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= 039560
(344 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 = 75.9 bits (185), Expect = 4e-14, Method: Composition-based stats.
Identities = 34/58 (58%), Positives = 47/58 (81%)
Query: 1 MGRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFS 58
MGR K++I RI + NRQVTF+KR+ GL+KKAYELS+LCD +IALI+F+ + RL ++
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYA 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 = 74.7 bits (182), Expect = 7e-14, Method: Composition-based stats.
Identities = 33/57 (57%), Positives = 46/57 (80%)
Query: 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFS 58
GR K++I RI + NRQVTF+KR+ GL+KKAYELS+LCD +IALI+F+ S +L ++
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYA 57
>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 = 74.3 bits (181), Expect = 9e-14, Method: Composition-based stats.
Identities = 39/84 (46%), Positives = 58/84 (69%), Gaps = 3/84 (3%)
Query: 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRK 61
GR K++I RI + NRQVTF+KR+ GL+KKAYELS+LCD +IALI+F+ S +L ++
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 RIEDVFSRYV--NLPDQEREHAII 83
++ V +Y N P + R ++ I
Sbjct: 61 -MDKVLLKYTEYNEPHESRTNSDI 83
>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 = 2e-13, Method: Composition-based stats.
Identities = 33/57 (57%), Positives = 46/57 (80%)
Query: 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFS 58
GR K++I RI + NRQVTF+KR+ GL+KKAYELS+LCD +IALI+F+ + RL ++
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYA 57
>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 = 73.6 bits (179), Expect = 2e-13, Method: Composition-based stats.
Identities = 33/57 (57%), Positives = 46/57 (80%)
Query: 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFS 58
GR K++I RI + NRQVTF+KR+ GL+KKAYELS+LCD +IALI+F+ S +L ++
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYA 57
>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 = 69.7 bits (169), Expect = 2e-12, Method: Composition-based stats.
Identities = 38/84 (45%), Positives = 57/84 (67%), Gaps = 3/84 (3%)
Query: 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRK 61
GR K++I RI + NRQVTF+KR+ GL+KKAYELS+L D +IALI+F+ S +L ++
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTD 60
Query: 62 RIEDVFSRYV--NLPDQEREHAII 83
++ V +Y N P + R ++ I
Sbjct: 61 -MDKVLLKYTEYNEPHESRTNSDI 83
>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 = 4e-09, Method: Composition-based stats.
Identities = 30/59 (50%), Positives = 42/59 (71%)
Query: 3 RVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRK 61
R K+EIK IEN T R VTFSKR++G++KKA+ELS+L + L++ S +G + FS K
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPK 76
>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 = 58.5 bits (140), Expect = 5e-09, Method: Composition-based stats.
Identities = 27/60 (45%), Positives = 41/60 (68%)
Query: 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRK 61
GRVK++++ I+N R TFSKR+ G++KKAYELS L + L++ S +G + F+ RK
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRK 70
>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 = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 27/60 (45%), Positives = 41/60 (68%)
Query: 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRK 61
GRVK++++ I+N R TFSKR+ G++KKAYELS L + L++ S +G + F+ RK
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRK 69
>pdb|3UGV|A Chain A, Crystal Structure Of An Enolase From Alpha Pretobacterium
Bal199 (Efi Target Efi-501650) With Bound Mg
pdb|3UGV|B Chain B, Crystal Structure Of An Enolase From Alpha Pretobacterium
Bal199 (Efi Target Efi-501650) With Bound Mg
pdb|3UGV|C Chain C, Crystal Structure Of An Enolase From Alpha Pretobacterium
Bal199 (Efi Target Efi-501650) With Bound Mg
pdb|3UGV|D Chain D, Crystal Structure Of An Enolase From Alpha Pretobacterium
Bal199 (Efi Target Efi-501650) With Bound Mg
pdb|3UGV|E Chain E, Crystal Structure Of An Enolase From Alpha Pretobacterium
Bal199 (Efi Target Efi-501650) With Bound Mg
pdb|3UGV|F Chain F, Crystal Structure Of An Enolase From Alpha Pretobacterium
Bal199 (Efi Target Efi-501650) With Bound Mg
pdb|3UGV|G Chain G, Crystal Structure Of An Enolase From Alpha Pretobacterium
Bal199 (Efi Target Efi-501650) With Bound Mg
pdb|3UGV|H Chain H, Crystal Structure Of An Enolase From Alpha Pretobacterium
Bal199 (Efi Target Efi-501650) With Bound Mg
Length = 390
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 13/93 (13%)
Query: 259 GECHVTNPSG---ENFATWPQAFVSAGLHSAPLSPSLYPQIQQHGMMGTDTNEILPRDQV 315
G C + P + W +A AG P+S LYP++ H M T+T L
Sbjct: 292 GACDLVMPDFMRIGGVSGWMRAAGVAGAWGIPMSTHLYPEVGAHVMRVTETAHWLEWQSW 351
Query: 316 EIPI-NAPHVQADNE---------GANYDQNKI 338
PI P+ +D + G ++D++ +
Sbjct: 352 ADPILQEPYALSDGDLIVPDKPGLGLDWDEDVV 384
>pdb|2AU3|A Chain A, Crystal Structure Of The Aquifex Aeolicus Primase (Zinc
Binding And Rna Polymerase Domains)
Length = 407
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 50 PSGRLSHFSGRKRIEDVFSRYVNLPD 75
P GR+ F GR+ +ED +Y+N PD
Sbjct: 196 PRGRVIGFGGRRIVEDKSPKYINSPD 221
>pdb|3EK1|A Chain A, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|B Chain B, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|C Chain C, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|D Chain D, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|E Chain E, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|F Chain F, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|G Chain G, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|H Chain H, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
Length = 504
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 22 SKRRNGLIKKAYELSILCDIDIALIMFSPSGR 53
+K R G+++K ++L I DIALIM S G+
Sbjct: 91 AKERAGILRKWFDLIIANADDIALIMTSEQGK 122
>pdb|2I9L|B Chain B, Structure Of Fab 7d11 From A Neutralizing Antibody Against
The Poxvirus L1 Protein
pdb|2I9L|D Chain D, Structure Of Fab 7d11 From A Neutralizing Antibody Against
The Poxvirus L1 Protein
pdb|2I9L|F Chain F, Structure Of Fab 7d11 From A Neutralizing Antibody Against
The Poxvirus L1 Protein
pdb|2I9L|H Chain H, Structure Of Fab 7d11 From A Neutralizing Antibody Against
The Poxvirus L1 Protein
Length = 219
Score = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 209 EVVGWL-PGGGHNQA-QIFESSASLNELRDLSTTMYDPLLQGTSSNAGPHSIGECHVTNP 266
E +G++ P G+ + Q F+ A+L + S+T+Y L TS ++ ++ C T
Sbjct: 46 EWIGYINPSTGYTEYNQKFKDKATLTADKS-SSTVYMQLSSLTSEDS---AVYYCARTTV 101
Query: 267 SGENFATWPQAFVSAGLHSAPLSPSLYP 294
G +FA W Q + + +PS+YP
Sbjct: 102 DGYDFAYWGQGTLVTVSAAKTTAPSVYP 129
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 0.133 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,700,266
Number of Sequences: 62578
Number of extensions: 383951
Number of successful extensions: 767
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 754
Number of HSP's gapped (non-prelim): 17
length of query: 344
length of database: 14,973,337
effective HSP length: 100
effective length of query: 244
effective length of database: 8,715,537
effective search space: 2126591028
effective search space used: 2126591028
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: 52 (24.6 bits)