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= 005589
(689 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OSF|A Chain A, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSF|D Chain D, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSG|A Chain A, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-1-12 Dna
pdb|3OSG|D Chain D, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-1-12 Dna
Length = 126
Score = 33.5 bits (75), Expect = 0.38, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 568 QSFMKKTPTVRWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVKLKYK 618
Q +K +++ +E E+ A+ Q G+D MI FP R +Q + ++K
Sbjct: 3 QVNLKAAKKQKFTPEEDEMLKRAVAQHGSDWKMIAATFPNRNARQCRDRWK 53
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 553 PATDRVQPRVHFFNYQS-FMKKTPTVRWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQ 611
P + Q R + NY + + TP W+ +E L + I+++G ++I + FPGRT
Sbjct: 41 PNRNARQCRDRWKNYLAPSISHTP---WTAEEDALLVQKIQEYGRQWAIIAKFFPGRTDI 97
Query: 612 QVKLKY 617
+K ++
Sbjct: 98 HIKNRW 103
>pdb|1MSE|C Chain C, Solution Structure Of A Specific Dna Complex Of The Myb
Dna- Binding Domain With Cooperative Recognition Helices
pdb|1MSF|C Chain C, Solution Structure Of A Specific Dna Complex Of The Myb
Dna- Binding Domain With Cooperative Recognition Helices
Length = 105
Score = 33.5 bits (75), Expect = 0.42, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 571 MKKTPTVRWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVKLKYKKEER 622
+KKT W+++E + Y+A ++ G + I +L PGRT +K + R
Sbjct: 54 VKKT---SWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMR 102
>pdb|2CNR|A Chain A, Structural Studies On The Interaction Of Scfas Acp With
Acps
Length = 82
Score = 33.1 bits (74), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 166 MFLTQDPISCGQAALTNNAGGIPVDDARLEREVQQDGAFPDLNFLDSTSEEAVASGQRAA 225
M TQ+ I G A + N GIPV+D +L++ D D++ L S E VA+ +R
Sbjct: 1 MAATQEEIVAGLAEIVNEIAGIPVEDVKLDKSFTDD---LDVDSL-SMVEVVVAAEERFD 56
Query: 226 KYKPRPQVR 234
P V+
Sbjct: 57 VKIPDDDVK 65
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 571 MKKTPTVRWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVKLKYKKEER 622
+KKT W+++E + Y+A ++ G + I +L PGRT +K + R
Sbjct: 54 VKKT---SWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMR 102
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 32.7 bits (73), Expect = 0.62, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 579 WSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVKLKYKKEER 622
W+++E + Y+A ++ G + I +L PGRT VK + R
Sbjct: 82 WTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAVKNHWNSTMR 125
>pdb|1H88|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H89|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex2
Length = 159
Score = 32.7 bits (73), Expect = 0.63, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 571 MKKTPTVRWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVKLKYKKEER 622
+KKT W+++E + Y+A ++ G + I +L PGRT +K + R
Sbjct: 108 VKKT---SWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMR 156
>pdb|2CU7|A Chain A, Solution Structure Of The Sant Domain Of Human Kiaa1915
Protein
Length = 72
Score = 32.7 bits (73), Expect = 0.65, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 577 VRWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVK 614
V+W+ +E ELF + + +FG + I +L RT QVK
Sbjct: 10 VKWTIEEKELFEQGLAKFGRRWTKISKLIGSRTVLQVK 47
>pdb|1IDY|A Chain A, Structure Of Myb Transforming Protein, Nmr, Minimized
Average Structure
pdb|1IDZ|A Chain A, Structure Of Myb Transforming Protein, Nmr, 20 Structures
Length = 54
Score = 32.7 bits (73), Expect = 0.75, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 579 WSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVKLKYKKEER 622
W+++E + Y+A ++ G + I +L PGRT +K + R
Sbjct: 8 WTEEEDRILYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMR 51
>pdb|1MBJ|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 3
pdb|1MBK|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 3
Length = 53
Score = 32.7 bits (73), Expect = 0.77, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 579 WSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVKLKYKKEER 622
W+++E + Y+A ++ G + I +L PGRT +K + R
Sbjct: 6 WTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMR 49
>pdb|2KOO|A Chain A, Nmr Solution Structures Of Hexanoyl-Acp From The
Streptomyces Coelicolor Fatty Acid Synthase
pdb|2KOP|A Chain A, Nmr Solution Structures Of 3-Oxooctanyl-Acp From
Streptomyces Coelicolor Fatty Acid Synthase
pdb|2KOQ|A Chain A, Nmr Solution Structures Of 3-Hydroxyoctanoyl-Acp From
Streptomyces Coelicolor Fatty Acid Synthase
pdb|2KOR|A Chain A, Nmr Solution Structures Of 2-Octenoyl-Acp From
Streptomyces Coelicolor Fatty Acid Synthase
pdb|2KOS|A Chain A, Nmr Solution Structures Of Octanoyl-Acp From Streptomyces
Coelicolor Fatty Acid Synthase
Length = 81
Score = 32.3 bits (72), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 169 TQDPISCGQAALTNNAGGIPVDDARLEREVQQDGAFPDLNFLDSTSEEAVASGQRAAKYK 228
TQ+ I G A + N GIPV+D +L++ D D++ L S E VA+ +R
Sbjct: 3 TQEEIVAGLAEIVNEIAGIPVEDVKLDKSFTDD---LDVDSL-SMVEVVVAAEERFDVKI 58
Query: 229 PRPQVR 234
P V+
Sbjct: 59 PDDDVK 64
>pdb|3ZQC|A Chain A, Structure Of The Trichomonas Vaginalis Myb3 Dna-Binding
Domain Bound To A Promoter Sequence Reveals A Unique C-
Terminal Beta-Hairpin Conformation
pdb|3ZQC|D Chain D, Structure Of The Trichomonas Vaginalis Myb3 Dna-Binding
Domain Bound To A Promoter Sequence Reveals A Unique C-
Terminal Beta-Hairpin Conformation
pdb|3ZQC|G Chain G, Structure Of The Trichomonas Vaginalis Myb3 Dna-Binding
Domain Bound To A Promoter Sequence Reveals A Unique C-
Terminal Beta-Hairpin Conformation
pdb|3ZQC|J Chain J, Structure Of The Trichomonas Vaginalis Myb3 Dna-Binding
Domain Bound To A Promoter Sequence Reveals A Unique C-
Terminal Beta-Hairpin Conformation
Length = 131
Score = 32.3 bits (72), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 579 WSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVKLKY 617
W+ +E E + + G+ S+I +L PGRT +K ++
Sbjct: 57 WTPEEDETIFRNYLKLGSKWSVIAKLIPGRTDNAIKNRW 95
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 32.3 bits (72), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 577 VRWSKQETELFYEAIRQFG-TDLSMIQQLFPGRTRQQVKLKY 617
V+W+ +E E +RQFG D + FP RT QQ + ++
Sbjct: 9 VKWTHEEDEQLRALVRQFGQQDWKFLASHFPNRTDQQCQYRW 50
>pdb|1A5J|A Chain A, Chicken B-Myb Dna Binding Domain, Repeat 2 And Repeat3,
Nmr, 32 Structures
Length = 110
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 579 WSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVK 614
W+++E + +EA + G + I +L PGRT VK
Sbjct: 62 WTEEEDRIIFEAHKVLGNRWAEIAKLLPGRTDNAVK 97
>pdb|1U2J|A Chain A, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P21 21 21)
pdb|1U2J|B Chain B, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P21 21 21)
pdb|1U2J|C Chain C, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P21 21 21)
pdb|1U2J|D Chain D, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P21 21 21)
pdb|1U2J|E Chain E, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P21 21 21)
pdb|1U2J|F Chain F, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P21 21 21)
pdb|1U2J|G Chain G, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P21 21 21)
pdb|1U2J|H Chain H, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P21 21 21)
Length = 326
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 102 NADVLSGLESLNDFQSQSSNGTEMPALIVSDYNGGE-AVVFEGLSSDNNAAPGVCDAAQA 160
NA + L L Q +S + ++++ G E A GLS APG DA Q
Sbjct: 103 NAAAVRALPVLEKIQKESGKASLADIIVLAGVVGVEKAASAAGLSIHVPFAPGRVDARQD 162
Query: 161 ETSADMFLTQDPISCG 176
+T +MF +PI+ G
Sbjct: 163 QTDIEMFELLEPIADG 178
>pdb|1U2K|A Chain A, Crystal Structure Of The C-Terminal Domain From The
Catalase- Peroxidase Katg Of Escherichia Coli (I41)
pdb|1U2L|A Chain A, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P1)
pdb|1U2L|B Chain B, Crystal Structure Of The C-Terminal Domain From The
Catalase-Peroxidase Katg Of Escherichia Coli (P1)
Length = 309
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 102 NADVLSGLESLNDFQSQSSNGTEMPALIVSDYNGGE-AVVFEGLSSDNNAAPGVCDAAQA 160
NA + L L Q +S + ++++ G E A GLS APG DA Q
Sbjct: 86 NAAAVRALPVLEKIQKESGKASLADIIVLAGVVGVEKAASAAGLSIHVPFAPGRVDARQD 145
Query: 161 ETSADMFLTQDPISCG 176
+T +MF +PI+ G
Sbjct: 146 QTDIEMFELLEPIADG 161
>pdb|2XAF|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 482
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 578 RWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVK 614
RW+ +E L +AIR++G D I + ++ QVK
Sbjct: 382 RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVK 418
>pdb|2V1D|B Chain B, Structural Basis Of Lsd1-Corest Selectivity In Histone H3
Recognition
pdb|2Y48|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A N-
Terminal Snail Peptide
Length = 178
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 578 RWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVK 614
RW+ +E L +AIR++G D I + ++ QVK
Sbjct: 78 RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVK 114
>pdb|2IW5|B Chain B, Structural Basis For Corest-dependent Demethylation Of
Nucleosomes By The Human Lsd1 Histone Demethylase
pdb|2UXN|B Chain B, Structural Basis Of Histone Demethylation By Lsd1 Revealed
By Suicide Inactivation
pdb|2UXX|B Chain B, Human Lsd1 Histone Demethylase-Corest In Complex With An
Fad-Tranylcypromine Adduct
Length = 235
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 578 RWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVK 614
RW+ +E L +AIR++G D I + ++ QVK
Sbjct: 135 RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVK 171
>pdb|2X0L|B Chain B, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 133
Score = 29.3 bits (64), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 578 RWSKQETELFYEAIRQFGTDLSMIQQLFPGRTRQQVK 614
RW+ +E L +AIR++G D I + ++ QVK
Sbjct: 75 RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVK 111
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
0.308 0.125 0.346
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,699,859
Number of Sequences: 62578
Number of extensions: 794645
Number of successful extensions: 1343
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1321
Number of HSP's gapped (non-prelim): 28
length of query: 689
length of database: 14,973,337
effective HSP length: 105
effective length of query: 584
effective length of database: 8,402,647
effective search space: 4907145848
effective search space used: 4907145848
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 55 (25.8 bits)