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= 039538
         (311 letters)

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

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



>pdb|3D23|B Chain B, Main Protease Of Hcov-Hku1
 pdb|3D23|A Chain A, Main Protease Of Hcov-Hku1
 pdb|3D23|C Chain C, Main Protease Of Hcov-Hku1
 pdb|3D23|D Chain D, Main Protease Of Hcov-Hku1
          Length = 302

 Score = 32.7 bits (73), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 3/47 (6%)

Query: 234 YGRYNIDKIWRDDILPCRVYLRHCVLAAKNLGDEAYNNFLDHTSLGD 280
           YG   ++ +W DD + C    RH + ++ N+ +  Y+  L   +LGD
Sbjct: 24  YGSMTLNGLWLDDKVYCP---RHVICSSSNMNEPDYSALLCRVTLGD 67


>pdb|3G7U|A Chain A, Crystal Structure Of Putative Dna Modification
           Methyltransferase Encoded Within Prophage Cp-933r
           (E.Coli)
          Length = 376

 Score = 28.9 bits (63), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 16/28 (57%)

Query: 105 FPNLINFRVAKLHGFRRVFAHVAPIFFE 132
           FP+   F V K H FR++   V+PI  E
Sbjct: 330 FPDWFRFHVTKWHSFRQIGNSVSPIVAE 357


  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
   0.323    0.137    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,065,682
Number of Sequences: 62578
Number of extensions: 352062
Number of successful extensions: 583
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 582
Number of HSP's gapped (non-prelim): 2
length of query: 311
length of database: 14,973,337
effective HSP length: 99
effective length of query: 212
effective length of database: 8,778,115
effective search space: 1860960380
effective search space used: 1860960380
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)