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= 027395
(224 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 = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/80 (41%), Positives = 56/80 (70%), Gaps = 3/80 (3%)
Query: 2 GRRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSSR 61
GR+K+ + +I + QVT+TKR+ G++KKA ELSVLCD ++ L++F+ S KL +Y+S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST- 59
Query: 62 RIEDIFLRFICDEKQEPLEN 81
++ + L++ E EP E+
Sbjct: 60 DMDKVLLKYT--EYNEPHES 77
>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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/80 (41%), Positives = 56/80 (70%), Gaps = 3/80 (3%)
Query: 2 GRRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSSR 61
GR+K+ + +I + QVT+TKR+ G++KKA ELSVLCD ++ L++F+ S KL +Y+S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST- 59
Query: 62 RIEDIFLRFICDEKQEPLEN 81
++ + L++ E EP E+
Sbjct: 60 DMDKVLLKYT--EYNEPHES 77
>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 = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 57/81 (70%), Gaps = 3/81 (3%)
Query: 1 MGRRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSS 60
MGR+K+ + +I + QVT+TKR+ G++KKA ELSVLCD ++ L++F+ + +L +Y+S+
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
Query: 61 RRIEDIFLRFICDEKQEPLEN 81
++ + L++ E EP E+
Sbjct: 61 -DMDRVLLKY--TEYSEPHES 78
>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 = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/80 (40%), Positives = 55/80 (68%), Gaps = 3/80 (3%)
Query: 2 GRRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSSR 61
GR+K+ + +I + QVT+TKR+ G++KKA ELSVL D ++ L++F+ S KL +Y+S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYAST- 59
Query: 62 RIEDIFLRFICDEKQEPLEN 81
++ + L++ E EP E+
Sbjct: 60 DMDKVLLKYT--EYNEPHES 77
>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 = 59.3 bits (142), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/80 (38%), Positives = 56/80 (70%), Gaps = 3/80 (3%)
Query: 2 GRRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSSR 61
GR+K+ + +I + QVT+TKR+ G++KKA ELSVLCD ++ L++F+ + +L +Y+S+
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST- 59
Query: 62 RIEDIFLRFICDEKQEPLEN 81
++ + L++ E EP E+
Sbjct: 60 DMDRVLLKYT--EYSEPHES 77
>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 = 59.3 bits (142), Expect = 2e-09, Method: Composition-based stats.
Identities = 29/69 (42%), Positives = 51/69 (73%), Gaps = 1/69 (1%)
Query: 2 GRRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSSR 61
GR+K+ + +I + QVT+TKR+ G++KKA ELSVLCD ++ L++F+ S KL +Y+S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST- 59
Query: 62 RIEDIFLRF 70
++ + L++
Sbjct: 60 DMDKVLLKY 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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 40/59 (67%)
Query: 3 RRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSSR 61
RRK+ ++ I+N VT++KR+ GI+KKA ELSVL T V LL+ S +G + +S+ +
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPK 76
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 38/60 (63%)
Query: 2 GRRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSSR 61
GR K+ M+ IDN T++KR+ GI+KKA ELS L T V LL+ S +G + +++ +
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRK 70
>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 = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 38/60 (63%)
Query: 2 GRRKLLMQKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDVGLLMFSPSGKLTKYSSSR 61
GR K+ M+ IDN T++KR+ GI+KKA ELS L T V LL+ S +G + +++ +
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRK 69
>pdb|3B1V|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob E67a
Mutant Bound To Mgmppnp
pdb|3B1W|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob E67a
Mutant Bound To Gdp
pdb|3B1W|B Chain B, Crystal Structure Of An S. Thermophilus Nfeob E67a
Mutant Bound To Gdp
pdb|3B1W|C Chain C, Crystal Structure Of An S. Thermophilus Nfeob E67a
Mutant Bound To Gdp
pdb|3B1W|D Chain D, Crystal Structure Of An S. Thermophilus Nfeob E67a
Mutant Bound To Gdp
Length = 272
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 9 QKIDNYPALQVTYTKRRDGIVKKAKELSVLCDTDV-GLLMFSPSGKLTK-YSSSRRIEDI 66
Q++ N+P + V +R+ G+VKK K+L + + + +SP K+ + Y S+R + I
Sbjct: 28 QRVGNWPGVTV---ERKSGLVKKNKDLEIQDLPGIYSMSPYSPEAKVARDYLLSQRADSI 84
Query: 67 F 67
Sbjct: 85 L 85
>pdb|2KU6|A Chain A, Mouse Prion Protein (121-231) With Mutations D167s And
N173k
Length = 113
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 190 PVPPNSKKKGGIHQCVNITMHEQT 213
PV S +K +H CVNIT+ + T
Sbjct: 46 PVSQYSNQKNFVHDCVNITIKQHT 69
>pdb|3B1Z|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob T35s
Mutant Without Nucleotide
Length = 272
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 9 QKIDNYPALQVTYTKRRDGIVKKAKELSV 37
Q++ N+P + V +R+ G+VKK K+L +
Sbjct: 28 QRVGNWPGVSV---ERKSGLVKKNKDLEI 53
>pdb|2KU4|A Chain A, Horse Prion Protein
Length = 113
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 190 PVPPNSKKKGGIHQCVNITMHEQT 213
PV S +K +H CVNIT+ + T
Sbjct: 47 PVSEYSNQKNFVHDCVNITVKQHT 70
>pdb|3B1X|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob E66a
Mutant Bound To Gmppnp
pdb|3B1X|B Chain B, Crystal Structure Of An S. Thermophilus Nfeob E66a
Mutant Bound To Gmppnp
Length = 272
Score = 26.9 bits (58), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 9 QKIDNYPALQVTYTKRRDGIVKKAKELSV 37
Q++ N+P + V +R+ G+VKK K+L +
Sbjct: 28 QRVGNWPGVTV---ERKSGLVKKNKDLEI 53
>pdb|3TAH|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob N11a
Mutant Bound To Mgdp
pdb|3TAH|B Chain B, Crystal Structure Of An S. Thermophilus Nfeob N11a
Mutant Bound To Mgdp
Length = 272
Score = 26.9 bits (58), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 9 QKIDNYPALQVTYTKRRDGIVKKAKELSV 37
Q++ N+P + V +R+ G+VKK K+L +
Sbjct: 28 QRVGNWPGVTV---ERKSGLVKKNKDLEI 53
>pdb|3B1Y|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob T35a
Mutant Bound To Gdp
Length = 272
Score = 26.9 bits (58), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 9 QKIDNYPALQVTYTKRRDGIVKKAKELSV 37
Q++ N+P + V +R+ G+VKK K+L +
Sbjct: 28 QRVGNWPGVAV---ERKSGLVKKNKDLEI 53
>pdb|3LX5|A Chain A, Crystal Structure Of Mgmppnp-Bound Nfeob From S.
Thermophilus
pdb|3LX8|A Chain A, Crystal Structure Of Gdp-Bound Nfeob From S.
Thermophilus
pdb|3SS8|A Chain A, Crystal Structure Of Nfeob From S. Thermophilus Bound To
Gdp.Alf4- And K+
pdb|3SS8|B Chain B, Crystal Structure Of Nfeob From S. Thermophilus Bound To
Gdp.Alf4- And K+
Length = 272
Score = 26.9 bits (58), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 9 QKIDNYPALQVTYTKRRDGIVKKAKELSV 37
Q++ N+P + V +R+ G+VKK K+L +
Sbjct: 28 QRVGNWPGVTV---ERKSGLVKKNKDLEI 53
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
0.317 0.133 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,646,352
Number of Sequences: 62578
Number of extensions: 192978
Number of successful extensions: 563
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 549
Number of HSP's gapped (non-prelim): 20
length of query: 224
length of database: 14,973,337
effective HSP length: 95
effective length of query: 129
effective length of database: 9,028,427
effective search space: 1164667083
effective search space used: 1164667083
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)