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= 022404
         (297 letters)

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

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



>pdb|1D9N|A Chain A, Solution Structure Of The Methyl-Cpg-Binding Domain Of
          The Methylation-Dependent Transcriptional Repressor
          Mbd1PCM1
 pdb|1IG4|A Chain A, Solution Structure Of The Methyl-Cpg-Binding Domain Of
          Human Mbd1 In Complex With Methylated Dna
          Length = 75

 Score = 35.4 bits (80), Expect = 0.043,   Method: Composition-based stats.
 Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 8/59 (13%)

Query: 21 GWKKKIVPRK-GGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPAS--SEFDWGTG 76
          GWK++ V RK G T  +S+  + +PTG+ I +K +L +YL     GPA   + FD+  G
Sbjct: 14 GWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYL-----GPACDLTLFDFKQG 67


>pdb|2KY8|A Chain A, Solution Structure And Dynamic Analysis Of Chicken Mbd2
          Methyl Binding Domain Bound To A Target Methylated Dna
          Sequence
          Length = 72

 Score = 34.3 bits (77), Expect = 0.096,   Method: Composition-based stats.
 Identities = 21/53 (39%), Positives = 35/53 (66%), Gaps = 2/53 (3%)

Query: 9  EEQVSFELPA-PFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYL 59
          ++Q   + PA P GWKK+ V RK G +  KS++ + +P+G++  +K QL +YL
Sbjct: 3  DKQGRTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYL 55


>pdb|3VYQ|A Chain A, Crystal Structure Of The Methyl Cpg Binding Domain Of
          Mbd4 In Complex With The 5mcg/tg Sequence In Space
          Group P1
 pdb|3VYQ|D Chain D, Crystal Structure Of The Methyl Cpg Binding Domain Of
          Mbd4 In Complex With The 5mcg/tg Sequence In Space
          Group P1
          Length = 74

 Score = 32.3 bits (72), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 17 PAPFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYL 59
          P P GW++ +  R  G T  K ++ F +P G +  +K+ L  YL
Sbjct: 10 PVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYL 53


>pdb|3VXV|A Chain A, Crystal Structure Of Methyl Cpg Binding Domain Of Mbd4
          In Complex With The 5mcg/tg Sequence
 pdb|3VXX|A Chain A, Crystal Structure Of Methyl Cpg Binding Domain Of Mbd4
          In Complex With The 5mcg/5mcg Sequence
 pdb|3VYB|A Chain A, Crystal Structure Of Methyl Cpg Binding Domain Of Mbd4
          In Complex With The 5mcg/hmcg Sequence
          Length = 69

 Score = 30.8 bits (68), Expect = 0.88,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 17 PAPFGWKKKIVPR-KGGTPKKSEIVFTAPTGEEISNKKQLEQYL 59
          P P GW++ +  R  G T  K ++ F +P G +  +K+ L  YL
Sbjct: 5  PVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYL 48


>pdb|4IHA|A Chain A, Crystal Structure Of Rice Dwarf14 (d14) In Complex With A
           Gr24 Hydrolysis Intermediate
 pdb|4IHA|B Chain B, Crystal Structure Of Rice Dwarf14 (d14) In Complex With A
           Gr24 Hydrolysis Intermediate
 pdb|4IH9|A Chain A, Crystal Structure Of Rice Dwarf14 (d14)
 pdb|4IH9|B Chain B, Crystal Structure Of Rice Dwarf14 (d14)
          Length = 268

 Score = 30.0 bits (66), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 15/39 (38%), Positives = 19/39 (48%)

Query: 45  TGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETPRRSA 83
           T  ++S    +  YLKAH GG  + EF    G  P  SA
Sbjct: 215 TTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSA 253


>pdb|3W04|A Chain A, Crystal Structure Of Oryza Sativa Dwarf14 (d14)
 pdb|3W04|B Chain B, Crystal Structure Of Oryza Sativa Dwarf14 (d14)
 pdb|3W05|A Chain A, Crystal Structure Of Oryza Sativa Dwarf14 (d14) In Complex
           With Pmsf
 pdb|3W05|B Chain B, Crystal Structure Of Oryza Sativa Dwarf14 (d14) In Complex
           With Pmsf
          Length = 266

 Score = 29.6 bits (65), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 15/39 (38%), Positives = 19/39 (48%)

Query: 45  TGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETPRRSA 83
           T  ++S    +  YLKAH GG  + EF    G  P  SA
Sbjct: 213 TTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSA 251


  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
   0.297    0.120    0.322 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,459,039
Number of Sequences: 62578
Number of extensions: 346263
Number of successful extensions: 427
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 415
Number of HSP's gapped (non-prelim): 23
length of query: 297
length of database: 14,973,337
effective HSP length: 98
effective length of query: 199
effective length of database: 8,840,693
effective search space: 1759297907
effective search space used: 1759297907
T: 11
A: 40
X1: 17 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 44 (21.9 bits)
S2: 51 (24.3 bits)