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= 028923
(202 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 78.6 bits (192), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 40/84 (47%), Positives = 60/84 (71%), Gaps = 2/84 (2%)
Query: 3 RGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSSCSI 62
R K Q+ RI + +RQVTF+KR+ GL+KKA+ELSVLCD E+ALIIF+ KL++++S +
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 63 NKTIERYQKKTK--DIGINSKIVE 84
+K + +Y + + + NS IVE
Sbjct: 62 DKVLLKYTEYNEPHESRTNSDIVE 85
>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 = 78.2 bits (191), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 35/67 (52%), Positives = 52/67 (77%)
Query: 3 RGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSSCSI 62
R K Q+ RI + +RQVTF+KR+ GL+KKA+ELSVLCD E+ALIIF+ KL++++S +
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 63 NKTIERY 69
+K + +Y
Sbjct: 62 DKVLLKY 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 = 78.2 bits (191), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 35/67 (52%), Positives = 52/67 (77%)
Query: 3 RGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSSCSI 62
R K Q+ RI + +RQVTF+KR+ GL+KKA+ELSVLCD E+ALIIF+ KL++++S +
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 63 NKTIERY 69
+K + +Y
Sbjct: 62 DKVLLKY 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 = 78.2 bits (191), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 40/84 (47%), Positives = 60/84 (71%), Gaps = 2/84 (2%)
Query: 3 RGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSSCSI 62
R K Q+ RI + +RQVTF+KR+ GL+KKA+ELSVL DAE+ALIIF+ KL++++S +
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTDM 61
Query: 63 NKTIERYQKKTK--DIGINSKIVE 84
+K + +Y + + + NS IVE
Sbjct: 62 DKVLLKYTEYNEPHESRTNSDIVE 85
>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 = 76.6 bits (187), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 34/69 (49%), Positives = 53/69 (76%)
Query: 1 MVRGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSSC 60
M R K Q+ RI + +RQVTF+KR+ GL+KKA+ELSVLCD E+ALIIF+ +L++++S
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
Query: 61 SINKTIERY 69
+++ + +Y
Sbjct: 61 DMDRVLLKY 69
>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 = 75.5 bits (184), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 33/67 (49%), Positives = 52/67 (77%)
Query: 3 RGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSSCSI 62
R K Q+ RI + +RQVTF+KR+ GL+KKA+ELSVLCD E+ALIIF+ +L++++S +
Sbjct: 2 RKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDM 61
Query: 63 NKTIERY 69
++ + +Y
Sbjct: 62 DRVLLKY 68
>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 = 65.1 bits (157), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 42/57 (73%)
Query: 3 RGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSS 59
R K ++K IEN T R VTFSKR++G++KKAFELSVL +V L++ S G +Y FS+
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 = 53.9 bits (128), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 38/57 (66%)
Query: 3 RGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSS 59
R K +M+ I+N R TFSKR+ G++KKA+ELS L +V L++ S G +Y F++
Sbjct: 12 RVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 68
>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 = 53.9 bits (128), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 38/57 (66%)
Query: 3 RGKTQMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSS 59
R K +M+ I+N R TFSKR+ G++KKA+ELS L +V L++ S G +Y F++
Sbjct: 11 RVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 67
>pdb|3J21|P Chain P, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 120
Score = 30.8 bits (68), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 8/97 (8%)
Query: 28 LLKKAFELSVLCDAEVALIIFSPRGKLYEFSSCSINKTIERYQKKTKDIGINSKIVEDHS 87
L KK+ E V +VA + PR + E + IN RY + I + ++
Sbjct: 18 LRKKSNEYGVKIWKDVAWRLERPRRQRAEVNVSKIN----RYANDGEMIVVPGSVL---- 69
Query: 88 QHAKEETSNMMTKLEFLEVAKRKLLGDGLEPCTIDEL 124
K E ++ +F E A+RK++ G E TI+EL
Sbjct: 70 GAGKLEKKVIVAAWKFSETARRKIIEAGGEAITIEEL 106
>pdb|2NZ8|B Chain B, N-Terminal Dhph Cassette Of Trio In Complex With
Nucleotide- Free Rac1
Length = 313
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 45 LIIFSPRGKLYEFSSCSINKTIERYQKKTKDIG 77
LIIF ++YEF + K +E+Y++ +D+G
Sbjct: 57 LIIFGNMQEIYEFHNNIFLKELEKYEQLPEDVG 89
>pdb|1NTY|A Chain A, Crystal Structure Of The First DhPH DOMAIN OF TRIO TO
1.7 A
Length = 311
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 45 LIIFSPRGKLYEFSSCSINKTIERYQKKTKDIG 77
LIIF ++YEF + K +E+Y++ +D+G
Sbjct: 55 LIIFGNMQEIYEFHNNIFLKELEKYEQLPEDVG 87
>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 = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 22 SKRRNGLLKKAFELSVLCDAEVALIIFSPRGK 53
+K R G+L+K F+L + ++ALI+ S +GK
Sbjct: 91 AKERAGILRKWFDLIIANADDIALIMTSEQGK 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
0.316 0.130 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,403,947
Number of Sequences: 62578
Number of extensions: 139041
Number of successful extensions: 379
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 366
Number of HSP's gapped (non-prelim): 15
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
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: 49 (23.5 bits)