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= 040046
(221 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 = 67.0 bits (162), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 31/60 (51%), Positives = 45/60 (75%)
Query: 1 MARGKIQIKRIENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVSS 60
M R KIQI RI + NRQVTF+KR+ GL KKA EL+VLCD ++++I+ +S ++ +Y S+
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
>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 = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 45/59 (76%)
Query: 2 ARGKIQIKRIENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVSS 60
R KIQI RI + NRQVTF+KR+ GL KKA EL+VLCD ++++I+ +S+ K+ +Y S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59
>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 = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 45/59 (76%)
Query: 2 ARGKIQIKRIENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVSS 60
R KIQI RI + NRQVTF+KR+ GL KKA EL+VLCD ++++I+ +S+ K+ +Y S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59
>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 = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 45/59 (76%)
Query: 2 ARGKIQIKRIENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVSS 60
R KIQI RI + NRQVTF+KR+ GL KKA EL+VLCD ++++I+ +S+ K+ +Y S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 45/59 (76%)
Query: 2 ARGKIQIKRIENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVSS 60
R KIQI RI + NRQVTF+KR+ GL KKA EL+VL DA++++I+ +S+ K+ +Y S+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYAST 59
>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 = 64.3 bits (155), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 44/59 (74%)
Query: 2 ARGKIQIKRIENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVSS 60
R KIQI RI + NRQVTF+KR+ GL KKA EL+VLCD ++++I+ +S ++ +Y S+
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 59
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 39/55 (70%)
Query: 3 RGKIQIKRIENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEY 57
R KI+IK IEN T R VTFSKR++G+ KKA EL+VL +V +++ S TG V +
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTF 72
>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 = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 2 ARGKIQIKR--IENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVS 59
RG+++IK I+N R TFSKR+ G+ KKA EL+ L +V +++ S TG V + +
Sbjct: 8 TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 67
>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 = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 2 ARGKIQIKR--IENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVS 59
RG+++IK I+N R TFSKR+ G+ KKA EL+ L +V +++ S TG V + +
Sbjct: 9 TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 68
>pdb|2QKM|B Chain B, The Crystal Structure Of Fission Yeast Mrna Decapping
Enzyme Dcp1-Dcp2 Complex
pdb|2QKM|D Chain D, The Crystal Structure Of Fission Yeast Mrna Decapping
Enzyme Dcp1-Dcp2 Complex
pdb|2QKM|F Chain F, The Crystal Structure Of Fission Yeast Mrna Decapping
Enzyme Dcp1-Dcp2 Complex
pdb|2QKM|H Chain H, The Crystal Structure Of Fission Yeast Mrna Decapping
Enzyme Dcp1-Dcp2 Complex
Length = 266
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 168 FIINAKEEDQH------YELVDNEGHYDSVIRFQNG-----GPGIFALRLQPNEPLSSQW 216
FI+N E+Q +++ Y+ IR QN G +F+ +L + PL +W
Sbjct: 19 FILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKW 78
Query: 217 MSIHE 221
+HE
Sbjct: 79 SKVHE 83
>pdb|2A6T|A Chain A, Crystal Structure Of S.Pombe Mrna Decapping Enzyme Dcp2p
pdb|2A6T|B Chain B, Crystal Structure Of S.Pombe Mrna Decapping Enzyme Dcp2p
Length = 271
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 168 FIINAKEEDQH------YELVDNEGHYDSVIRFQNG-----GPGIFALRLQPNEPLSSQW 216
FI+N E+Q +++ Y+ IR QN G +F+ +L + PL +W
Sbjct: 24 FILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKW 83
Query: 217 MSIHE 221
+HE
Sbjct: 84 SKVHE 88
>pdb|2QKL|B Chain B, The Crystal Structure Of Fission Yeast Mrna Decapping
Enzyme Dcp1-Dcp2 Complex
Length = 95
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 11/69 (15%)
Query: 164 LRNGFIINAKEEDQH------YELVDNEGHYDSVIRFQNG-----GPGIFALRLQPNEPL 212
L FI+N E+Q +++ Y+ IR QN G +F+ +L + PL
Sbjct: 15 LSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPL 74
Query: 213 SSQWMSIHE 221
+W +HE
Sbjct: 75 LWKWSKVHE 83
>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 555
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 3 RGKIQIKRIENATNRQVTFSKRRNGLFKKAQELTVLCDAKVSIIMCSSTGKVQEYVSSST 62
RGK ++K++E TN+Q L ++ ++ D++ + + +S Q S S
Sbjct: 460 RGKDKVKKLEQTTNQQAELEAFAMALTDSGPKVNIIVDSQYVMGIVAS----QPTESESK 515
Query: 63 TTKQLLDE 70
Q+++E
Sbjct: 516 IVNQIIEE 523
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 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,368,345
Number of Sequences: 62578
Number of extensions: 178206
Number of successful extensions: 503
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 494
Number of HSP's gapped (non-prelim): 14
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)