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= 030090
(183 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 = 75.9 bits (185), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 35/73 (47%), Positives = 53/73 (72%)
Query: 1 MAREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSS 60
M R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF++ +LF+ +S+
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
Query: 61 SMKDIIARYNMHS 73
M ++ +Y +S
Sbjct: 61 DMDRVLLKYTEYS 73
>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 = 74.7 bits (182), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 52/71 (73%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF+++ KLF+ +S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 MKDIIARYNMH 72
M ++ +Y +
Sbjct: 61 MDKVLLKYTAY 71
>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 = 74.3 bits (181), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 34/72 (47%), Positives = 53/72 (73%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF+++ KLF+ +S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 MKDIIARYNMHS 73
M ++ +Y ++
Sbjct: 61 MDKVLLKYTEYN 72
>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 = 74.3 bits (181), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 34/72 (47%), Positives = 53/72 (73%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF+++ KLF+ +S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 MKDIIARYNMHS 73
M ++ +Y ++
Sbjct: 61 MDKVLLKYTEYN 72
>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 = 73.2 bits (178), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 34/72 (47%), Positives = 52/72 (72%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVLCD E+ +IIF++ +LF+ +S+
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD 60
Query: 62 MKDIIARYNMHS 73
M ++ +Y +S
Sbjct: 61 MDRVLLKYTEYS 72
>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 = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 34/72 (47%), Positives = 53/72 (73%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R+KI+I +I + RQVTF+KR+ GL KKA ELSVL DAE+ +IIF+++ KLF+ +S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTD 60
Query: 62 MKDIIARYNMHS 73
M ++ +Y ++
Sbjct: 61 MDKVLLKYTEYN 72
>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 = 57.4 bits (137), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 50/83 (60%)
Query: 3 REKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSSM 62
R KI+I+ I+N T R VTFSKR+ G+ KKA ELSVL +V +++ S TG ++ S+
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKF 77
Query: 63 KDIIARYNMHSSNISKLNHPSLE 85
+ I+ + + + LN P E
Sbjct: 78 EPIVTQQEGRNLIQACLNAPDDE 100
>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 = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 45/81 (55%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R KIK+ IDN R TFSKR+ G+ KKA ELS L +V +++ S TG ++ ++
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRK 70
Query: 62 MKDIIARYNMHSSNISKLNHP 82
++ +I + + LN P
Sbjct: 71 LQPMITSETGKALIQTCLNSP 91
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 45/81 (55%)
Query: 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS 61
R KIK+ IDN R TFSKR+ G+ KKA ELS L +V +++ S TG ++ ++
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRK 69
Query: 62 MKDIIARYNMHSSNISKLNHP 82
++ +I + + LN P
Sbjct: 70 LQPMITSETGKALIQTCLNSP 90
>pdb|3IKB|A Chain A, The Structure Of A Conserved Protein From Streptococcus
Mutans Ua159.
pdb|3IKB|B Chain B, The Structure Of A Conserved Protein From Streptococcus
Mutans Ua159
Length = 198
Score = 31.2 bits (69), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 4/89 (4%)
Query: 25 RRGLFKKAEE--LSVLCDAEVGVIIFSATGKLF--ESSSSSMKDIIARYNMHSSNISKLN 80
R+G +K + L +L D ++ ++I + K + + SS + D +A Y + + L
Sbjct: 104 RKGFAQKWHQPILDLLPDIQLTILIGNYAQKYYLHQKSSVKLTDTVAHYKKYLPDYFPLV 163
Query: 81 HPSLELQLENSKYLSLSREIADKSRQLRQ 109
HPS Q+ S++ ++ +++ Q
Sbjct: 164 HPSPRNQIWXSRHPWFEAQVVPDLKKIIQ 192
>pdb|2B8E|A Chain A, Copa Atp Binding Domain
pdb|2B8E|B Chain B, Copa Atp Binding Domain
pdb|2B8E|C Chain C, Copa Atp Binding Domain
Length = 273
Score = 26.9 bits (58), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 38 LCDAEVGVIIFSATGKLFESSS-----SSMKDIIARYNMHSSNISKLNHPSLE 85
L A++G+ + S + ES ++D++A + SK +HP E
Sbjct: 220 LAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSRKTXSKWSHPQFE 272
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
0.318 0.132 0.360
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,186,270
Number of Sequences: 62578
Number of extensions: 130608
Number of successful extensions: 445
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 436
Number of HSP's gapped (non-prelim): 19
length of query: 183
length of database: 14,973,337
effective HSP length: 93
effective length of query: 90
effective length of database: 9,153,583
effective search space: 823822470
effective search space used: 823822470
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)