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= 028296
(211 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 = 62.8 bits (151), Expect = 1e-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|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 = 62.8 bits (151), Expect = 1e-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|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 = 62.8 bits (151), Expect = 2e-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|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 = 62.8 bits (151), Expect = 2e-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 = 61.6 bits (148), Expect = 3e-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 = 60.5 bits (145), Expect = 6e-10, 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 = 57.8 bits (138), Expect = 5e-09, 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|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 = 3e-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|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 = 48.1 bits (113), Expect = 4e-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|2QEZ|A Chain A, Crystal Structure Of Ethanolamine Ammonia-Lyase Heavy
Chain (Yp_013784.1) From Listeria Monocytogenes 4b F2365
At 2.15 A Resolution
pdb|2QEZ|B Chain B, Crystal Structure Of Ethanolamine Ammonia-Lyase Heavy
Chain (Yp_013784.1) From Listeria Monocytogenes 4b F2365
At 2.15 A Resolution
pdb|2QEZ|C Chain C, Crystal Structure Of Ethanolamine Ammonia-Lyase Heavy
Chain (Yp_013784.1) From Listeria Monocytogenes 4b F2365
At 2.15 A Resolution
pdb|2QEZ|D Chain D, Crystal Structure Of Ethanolamine Ammonia-Lyase Heavy
Chain (Yp_013784.1) From Listeria Monocytogenes 4b F2365
At 2.15 A Resolution
pdb|2QEZ|E Chain E, Crystal Structure Of Ethanolamine Ammonia-Lyase Heavy
Chain (Yp_013784.1) From Listeria Monocytogenes 4b F2365
At 2.15 A Resolution
pdb|2QEZ|F Chain F, Crystal Structure Of Ethanolamine Ammonia-Lyase Heavy
Chain (Yp_013784.1) From Listeria Monocytogenes 4b F2365
At 2.15 A Resolution
Length = 455
Score = 34.7 bits (78), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 35/122 (28%), Positives = 55/122 (45%), Gaps = 32/122 (26%)
Query: 95 EQVNRILKKQIRQRMGESLNDLTLEELTGLEQDILDGLKIIHECKDQVLARQINTFKRKV 154
++V RI++ Q+ R+ +S+ + T+EE L + ILD H+ D + KR
Sbjct: 71 DEVTRIIQDQVNDRIHDSIKNWTVEE---LREWILD-----HKTTDADI-------KRVA 115
Query: 155 RGVQKENKSLQDGFIINAKEE-----DPHYEYELVDNGEHCDSDFGFQNEGPGIFALRLQ 209
RG+ E II A + D Y + + H ++ G PG F+ RLQ
Sbjct: 116 RGLTSE--------IIAAVTKLXSNLDLIYGAKKIRVIAHANTTIGL----PGTFSARLQ 163
Query: 210 PN 211
PN
Sbjct: 164 PN 165
>pdb|3T7I|A Chain A, Crystal Structure Of Se-Met Rtt107p (Residues 820-1070)
pdb|3T7I|B Chain B, Crystal Structure Of Se-Met Rtt107p (Residues 820-1070)
Length = 256
Score = 30.4 bits (67), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 86 KMLENLGAVEQVNRILKKQIRQRMGESLNDLTLEELT-GLEQD-ILDGLKIIHECKDQVL 143
K+ +N+ +++N I +I R + L L+ E L L+ + I+D LK IH KD++
Sbjct: 49 KIFDNIKETDKLNCIFAPKIL-RTEKFLKSLSFEPLKFALKPEFIIDXLKQIHSKKDKLS 107
Query: 144 ARQINTFKRKVRGVQ 158
IN F ++ G+
Sbjct: 108 QININLFDYEINGIN 122
>pdb|3T7J|A Chain A, Crystal Structure Of Rtt107p (Residues 820-1070)
pdb|3T7J|B Chain B, Crystal Structure Of Rtt107p (Residues 820-1070)
pdb|3T7K|A Chain A, Complex Structure Of Rtt107p And Phosphorylated Histone
H2a
pdb|3T7K|B Chain B, Complex Structure Of Rtt107p And Phosphorylated Histone
H2a
Length = 256
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 86 KMLENLGAVEQVNRILKKQIRQRMGESLNDLTLEELT-GLEQD-ILDGLKIIHECKDQVL 143
K+ +N+ +++N I +I R + L L+ E L L+ + I+D LK IH KD++
Sbjct: 49 KIFDNIKETDKLNCIFAPKIL-RTEKFLKSLSFEPLKFALKPEFIIDLLKQIHSKKDKLS 107
Query: 144 ARQINTFKRKVRGVQ 158
IN F ++ G+
Sbjct: 108 QININLFDYEINGIN 122
>pdb|2P67|A Chain A, Crystal Structure Of LaoAO TRANSPORT SYSTEM KINASE
Length = 341
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 7 EMKRIENATNRQVTFSKRRNGLFKKARELTILCDA 41
++ R E A R V S G ++AREL +LC+A
Sbjct: 112 DLARAEAAFIRPVPSSGHLGGASQRARELMLLCEA 146
>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 = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 13/89 (14%)
Query: 82 SHYEKMLENLGAVEQVNRILKKQIRQRMGES--LNDLTLEELTGLEQDILDGLKI----- 134
++ +K+LENLG VE+ RIL+ + ++ S LND+ + + + +++++ L I
Sbjct: 50 AYLKKLLENLGYVEK--RILEAEEINQLXNSINLNDIEINAFSKVAKNLIEKLNIRDDEI 107
Query: 135 ---IHECKDQVLARQINTFKRKVRGVQKE 160
I C + ++FK K+ + KE
Sbjct: 108 EIYIDACSTNTKKFE-DSFKDKIEDIIKE 135
>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 = 5.0, 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 = 5.1, 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|2Z6B|A Chain A, Crystal Structure Analysis Of (Gp27-Gp5)3 Conjugated With
Fe(Iii) Protoporphyrin
Length = 584
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 94 VEQVNRILKKQIRQRMGESLNDLTLEELTGL-EQDILD 130
+ Q+N++L KQ+ + + + +T+EE T L E+D+ D
Sbjct: 214 MAQINKVLSKQVGREITGNPGSITMEEATTLFERDLAD 251
>pdb|1WTH|A Chain A, Crystal Structure Of Gp5-S351l Mutant And Gp27 Complex
Length = 584
Score = 27.7 bits (60), Expect = 5.3, 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|3PC8|A Chain A, X-Ray Crystal Structure Of The Heterodimeric Complex Of
Xrcc1 And Dna Ligase Iii-Alpha Brct Domains.
pdb|3PC8|B Chain B, X-Ray Crystal Structure Of The Heterodimeric Complex Of
Xrcc1 And Dna Ligase Iii-Alpha Brct Domains
Length = 98
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 151 KRKVRGVQKENKSLQD------GFIINAKEEDPHYEYELVDN 186
+R +R V N L+D F+I A+E DP++E L++N
Sbjct: 25 RRLIRYVTAFNGELEDRMNERVQFVITAQEWDPNFEEALMEN 66
>pdb|3PC6|A Chain A, X-Ray Crystal Structure Of The Second Xrcc1 Brct Domain.
pdb|3PC6|B Chain B, X-Ray Crystal Structure Of The Second Xrcc1 Brct Domain
Length = 104
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 151 KRKVRGVQKENKSLQD------GFIINAKEEDPHYEYELVDN 186
+R +R V N L+D F+I A+E DP++E L++N
Sbjct: 25 RRLIRYVTAFNGELEDYMNERVQFVITAQEWDPNFEEALMEN 66
>pdb|3QVG|B Chain B, Xrcc1 Bound To Dna Ligase
pdb|3QVG|D Chain D, Xrcc1 Bound To Dna Ligase
Length = 106
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 151 KRKVRGVQKENKSLQD------GFIINAKEEDPHYEYELVDN 186
+R +R V N L+D F+I A+E DP++E L++N
Sbjct: 33 RRLIRYVTAFNGELEDRMNERVQFVITAQEWDPNFEEALMEN 74
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 0.134 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,909,371
Number of Sequences: 62578
Number of extensions: 229090
Number of successful extensions: 743
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 729
Number of HSP's gapped (non-prelim): 32
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
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)