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= 016673
         (385 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 =  124 bits (311), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 100/360 (27%), Positives = 168/360 (46%), Gaps = 55/360 (15%)

Query: 23  TSYFLIACMVAAMGGSLFGYDLGV-SGGVTSMDDFLKEFFPKVYRRKQAHLTETDYCKYD 81
           +SY     +VA +GG LFGYD  V SG V S++         V+   Q +L+E+      
Sbjct: 7   SSYIFSITLVATLGGLLFGYDTAVISGTVESLNT--------VFVAPQ-NLSESA----A 53

Query: 82  NQVLTLFTSSLYFAGLVSTFGASYVTRSRGRRASIMVGSVSFFIGAILNAC--------- 132
           N +L    +S     ++      Y +   GRR S+ + +V FFI  + +A          
Sbjct: 54  NSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSIN 113

Query: 133 ---------AVHISMLLLGRIFLGMGIGFGNQAVPLYLSEMAPAKIRGAVNQLFQLTTCL 183
                    A ++   ++ RI  G+G+G  +   P+Y++E+APA IRG +    Q     
Sbjct: 114 PDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIF 173

Query: 184 GILVANLINYGTEK------IHPWGWRLSLGLATVPATLMFVGGLFLPETPNSLVEQGKL 237
           G L+   +NY   +      ++  GWR       +PA L  +    +PE+P  L+ +GK 
Sbjct: 174 GQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQ 233

Query: 238 DEARKVLEKVRGTANVDAEFSDLIDASNAARAIKNPFRNLFKKKNR------PQLVIGAL 291
           ++A  +L K+ G             A+ A + IK+   +  K   R        +VIG +
Sbjct: 234 EQAEGILRKIMGNT----------LATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVM 283

Query: 292 GIPAFQQLTGMNSILFYAPVIFQSLGFGSGAALYSSVITGIALCIAALISMAFVDKFGRR 351
            +  FQQ  G+N +L+YAP +F++LG  +  AL  ++I G+      ++++  VDKFGR+
Sbjct: 284 -LSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRK 342


>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 = 30.8 bits (68), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 32/131 (24%), Positives = 55/131 (41%), Gaps = 31/131 (23%)

Query: 236 KLDEARKVLEKVRGTANVDAEFSD-----------------LIDASNAARAIKNP-FRNL 277
           K+ + RK+LEKV   +   +E  D                 L+   +A + +++  F  +
Sbjct: 76  KIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHHILRVEPLLKIRSAGQKVQDCYFYQI 135

Query: 278 FKKKNRPQLVIGALGIPAFQQL---TGMNSILFYAP----VIFQSLGFGSGAALYSSVIT 330
           F +KN        +G+P  QQL   + +NS L +A     +I Q   FG    L+  +  
Sbjct: 136 FMEKNE------KVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKDFKLFKKIFP 189

Query: 331 GIALCIAALIS 341
            + L I  L+ 
Sbjct: 190 SLELNITDLLE 200


>pdb|3GSN|B Chain B, Crystal Structure Of The Public Ra14 Tcr In Complex With
           The Hcmv Dominant NlvHLA-A2 Epitope
          Length = 243

 Score = 29.6 bits (65), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 15/88 (17%)

Query: 3   GGGFTDAGDLKRAHLYEYRITSYFLIA-------------CMVAAMGGSLFGYDLGVSGG 49
           G G TD G++   +      T  F +              C  + + G ++GY  G    
Sbjct: 50  GAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSPVTGGIYGYTFGSGTR 109

Query: 50  VTSMDDFLKEFFPK--VYRRKQAHLTET 75
           +T ++D  K F P+  V+   +A ++ T
Sbjct: 110 LTVVEDLNKVFPPEVAVFEPSEAEISHT 137


  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
   0.326    0.140    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,427,468
Number of Sequences: 62578
Number of extensions: 411132
Number of successful extensions: 1346
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1340
Number of HSP's gapped (non-prelim): 7
length of query: 385
length of database: 14,973,337
effective HSP length: 101
effective length of query: 284
effective length of database: 8,652,959
effective search space: 2457440356
effective search space used: 2457440356
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: 52 (24.6 bits)