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= 028961
(201 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 = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/79 (39%), Positives = 54/79 (68%), Gaps = 1/79 (1%)
Query: 1 MARGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELATN 60
M R K+Q+ RI + +RQVTF KR+ GL+KKA ELS+LCD ++ + IF++ +L++ A+
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
Query: 61 GTMQGLIEKYLKSTQGAQA 79
M ++ KY + ++ ++
Sbjct: 61 D-MDRVLLKYTEYSEPHES 78
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 3 RGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELATNGT 62
R K+Q+ RI + +RQVTF KR+ GL+KKA ELS+LCD ++ + IF++ KL++ A+
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD- 60
Query: 63 MQGLIEKY 70
M ++ KY
Sbjct: 61 MDKVLLKY 68
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 3 RGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELATNGT 62
R K+Q+ RI + +RQVTF KR+ GL+KKA ELS+LCD ++ + IF++ KL++ A+
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD- 60
Query: 63 MQGLIEKY 70
M ++ KY
Sbjct: 61 MDKVLLKY 68
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 3 RGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELATNGT 62
R K+Q+ RI + +RQVTF KR+ GL+KKA ELS+LCD ++ + IF++ KL++ A+
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD- 60
Query: 63 MQGLIEKY 70
M ++ KY
Sbjct: 61 MDKVLLKY 68
>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 = 64.7 bits (156), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 3 RGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELATNGT 62
R K+Q+ RI + +RQVTF KR+ GL+KKA ELS+L DA++ + IF++ KL++ A+
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTD- 60
Query: 63 MQGLIEKY 70
M ++ KY
Sbjct: 61 MDKVLLKY 68
>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 = 63.5 bits (153), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 53/78 (67%), Gaps = 1/78 (1%)
Query: 2 ARGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELATNG 61
R K+Q+ RI + +RQVTF KR+ GL+KKA ELS+LCD ++ + IF++ +L++ A+
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD 60
Query: 62 TMQGLIEKYLKSTQGAQA 79
M ++ KY + ++ ++
Sbjct: 61 -MDRVLLKYTEYSEPHES 77
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 3 RGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELAT 59
R K+++K IEN R VTF KR+ G++KKA ELS+L V + + S G +Y +T
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFST 74
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 35/59 (59%)
Query: 2 ARGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELATN 60
R K++M+ I+N + R TF KR+ G++KKA ELS L V + + S G +Y AT
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATR 69
>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 = 2e-06, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 35/59 (59%)
Query: 2 ARGKVQMKRIENPVHRQVTFCKRRAGLLKKAKELSILCDADVGVFIFSNHGKLYELATN 60
R K++M+ I+N + R TF KR+ G++KKA ELS L V + + S G +Y AT
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATR 68
>pdb|1ZI0|A Chain A, A Superhelical Spiral In Escherichia Coli Dna Gyrase A C-
Terminal Domain Imparts Unidirectional Supercoiling Bias
pdb|1ZI0|B Chain B, A Superhelical Spiral In Escherichia Coli Dna Gyrase A C-
Terminal Domain Imparts Unidirectional Supercoiling Bias
Length = 307
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 45 VFIFSNHGKLYELATNGTMQGLIEKYLKSTQGAQAEPVMQTQPLDAKDEINMLKQEIEIL 104
+ FS+ G++Y + + + ++T+GA+ P++ PL+ + I + E
Sbjct: 56 ILCFSSRGRVYSMK--------VYQLPEATRGARGRPIVNLLPLEQDERITAILPVTE-F 106
Query: 105 QKGLRYMFGGGTGTM 119
++G++ GT+
Sbjct: 107 EEGVKVFMATANGTV 121
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 0.137 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,711,446
Number of Sequences: 62578
Number of extensions: 225599
Number of successful extensions: 549
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 539
Number of HSP's gapped (non-prelim): 13
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
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: 49 (23.5 bits)