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= 012627
         (459 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 =  152 bits (384), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 116/424 (27%), Positives = 200/424 (47%), Gaps = 59/424 (13%)

Query: 53  YVTRSRGRRASIMVGSVSFFIGAILNA------------------CAVHISMLLLGRIFL 94
           Y +   GRR S+ + +V FFI  + +A                   A ++   ++ RI  
Sbjct: 77  YCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRIIG 136

Query: 95  GMGIGFGNQAVPLYLSEMAPAKIRGAVNQLFQLTTCLGILVANLINYGTEK------IHP 148
           G+G+G  +   P+Y++E+APA IRG +    Q     G L+   +NY   +      ++ 
Sbjct: 137 GIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNT 196

Query: 149 WGWRLSLGLATVPATLMFVGGLFLPETPNSLVEQGKLDEARKVLEKVRGTANVDAEFSDL 208
            GWR       +PA L  +    +PE+P  L+ +GK ++A  +L K+ G           
Sbjct: 197 DGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNT--------- 247

Query: 209 IDASNAARAIKNPFRNLFKKKNR------PQLVIGALGIPAFQQLTGMNSILFYAPVIFQ 262
             A+ A + IK+   +  K   R        +VIG + +  FQQ  G+N +L+YAP +F+
Sbjct: 248 -LATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVM-LSIFQQFVGINVVLYYAPEVFK 305

Query: 263 SLGFGSGAALYSSVITGIALCIAALISMAFVDKFGRRAFFLEAGTEMIIYMVIVAITLAL 322
           +LG  +  AL  ++I G+      ++++  VDKFGR+   +     M I M     +L  
Sbjct: 306 TLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGM----FSLGT 361

Query: 323 EFGEGKPLPKGIGIFLVIVICLFVLAYGRSWGPLGWLVPSELFPLEMRSAGQSVVVCNNL 382
            F    P     GI  ++ +  +V A+  SWGP+ W++ SE+FP  +R    ++ V    
Sbjct: 362 AFYTQAP-----GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQW 416

Query: 383 L--------FTALIAQAFLAALCHLKFGIFLVFGGLVVIMSAFIYFFLPETKQVPIEEIY 434
           L        F  +   ++L A  H  F  + ++G + V+ + F++ F+PETK   +EE+ 
Sbjct: 417 LANYFVSWTFPMMDKNSWLVAHFHNGFS-YWIYGCMGVLAALFMWKFVPETKGKTLEELE 475

Query: 435 LLFE 438
            L+E
Sbjct: 476 ALWE 479


>pdb|2VHF|A Chain A, Structure Of The Cyld Usp Domain
 pdb|2VHF|B Chain B, Structure Of The Cyld Usp Domain
          Length = 374

 Score = 29.6 bits (65), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 32/131 (24%), Positives = 55/131 (41%), Gaps = 31/131 (23%)

Query: 184 KLDEARKVLEKVRGTANVDAEFSD-----------------LIDASNAARAIKNP-FRNL 225
           K+ + RK+LEKV   +   +E  D                 L+   +A + +++  F  +
Sbjct: 76  KIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHHILRVEPLLKIRSAGQKVQDCYFYQI 135

Query: 226 FKKKNRPQLVIGALGIPAFQQL---TGMNSILFYAP----VIFQSLGFGSGAALYSSVIT 278
           F +KN        +G+P  QQL   + +NS L +A     +I Q   FG    L+  +  
Sbjct: 136 FMEKNE------KVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKDFKLFKKIFP 189

Query: 279 GIALCIAALIS 289
            + L I  L+ 
Sbjct: 190 SLELNITDLLE 200


  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    0.143    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,541,261
Number of Sequences: 62578
Number of extensions: 496499
Number of successful extensions: 1267
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1261
Number of HSP's gapped (non-prelim): 7
length of query: 459
length of database: 14,973,337
effective HSP length: 102
effective length of query: 357
effective length of database: 8,590,381
effective search space: 3066766017
effective search space used: 3066766017
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)