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= psy10561
         (73 letters)

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

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



>pdb|1CQQ|A Chain A, Type 2 Rhinovirus 3c Protease With Ag7088 Inhibitor
          Length = 180

 Score = 28.5 bits (62), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 7/63 (11%)

Query: 9   NVEPAVGSGERCLPGDEAHCGDGAPARDAKLAYPKGKNYNRSLCSRVGITVGLHSGGLGF 68
           NV   V  G   L G++        AR  K +YP    Y   +  ++G  +G+H GG G 
Sbjct: 115 NVGDVVSYGNILLSGNQT-------ARMLKYSYPTKSGYCGGVLYKIGQVLGIHVGGNGR 167

Query: 69  DSW 71
           D +
Sbjct: 168 DGF 170


>pdb|2XYA|A Chain A, Non-Covalent Inhibtors Of Rhinovirus 3c Protease
          Length = 182

 Score = 28.5 bits (62), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 7/63 (11%)

Query: 9   NVEPAVGSGERCLPGDEAHCGDGAPARDAKLAYPKGKNYNRSLCSRVGITVGLHSGGLGF 68
           NV   V  G   L G++        AR  K +YP    Y   +  ++G  +G+H GG G 
Sbjct: 117 NVGDVVSYGNILLSGNQT-------ARMLKYSYPTKSGYCGGVLYKIGQVLGIHVGGNGR 169

Query: 69  DSW 71
           D +
Sbjct: 170 DGF 172


>pdb|4GFP|A Chain A, 2.7 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In A Second Conformational State
          Length = 462

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 1/24 (4%)

Query: 4  SAPDYNVEPAVG-SGERCLPGDEA 26
          +A DY   P+ G SGE C+PGD++
Sbjct: 23 NAMDYQTIPSQGLSGEICVPGDKS 46


>pdb|3ROI|A Chain A, 2.20 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii
 pdb|3ROI|B Chain B, 2.20 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii
 pdb|3SLH|A Chain A, 1.70 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Shikimate-3-Phosphate And
          Glyphosate
 pdb|3SLH|B Chain B, 1.70 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Shikimate-3-Phosphate And
          Glyphosate
 pdb|3SLH|C Chain C, 1.70 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Shikimate-3-Phosphate And
          Glyphosate
 pdb|3SLH|D Chain D, 1.70 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Shikimate-3-Phosphate And
          Glyphosate
 pdb|4EGR|A Chain A, 2.50 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Phosphoenolpyruvate
 pdb|4EGR|B Chain B, 2.50 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Phosphoenolpyruvate
 pdb|4EGR|C Chain C, 2.50 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Phosphoenolpyruvate
 pdb|4EGR|D Chain D, 2.50 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Phosphoenolpyruvate
 pdb|4EGR|E Chain E, 2.50 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Phosphoenolpyruvate
 pdb|4EGR|F Chain F, 2.50 Angstrom Resolution Structure Of 3-Phosphoshikimate
          1- Carboxyvinyltransferase (Aroa) From Coxiella
          Burnetii In Complex With Phosphoenolpyruvate
          Length = 441

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 1/24 (4%)

Query: 4  SAPDYNVEPAVG-SGERCLPGDEA 26
          +A DY   P+ G SGE C+PGD++
Sbjct: 2  NAMDYQTIPSQGLSGEICVPGDKS 25


  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
   0.316    0.139    0.454 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,835,219
Number of Sequences: 62578
Number of extensions: 109684
Number of successful extensions: 150
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 147
Number of HSP's gapped (non-prelim): 5
length of query: 73
length of database: 14,973,337
effective HSP length: 43
effective length of query: 30
effective length of database: 12,282,483
effective search space: 368474490
effective search space used: 368474490
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)