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= 038993
         (327 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|1FMD|2 Chain 2, The Structure And Antigenicity Of A Type C Foot-And-Mouth
           Disease Virus
 pdb|1QGC|2 Chain 2, Structure Of The Complex Of An Fab Fragment Of A
           Neutralizing Antibody With Foot And Mouth Disease Virus
          Length = 218

 Score = 29.6 bits (65), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 4/64 (6%)

Query: 112 PQTLAIWTHLRESTAFYRRQRLPWIPKRLVAFFMGLVRIARRSGDACFGGAAEVKVYSLA 171
           P T A+ T + ++  F++     W+P +       +V      G   +GG   VK Y+  
Sbjct: 46  PNTSALETRVHQAERFFKMALFDWVPSQNFGHMHKVVLPHEPKG--VYGGL--VKSYAYM 101

Query: 172 RNSW 175
           RN W
Sbjct: 102 RNGW 105


>pdb|3SAL|A Chain A, Crystal Structure Of Influenza A Virus Neuraminidase N5
 pdb|3SAL|B Chain B, Crystal Structure Of Influenza A Virus Neuraminidase N5
 pdb|3SAN|A Chain A, Crystal Structure Of Influenza A Virus Neuraminidase N5
           Complexed With Zanamivir
 pdb|3SAN|B Chain B, Crystal Structure Of Influenza A Virus Neuraminidase N5
           Complexed With Zanamivir
 pdb|3TI8|A Chain A, Crystal Structure Of Influenza A Virus Neuraminidase N5
           Complexed With Laninamivir
 pdb|3TI8|B Chain B, Crystal Structure Of Influenza A Virus Neuraminidase N5
           Complexed With Laninamivir
          Length = 395

 Score = 28.5 bits (62), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 7/52 (13%)

Query: 49  SRNQARDRS----IITVGLGSTDTLYEEKYENGCIATKLDHPWMDSKQWIEV 96
           S N  +DRS    +++V LGS+   Y+ K+E+   +    H   D K+W+ V
Sbjct: 64  SNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACH---DGKKWLAV 112


>pdb|2Q6P|A Chain A, The Chemical Control Of Protein Folding: Engineering A
           Superfolder Green Fluorescent Protein
          Length = 236

 Score = 27.7 bits (60), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 25  LRLRCVSKTWRDLIDGPDFIKLQLSRNQARDRSIITVGLGSTDTLYEEKYENGCIATKLD 84
           L ++C S+ + D +   DF K  +     ++R+I     G+  T  E K+E   +  +++
Sbjct: 64  LXVQCFSR-YXDHMKRHDFFKSAMXEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIE 122

Query: 85  HPWMDSKQWIEVVG 98
              +D K+   ++G
Sbjct: 123 LKGIDFKEDGNILG 136


  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    0.140    0.460 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,050,270
Number of Sequences: 62578
Number of extensions: 401202
Number of successful extensions: 1020
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1020
Number of HSP's gapped (non-prelim): 3
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)