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= 020809
         (321 letters)

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

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



>pdb|1YNY|A Chain A, Molecular Structure Of D-Hydantoinase From A Bacillus Sp.
           Ar9: Evidence For Mercury Inhibition
 pdb|1YNY|B Chain B, Molecular Structure Of D-Hydantoinase From A Bacillus Sp.
           Ar9: Evidence For Mercury Inhibition
          Length = 461

 Score = 33.1 bits (74), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 28/96 (29%), Positives = 41/96 (42%), Gaps = 28/96 (29%)

Query: 191 AKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLI-------ETHWNAHGKP-----AMD 238
           A+ EAT R+  LT +  + L     VH+  C S +       E  WN +G+      A+D
Sbjct: 216 AEGEATGRAIALTALAGSQL---YVVHV-SCASAVQRIAEAREKGWNVYGETCPQYLALD 271

Query: 239 VAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQW 274
           V+I              QP  E  K  W P ++E+W
Sbjct: 272 VSIMD------------QPDFEGAKYVWSPPLREKW 295


>pdb|3SFW|A Chain A, Crystal Structure Of Dihydropyrimidinase From
           Brevibacillus Agri Nchu1002
 pdb|3SFW|B Chain B, Crystal Structure Of Dihydropyrimidinase From
           Brevibacillus Agri Nchu1002
          Length = 461

 Score = 29.6 bits (65), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 39/93 (41%), Gaps = 22/93 (23%)

Query: 191 AKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLI-------ETHWNAHGK--PAMDVAI 241
           A+ EAT R+  LT +  A L     VH+  C   +       E  WN +G+  P   V  
Sbjct: 216 AEGEATGRAIALTALADAQL---YVVHV-SCADAVRRIAEAREKGWNVYGETCPQYLVLD 271

Query: 242 QKALEKKAQAGKWVQPHVETIKAKWIPAVKEQW 274
             ALEK         P  E  K  W P ++E+W
Sbjct: 272 ITALEK---------PDFEGAKYVWSPPLREKW 295


>pdb|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
            Chicken Gizzard Smooth Muscle Myosin With Regulatory
            Light Chain In The Dephosphorylated State. Only C Alphas
            Provided For Regulatory Light Chain. Only Backbone Atoms
            Provided For S2 Fragment.
 pdb|1I84|V Chain V, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
            Chicken Gizzard Smooth Muscle Myosin With Regulatory
            Light Chain In The Dephosphorylated State. Only C Alphas
            Provided For Regulatory Light Chain. Only Backbone Atoms
            Provided For S2 Fragment
          Length = 1184

 Score = 27.7 bits (60), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 53   KIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL 96
            KIR LESHI +  ++L+ +     + EK  +D SE + +L+ EL
Sbjct: 1117 KIRELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTEL 1160


>pdb|1K1D|A Chain A, Crystal Structure Of D-Hydantoinase
 pdb|1K1D|B Chain B, Crystal Structure Of D-Hydantoinase
 pdb|1K1D|C Chain C, Crystal Structure Of D-Hydantoinase
 pdb|1K1D|D Chain D, Crystal Structure Of D-Hydantoinase
 pdb|1K1D|E Chain E, Crystal Structure Of D-Hydantoinase
 pdb|1K1D|F Chain F, Crystal Structure Of D-Hydantoinase
 pdb|1K1D|G Chain G, Crystal Structure Of D-Hydantoinase
 pdb|1K1D|H Chain H, Crystal Structure Of D-Hydantoinase
          Length = 460

 Score = 27.7 bits (60), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 37/90 (41%), Gaps = 22/90 (24%)

Query: 194 EATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGK---------PAMDVAIQKA 244
           EAT R+ +LTE+  + L     VH+  C   +E    A  K         P   V  Q  
Sbjct: 219 EATGRACQLTELAGSQL---YVVHV-TCAQAVEKIAEARNKGLDVWGETCPQYLVLDQSY 274

Query: 245 LEKKAQAGKWVQPHVETIKAKWIPAVKEQW 274
           LEK         P+ E  K  W P ++E+W
Sbjct: 275 LEK---------PNFEGAKYVWSPPLREKW 295


>pdb|3NA7|A Chain A, 2.2 Angstrom Structure Of The Hp0958 Protein From
           Helicobacter Pylori Ccug 17874
          Length = 256

 Score = 27.7 bits (60), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 35/54 (64%), Gaps = 1/54 (1%)

Query: 75  VAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAE-QVDKAHARADELEKQIDN 127
           V++ E+ +QD + +I S+QK++S ++ +  L +   + D A  R+++  ++I+N
Sbjct: 62  VSKNEQTLQDTNAKIASIQKKMSEIKSERELRSLNIEEDIAKERSNQANREIEN 115


  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
   0.312    0.125    0.343 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,567,190
Number of Sequences: 62578
Number of extensions: 255762
Number of successful extensions: 759
Number of sequences better than 100.0: 78
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 62
Number of HSP's that attempted gapping in prelim test: 702
Number of HSP's gapped (non-prelim): 115
length of query: 321
length of database: 14,973,337
effective HSP length: 99
effective length of query: 222
effective length of database: 8,778,115
effective search space: 1948741530
effective search space used: 1948741530
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)