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= psy15864
         (553 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 = 84.0 bits (206), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 93/370 (25%), Positives = 155/370 (41%), Gaps = 60/370 (16%)

Query: 90  GTFLYKMAAPLVLVLTYVAEITQPHLRGMLSATASMTTIFGTVSQLFLGSFLH------- 142
           G  L  M +P+     Y+AE+   H+RG L +      IFG +    +  F+        
Sbjct: 139 GVGLASMLSPM-----YIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASW 193

Query: 143 -----WR----SAAILNLLFPILALCALYFIPESPHWLISQGRMQEASASLCWLRGWVTP 193
                WR    S  I  LLF +L    LY +PESP WL+S+G+ ++A   L  + G    
Sbjct: 194 LNTDGWRYMFASECIPALLFLML----LYTVPESPRWLMSRGKQEQAEGILRKIMG---- 245

Query: 194 DKVQTELSQITKAIEESELKRLGKDGQRRPNYRMYMRRTFLLPYAIVTSLFFIGQFGGMT 253
               T  +Q  + I+ S       D  R+   R+ M    ++   ++ S+F   QF G+ 
Sbjct: 246 ---NTLATQAVQEIKHS------LDHGRKTGGRLLMFGVGVIVIGVMLSIF--QQFVGIN 294

Query: 254 TLQTYAVGIFESIHAPLD-PYFXXXXXXXXXXXXXXXXXXXIHYTGKRPLALISTGGSAA 312
            +  YA  +F+++ A  D                       +   G++PL +I   G A 
Sbjct: 295 VVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAI 354

Query: 313 CFIVVAVYAQFHLSYGWDSPLVPTVFLVLAAFLTH---ICIRLLPWMLIGEVFPNNIRAT 369
               +     F+        L+  +F V AAF      +C     W+L+ E+FPN IR  
Sbjct: 355 GMFSLG--TAFYTQAPGIVALLSMLFYV-AAFAMSWGPVC-----WVLLSEIFPNAIRGK 406

Query: 370 XXXXXXXXXYIFAFAVNKLYYPMLDT-------FHLWGTLYFYAAISVVGTLYMYFVMPE 422
                    ++  + V+   +PM+D        FH   + + Y  + V+  L+M+  +PE
Sbjct: 407 ALAIAVAAQWLANYFVS-WTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPE 465

Query: 423 TEGRTLRDIE 432
           T+G+TL ++E
Sbjct: 466 TKGKTLEELE 475


>pdb|3IFU|A Chain A, The Crystal Structure Of Porcine Reproductive And
           Respiratory Syndrome Virus (Prrsv) Leader Protease Nsp1
          Length = 180

 Score = 31.6 bits (70), Expect = 1.2,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 128 IFGTVSQLFLGSFLHWRSAAILNLLFPILALCALYFIPESP-HWLISQG--RMQEASASL 184
           +F    Q++    L  RS   LNL  P L +  L++ PE P  W + +    ++ + A  
Sbjct: 16  VFVAEGQVYCTRCLSARSLLPLNLQVPELGVLGLFYRPEEPLRWTLPRAFPTVECSPAGA 75

Query: 185 CWL 187
           CWL
Sbjct: 76  CWL 78


>pdb|1VQT|A Chain A, Crystal Structure Of Orotidine 5'-Phosphate Decarboxylase
           (Tm0332) From Thermotoga Maritima At 2.00 A Resolution
          Length = 213

 Score = 30.0 bits (66), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 471 GMEGEDGKYISRV--VGTLYMYFVMPETEGRTLRDIEEHFADKGKTFVTNIRRAEKKRHA 528
            MEG    Y+ R+  +  L   FV+P    + LR+       KGK  V  IR   K    
Sbjct: 119 SMEGSLEDYMDRIEKLNKLGCDFVLPGPWAKALRE-----KIKGKILVPGIRMEVKADDQ 173

Query: 529 AKVEGQEEVKGEDNFGMEGED 549
             V   EE+KG  NF + G +
Sbjct: 174 KDVVTLEEMKGIANFAVLGRE 194


  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
   0.324    0.139    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,378,324
Number of Sequences: 62578
Number of extensions: 499327
Number of successful extensions: 1232
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: 1226
Number of HSP's gapped (non-prelim): 7
length of query: 553
length of database: 14,973,337
effective HSP length: 104
effective length of query: 449
effective length of database: 8,465,225
effective search space: 3800886025
effective search space used: 3800886025
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)