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= 011657
         (480 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 = 83.2 bits (204), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 127/284 (44%), Gaps = 29/284 (10%)

Query: 178 GWRYMYGASTPLAVIMGMGMWWLPASPRWLLLCAMKRKGDMQDLRESAISCLCRLRGQSI 237
           GWRYM+ +    A++  M ++ +P SPRWL+      +G     +E A   L ++ G ++
Sbjct: 198 GWRYMFASECIPALLFLMLLYTVPESPRWLM-----SRGK----QEQAEGILRKIMGNTL 248

Query: 238 GDSAPTEVDEILTELSYVGEDKEVSLREVFHGKCLKALIIGAGLVLFQQITGQPSVLYYA 297
              A  E+   L         ++   R +  G  +  ++IG  L +FQQ  G   VLYYA
Sbjct: 249 ATQAVQEIKHSLD------HGRKTGGRLLMFG--VGVIVIGVMLSIFQQFVGINVVLYYA 300

Query: 298 ASILQSAGFSAASD-ATRVSILLGLFKLIMTGLAXXXXXXXXXXXXXXXXXXXIVIXXXX 356
             + ++ G  A++D A   +I++G+  L  T LA                   + I    
Sbjct: 301 PEVFKTLG--ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFS 358

Query: 357 XXXXXXXXXXVPXXXXXXXXXYVGCYQLSFGPIGWLMISEVFPLRLRGRGLSVAVLVNFG 416
                                YV  + +S+GP+ W+++SE+FP  +RG+ L++AV   + 
Sbjct: 359 LGTAFYTQAP-GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWL 417

Query: 417 ANALVTFAFSPLKD-------LLGAGILFYAFGVIAVLSLAFIF 453
           AN  V++ F P+ D           G  ++ +G + VL+  F++
Sbjct: 418 ANYFVSWTF-PMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMW 460


>pdb|4GMO|A Chain A, Crystal Structure Of Syo1
          Length = 684

 Score = 28.9 bits (63), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 6/41 (14%)

Query: 219 QDLRESAISCLCRLR------GQSIGDSAPTEVDEILTELS 253
           QD+ E AISCL  L       GQ+I D   T V ++L +L+
Sbjct: 199 QDIYEEAISCLTTLSEDNLKVGQAITDDQETHVYDVLLKLA 239


>pdb|4GMN|A Chain A, Structural Basis Of Rpl5 Recognition By Syo1
          Length = 676

 Score = 28.9 bits (63), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 6/41 (14%)

Query: 219 QDLRESAISCLCRLR------GQSIGDSAPTEVDEILTELS 253
           QD+ E AISCL  L       GQ+I D   T V ++L +L+
Sbjct: 199 QDIYEEAISCLTTLSEDNLKVGQAITDDQETHVYDVLLKLA 239


  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
   0.322    0.139    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,646,497
Number of Sequences: 62578
Number of extensions: 312942
Number of successful extensions: 676
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 670
Number of HSP's gapped (non-prelim): 5
length of query: 480
length of database: 14,973,337
effective HSP length: 103
effective length of query: 377
effective length of database: 8,527,803
effective search space: 3214981731
effective search space used: 3214981731
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: 53 (25.0 bits)