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= 041627
         (204 letters)

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

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



>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score = 83.6 bits (205), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 57/199 (28%), Positives = 91/199 (45%), Gaps = 14/199 (7%)

Query: 1   MQAFQQFTGINTVMYYSPTIVQMAGFQSNQLALLPSLVVAGTNAVGTIVGIYLIDHFGRK 60
           +  FQQF GIN V+YY+P + +  G  S  +ALL +++V   N   T++ I  +D FGRK
Sbjct: 284 LSIFQQFVGINVVLYYAPEVFKTLG-ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRK 342

Query: 61  KLALSSLAGVIISLVLLSWAF-------ISVIGLALYITFFAPGMGPVPWTVNSEVYREQ 113
            L +    G+ I +  L  AF       ++++ +  Y+  FA   GPV W + SE++   
Sbjct: 343 PLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNA 402

Query: 114 YRGICGGMSATVNWISNLIVAQNFLTVAD---LVG---TGSTXXXXXXXXXXXXXXXXXX 167
            RG    ++    W++N  V+  F  +     LV     G +                  
Sbjct: 403 IRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKF 462

Query: 168 XPETQGLTFLEVEQRWKER 186
            PET+G T  E+E  W+  
Sbjct: 463 VPETKGKTLEELEALWEPE 481


>pdb|2AIV|A Chain A, Multiple Conformations In The Ligand-Binding Site Of The
          Yeast Nuclear Pore Targeting Domain Of Nup116p
          Length = 149

 Score = 32.0 bits (71), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 4/66 (6%)

Query: 9  GINTVMYYSPTIVQMAGFQSNQLALLPSLVVAGTNAVGTIVGIYLIDHFGRKKLALSSLA 68
          G N   Y SP++  ++ +   QL  +P LVV G  + G I  +  +D  G   + L+SL 
Sbjct: 1  GPNENYYISPSLDTLSSYSLLQLRKVPHLVV-GHKSYGKIEFLEPVDLAG---IPLTSLG 56

Query: 69 GVIISL 74
          GVII+ 
Sbjct: 57 GVIITF 62


>pdb|3PBP|B Chain B, Structure Of The Yeast Heterotrimeric
          Nup82-Nup159-Nup116 Nucleoporin Complex
 pdb|3PBP|E Chain E, Structure Of The Yeast Heterotrimeric
          Nup82-Nup159-Nup116 Nucleoporin Complex
 pdb|3PBP|H Chain H, Structure Of The Yeast Heterotrimeric
          Nup82-Nup159-Nup116 Nucleoporin Complex
 pdb|3PBP|K Chain K, Structure Of The Yeast Heterotrimeric
          Nup82-Nup159-Nup116 Nucleoporin Complex
          Length = 148

 Score = 30.4 bits (67), Expect = 0.72,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 4/64 (6%)

Query: 11 NTVMYYSPTIVQMAGFQSNQLALLPSLVVAGTNAVGTIVGIYLIDHFGRKKLALSSLAGV 70
          N   Y SP++  ++ +   QL  +P LVV G  + G I  +  +D  G   + L+SL GV
Sbjct: 2  NENYYISPSLDTLSSYSLLQLRKVPHLVV-GHKSYGKIEFLEPVDLAG---IPLTSLGGV 57

Query: 71 IISL 74
          II+ 
Sbjct: 58 IITF 61


  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
   0.321    0.135    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,257,542
Number of Sequences: 62578
Number of extensions: 177696
Number of successful extensions: 316
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 307
Number of HSP's gapped (non-prelim): 11
length of query: 204
length of database: 14,973,337
effective HSP length: 94
effective length of query: 110
effective length of database: 9,091,005
effective search space: 1000010550
effective search space used: 1000010550
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)