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= 039894
         (159 letters)

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

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



>pdb|3CLZ|A Chain A, The Set And Ring Associated (Sra) Domain Of Uhrf1 Bound
          To Methylated Dna
 pdb|3CLZ|B Chain B, The Set And Ring Associated (Sra) Domain Of Uhrf1 Bound
          To Methylated Dna
 pdb|3CLZ|C Chain C, The Set And Ring Associated (Sra) Domain Of Uhrf1 Bound
          To Methylated Dna
 pdb|3CLZ|D Chain D, The Set And Ring Associated (Sra) Domain Of Uhrf1 Bound
          To Methylated Dna
          Length = 212

 Score = 28.1 bits (61), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 40 ADHYEEDQDHDSFEDQSISSGRSLLQKKRTS 70
          A  YE+D DH +F   + S GR L   KRT+
Sbjct: 51 AGGYEDDVDHGNFFTYTGSGGRDLSGNKRTA 81


>pdb|3DWH|A Chain A, Structural And Functional Analysis Of Sra Domain
          Length = 208

 Score = 28.1 bits (61), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 40 ADHYEEDQDHDSFEDQSISSGRSLLQKKRTS 70
          A  YE+D DH +F   + S GR L   KRT+
Sbjct: 54 AGGYEDDVDHGNFFTYTGSGGRDLSGNKRTA 84


>pdb|3BI7|A Chain A, Crystal Structure Of The Sra Domain Of E3
          Ubiquitin-Protein Ligase Uhrf1
          Length = 212

 Score = 28.1 bits (61), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 40 ADHYEEDQDHDSFEDQSISSGRSLLQKKRTS 70
          A  YE+D DH +F   + S GR L   KRT+
Sbjct: 51 AGGYEDDVDHGNFFTYTGSGGRDLSGNKRTA 81


>pdb|2PB7|A Chain A, Crystal Structure Of The Sra Domain Of The Human Uhrf1
          Protein
          Length = 239

 Score = 28.1 bits (61), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 40 ADHYEEDQDHDSFEDQSISSGRSLLQKKRTS 70
          A  YE+D DH +F   + S GR L   KRT+
Sbjct: 59 AGGYEDDVDHGNFFTYTGSGGRDLSGNKRTA 89


>pdb|3LKD|A Chain A, Crystal Structure Of The Type I Restriction-Modification
           System Methyltransferase Subunit From Streptococcus
           Thermophilus, Northeast Structural Genomics Consortium
           Target Sur80
 pdb|3LKD|B Chain B, Crystal Structure Of The Type I Restriction-Modification
           System Methyltransferase Subunit From Streptococcus
           Thermophilus, Northeast Structural Genomics Consortium
           Target Sur80
          Length = 542

 Score = 27.7 bits (60), Expect = 2.9,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 23  SATTTVVHVEEENQNHDADHYEEDQDHDSFEDQSISSGRSLLQKKRTSYKTLRLTCDKFP 82
           S  TTV+ +++   N D    +  ++ D  ++Q+I +  + ++K   +YK+ R   DKF 
Sbjct: 397 SIPTTVIILKKNRTNRDVYFIDASKEFDKGKNQNIXTD-AHIEKILNAYKS-REDIDKFA 454

Query: 83  RICYFE 88
            +  FE
Sbjct: 455 HLASFE 460


  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
   0.320    0.133    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,315,233
Number of Sequences: 62578
Number of extensions: 149523
Number of successful extensions: 269
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 257
Number of HSP's gapped (non-prelim): 15
length of query: 159
length of database: 14,973,337
effective HSP length: 91
effective length of query: 68
effective length of database: 9,278,739
effective search space: 630954252
effective search space used: 630954252
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)