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= 029175
(197 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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 87 RPGIPKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 143
R P P G+K+ V+RK K D YY +P+GKK R+ ++A +L + V L
Sbjct: 7 RTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLG-----NAVDL 61
Query: 144 SDFTFSVPKVM 154
S F F K+M
Sbjct: 62 SCFDFRTGKMM 72
>pdb|1UB1|A Chain A, Solution Structure Of The Matrix Attachment Region-Binding
Domain Of Chicken Mecp2
Length = 133
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 33/107 (30%), Positives = 44/107 (41%), Gaps = 20/107 (18%)
Query: 91 PKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL--SD 145
P P G+ R L RK K D Y I P GK R+ E+ + + D SL +D
Sbjct: 36 PTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFE---KVGDTSLDPND 92
Query: 146 FTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGDGTARDEG 192
F F+V +GS S +R PK +K G+ R G
Sbjct: 93 FDFTV------------TGRGSPSRREQRPPKKAKSPKSPGSGRGRG 127
>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 = 33.5 bits (75), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 94 PGGFKRSLVLR---KDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSV 150
P G++R + R K K D Y+I+P G K R+ +A +L N E + + DF F+V
Sbjct: 12 PCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGE-TFLKPEDFNFTV 70
>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 = 33.5 bits (75), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 93 TPGGFKRSLVLR---KDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFS 149
P G++R + R K K D Y+I+P G K R+ +A +L N E + + DF F+
Sbjct: 6 VPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGE-TFLKPEDFNFT 64
Query: 150 V 150
V
Sbjct: 65 V 65
>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 = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 96 GFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDF 146
G+KR V RK + D YY +PTG ++R+ E+ +L D++L DF
Sbjct: 14 GWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPA---CDLTLFDF 64
>pdb|1QK9|A Chain A, The Solution Structure Of The Domain From Mecp2 That Binds
To Methylated Dna
Length = 92
Score = 31.6 bits (70), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 91 PKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL--SD 145
P P G+ R L RK K D Y I P GK R+ E+ + + D SL +D
Sbjct: 22 PTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFE---KVGDTSLDPND 78
Query: 146 FTFSV 150
F F+V
Sbjct: 79 FDFTV 83
>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 = 30.8 bits (68), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 91 PKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL--SD 145
P P G+ R L RK K D Y I P GK R+ E+ + + D SL +D
Sbjct: 22 PTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIXYFE---KVGDTSLDPND 78
Query: 146 FTFSV 150
F F+V
Sbjct: 79 FDFTV 83
>pdb|1ZUN|B Chain B, Crystal Structure Of A Gtp-Regulated Atp Sulfurylase
Heterodimer From Pseudomonas Syringae
Length = 434
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 15 PRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPAD 74
P G ++SI T+ + E+ + + + E +EI ++ D P VS
Sbjct: 280 PSGKSSRVKSIVTFEGELEQAGPGQAVTLTXE-DEIDISRGDLLVHADNVPQVSDA---- 334
Query: 75 IEYDASRVWVIDRPGIPKTPGGFKRS 100
+DA VW + P +P KR+
Sbjct: 335 --FDAXLVWXAEEPXLPGKKYDIKRA 358
>pdb|1UXI|A Chain A, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-Dimer Interface
pdb|1UXI|B Chain B, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-Dimer Interface
pdb|1UXJ|A Chain A, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-dimer Interface
pdb|1UXJ|C Chain C, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-dimer Interface
Length = 309
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 28/62 (45%)
Query: 23 RSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRV 82
+++D Y A + F RV ++ + + + RKPG+S ED + D +R
Sbjct: 42 KALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRA 101
Query: 83 WV 84
+
Sbjct: 102 CI 103
>pdb|1UXH|A Chain A, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-Dimer Interface
pdb|1UXH|B Chain B, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-Dimer Interface
pdb|1UXK|A Chain A, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-dimer Interface
pdb|1UXK|C Chain C, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-dimer Interface
Length = 309
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 28/62 (45%)
Query: 23 RSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRV 82
+++D Y A + F RV ++ + + + RKPG+S ED + D +R
Sbjct: 42 KALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRA 101
Query: 83 WV 84
+
Sbjct: 102 CI 103
>pdb|1GUY|A Chain A, Structural Basis For Thermophilic Protein Stability:
Structures Of Thermophilic And Mesophilic Malate
Dehydrogenases
pdb|1GUY|C Chain C, Structural Basis For Thermophilic Protein Stability:
Structures Of Thermophilic And Mesophilic Malate
Dehydrogenases
pdb|1UXG|A Chain A, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-Dimer Interface.
pdb|1UXG|B Chain B, Large Improvement In The Thermal Stability Of A Tetrameric
Malate Dehydrogenase By Single Point Mutations At The
Dimer-Dimer Interface
Length = 309
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 28/62 (45%)
Query: 23 RSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRV 82
+++D Y A + F RV ++ + + + RKPG+S ED + D +R
Sbjct: 42 KALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRA 101
Query: 83 WV 84
+
Sbjct: 102 CI 103
>pdb|1UR5|A Chain A, Stabilization Of A Tetrameric Malate Dehydrogenase By
Introduction Of A Disulfide Bridge At The DimerDIMER
Interface
pdb|1UR5|C Chain C, Stabilization Of A Tetrameric Malate Dehydrogenase By
Introduction Of A Disulfide Bridge At The DimerDIMER
Interface
Length = 309
Score = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 28/62 (45%)
Query: 23 RSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRV 82
+++D Y A + F RV ++ + + + RKPG+S ED + D +R
Sbjct: 42 KALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRA 101
Query: 83 WV 84
+
Sbjct: 102 CI 103
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
0.314 0.133 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,336,871
Number of Sequences: 62578
Number of extensions: 265875
Number of successful extensions: 377
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 369
Number of HSP's gapped (non-prelim): 14
length of query: 197
length of database: 14,973,337
effective HSP length: 94
effective length of query: 103
effective length of database: 9,091,005
effective search space: 936373515
effective search space used: 936373515
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: 49 (23.5 bits)