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= 008463
         (564 letters)

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

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



>pdb|1QK9|A Chain A, The Solution Structure Of The Domain From Mecp2 That
          Binds To Methylated Dna
          Length = 92

 Score = 35.4 bits (80), Expect = 0.087,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 4/58 (6%)

Query: 40 LPPGWTKEIKVTKTGRKV-RRDPYYIDPASGYIFRSMKDAVRYVETGEIGRLAYKPKD 96
          LP GWT+++K  K+GR   + D Y I+P  G  FRS  + + Y E  ++G  +  P D
Sbjct: 24 LPEGWTRKLKQRKSGRSAGKYDVYLINP-QGKAFRSKVELIAYFE--KVGDTSLDPND 78


>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 = 35.4 bits (80), Expect = 0.093,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 40 LPPGWTKEIKVTKTGRKV-RRDPYYIDPASGYIFRSMKDAVRYV 82
          LPPGW KE  + K+G    + D YY  P SG  FRS     RY+
Sbjct: 13 LPPGWKKEEVIRKSGLSAGKSDVYYFSP-SGKKFRSKPQLARYL 55


>pdb|3C2I|A Chain A, The Crystal Structure Of Methyl-Cpg Binding Domain Of
          Human Mecp2 In Complex With A Methylated Dna Sequence
          From Bdnf
          Length = 97

 Score = 35.0 bits (79), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 4/58 (6%)

Query: 40 LPPGWTKEIKVTKTGRKV-RRDPYYIDPASGYIFRSMKDAVRYVETGEIGRLAYKPKD 96
          LP GWT+++K  K+GR   + D Y I+P  G  FRS  + + Y E  ++G  +  P D
Sbjct: 24 LPEGWTRKLKQRKSGRSAGKYDVYLINP-QGKAFRSKVELIXYFE--KVGDTSLDPND 78


>pdb|1UB1|A Chain A, Solution Structure Of The Matrix Attachment
          Region-Binding Domain Of Chicken Mecp2
          Length = 133

 Score = 33.9 bits (76), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 4/58 (6%)

Query: 40 LPPGWTKEIKVTKTGRKV-RRDPYYIDPASGYIFRSMKDAVRYVETGEIGRLAYKPKD 96
          LP GWT+++K  K+GR   + D Y I+P  G  FRS  + + Y E  ++G  +  P D
Sbjct: 38 LPEGWTRKLKQRKSGRSAGKYDVYLINP-QGKAFRSKVELIAYFE--KVGDTSLDPND 92


>pdb|1TQY|B Chain B, The Actinorhodin KetosynthaseCHAIN LENGTH FACTOR
 pdb|1TQY|D Chain D, The Actinorhodin KetosynthaseCHAIN LENGTH FACTOR
 pdb|1TQY|F Chain F, The Actinorhodin KetosynthaseCHAIN LENGTH FACTOR
 pdb|1TQY|H Chain H, The Actinorhodin KetosynthaseCHAIN LENGTH FACTOR
          Length = 415

 Score = 30.0 bits (66), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 14/23 (60%), Positives = 16/23 (69%)

Query: 186 MDYRKDSDKNVLSTPVVVVLPQG 208
           MDY+ D DK+VL T V VV P G
Sbjct: 1   MDYKDDDDKSVLITGVGVVAPNG 23


  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
   0.308    0.127    0.357 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,912,149
Number of Sequences: 62578
Number of extensions: 710411
Number of successful extensions: 1296
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1288
Number of HSP's gapped (non-prelim): 14
length of query: 564
length of database: 14,973,337
effective HSP length: 104
effective length of query: 460
effective length of database: 8,465,225
effective search space: 3894003500
effective search space used: 3894003500
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 54 (25.4 bits)