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= psy3970
(104 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KY8|A Chain A, Solution Structure And Dynamic Analysis Of Chicken Mbd2
Methyl Binding Domain Bound To A Target Methylated Dna
Sequence
Length = 72
Score = 75.9 bits (185), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 32/65 (49%), Positives = 45/65 (69%)
Query: 23 RYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDF 82
R +CP LPPGW +EEV R GLS GK DV+Y+SP GKK R++ ++ + + + FDF
Sbjct: 7 RTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNAVDLSCFDF 66
Query: 83 RSGKL 87
R+GK+
Sbjct: 67 RTGKM 71
>pdb|1D9N|A Chain A, Solution Structure Of The Methyl-Cpg-Binding Domain Of
The Methylation-Dependent Transcriptional Repressor
Mbd1PCM1
pdb|1IG4|A Chain A, Solution Structure Of The Methyl-Cpg-Binding Domain Of
Human Mbd1 In Complex With Methylated Dna
Length = 75
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 25 ECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDFRS 84
+CP L PGW R EV R G + G+ D +Y SP G ++R++ E+ + + FDF+
Sbjct: 7 DCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLTLFDFKQ 66
Query: 85 GKL 87
G L
Sbjct: 67 GIL 69
>pdb|3C2I|A Chain A, The Crystal Structure Of Methyl-Cpg Binding Domain Of
Human Mecp2 In Complex With A Methylated Dna Sequence
From Bdnf
Length = 97
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 24 YECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVL 68
Y+ P LP GW R+ R G S GK DV+ +P GK R++ E++
Sbjct: 19 YDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELI 63
>pdb|1QK9|A Chain A, The Solution Structure Of The Domain From Mecp2 That
Binds To Methylated Dna
Length = 92
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 24 YECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVL 68
Y+ P LP GW R+ R G S GK DV+ +P GK R++ E++
Sbjct: 19 YDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELI 63
>pdb|1UB1|A Chain A, Solution Structure Of The Matrix Attachment
Region-Binding Domain Of Chicken Mecp2
Length = 133
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 24 YECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVL 68
Y+ P LP GW R+ R G S GK DV+ +P GK R++ E++
Sbjct: 33 YDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELI 77
>pdb|3VYQ|A Chain A, Crystal Structure Of The Methyl Cpg Binding Domain Of
Mbd4 In Complex With The 5mcg/tg Sequence In Space
Group P1
pdb|3VYQ|D Chain D, Crystal Structure Of The Methyl Cpg Binding Domain Of
Mbd4 In Complex With The 5mcg/tg Sequence In Space
Group P1
Length = 74
Score = 32.7 bits (73), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%)
Query: 29 LPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGN 74
+P GW R R G + GK DV++ SP G K R++ + + N
Sbjct: 11 VPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKN 56
>pdb|3VXV|A Chain A, Crystal Structure Of Methyl Cpg Binding Domain Of Mbd4
In Complex With The 5mcg/tg Sequence
pdb|3VXX|A Chain A, Crystal Structure Of Methyl Cpg Binding Domain Of Mbd4
In Complex With The 5mcg/5mcg Sequence
pdb|3VYB|A Chain A, Crystal Structure Of Methyl Cpg Binding Domain Of Mbd4
In Complex With The 5mcg/hmcg Sequence
Length = 69
Score = 32.7 bits (73), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%)
Query: 29 LPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGN 74
+P GW R R G + GK DV++ SP G K R++ + + N
Sbjct: 6 VPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKN 51
>pdb|4HC8|A Chain A, Crystal Structure Of Probable Enoyl-Coa Hydratase Echa3
(Rv0632c, Nysgrc-019494) From Mycobacterium Tuberculosis
H37rv
pdb|4HC8|B Chain B, Crystal Structure Of Probable Enoyl-Coa Hydratase Echa3
(Rv0632c, Nysgrc-019494) From Mycobacterium Tuberculosis
H37rv
Length = 255
Score = 29.3 bits (64), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 54 YSPCGKKLRTRSEVLQVIRGNIPGVSFDF 82
++ KLR+R++ L IR I G++ +F
Sbjct: 203 HAHAATKLRSRADALTAIRAGIDGIAAEF 231
>pdb|3R6H|A Chain A, Crystal Structure Of An Enoyl-Coa Hydratase (Echa3) From
Mycobacterium Marinum
Length = 233
Score = 28.5 bits (62), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 60 KLRTRSEVLQVIRGNIPGVSFDF 82
KLR R+E L+ IR I G+ +F
Sbjct: 209 KLRARAEALKAIRAGIDGIEAEF 231
>pdb|4F1I|A Chain A, Crystal Structure Of Semet Tdp2 From Caenorhabditis
Elegans
Length = 362
Score = 28.1 bits (61), Expect = 1.2, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 34 YREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDFRSGKLNSLQKH 93
Y + +K V K DV ++ G RT LQ++ G+I G+ + L S ++H
Sbjct: 185 YYTAILVSKXFDVEKHDVIHFQNSGX-YRT----LQILEGSIGGLKVFLLNTHLESTREH 239
Query: 94 RNKQRGNQFEY 104
R QR QF +
Sbjct: 240 R-PQRCAQFGF 249
>pdb|1Y3N|A Chain A, Structure Of Algq1, Alginate-binding Protein, Complexed
With An Alginate Disaccharide
pdb|1Y3P|A Chain A, Structure Of Algq1, Alginate-Binding Protein, Complexed
With An Alginate Tetrasaccharide
pdb|1Y3Q|A Chain A, Structure Of Algq1, Alginate-Binding Protein
pdb|3A09|A Chain A, Crystal Structure Of Sphingomonas Sp. A1 Alginate-Binding
Protein Algq1 In Complex With Unsaturated Trimannuronate
Length = 490
Score = 27.7 bits (60), Expect = 1.7, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 10/57 (17%)
Query: 30 PPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDFRSGK 86
P GW +N ++ D FY+ P G++L +PG+++D ++GK
Sbjct: 314 PDGWAITATNKNPVETIKLFD-FYFGPKGRELSNFG---------VPGLTYDIKNGK 360
>pdb|3VLU|A Chain A, Crystal Structure Of Sphingomonas Sp. A1 Alginate-Binding
Protein Algq1 In Complex With Saturated Trimannuronate
pdb|3VLV|A Chain A, Crystal Structure Of Sphingomonas Sp. A1 Alginate-Binding
Ptotein Algq1 In Complex With Unsaturated Triguluronate
pdb|3VLW|A Chain A, Crystal Structure Of Sphingomonas Sp. A1 Alginate-Binding
Protein Algq1 In Complex With Mannuronate-Guluronate
Disaccharide
pdb|3VLW|B Chain B, Crystal Structure Of Sphingomonas Sp. A1 Alginate-Binding
Protein Algq1 In Complex With Mannuronate-Guluronate
Disaccharide
Length = 502
Score = 27.7 bits (60), Expect = 1.7, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 10/57 (17%)
Query: 30 PPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDFRSGK 86
P GW +N ++ D FY+ P G++L +PG+++D ++GK
Sbjct: 314 PDGWAITATNKNPVETIKLFD-FYFGPKGRELSNFG---------VPGLTYDIKNGK 360
>pdb|4GEW|A Chain A, Crystal Structure Of Tdp2 From C. Elegans
Length = 362
Score = 27.3 bits (59), Expect = 1.9, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 34 YREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDFRSGKLNSLQKH 93
Y + +K V K DV ++ G RT LQ++ G+I G+ + L S ++H
Sbjct: 185 YYTAILVSKMFDVEKHDVIHFQNSGM-YRT----LQILEGSIGGLKVFLLNTHLESTREH 239
Query: 94 RNKQRGNQFEY 104
R QR QF +
Sbjct: 240 R-PQRCAQFGF 249
>pdb|4FVA|A Chain A, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|B Chain B, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|C Chain C, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|D Chain D, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
Length = 256
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 34 YREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDFRSGKLNSLQKH 93
Y + +K V K DV ++ G RT LQ++ G+I G+ + L S ++H
Sbjct: 79 YYTAILVSKMFDVEKHDVIHFQNSGM-YRT----LQILEGSIGGLKVFLLNTHLESTREH 133
Query: 94 RNKQRGNQFEY 104
R QR QF +
Sbjct: 134 R-PQRCAQFGF 143
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
0.318 0.137 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,039,453
Number of Sequences: 62578
Number of extensions: 108162
Number of successful extensions: 178
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 168
Number of HSP's gapped (non-prelim): 15
length of query: 104
length of database: 14,973,337
effective HSP length: 69
effective length of query: 35
effective length of database: 10,655,455
effective search space: 372940925
effective search space used: 372940925
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: 45 (21.9 bits)