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= 042235
(225 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 42/67 (62%), Gaps = 4/67 (5%)
Query: 6 KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTF-YTFGH 64
+R+I +K + K +R V+FSKR+HG++ KA E + T +Q+ LLV VS+T YTF
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLV---VSETGLVYTFST 74
Query: 65 SSVDAVL 71
+ ++
Sbjct: 75 PKFEPIV 81
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
G+++I + R + R V+F+KR+ GL+ KA E + +++AL++ + S + +
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFN--SSNKLFQYAS 58
Query: 65 SSVDAVLDAFVNNRAP 80
+ +D VL + P
Sbjct: 59 TDMDKVLLKYTEYNEP 74
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
G+++I + R + R V+F+KR+ GL+ KA E + ++AL++ + S + +
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFN--SSNKLFQYAS 58
Query: 65 SSVDAVLDAFVNNRAPEAA 83
+ +D VL + P +
Sbjct: 59 TDMDKVLLKYTEYNEPHES 77
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
G+++I + R + R V+F+KR+ GL+ KA E + ++AL++ + S + +
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFN--SSNKLFQYAS 58
Query: 65 SSVDAVLDAFVNNRAP 80
+ +D VL + P
Sbjct: 59 TDMDKVLLKYTEYNEP 74
>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 = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
G+ +I ++ D K +R +FSKR+ G++ KA E T +Q+ LLV+S YTF
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGH--VYTFAT 68
Query: 65 SSVDAVLDA 73
+ ++ +
Sbjct: 69 RKLQPMITS 77
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 4 VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
+G+++I + R + R V+F+KR+ GL+ KA E + ++AL++ + S + +
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFN--SANRLFQYA 58
Query: 64 HSSVDAVLDAFVNNRAP 80
+ +D VL + P
Sbjct: 59 STDMDRVLLKYTEYSEP 75
>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 = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
G+++I + R + R V+F+KR+ GL+ KA E + ++AL++ + S + +
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFN--SANRLFQYAS 58
Query: 65 SSVDAVLDAFVNNRAPEAA 83
+ +D VL + P +
Sbjct: 59 TDMDRVLLKYTEYSEPHES 77
>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 = 36.6 bits (83), Expect = 0.010, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
G+++I + R + R V+F+KR+ GL+ KA E + ++AL++ + S + +
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFN--SSNKLFQYAS 58
Query: 65 SSVDAVL 71
+ +D VL
Sbjct: 59 TDMDKVL 65
>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 = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
G+ +I ++ D K +R +FSKR+ G++ KA E T +Q+ LLV+S YTF
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGH--VYTFAT 67
Query: 65 SSVDAVLDA 73
+ ++ +
Sbjct: 68 RKLQPMITS 76
>pdb|2NPI|A Chain A, Clp1-Atp-Pcf11 Complex
pdb|2NPI|B Chain B, Clp1-Atp-Pcf11 Complex
Length = 460
Score = 30.4 bits (67), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 15/105 (14%)
Query: 51 SSPVSD---TTFYTFGHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLEL---- 103
++P+SD T+G S ++N+ P + G+ NE KDL L
Sbjct: 190 ATPISDILDAQLPTWGQSLTSGA--TLLHNKQPXVKN-----FGLERINENKDLYLECIS 242
Query: 104 -YDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKL 147
+ + + + D + R G D + DE++ EL I++KL
Sbjct: 243 QLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKL 287
>pdb|1KHV|A Chain A, Crystal Structure Of Rabbit Hemorrhagic Disease Virus
Rna-Dependent Rna Polymerase Complexed With Lu3+
pdb|1KHV|B Chain B, Crystal Structure Of Rabbit Hemorrhagic Disease Virus
Rna-Dependent Rna Polymerase Complexed With Lu3+
pdb|1KHW|A Chain A, Crystal Structure Of Rabbit Hemorrhagic Disease Virus
Rna-dependent Rna Polymerase Complexed With Mn2+
pdb|1KHW|B Chain B, Crystal Structure Of Rabbit Hemorrhagic Disease Virus
Rna-dependent Rna Polymerase Complexed With Mn2+
Length = 516
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 42/97 (43%), Gaps = 19/97 (19%)
Query: 1 MVAVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFY 60
M+ KR +P T ++ H LL AA Y ++ +++ L S+ D FY
Sbjct: 298 MIVQTKRGLPSGMPFTSVINSIC-----HWLLWSAAVY--KSCAEIGLHCSNLYEDAPFY 350
Query: 61 TFGHSSVDAV-------LDAFVNN-----RAPEAADK 85
T+G V A+ L A + N +P AADK
Sbjct: 351 TYGDDGVYAMTPMMVSLLPAIIENLRDYGLSPTAADK 387
>pdb|1ERZ|A Chain A, Crystal Structure Of N-Carbamyl-D-Amino Acid
Amidohydrolase With A Novel Catalytic Framework Common
To Amidohydrolases
pdb|1ERZ|B Chain B, Crystal Structure Of N-Carbamyl-D-Amino Acid
Amidohydrolase With A Novel Catalytic Framework Common
To Amidohydrolases
Length = 303
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 13/88 (14%)
Query: 1 MVAVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSP-VSDTTF 59
++AVG++ P+ R +T+EQ V R +L KAA S+ A + P ++ TTF
Sbjct: 5 ILAVGQQG-PIARAETREQVVV----RLLDMLTKAA-------SRGANFIVFPELALTTF 52
Query: 60 YTFGHSSVDAVLDAFVNNRAPEAADKEL 87
+ H + +A LD+F P + L
Sbjct: 53 FPRWHFTDEAELDSFYETEMPGPVVRPL 80
>pdb|1UF4|A Chain A, Crystal Structure Of C171aV236A MUTANT OF N-Carbamyl-D-
Amino Acid Amidohydrolase
pdb|1UF4|B Chain B, Crystal Structure Of C171aV236A MUTANT OF N-Carbamyl-D-
Amino Acid Amidohydrolase
pdb|1UF5|A Chain A, Crystal Structure Of C171aV236A MUTANT OF N-Carbamyl-D-
Amino Acid Amidohydrolase Complexed With N-Carbamyl-D-
Methionine
pdb|1UF5|B Chain B, Crystal Structure Of C171aV236A MUTANT OF N-Carbamyl-D-
Amino Acid Amidohydrolase Complexed With N-Carbamyl-D-
Methionine
pdb|1UF7|A Chain A, Crystal Structure Of C171aV236A MUTANT OF N-Carbamyl-D-
Amino Acid Amidohydrolase Complexed With N-Carbamyl-D-
Valine
pdb|1UF7|B Chain B, Crystal Structure Of C171aV236A MUTANT OF N-Carbamyl-D-
Amino Acid Amidohydrolase Complexed With N-Carbamyl-D-
Valine
pdb|1UF8|A Chain A, Crystal Structure Of C171aV236A MUTANT OF N-Carbamyl-D-
Amino Acid Amidohydrolase Complexed With N-Carbamyl-D-
Phenylalanine
pdb|1UF8|B Chain B, Crystal Structure Of C171aV236A MUTANT OF N-Carbamyl-D-
Amino Acid Amidohydrolase Complexed With N-Carbamyl-D-
Phenylalanine
Length = 303
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 13/88 (14%)
Query: 1 MVAVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSP-VSDTTF 59
++AVG++ P+ R +T+EQ V R +L KAA S+ A + P ++ TTF
Sbjct: 5 ILAVGQQG-PIARAETREQVVV----RLLDMLTKAA-------SRGANFIVFPELALTTF 52
Query: 60 YTFGHSSVDAVLDAFVNNRAPEAADKEL 87
+ H + +A LD+F P + L
Sbjct: 53 FPRWHFTDEAELDSFYETEMPGPVVRPL 80
>pdb|2VBF|A Chain A, The Holostructure Of The Branched-Chain Keto Acid
Decarboxylase (Kdca) From Lactococcus Lactis
pdb|2VBF|B Chain B, The Holostructure Of The Branched-Chain Keto Acid
Decarboxylase (Kdca) From Lactococcus Lactis
pdb|2VBG|A Chain A, The Complex Structure Of The Branched-Chain Keto Acid
Decarboxylase (Kdca) From Lactococcus Lactis With 2r-1-
Hydroxyethyl-Deazathdp
pdb|2VBG|B Chain B, The Complex Structure Of The Branched-Chain Keto Acid
Decarboxylase (Kdca) From Lactococcus Lactis With 2r-1-
Hydroxyethyl-Deazathdp
Length = 570
Score = 26.9 bits (58), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 89 RLGISMFNEVKDLEL----YDKKISKAIKSDGNLEREGFWEDYEKLGNSDESI 137
R +S +E+K +E DK+ + I S L ++ W+ E L S+E+I
Sbjct: 344 RAVVSSLSELKGIEYEGQYIDKQYEEFIPSSAPLSQDRLWQAVESLTQSNETI 396
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 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,848,901
Number of Sequences: 62578
Number of extensions: 202759
Number of successful extensions: 480
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 468
Number of HSP's gapped (non-prelim): 21
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
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: 50 (23.9 bits)