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= 037442
(180 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 = 69.7 bits (169), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 51/84 (60%)
Query: 1 MGRRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSFGHP 60
MGR+KI++ + D +RQVTF+KR+ GL KKA EL+ LC IA+++F+ + F +
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
Query: 61 SVDVVVQRLLNWEMDPKDETNSHV 84
+D V+ + + + TN+ +
Sbjct: 61 DMDRVLLKYTEYSEPHESRTNTDI 84
>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 = 69.7 bits (169), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 35/97 (36%), Positives = 56/97 (57%), Gaps = 7/97 (7%)
Query: 2 GRRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSFGHPS 61
GR+KI++ + D +RQVTF+KR+ GL KKA EL+ LC IA+++F+ K F +
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 VDVVVQRLLNWEMDPKDETNSHVDAEQEAKVEQLNEQ 98
+D V+ + + + TNS + VE LN++
Sbjct: 61 MDKVLLKYTEYNEPHESRTNSDI-------VEALNKK 90
>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 = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 50/83 (60%)
Query: 2 GRRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSFGHPS 61
GR+KI++ + D +RQVTF+KR+ GL KKA EL+ LC IA+++F+ + F +
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD 60
Query: 62 VDVVVQRLLNWEMDPKDETNSHV 84
+D V+ + + + TN+ +
Sbjct: 61 MDRVLLKYTEYSEPHESRTNTDI 83
>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 = 66.6 bits (161), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 50/83 (60%)
Query: 2 GRRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSFGHPS 61
GR+KI++ + D +RQVTF+KR+ GL KKA EL+ L A IA+++F+ K F +
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTD 60
Query: 62 VDVVVQRLLNWEMDPKDETNSHV 84
+D V+ + + + TNS +
Sbjct: 61 MDKVLLKYTEYNEPHESRTNSDI 83
>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 = 65.5 bits (158), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 45/71 (63%)
Query: 2 GRRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSFGHPS 61
GR+KI++ + D +RQVTF+KR+ GL KKA EL+ LC IA+++F+ K F +
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 VDVVVQRLLNW 72
+D V+ + +
Sbjct: 61 MDKVLLKYTEY 71
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 43/65 (66%)
Query: 2 GRRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSFGHPS 61
GR+KI++ + D +RQVTF+KR+ GL KKA EL+ LC IA+++F+ K F +
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 VDVVV 66
+D V+
Sbjct: 61 MDKVL 65
>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 = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 41/64 (64%)
Query: 3 RRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSFGHPSV 62
RRKIE+K +++ R VTFSKR++G+ KKA EL+ L + ++V S G ++F P
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKF 77
Query: 63 DVVV 66
+ +V
Sbjct: 78 EPIV 81
>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 = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 35/56 (62%)
Query: 2 GRRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSF 57
GR KI+M+ + + R TFSKR+ G+ KKA EL+TL + ++V S G ++F
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTF 66
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 2 GRRKIEMKMVKDSNSRQVTFSKRRNGLFKKANELATLCAAHIAIVVFSPGGKPFSFG 58
GR KI+M+ + + R TFSKR+ G+ KKA EL+TL + ++V S G ++F
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFA 66
>pdb|1IWP|G Chain G, Glycerol Dehydratase-Cyanocobalamin Complex Of Klebsiella
Pneumoniae
pdb|1IWP|M Chain M, Glycerol Dehydratase-Cyanocobalamin Complex Of Klebsiella
Pneumoniae
pdb|1MMF|G Chain G, Crystal Structure Of Substrate Free Form Of Glycerol
Dehydratase
pdb|1MMF|M Chain M, Crystal Structure Of Substrate Free Form Of Glycerol
Dehydratase
Length = 141
Score = 33.1 bits (74), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 11/67 (16%)
Query: 35 LATLCAAHIAIVVFSPGGKPFSFGHPSVDVVVQRLLNWEMDPKDETNSHVDAEQEAKV-E 93
LAT C HI +P GKP + D+ ++++L+ E+ P+D S E +A++ E
Sbjct: 13 LATRCPEHI----LTPTGKPLT------DITLEKVLSGEVGPQDVRISRQTLEYQAQIAE 62
Query: 94 QLNEQLI 100
Q+ +
Sbjct: 63 QMQRHAV 69
>pdb|3S4W|B Chain B, Structure Of The Fanci-Fancd2 Complex
Length = 1323
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 14/80 (17%)
Query: 104 NQLEIEKKRGEMLDKALKAKGLSKYCKKSINDLGLDELLHMKASLEKLREN--------- 154
N E+E+ G + K LKA GL+ ++ N LG+D+++ + + LR++
Sbjct: 3 NSHEVEEN-GSVFVKLLKASGLTLKTGENQNQLGVDQVIFQRKLFQALRKHPAYPKVIEE 61
Query: 155 ----LKSHIDDMEASSSLLL 170
L+S+ +D E+ + LL
Sbjct: 62 FVNGLESYTEDSESLRNCLL 81
>pdb|4G63|A Chain A, Crystal Structure Of Cytosolic Imp-Gmp Specific
5'-Nucleotidase (Lpg0095) In Complex With Phosphate Ions
From Legionella Pneumophila, Northeast Structural
Genomics Consortium Target Lgr1
Length = 470
Score = 26.6 bits (57), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 5/47 (10%)
Query: 92 VEQLNEQLIDLVNQLEIEKKRGEMLDKALKAKGLSKY---CKKSIND 135
VE+L E++ + L IEKK GE + A+K + KY C +SI++
Sbjct: 324 VEELGEEIASQIRALPIEKKIGEAM--AIKKELEQKYVDLCTRSIDE 368
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
0.313 0.130 0.357
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,952,572
Number of Sequences: 62578
Number of extensions: 193329
Number of successful extensions: 583
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 571
Number of HSP's gapped (non-prelim): 30
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)