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= 040972
(87 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 = 68.6 bits (166), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 37/87 (42%), Positives = 54/87 (62%), Gaps = 8/87 (9%)
Query: 1 MAREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSS 60
M R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF++ +LF+ +S+
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
Query: 61 SFITLWF--------HKSSHITSFLES 79
+ H+S T LE+
Sbjct: 61 DMDRVLLKYTEYSEPHESRTNTDILET 87
>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 = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/60 (53%), Positives = 46/60 (76%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF+++ KLF+ +S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
>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 = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/60 (53%), Positives = 46/60 (76%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF+++ KLF+ +S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
>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 = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 32/61 (52%), Positives = 46/61 (75%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF+++ KLF+ +S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 F 62
Sbjct: 61 M 61
>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 = 66.2 bits (160), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 36/86 (41%), Positives = 53/86 (61%), Gaps = 8/86 (9%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF++ +LF+ +S+
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD 60
Query: 62 FITLWF--------HKSSHITSFLES 79
+ H+S T LE+
Sbjct: 61 MDRVLLKYTEYSEPHESRTNTDILET 86
>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 = 65.5 bits (158), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 32/61 (52%), Positives = 46/61 (75%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVL DAE+ +IIF+++ KLF+ +S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTD 60
Query: 62 F 62
Sbjct: 61 M 61
>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 = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 41/60 (68%)
Query: 3 REKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSSF 62
R KI+I+ I+N T R VTFSKR+ G+ KKA ELSVL +V +++ S TG ++ S+ F
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKF 77
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLF 55
R KIK+ IDN R TFSKR+ G+ KKA ELS L +V +++ S TG ++
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVY 64
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLF 55
R KIK+ IDN R TFSKR+ G+ KKA ELS L +V +++ S TG ++
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVY 63
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
0.322 0.131 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,865,291
Number of Sequences: 62578
Number of extensions: 50295
Number of successful extensions: 133
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 124
Number of HSP's gapped (non-prelim): 9
length of query: 87
length of database: 14,973,337
effective HSP length: 55
effective length of query: 32
effective length of database: 11,531,547
effective search space: 369009504
effective search space used: 369009504
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)