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= 039654
(225 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 = 68.9 bits (167), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 54/85 (63%), Gaps = 1/85 (1%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCV 71
R+K+++ ++ +E N QVTF+KR+ GL KKA EL LC +IA+I+F+ K+F + +
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 72 ETIVDRYLTRNPPQISGT-MQLIEA 95
+ ++ +Y N P S T ++EA
Sbjct: 62 DKVLLKYTEYNEPHESRTNSDIVEA 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 = 68.2 bits (165), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 50/78 (64%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCV 71
R+K+++ ++ +E N QVTF+KR+ GL KKA EL L A+IA+I+F+ K+F + +
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTDM 61
Query: 72 ETIVDRYLTRNPPQISGT 89
+ ++ +Y N P S T
Sbjct: 62 DKVLLKYTEYNEPHESRT 79
>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 = 67.0 bits (162), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 48/74 (64%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCV 71
R+K+++ ++ +E N QVTF+KR+ GL KKA EL LC +IA+I+F+ K+F + +
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 72 ETIVDRYLTRNPPQ 85
+ ++ +Y N P
Sbjct: 62 DKVLLKYTEYNEPH 75
>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 = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 50/78 (64%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCV 71
R+K+++ ++ ++ N QVTF+KR+ GL KKA EL LC +IA+I+F+ ++F + +
Sbjct: 3 RKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDM 62
Query: 72 ETIVDRYLTRNPPQISGT 89
+ ++ +Y + P S T
Sbjct: 63 DRVLLKYTEYSEPHESRT 80
>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 = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 50/78 (64%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCV 71
R+K+++ ++ ++ N QVTF+KR+ GL KKA EL LC +IA+I+F+ ++F + +
Sbjct: 2 RKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDM 61
Query: 72 ETIVDRYLTRNPPQISGT 89
+ ++ +Y + P S T
Sbjct: 62 DRVLLKYTEYSEPHESRT 79
>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 = 62.8 bits (151), Expect = 2e-10, Method: Composition-based stats.
Identities = 26/67 (38%), Positives = 46/67 (68%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCV 71
R+K+++ ++ +E N QVTF+KR+ GL KKA EL LC +IA+I+F+ K+F + +
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 72 ETIVDRY 78
+ ++ +Y
Sbjct: 62 DKVLLKY 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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 42/71 (59%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCV 71
R+K+E+ + N++ VTFSKR+ G+ KKA EL L G + ++V S V++F P
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKF 77
Query: 72 ETIVDRYLTRN 82
E IV + RN
Sbjct: 78 EPIVTQQEGRN 88
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 34/56 (60%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFG 67
R K++M + N+ TFSKR+TG+ KKA EL TL G + ++V S V++F
Sbjct: 12 RVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFA 67
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 34/56 (60%)
Query: 12 RQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFG 67
R K++M + N+ TFSKR+TG+ KKA EL TL G + ++V S V++F
Sbjct: 11 RVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFA 66
>pdb|2X24|A Chain A, Bovine Acc2 Ct Domain In Complex With Inhibitor
pdb|2X24|B Chain B, Bovine Acc2 Ct Domain In Complex With Inhibitor
Length = 793
Score = 27.3 bits (59), Expect = 6.2, Method: Composition-based stats.
Identities = 21/106 (19%), Positives = 48/106 (45%), Gaps = 9/106 (8%)
Query: 70 CVETIVDRYLTRNPPQISGTMQLIEAHRN--ASVRELNMQLTQVLNQLEIEKKRGEELNQ 127
C+E DR + + GT+++ ++ ++R L+ +++ QL + + + +
Sbjct: 550 CIEMYADRESRASVLEPEGTVEIKYQKKDLVKTIRRLDPISKKLVEQLGVSELSDTDRKE 609
Query: 128 MRKASQAQCWWEAPIEELNLPQLEQLKMSLEELKKNVGKQAEKMLI 173
+ +A+ E+L LP Q+ + +L G+ EK +I
Sbjct: 610 LEGQLKAR-------EDLLLPMYHQVALHFADLHDTAGRMLEKGVI 648
>pdb|2NVU|C Chain C, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 180
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 118 EKKRGEELNQMRKASQAQCWWEAPIEELNLPQLEQLKMS 156
++K+ EE +KAS AQ + I ELNLP+ + S
Sbjct: 11 QQKKEEEKGSSKKASAAQLRIQKDINELNLPKTCDISFS 49
>pdb|1B92|A Chain A, Mobility Of An Hiv-1 Integrase Active Site Loop Is
Correlated With Catalytic Activity
Length = 163
Score = 26.9 bits (58), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 7/46 (15%)
Query: 133 QAQCWWEAPIEELNLPQLEQLKMSLE----ELKKNVGK---QAEKM 171
+A CWW +E +P Q + +E ELKK +G+ QAE +
Sbjct: 78 KAACWWAGIKQEFGIPYNPQSQAVIESMNKELKKIIGQVRDQAEHL 123
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 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,619,910
Number of Sequences: 62578
Number of extensions: 192387
Number of successful extensions: 617
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 606
Number of HSP's gapped (non-prelim): 14
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
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: 50 (23.9 bits)