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= 038783
         (76 letters)

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

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



>pdb|1TQE|P Chain P, Mechanism Of Recruitment Of Class Ii Histone
          Deacetylases By Myocyte Enhancer Factor-2
 pdb|1TQE|Q Chain Q, Mechanism Of Recruitment Of Class Ii Histone
          Deacetylases By Myocyte Enhancer Factor-2
 pdb|1TQE|R Chain R, Mechanism Of Recruitment Of Class Ii Histone
          Deacetylases By Myocyte Enhancer Factor-2
 pdb|1TQE|S Chain S, Mechanism Of Recruitment Of Class Ii Histone
          Deacetylases By Myocyte Enhancer Factor-2
          Length = 93

 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 39/44 (88%)

Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  RL++YA+
Sbjct: 16 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAS 59


>pdb|1N6J|A Chain A, Structural Basis Of Sequence-Specific Recruitment Of
          Histone Deacetylases By Myocyte Enhancer Factor-2
 pdb|1N6J|B Chain B, Structural Basis Of Sequence-Specific Recruitment Of
          Histone Deacetylases By Myocyte Enhancer Factor-2
          Length = 93

 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 39/44 (88%)

Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  RL++YA+
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAS 58


>pdb|3KOV|A Chain A, Structure Of Mef2a Bound To Dna Reveals A Completely
          Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND
          RECRUITS Transcription Co-Factors
 pdb|3KOV|B Chain B, Structure Of Mef2a Bound To Dna Reveals A Completely
          Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND
          RECRUITS Transcription Co-Factors
 pdb|3KOV|I Chain I, Structure Of Mef2a Bound To Dna Reveals A Completely
          Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND
          RECRUITS Transcription Co-Factors
 pdb|3KOV|J Chain J, Structure Of Mef2a Bound To Dna Reveals A Completely
          Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND
          RECRUITS Transcription Co-Factors
 pdb|3P57|A Chain A, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
          On Dna
 pdb|3P57|B Chain B, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
          On Dna
 pdb|3P57|C Chain C, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
          On Dna
 pdb|3P57|D Chain D, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
          On Dna
 pdb|3P57|I Chain I, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
          On Dna
 pdb|3P57|J Chain J, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
          On Dna
          Length = 90

 Score = 69.3 bits (168), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 30/43 (69%), Positives = 38/43 (88%)

Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 74
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYA 57


>pdb|1C7U|A Chain A, Complex Of The Dna Binding Core Domain Of The
          Transcription Factor Mef2a With A 20mer Oligonucleotide
 pdb|1C7U|B Chain B, Complex Of The Dna Binding Core Domain Of The
          Transcription Factor Mef2a With A 20mer Oligonucleotide
          Length = 85

 Score = 68.9 bits (167), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 30/44 (68%), Positives = 39/44 (88%)

Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          NRQVTF KR+ GL+KKAYELSVL DAE+ALI+F+S  +L++YA+
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYAS 58


>pdb|1EGW|A Chain A, Crystal Structure Of Mef2a Core Bound To Dna
 pdb|1EGW|B Chain B, Crystal Structure Of Mef2a Core Bound To Dna
 pdb|1EGW|C Chain C, Crystal Structure Of Mef2a Core Bound To Dna
 pdb|1EGW|D Chain D, Crystal Structure Of Mef2a Core Bound To Dna
          Length = 77

 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 30/44 (68%), Positives = 39/44 (88%)

Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA+
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAS 58


>pdb|3MU6|A Chain A, Inhibiting The Binding Of Class Iia Histone Deacetylases
          To Myocyte Enhancer Factor-2 By Small Molecules
 pdb|3MU6|B Chain B, Inhibiting The Binding Of Class Iia Histone Deacetylases
          To Myocyte Enhancer Factor-2 By Small Molecules
 pdb|3MU6|C Chain C, Inhibiting The Binding Of Class Iia Histone Deacetylases
          To Myocyte Enhancer Factor-2 By Small Molecules
 pdb|3MU6|D Chain D, Inhibiting The Binding Of Class Iia Histone Deacetylases
          To Myocyte Enhancer Factor-2 By Small Molecules
          Length = 71

 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 30/45 (66%), Positives = 39/45 (86%)

Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA+ 
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59


>pdb|1MNM|A Chain A, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
          Crystal Structure
 pdb|1MNM|B Chain B, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
          Crystal Structure
          Length = 100

 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 33/46 (71%)

Query: 29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 74
          N T R VTF KR++G++KKA+ELSVL   +V L+V S  G +Y ++
Sbjct: 28 NKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFS 73


>pdb|1K6O|B Chain B, Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dna
          Complex
 pdb|1K6O|C Chain C, Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dna
          Complex
          Length = 103

 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 29/47 (61%)

Query: 29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          N   R  TF KR+ G++KKAYELS L   +V L+V S  G +Y +A 
Sbjct: 21 NKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 67


>pdb|1SRS|A Chain A, Serum Response Factor (Srf) Core Complexed With Specific
          Sre Dna
 pdb|1SRS|B Chain B, Serum Response Factor (Srf) Core Complexed With Specific
          Sre Dna
 pdb|1HBX|A Chain A, Ternary Complex Of Sap-1 And Srf With Specific Sre Dna
 pdb|1HBX|B Chain B, Ternary Complex Of Sap-1 And Srf With Specific Sre Dna
 pdb|1HBX|D Chain D, Ternary Complex Of Sap-1 And Srf With Specific Sre Dna
 pdb|1HBX|E Chain E, Ternary Complex Of Sap-1 And Srf With Specific Sre Dna
          Length = 92

 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 29/47 (61%)

Query: 29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          N   R  TF KR+ G++KKAYELS L   +V L+V S  G +Y +A 
Sbjct: 22 NKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 68


>pdb|3EK1|A Chain A, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
           Melitensis Biovar Abortus 2308
 pdb|3EK1|B Chain B, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
           Melitensis Biovar Abortus 2308
 pdb|3EK1|C Chain C, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
           Melitensis Biovar Abortus 2308
 pdb|3EK1|D Chain D, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
           Melitensis Biovar Abortus 2308
 pdb|3EK1|E Chain E, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
           Melitensis Biovar Abortus 2308
 pdb|3EK1|F Chain F, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
           Melitensis Biovar Abortus 2308
 pdb|3EK1|G Chain G, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
           Melitensis Biovar Abortus 2308
 pdb|3EK1|H Chain H, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
           Melitensis Biovar Abortus 2308
          Length = 504

 Score = 26.2 bits (56), Expect = 5.4,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 21/31 (67%)

Query: 39  KRRNGLLKKAYELSVLCDAEVALIVFSSRGR 69
           K R G+L+K ++L +    ++ALI+ S +G+
Sbjct: 92  KERAGILRKWFDLIIANADDIALIMTSEQGK 122


  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
   0.315    0.128    0.358 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,498,545
Number of Sequences: 62578
Number of extensions: 31705
Number of successful extensions: 53
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 43
Number of HSP's gapped (non-prelim): 10
length of query: 76
length of database: 14,973,337
effective HSP length: 45
effective length of query: 31
effective length of database: 12,157,327
effective search space: 376877137
effective search space used: 376877137
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)