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= 041581
(261 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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%)
Query: 1 MGRGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMIIYGP 50
MGR K+ + I ++ R +T+ KRK GL KKA E S LC +II+
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNS 50
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 2 GRGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMIIYGP 50
GR K+ + I E+ R +T+ KRK GL KKA E S LC +II+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNS 49
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 2 GRGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMIIYGP 50
GR K+ + I E+ R +T+ KRK GL KKA E S LC +II+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNS 49
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 2 GRGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMIIYGP 50
GR K+ + I E+ R +T+ KRK GL KKA E S LC +II+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNS 49
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 28/49 (57%)
Query: 2 GRGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMIIYGP 50
GR K+ + I ++ R +T+ KRK GL KKA E S LC +II+
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNS 49
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 27/49 (55%)
Query: 2 GRGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMIIYGP 50
GR K+ + I E+ R +T+ KRK GL KKA E S L +II+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNS 49
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 2 GRGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMII 47
GR K+ M+ I+ + R T+ KRK G+ KKA E STL G +++
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLV 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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 2 GRGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMII 47
GR K+ M+ I+ + R T+ KRK G+ KKA E STL G +++
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLV 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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 3 RGKLTMQLIEKEKARMITYQKRKRGLKKKAEEFSTLCGVPTCMII 47
R K+ ++ IE + R +T+ KRK G+ KKA E S L G +++
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLV 62
>pdb|2IFT|A Chain A, Crystal Structure Of Putative Methylase Hi0767 From
Haemophilus Influenzae. Nesg Target Ir102.
pdb|2IFT|B Chain B, Crystal Structure Of Putative Methylase Hi0767 From
Haemophilus Influenzae. Nesg Target Ir102
Length = 201
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 75 LYKDKAYSSVRGVKSLSLFDFFADRKRKV-----DENIAKTRKANYESLFSTDDWDEMIN 129
+++ + G SL F+ + + +KV D+ +A K N ++L + + E+IN
Sbjct: 52 IHQSECLDGFAGSGSLG-FEALSRQAKKVTFLELDKTVANQLKKNLQTLKCSSEQAEVIN 110
Query: 130 RFSIDQLKQ 138
+ S+D LKQ
Sbjct: 111 QSSLDFLKQ 119
>pdb|3LYU|A Chain A, Crystal Structure Of The C-Terminal Domain (Residues
83-215) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LYU|B Chain B, Crystal Structure Of The C-Terminal Domain (Residues
83-215) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LYU|C Chain C, Crystal Structure Of The C-Terminal Domain (Residues
83-215) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LYU|D Chain D, Crystal Structure Of The C-Terminal Domain (Residues
83-215) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LYU|E Chain E, Crystal Structure Of The C-Terminal Domain (Residues
83-215) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LYU|F Chain F, Crystal Structure Of The C-Terminal Domain (Residues
83-215) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
Length = 142
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 94 DFFADRKRKVDENIAKTRKANYESLFSTDDWDEMINRFSIDQLKQMLVVFDEY 146
DF A+ K N+++ K L ++DWD + + KQ+ V EY
Sbjct: 83 DFLANXK-----NVSQRLKEKVRELLESEDWDLVFXVGPVGDQKQVFEVVKEY 130
>pdb|3LRX|A Chain A, Crystal Structure Of The C-Terminal Domain (Residues
78-226) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LRX|B Chain B, Crystal Structure Of The C-Terminal Domain (Residues
78-226) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LRX|C Chain C, Crystal Structure Of The C-Terminal Domain (Residues
78-226) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LRX|D Chain D, Crystal Structure Of The C-Terminal Domain (Residues
78-226) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LRX|E Chain E, Crystal Structure Of The C-Terminal Domain (Residues
78-226) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
pdb|3LRX|F Chain F, Crystal Structure Of The C-Terminal Domain (Residues
78-226) Of Pf1911 Hydrogenase From Pyrococcus Furiosus,
Northeast Structural Genomics Consortium Target Pfr246a
Length = 158
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 94 DFFADRKRKVDENIAKTRKANYESLFSTDDWDEMINRFSIDQLKQMLVVFDEY 146
DF A+ K N+++ K L ++DWD + + KQ+ V EY
Sbjct: 88 DFLANXK-----NVSQRLKEKVRELLESEDWDLVFXVGPVGDQKQVFEVVKEY 135
>pdb|4E3A|A Chain A, Crystal Structure Of Probable Sugar Kinase Protein From
Rhizobium Etli Cfn 42
pdb|4E3A|B Chain B, Crystal Structure Of Probable Sugar Kinase Protein From
Rhizobium Etli Cfn 42
Length = 352
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 99 RKRKVDENIAKTRKANYESLFSTDDWDEMINRFSID 134
R KVD A ++A SL+ TDD++E +NR + D
Sbjct: 227 RSGKVDIVFANRQEA--LSLYQTDDFEEALNRIAAD 260
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
0.322 0.136 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,035,763
Number of Sequences: 62578
Number of extensions: 258551
Number of successful extensions: 489
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 478
Number of HSP's gapped (non-prelim): 24
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)