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= 045019
(248 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 = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 22/44 (50%), Positives = 31/44 (70%), Gaps = 1/44 (2%)
Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
LPPGW+ E+ +R SG +AG D YYF SG++FRSK ++ +L
Sbjct: 13 LPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYL 55
>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 = 0.008, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 101 TATEAW--LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVL-YFLETG 153
TATE +P GWE + R SG TAG D YF G +FRSK+ + Y L+ G
Sbjct: 3 TATEGHKPVPCGWERVVKQRLSGKTAGKFD-VYFISPQGLKFRSKRSLANYLLKNG 57
>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 = 37.0 bits (84), Expect = 0.011, Method: Composition-based stats.
Identities = 20/44 (45%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
L PGW+ + R SGAT G D YY +G R RSK E+ +L
Sbjct: 11 LGPGWKRREVFRKSGATCGRSDTYY-QSPTGDRIRSKVELTRYL 53
>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 = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVL-YFLETG 153
+P GWE + R SG TAG D YF G +FRSK+ + Y L+ G
Sbjct: 6 VPCGWERVVKQRLSGKTAGKFD-VYFISPQGLKFRSKRSLANYLLKNG 52
>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 = 34.7 bits (78), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
LP GW + + R SG +AG D Y + G+ FRSK E++ + E
Sbjct: 24 LPEGWTRKLKQRKSGRSAGKYDVYLIN-PQGKAFRSKVELIXYFE 67
>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 = 0.047, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
LP GW + + R SG +AG D Y + G+ FRSK E++ + E
Sbjct: 38 LPEGWTRKLKQRKSGRSAGKYDVYLIN-PQGKAFRSKVELIAYFE 81
>pdb|1QK9|A Chain A, The Solution Structure Of The Domain From Mecp2 That Binds
To Methylated Dna
Length = 92
Score = 34.7 bits (78), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
LP GW + + R SG +AG D Y + G+ FRSK E++ + E
Sbjct: 24 LPEGWTRKLKQRKSGRSAGKYDVYLIN-PQGKAFRSKVELIAYFE 67
>pdb|2WAF|A Chain A, Penicillin-Binding Protein 2b (Pbp-2b) From Streptococcus
Pneumoniae (Strain R6)
Length = 682
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 56/138 (40%), Gaps = 28/138 (20%)
Query: 18 HKPEPKESVNLFSTVN---------VPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKK 68
+ + K+ + LFS +N + DPL DS A A+ + TS
Sbjct: 167 YTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDS----QVAVIASISKEMPGISISTSWD 222
Query: 69 RGTIREHKSENLATTNGTESALTPETASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVD 128
R + S + + + ++ L E A EA+L G+ + DRV TS ++
Sbjct: 223 RKVLETSLSSIVGSVSSEKAGLPAEEA--------EAYLKKGYSLNDRVGTS-----YLE 269
Query: 129 KYYFHVASGRRFRSKKEV 146
K Y G+ RS KE+
Sbjct: 270 KQYEETLQGK--RSVKEI 285
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
0.309 0.125 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,231,363
Number of Sequences: 62578
Number of extensions: 271249
Number of successful extensions: 487
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 481
Number of HSP's gapped (non-prelim): 12
length of query: 248
length of database: 14,973,337
effective HSP length: 96
effective length of query: 152
effective length of database: 8,965,849
effective search space: 1362809048
effective search space used: 1362809048
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: 50 (23.9 bits)