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= 024093
(272 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 = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 44/59 (74%)
Query: 1 MGRGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYIS 59
MGR K+++ RI + NRQVTF+KR+ GL KKA EL++LCD +++++I +S + +Y S
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAS 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 = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 44/59 (74%)
Query: 2 GRGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYISP 60
GR K+++ RI + NRQVTF+KR+ GL KKA EL++LCD +++++I +S+ K +Y S
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59
>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 = 4e-10, Method: Compositional matrix adjust.
Identities = 28/58 (48%), Positives = 44/58 (75%)
Query: 2 GRGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYIS 59
GR K+++ RI + NRQVTF+KR+ GL KKA EL++LCD +++++I +S+ K +Y S
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAS 58
>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 = 61.6 bits (148), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 28/58 (48%), Positives = 44/58 (75%)
Query: 2 GRGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYIS 59
GR K+++ RI + NRQVTF+KR+ GL KKA EL++LCD +++++I +S+ K +Y S
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAS 58
>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 = 61.2 bits (147), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 28/58 (48%), Positives = 44/58 (75%)
Query: 2 GRGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYIS 59
GR K+++ RI + NRQVTF+KR+ GL KKA EL++L DA+++++I +S+ K +Y S
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYAS 58
>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 = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 43/58 (74%)
Query: 2 GRGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYIS 59
GR K+++ RI + NRQVTF+KR+ GL KKA EL++LCD +++++I +S + +Y S
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAS 58
>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 = 27/58 (46%), Positives = 40/58 (68%)
Query: 3 RGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYISP 60
R K+E+K IEN T R VTFSKR++G+ KKA EL++L +V +L+ S T + + +P
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTP 75
>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 = 7e-06, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 36/58 (62%)
Query: 2 GRGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYIS 59
GR K++M+ I+N R TFSKR+ G+ KKA EL+ L +V +L+ S T + + +
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 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 = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 36/58 (62%)
Query: 2 GRGKMEMKRIENATNRQVTFSKRRNGLFKKARELTILCDAKVSILICSSTAKAHEYIS 59
GR K++M+ I+N R TFSKR+ G+ KKA EL+ L +V +L+ S T + + +
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 67
>pdb|1USY|A Chain A, Atp Phosphoribosyl Transferase (Hisg:hisz) Complex From
Thermotoga Maritima
pdb|1USY|B Chain B, Atp Phosphoribosyl Transferase (Hisg:hisz) Complex From
Thermotoga Maritima
pdb|1USY|D Chain D, Atp Phosphoribosyl Transferase (Hisg:hisz) Complex From
Thermotoga Maritima
Length = 275
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 2/90 (2%)
Query: 94 VEQVNRILKKQIRQRMGESLNDLTLEELTGLEQDILDGLKIIHECKDQVLARQINTFKRK 153
+ +V +I++ I +R E L + L + +D+L + E V T R
Sbjct: 173 LSRVEKIIEDSIYRRSPEHLKTMDLP--LSVREDLLSASSFLQEKFPTVSVEIDLTLART 230
Query: 154 VCSVCHIILKTYDSSLSFILLFVGNFQVRG 183
+ C +I YD+S S ++ G + V G
Sbjct: 231 IEEYCGLIFTIYDTSSSRLVAAGGEYTVNG 260
>pdb|1USY|C Chain C, Atp Phosphoribosyl Transferase (Hisg:hisz) Complex From
Thermotoga Maritima
Length = 275
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 2/90 (2%)
Query: 94 VEQVNRILKKQIRQRMGESLNDLTLEELTGLEQDILDGLKIIHECKDQVLARQINTFKRK 153
+ +V +I++ I +R E L + L + +D+L + E V T R
Sbjct: 173 LSRVEKIIEDSIYRRSPEHLKTMDLP--LSVREDLLSASSFLQEKFPTVSVEIDLTLART 230
Query: 154 VCSVCHIILKTYDSSLSFILLFVGNFQVRG 183
+ C +I YD+S S ++ G + V G
Sbjct: 231 IEEYCGLIFTIYDTSSSRLVAAGGEYTVNG 260
>pdb|2Z6B|A Chain A, Crystal Structure Analysis Of (Gp27-Gp5)3 Conjugated With
Fe(Iii) Protoporphyrin
Length = 584
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 96 QVNRILKKQIRQRMGESLNDLTLEELTGL-EQDILD 130
Q+N++L KQ+ + + + +T+EE T L E+D+ D
Sbjct: 216 QINKVLSKQVGREITGNPGSITMEEATTLFERDLAD 251
>pdb|1PDL|A Chain A, Fitting Of Gp5 In The Cryoem Reconstruction Of The
Bacteriophage T4 Baseplate
pdb|1PDL|B Chain B, Fitting Of Gp5 In The Cryoem Reconstruction Of The
Bacteriophage T4 Baseplate
pdb|1PDL|C Chain C, Fitting Of Gp5 In The Cryoem Reconstruction Of The
Bacteriophage T4 Baseplate
Length = 575
Score = 27.7 bits (60), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 96 QVNRILKKQIRQRMGESLNDLTLEELTGL-EQDILD 130
Q+N++L KQ+ + + + +T+EE T L E+D+ D
Sbjct: 216 QINKVLSKQVGREITGNPGSITMEEATTLFERDLAD 251
>pdb|1K28|A Chain A, The Structure Of The Bacteriophage T4 Cell-Puncturing
Device
Length = 584
Score = 27.7 bits (60), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 96 QVNRILKKQIRQRMGESLNDLTLEELTGL-EQDILD 130
Q+N++L KQ+ + + + +T+EE T L E+D+ D
Sbjct: 216 QINKVLSKQVGREITGNPGSITMEEATTLFERDLAD 251
>pdb|1WTH|A Chain A, Crystal Structure Of Gp5-S351l Mutant And Gp27 Complex
Length = 584
Score = 27.7 bits (60), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 96 QVNRILKKQIRQRMGESLNDLTLEELTGL-EQDILD 130
Q+N++L KQ+ + + + +T+EE T L E+D+ D
Sbjct: 216 QINKVLSKQVGREITGNPGSITMEEATTLFERDLAD 251
>pdb|1EKE|A Chain A, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
pdb|1EKE|B Chain B, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
Length = 230
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 35/55 (63%), Gaps = 4/55 (7%)
Query: 82 SHYEKMLENLGAVEQVNRILKKQIRQRMGES--LNDLTLEELTGLEQDILDGLKI 134
++ +K+LENLG VE+ RIL+ + ++ S LND+ + + + +++++ L I
Sbjct: 50 AYLKKLLENLGYVEK--RILEAEEINQLXNSINLNDIEINAFSKVAKNLIEKLNI 102
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
0.320 0.136 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,404,377
Number of Sequences: 62578
Number of extensions: 284266
Number of successful extensions: 761
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 751
Number of HSP's gapped (non-prelim): 29
length of query: 272
length of database: 14,973,337
effective HSP length: 97
effective length of query: 175
effective length of database: 8,903,271
effective search space: 1558072425
effective search space used: 1558072425
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)