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= 010239
         (514 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 =  107 bits (268), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 90/340 (26%), Positives = 154/340 (45%), Gaps = 36/340 (10%)

Query: 163 LAMHAAPMYIAETAPTPMRGQLISLKEFFIVLGMVGGYGIGSLLVDL-------VAGWRY 215
           LA   +PMYIAE AP  +RG+L+S  +F I+ G +  Y +   +            GWRY
Sbjct: 142 LASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRY 201

Query: 216 MYGASTPLAVIMGMGMWWLPASPRWLLLCAMKRKGDMQDLRESAISCLCRLRGQSIGDSA 275
           M+ +    A++  M ++ +P SPRWL+      +G     +E A   L ++ G ++   A
Sbjct: 202 MFASECIPALLFLMLLYTVPESPRWLM-----SRGK----QEQAEGILRKIMGNTLATQA 252

Query: 276 PTEVDEILTELSYVGEDKEVSLREVFHGKCLKALIIGAGLVLFQQITGQPSVLYYAASIL 335
             E+   L         ++   R +  G  +  ++IG  L +FQQ  G   VLYYA  + 
Sbjct: 253 VQEIKHSLD------HGRKTGGRLLMFG--VGVIVIGVMLSIFQQFVGINVVLYYAPEVF 304

Query: 336 QSAGFSAASD-ATRVSILLGLFKLIMTGLAXXXXXXXXXXXXXXXXXXXIVIXXXXXXXX 394
           ++ G  A++D A   +I++G+  L  T LA                   + I        
Sbjct: 305 KTLG--ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTA 362

Query: 395 XXXXXXVPXXXXXXXXXYVGCYQLSFGPIGWLMISEVFPLRLRGRGLSVAVLVNFGANAL 454
                            YV  + +S+GP+ W+++SE+FP  +RG+ L++AV   + AN  
Sbjct: 363 FYTQAP-GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYF 421

Query: 455 VTFAFSPLKD-------LLGAGILFYAFGVIAVLSLAFIF 487
           V++ F P+ D           G  ++ +G + VL+  F++
Sbjct: 422 VSWTF-PMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMW 460


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

 Score = 28.9 bits (63), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 6/41 (14%)

Query: 253 QDLRESAISCLCRLR------GQSIGDSAPTEVDEILTELS 287
           QD+ E AISCL  L       GQ+I D   T V ++L +L+
Sbjct: 199 QDIYEEAISCLTTLSEDNLKVGQAITDDQETHVYDVLLKLA 239


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

 Score = 28.9 bits (63), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 6/41 (14%)

Query: 253 QDLRESAISCLCRLR------GQSIGDSAPTEVDEILTELS 287
           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
   0.323    0.139    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,882,044
Number of Sequences: 62578
Number of extensions: 373624
Number of successful extensions: 802
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: 795
Number of HSP's gapped (non-prelim): 5
length of query: 514
length of database: 14,973,337
effective HSP length: 103
effective length of query: 411
effective length of database: 8,527,803
effective search space: 3504927033
effective search space used: 3504927033
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)