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= 019469
(340 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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 185 PPGWQRLLRIRGEG-STKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
PPGW++ IR G S +DVYY +PSGKK RS ++ +Y V +S F F
Sbjct: 14 PPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGN-------AVDLSCFDF 66
Query: 244 QIPKPL 249
+ K +
Sbjct: 67 RTGKMM 72
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 176 IDKPNIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARA 234
+D P + PGW+R R G+T +D YY++P+G ++RS VE+ +Y +
Sbjct: 6 LDCPALG---PGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLTLF 62
Query: 235 GVKMSQFSFQIPK 247
K + PK
Sbjct: 63 DFKQGILCYPAPK 75
>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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 3/48 (6%)
Query: 185 PPGWQRLL--RIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPE 230
P GW+R++ R+ G+ + KF DVY+ +P G K RS + Y L++ E
Sbjct: 12 PCGWERVVKQRLSGKTAGKF-DVYFISPQGLKFRSKRSLANYLLKNGE 58
>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 = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 3/48 (6%)
Query: 185 PPGWQRLL--RIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPE 230
P GW+R++ R+ G+ + KF DVY+ +P G K RS + Y L++ E
Sbjct: 7 PCGWERVVKQRLSGKTAGKF-DVYFISPQGLKFRSKRSLANYLLKNGE 53
>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 = 35.0 bits (79), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 185 PPGWQRLLRIRGEG-STKFADVYYEAPSGKKLRSMVEIQKYF 225
P GW R L+ R G S DVY P GK RS VE+ YF
Sbjct: 25 PEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIXYF 66
>pdb|1QK9|A Chain A, The Solution Structure Of The Domain From Mecp2 That Binds
To Methylated Dna
Length = 92
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 185 PPGWQRLLRIRGEG-STKFADVYYEAPSGKKLRSMVEIQKYF 225
P GW R L+ R G S DVY P GK RS VE+ YF
Sbjct: 25 PEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYF 66
>pdb|1UB1|A Chain A, Solution Structure Of The Matrix Attachment Region-Binding
Domain Of Chicken Mecp2
Length = 133
Score = 34.7 bits (78), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 185 PPGWQRLLRIRGEG-STKFADVYYEAPSGKKLRSMVEIQKYF 225
P GW R L+ R G S DVY P GK RS VE+ YF
Sbjct: 39 PEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYF 80
>pdb|2L7P|A Chain A, Ashh2 A Cw Domain
Length = 100
Score = 29.3 bits (64), Expect = 3.1, Method: Composition-based stats.
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 117 VQCADCFKWRLIP 129
V+C DCFKWR IP
Sbjct: 29 VRCDDCFKWRRIP 41
>pdb|2SHP|A Chain A, Tyrosine Phosphatase Shp-2
pdb|2SHP|B Chain B, Tyrosine Phosphatase Shp-2
Length = 525
Score = 28.1 bits (61), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 16/89 (17%)
Query: 150 KAREW-RPDVSCDDPTDI----SQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFAD 204
K+R W P+++ + ++ DGS L K N PG L +R G+
Sbjct: 2 KSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSN-----PG-DLTLSVRRNGAVTHIK 55
Query: 205 V-----YYEAPSGKKLRSMVEIQKYFLEH 228
+ YY+ G+K ++ E+ +Y++EH
Sbjct: 56 IQNTGDYYDLYGGEKFATLAELVQYYMEH 84
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
0.313 0.132 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,074,858
Number of Sequences: 62578
Number of extensions: 490844
Number of successful extensions: 624
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 610
Number of HSP's gapped (non-prelim): 27
length of query: 340
length of database: 14,973,337
effective HSP length: 99
effective length of query: 241
effective length of database: 8,778,115
effective search space: 2115525715
effective search space used: 2115525715
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)