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= 016882
         (381 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 = 78.6 bits (192), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 103/213 (48%), Gaps = 27/213 (12%)

Query: 163 LAMHAAPMYIAETAPTPMRGQLISLKEFFIVLGMVGGYGIGSLLVD-------LVAGWRY 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-ATRVSILLGLFKVGSCTLFFMS 367
           ++ G  A++D A   +I++G+  +    L  M+
Sbjct: 305 KTLG--ASTDIALLQTIIVGVINLTFTVLAIMT 335


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

 Score = 28.5 bits (62), Expect = 5.7,   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 = 28.5 bits (62), Expect = 5.8,   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|2VK9|A Chain A, Crystal Structure Of The Catalytic Domain Of Alpha-Toxin
           From Clostridium Novyi
          Length = 551

 Score = 28.1 bits (61), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 22/42 (52%)

Query: 311 IGAGLVLFQQITGQPSVLYYAASILQSAGFSAASDATRVSIL 352
           IGA  +  + I       YY   ++Q+   +AASD  R++IL
Sbjct: 234 IGATDINTENILTNKLKSYYYQELIQTNNLAAASDILRIAIL 275


  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    0.137    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,228,653
Number of Sequences: 62578
Number of extensions: 326817
Number of successful extensions: 767
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 761
Number of HSP's gapped (non-prelim): 5
length of query: 381
length of database: 14,973,337
effective HSP length: 101
effective length of query: 280
effective length of database: 8,652,959
effective search space: 2422828520
effective search space used: 2422828520
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: 52 (24.6 bits)