRYVLAYAFNSDKD 238
            +G+A + R+   LG      A+  + V +V     AVI    L   R  LA  +N D  
Sbjct: 295 SVGSAGTVRIGFSLGRREFSRARYISGVSLVSGWVLAVITVLSLVLFRSPLASMYNDDPA 354

Query: 239 VVNYVSELVPLLSFSIIMDSLQSVLSGVARGTGWQHIGAYVNLGAYYIVGIPLASVLCFV 298
           V++  S ++         D  Q + S   RG     +  +++  A++  G+    +L + 
Sbjct: 355 VLSIASTVLLFAGLFQPADFTQCIASYALRGYKVTKVPMFIHAAAFWGCGLLPGYLLAYR 414

Query: 299 LNLRGKGLWIGIMTGSAVQAIVL 321
            ++   G W  ++    + A+ L
Sbjct: 415 FDMGIYGFWTALIASLTIAAVAL 437


>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
           Cell Carcinoma Antigen Recognized By T Cells 3
          Length = 100

 Score = 29.3 bits (64), Expect = 3.3,   Method: Composition-based stats.
 Identities = 13/23 (56%), Positives = 16/23 (69%)

Query: 102 RYSSSCEKTRVFIFSDIFSCIKE 124
           RYS+S EK ++FI    FSC KE
Sbjct: 10  RYSTSLEKHKLFISGLPFSCTKE 32


>pdb|2GQD|A Chain A, The Crystal Structure Of B-Ketoacyl-Acp Synthase Ii (Fabf)
           From Staphylococcus Aureus
 pdb|2GQD|B Chain B, The Crystal Structure Of B-Ketoacyl-Acp Synthase Ii (Fabf)
           From Staphylococcus Aureus
          Length = 437

 Score = 28.9 bits (63), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 23/42 (54%)

Query: 174 YFIPYGIGAAASTRVSNELGAGNPQAAQLAACVVMVLAVTEA 215
           +F+P  I   A+ +VS +LGA  P  A + AC     ++ EA
Sbjct: 157 FFVPMLIPDMATGQVSIDLGAKGPNGATVTACATGTNSIGEA 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
   0.328    0.139    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,895,417
Number of Sequences: 62578
Number of extensions: 321891
Number of successful extensions: 611
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 601
Number of HSP's gapped (non-prelim): 9
length of query: 353
length of database: 14,973,337
effective HSP length: 100
effective length of query: 253
effective length of database: 8,715,537
effective search space: 2205030861
effective search space used: 2205030861
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 bits)