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= psy10231
         (607 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 =  114 bits (285), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 103/375 (27%), Positives = 174/375 (46%), Gaps = 40/375 (10%)

Query: 234 ITGMAIGMSSACY-VYVAEICLPNDRGYLSAFGPVFVSLGVLIVYSLGYIVT-------- 284
           I G+ +G++S    +Y+AE+   + RG L +F    +  G L+VY + Y +         
Sbjct: 135 IGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWL 194

Query: 285 ----WQYTSAACAVVALVGFAAMHAVPETPSWLARQGCTKEARNSLVWFRRSTAVADAEL 340
               W+Y  A+  + AL+    ++ VPE+P WL  +G  ++A   L     +T +A   +
Sbjct: 195 NTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNT-LATQAV 253

Query: 341 KEIQQSLKVQMAGSSMDHCAQTFTNSAVWKPFFILIGFFL--FQEASGMYIVLYYAVNFF 398
           +EI+ SL         DH  +T     ++    I+IG  L  FQ+  G+ +VLYYA   F
Sbjct: 254 QEIKHSL---------DHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVF 304

Query: 399 EDAGSSLD-DYVASIIVAGLRFFMAIIGSACIQMFSRRALATTSAFFMALSMGISGTYEY 457
           +  G+S D   + +IIV  +     ++    +  F R+ L    A  MA+ M   GT  Y
Sbjct: 305 KTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFY 364

Query: 458 YFSELSMDDRPLNWIPLACILANVCASMLGMLQLPWVMIAELFPLSVRGIMGGIVCSLGY 517
                    +    + L  +L  V A  +    + WV+++E+FP ++RG    I  +  +
Sbjct: 365 --------TQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQW 416

Query: 518 L---FIFTTVKMYPDLMYLL---NMGGMMWAFSCACLLAMVFIQAFLPETQGKTLLEIEN 571
           L   F+  T  M     +L+   + G   W + C  +LA +F+  F+PET+GKTL E+E 
Sbjct: 417 LANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEA 476

Query: 572 HFRGKKNMADSTEHL 586
            +  +      T  L
Sbjct: 477 LWEPETKKTQQTATL 491



 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/162 (24%), Positives = 71/162 (43%), Gaps = 31/162 (19%)

Query: 77  VGSLFAGIFMDLLGRKTTVQLTAIPFII----------GWTIITVSKGFTLLCVG----- 121
           +G    G   +  GR+ ++++ A+ F I          G+T I       +   G     
Sbjct: 70  IGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEF 129

Query: 122 ---RFITGMAIGMSSACY-VYVAEICLPNDRGYLSAFGPVFVSLGVLIVYSLGYIVT--- 174
              R I G+ +G++S    +Y+AE+   + RG L +F    +  G L+VY + Y +    
Sbjct: 130 VIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSG 189

Query: 175 ---------WQYTSAACAVVALVGFAAMHAVPETPSWLARQG 207
                    W+Y  A+  + AL+    ++ VPE+P WL  +G
Sbjct: 190 DASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRG 231


>pdb|3HDB|A Chain A, Crystal Structure Of Aahiv, A Metalloproteinase From Venom
           Of Agkistrodon Acutus
          Length = 417

 Score = 29.6 bits (65), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 226 QYHIHTWFITGMAIGMSSACYVYVAEICLPNDR-GYLSAFGPVFVSLGVLIVYSLGYIVT 284
           + H +   ITG+    S   Y Y+  +C P    G +  + P+ + L V++ + +G+ + 
Sbjct: 89  KKHDNAQLITGIDFRGSIIGYAYIGSMCHPKRSVGIIQDYSPINLVLAVIMAHEMGHNLG 148

Query: 285 WQYTSAAC 292
             +    C
Sbjct: 149 IHHDDGYC 156


  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    0.139    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,782,007
Number of Sequences: 62578
Number of extensions: 634881
Number of successful extensions: 1307
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1296
Number of HSP's gapped (non-prelim): 7
length of query: 607
length of database: 14,973,337
effective HSP length: 104
effective length of query: 503
effective length of database: 8,465,225
effective search space: 4258008175
effective search space used: 4258008175
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (25.4 bits)