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= 024893
(261 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/30 (60%), Positives = 22/30 (73%)
Query: 19 ATFKKRKNSLMKKAYEFTTLCDVEVCIIIY 48
TF KRK LMKKAYE + LCD E+ +II+
Sbjct: 18 VTFTKRKFGLMKKAYELSVLCDCEIALIIF 47
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 22/31 (70%)
Query: 19 ATFKKRKNSLMKKAYEFTTLCDVEVCIIIYG 49
TF KRK LMKKAYE + LCD E+ +II+
Sbjct: 19 VTFTKRKFGLMKKAYELSVLCDCEIALIIFN 49
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 22/31 (70%)
Query: 19 ATFKKRKNSLMKKAYEFTTLCDVEVCIIIYG 49
TF KRK LMKKAYE + LCD E+ +II+
Sbjct: 18 VTFTKRKFGLMKKAYELSVLCDCEIALIIFN 48
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 22/31 (70%)
Query: 19 ATFKKRKNSLMKKAYEFTTLCDVEVCIIIYG 49
TF KRK LMKKAYE + LCD E+ +II+
Sbjct: 18 VTFTKRKFGLMKKAYELSVLCDCEIALIIFN 48
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 22/31 (70%)
Query: 19 ATFKKRKNSLMKKAYEFTTLCDVEVCIIIYG 49
TF KRK LMKKAYE + LCD E+ +II+
Sbjct: 18 VTFTKRKFGLMKKAYELSVLCDCEIALIIFN 48
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 23/36 (63%)
Query: 14 EKACLATFKKRKNSLMKKAYEFTTLCDVEVCIIIYG 49
E+ TF KRK LMKKAYE + L D E+ +II+
Sbjct: 13 ERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFN 48
>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 = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 20 TFKKRKNSLMKKAYEFTTLCDVEVCIII 47
TF KRK +MKKAYE +TL +V +++
Sbjct: 28 TFSKRKTGIMKKAYELSTLTGTQVLLLV 55
>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 = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 20 TFKKRKNSLMKKAYEFTTLCDVEVCIII 47
TF KRK +MKKAYE +TL +V +++
Sbjct: 29 TFSKRKTGIMKKAYELSTLTGTQVLLLV 56
>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 = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 19 ATFKKRKNSLMKKAYEFTTLCDVEVCIII 47
TF KRK+ +MKKA+E + L +V +++
Sbjct: 34 VTFSKRKHGIMKKAFELSVLTGTQVLLLV 62
>pdb|1YF2|A Chain A, Three-dimensional Structure Of Dna Sequence Specificity
(s) Subunit Of A Type I Restriction-modification Enzyme
And Its Functional Implications
pdb|1YF2|B Chain B, Three-dimensional Structure Of Dna Sequence Specificity
(s) Subunit Of A Type I Restriction-modification Enzyme
And Its Functional Implications
Length = 425
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 61/122 (50%), Gaps = 20/122 (16%)
Query: 132 EDQLKMILSTMDDKLKDVDRKLNTIKR-DQNVVNKATSRKLEHDHSNDAKSLVNLQPAYQ 190
+ Q+ IL+ +D+ ++ +++ +N ++R + +++K ++ + HS KS +
Sbjct: 171 QKQIAKILTKIDEGIEIIEKSINKLERIKKGLMHKLLTKGI--GHSRFKKSEIG------ 222
Query: 191 VSQKLPSDSSFMEIQ--CGGGSGSTIPFTPL-----QGQINWNSSLTMSPTSSGIYDGSA 243
++P D EI+ +G+T P T G+INW + L +S + IY GS+
Sbjct: 223 ---EIPEDWEVFEIKDIFEVKTGTT-PSTKKSEYWENGEINWITPLDLSRLNEKIYIGSS 278
Query: 244 AQ 245
+
Sbjct: 279 ER 280
>pdb|3THF|A Chain A, Crystal Structure Of The Sd2 Domain From Drosophila Shroom
pdb|3THF|B Chain B, Crystal Structure Of The Sd2 Domain From Drosophila Shroom
Length = 190
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 28/43 (65%)
Query: 126 GMDSLSEDQLKMILSTMDDKLKDVDRKLNTIKRDQNVVNKATS 168
G+D +E+ +I MD+ +K +++K+ ++KR+Q +++ S
Sbjct: 1 GIDPFTEEPTNLIKQKMDELIKHLNQKIVSLKREQQTISEECS 43
>pdb|1XSI|A Chain A, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSI|B Chain B, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSI|C Chain C, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSI|D Chain D, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSI|E Chain E, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSI|F Chain F, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSJ|A Chain A, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSJ|B Chain B, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSJ|C Chain C, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSJ|D Chain D, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSJ|E Chain E, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSJ|F Chain F, Structure Of A Family 31 Alpha Glycosidase
pdb|1XSK|A Chain A, Structure Of A Family 31 Alpha Glycosidase Glycosyl-Enzyme
Intermediate
pdb|1XSK|B Chain B, Structure Of A Family 31 Alpha Glycosidase Glycosyl-Enzyme
Intermediate
pdb|1XSK|C Chain C, Structure Of A Family 31 Alpha Glycosidase Glycosyl-Enzyme
Intermediate
pdb|1XSK|D Chain D, Structure Of A Family 31 Alpha Glycosidase Glycosyl-Enzyme
Intermediate
pdb|1XSK|E Chain E, Structure Of A Family 31 Alpha Glycosidase Glycosyl-Enzyme
Intermediate
pdb|1XSK|F Chain F, Structure Of A Family 31 Alpha Glycosidase Glycosyl-Enzyme
Intermediate
Length = 778
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 175 HSNDAKSLVNLQPAYQVSQKLPS-DSSFMEIQCGGGSGSTIPFTPLQGQINWNSSLTMSP 233
H A L NLQ ++ ++P+ D S + +G+TI T NW L
Sbjct: 683 HEGTAFHLFNLQDGHEAVCEVPAADGSVIFTLKAARTGNTITVTGAGEAKNWTLCLRNVV 742
Query: 234 TSSGIYDGSAAQAKKS 249
+G+ DGS A++++
Sbjct: 743 KVNGLQDGSQAESEQG 758
>pdb|2F2H|A Chain A, Structure Of The Yici Thiosugar Michaelis Complex
pdb|2F2H|B Chain B, Structure Of The Yici Thiosugar Michaelis Complex
pdb|2F2H|C Chain C, Structure Of The Yici Thiosugar Michaelis Complex
pdb|2F2H|D Chain D, Structure Of The Yici Thiosugar Michaelis Complex
pdb|2F2H|E Chain E, Structure Of The Yici Thiosugar Michaelis Complex
pdb|2F2H|F Chain F, Structure Of The Yici Thiosugar Michaelis Complex
Length = 773
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 175 HSNDAKSLVNLQPAYQVSQKLPS-DSSFMEIQCGGGSGSTIPFTPLQGQINWNSSLTMSP 233
H A L NLQ ++ ++P+ D S + +G+TI T NW L
Sbjct: 683 HEGTAFHLFNLQDGHEAVCEVPAADGSVIFTLKAARTGNTITVTGAGEAKNWTLCLRNVV 742
Query: 234 TSSGIYDGSAAQAKKS 249
+G+ DGS A++++
Sbjct: 743 KVNGLQDGSQAESEQG 758
>pdb|1WE5|A Chain A, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|B Chain B, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|C Chain C, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|D Chain D, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|E Chain E, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|F Chain F, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
Length = 772
Score = 28.1 bits (61), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 175 HSNDAKSLVNLQPAYQVSQKLPS-DSSFMEIQCGGGSGSTIPFTPLQGQINWNSSLTMSP 233
H A L NLQ ++ ++P+ D S + +G+TI T NW L
Sbjct: 683 HEGTAFHLFNLQDGHEAVCEVPAADGSVIFTLKAARTGNTITVTGAGEAKNWTLCLRNVV 742
Query: 234 TSSGIYDGSAAQAKKS 249
+G+ DGS A++++
Sbjct: 743 KVNGLQDGSQAESEQG 758
>pdb|2P1I|A Chain A, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2
(Py03671)
pdb|2P1I|B Chain B, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2
(Py03671)
pdb|2P1I|C Chain C, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2
(Py03671)
pdb|2P1I|D Chain D, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2
(Py03671)
pdb|2P1I|E Chain E, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2
(Py03671)
pdb|2P1I|F Chain F, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2
(Py03671)
pdb|2P1I|G Chain G, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2
(Py03671)
pdb|2P1I|H Chain H, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2
(Py03671)
Length = 349
Score = 27.7 bits (60), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 37/161 (22%), Positives = 78/161 (48%), Gaps = 22/161 (13%)
Query: 11 TKQEKACLATFKKRKNS----LMKKAYEFTTLCDVEVCIIIYGPKVKGHSLKPET--WTS 64
+KQEK + F+K K S L K++ FT + I+Y P+V K E WT+
Sbjct: 14 SKQEKE-FSDFQKSKESNEKILNKESNRFT------LHPIMY-PEVWNFYKKAEASFWTA 65
Query: 65 KEGELTSIIRKYEKKISAVDHGQHRTLSLSKFDESKMRQVDDAATRACKKICVGD---FT 121
+E +L+S ++ +EK H L+ F S +++ A++ +++ + + F
Sbjct: 66 EEIDLSSDLKDFEKLNVNEKHFIKHVLAF--FAASDGIVLENLASKFLREVEIIEAKKFY 123
Query: 122 TWDQGMDSLSEDQLKMILSTMDDKLKDVDRKLNTIKRDQNV 162
++ ++++ + +++ D+ +KD +LN +N+
Sbjct: 124 SFQIAVENIHSETYSLLI---DNYIKDEKERLNLFHAIENI 161
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
0.312 0.126 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,374,113
Number of Sequences: 62578
Number of extensions: 281911
Number of successful extensions: 603
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 586
Number of HSP's gapped (non-prelim): 37
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)