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= 042044
(218 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 = 76.3 bits (186), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 35/73 (47%), Positives = 53/73 (72%)
Query: 1 MGRGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSSA 60
MGR KI+I RI + NRQVT++KR+ GL+KKA E++VLCD +++LIIF ++ ++ Y+S
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
Query: 61 PMFEILEAYHKQS 73
M +L Y + S
Sbjct: 61 DMDRVLLKYTEYS 73
>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 = 75.5 bits (184), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 35/68 (51%), Positives = 51/68 (75%)
Query: 2 GRGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSSAP 61
GR KI+I RI + NRQVT++KR+ GL+KKA E++VLCD +++LIIF +S K+ Y+S
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 MFEILEAY 69
M ++L Y
Sbjct: 61 MDKVLLKY 68
>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 = 75.5 bits (184), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 35/68 (51%), Positives = 51/68 (75%)
Query: 2 GRGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSSAP 61
GR KI+I RI + NRQVT++KR+ GL+KKA E++VLCD +++LIIF +S K+ Y+S
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 MFEILEAY 69
M ++L Y
Sbjct: 61 MDKVLLKY 68
>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 = 73.6 bits (179), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 34/72 (47%), Positives = 52/72 (72%)
Query: 2 GRGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSSAP 61
GR KI+I RI + NRQVT++KR+ GL+KKA E++VLCD +++LIIF ++ ++ Y+S
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD 60
Query: 62 MFEILEAYHKQS 73
M +L Y + S
Sbjct: 61 MDRVLLKYTEYS 72
>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 = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 35/68 (51%), Positives = 51/68 (75%)
Query: 2 GRGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSSAP 61
GR KI+I RI + NRQVT++KR+ GL+KKA E++VL DA+++LIIF +S K+ Y+S
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTD 60
Query: 62 MFEILEAY 69
M ++L Y
Sbjct: 61 MDKVLLKY 68
>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 = 70.9 bits (172), Expect = 6e-13, Method: Composition-based stats.
Identities = 35/68 (51%), Positives = 51/68 (75%)
Query: 2 GRGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSSAP 61
GR KI+I RI + NRQVT++KR+ GL+KKA E++VLCD +++LIIF +S K+ Y+S
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 MFEILEAY 69
M ++L Y
Sbjct: 61 MDKVLLKY 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 = 60.8 bits (146), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 33/78 (42%), Positives = 53/78 (67%), Gaps = 3/78 (3%)
Query: 3 RGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSSAPM 62
R KIEIK IEN + R VT+SKR++G++KKA E++VL +V L++ + +G ++ +S+ P
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFST-PK 76
Query: 63 FEILEAYHKQSGKKLWDA 80
FE + +Q G+ L A
Sbjct: 77 FEPI--VTQQEGRNLIQA 92
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 40/58 (68%)
Query: 2 GRGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSS 59
GR KI+++ I+N R T+SKR+ G++KKA E++ L +V L++ + +G ++ +++
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 40/58 (68%)
Query: 2 GRGKIEIKRIENLSNRQVTYSKRRNGLIKKAKEIAVLCDAKVSLIIFATSGKMHDYSS 59
GR KI+++ I+N R T+SKR+ G++KKA E++ L +V L++ + +G ++ +++
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 68
>pdb|1VMA|A Chain A, Crystal Structure Of Cell Division Protein Ftsy (Tm0570)
From Thermotoga Maritima At 1.60 A Resolution
pdb|1VMA|B Chain B, Crystal Structure Of Cell Division Protein Ftsy (Tm0570)
From Thermotoga Maritima At 1.60 A Resolution
Length = 306
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 45 LIIFATSGKMHDYSSAPMFEILEAYHKQSGKKLWDAKHENLYNEIDRIKKENDSMQIKL 103
++I T+G++H + + E L H+ KK+ DA HE L ID +N +Q K+
Sbjct: 189 VVIIDTAGRLHTKKN--LMEELRKVHRVVKKKIPDAPHETLLV-IDATTGQNGLVQAKI 244
>pdb|1G5I|A Chain A, Crystal Structure Of The Accessory Subunit Of Murine
Mitochondrial Polymerase Gamma
pdb|1G5I|B Chain B, Crystal Structure Of The Accessory Subunit Of Murine
Mitochondrial Polymerase Gamma
pdb|1G5I|C Chain C, Crystal Structure Of The Accessory Subunit Of Murine
Mitochondrial Polymerase Gamma
pdb|1G5I|D Chain D, Crystal Structure Of The Accessory Subunit Of Murine
Mitochondrial Polymerase Gamma
Length = 454
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 14/73 (19%)
Query: 72 QSGKKLWDAKHENLYNEIDRIKKENDSMQIKLRHLKGEDVTSLNHKELMALEDALENGLT 131
++G +W E +++ ++++ + D M + ++ E LENGL
Sbjct: 366 ENGISVWPGYSETVHSSLEQLHSKYDEMSVLF--------------SVLVTETTLENGLI 411
Query: 132 GIRDKQSEMMERM 144
+R + + M E M
Sbjct: 412 QLRSRDTTMKEMM 424
>pdb|2ZKR|2 Chain 2, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 97
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 67 EAYHKQ---SGKKLWDAKHENLYNEIDRIKKENDSMQIKLRHLK 107
+AYH Q GK + AK + YN + K+ N + ++RHLK
Sbjct: 25 KAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLK 68
>pdb|1VKO|A Chain A, Crystal Structure Of Inositol-3-Phosphate Synthase
(Ce21227) From Caenorhabditis Elegans At 2.30 A
Resolution
Length = 537
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 78 WDAKHENLYNEIDRIKKENDSMQIKLRHLKGEDV--TSLNHKELMALE--DALENGLTGI 133
WD NLY + R K +Q KLR V S+ + + +A D N + G
Sbjct: 159 WDISDSNLYEAMGRAKVFEPELQEKLRPFMEPIVPLPSIYYPDFIASNQGDRANNVIPG- 217
Query: 134 RDKQSEMMERMRKNGKMLEEEH 155
D + E +E +R + + ++EH
Sbjct: 218 -DNKLEHLEHIRADIRKFKQEH 238
>pdb|1YU9|A Chain A, Gppnhp-Bound Rab4a
Length = 175
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 75 KKLWDAKHENLYNEIDRIKKENDSMQIKLRHLKGEDV 111
KK DA E + E R +EN+ M ++ L GEDV
Sbjct: 125 KKDLDADREVTFLEASRFAQENELMFLETSALTGEDV 161
>pdb|1Z0K|A Chain A, Structure Of Gtp-Bound Rab4q67l Gtpase In Complex With The
Central Rab Binding Domain Of Rabenosyn-5
pdb|1Z0K|C Chain C, Structure Of Gtp-Bound Rab4q67l Gtpase In Complex With The
Central Rab Binding Domain Of Rabenosyn-5
Length = 172
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 75 KKLWDAKHENLYNEIDRIKKENDSMQIKLRHLKGEDV 111
KK DA E + E R +EN+ M ++ L GEDV
Sbjct: 122 KKDLDADREVTFLEASRFAQENELMFLETSALTGEDV 158
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
0.315 0.132 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,065,280
Number of Sequences: 62578
Number of extensions: 227383
Number of successful extensions: 684
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 672
Number of HSP's gapped (non-prelim): 23
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
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: 49 (23.5 bits)