Citrus Sinensis ID: 019505

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340
Protein Sequence
MQSHSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPSSTSSSASEGQSDETVEGDDQINGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPPVEAPISDPNPRPAKQARRAPKQMYSGSPISSDHKFRAEE
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccEEEEccccccccEEccHHHHHHHHHHcccccEEcccccccccccccccccccccccccEEEccccccccccccccEEEEEcccccccccEEEEEccccccEEcHHHHHHHHHHccccccccccccEEEEccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEcccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccccccccEEEEEEHHHcccEEEcccHHHHHHHHHHHcccccEccccccccccccccccccccccccEEEEEEcccccccccccEEEEEEEccccccccEEEEEcccccccccHHHHHHHHHHcHHHHcccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mqshsgkasVRVEKEANEFLGSSLLSnldeslhepidvpsstsssasegqsdetvegddqingdaskqlvlydptangtseiepvpesfqynrapfgrysgpntqsrvlpsvgaftVQCAdcfkwrliptkeKYEEIREHVlenpftcekarewrpdvscddptdisqdgsrlwaidkpniaqpppgwQRLLRirgegstkfadvyyeapsgkklRSMVEIQKYFLEHpeyaragvkmsqfsfqipkplqenyvrkrvpkahtshdtpkalepravsplswvspdnftdlqlgrpalpappveapisdpnprpakqarrapkqmysgspissdhkfraee
Flexible Loop (DISEMBL)
mqshsgkasvrVEKEANEFLGSSLLSNLDESLHEPIDvpsstsssasegqsdETVEGDDQINGDASKQLVLYDPTANgtseiepvpesFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVlenpftcekarewrpdvscddPTDISQDgsrlwaidkpniaqpppgWQRLLRIRGEGSTKFADVyyeapsgkklrSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRKRVpkahtshdtpkalepraVSPLSWVSPDNFTDLQLGRPALPAPpveapisdpnprpakqarrapkqmysgspissdhkfraee
Low Complexity Region (SEG)
MQSHSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPsstsssasegqsDETVEGDDQINGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPPVEAPISDPNPRPAKQARRAPKQMYSGSPISSDHKFRAEE
Disordered region (IsUnstruct)
**********************************************************************************************************RVLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSC**********SRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQI***********************************************************************************************
Disordered Region (DISOPRED)
*******************************************************************QLVL****************************************VGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF*************************************************************************************************
Disordered Region (DISEMBL)
**********RVEKEANEFLGSSLLSNLDESLHE***********************DDQINGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPPVEAPISD********************************
Disordered Region (DISPRO)
******KASVRVEKEANEFLGSS****************************************DASKQLVLYDPT********************************VLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQ***************************PLSW***********************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQSHSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPSSTSSSASEGQSDETVEGDDQINGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPPVEAPISDPNPRPAKQARRAPKQMYSGSPISSDHKFRAEE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	340	2.2.26 [Sep-21-2011]
Q8LA53	272	Methyl-CpG-binding domain	yes	no	0.708	0.886	0.538	1e-76
Q9FZP6	155	Putative methyl-CpG-bindi	no	no	0.391	0.858	0.527	1e-34
Q9LYB9	186	Methyl-CpG-binding domain	no	no	0.388	0.709	0.4	3e-25
Q5XEN5	204	Methyl-CpG-binding domain	no	no	0.429	0.715	0.408	5e-25
Q4PSK1	163	Methyl-CpG-binding domain	no	no	0.352	0.736	0.294	9e-10
Q9Z2E1	414	Methyl-CpG-binding domain	yes	no	0.194	0.159	0.384	0.0004
Q9UBB5	411	Methyl-CpG-binding domain	yes	no	0.194	0.160	0.384	0.0005

>sp|Q8LA53|MBD2_ARATH Methyl-CpG-binding domain-containing protein 2 OS=Arabidopsis thaliana GN=MBD2 PE=1 SV=1

 Score =  286 bits (733), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 139/258 (53%), Positives = 179/258 (69%), Gaps = 17/258 (6%)

Query: 68  QLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCFKWRL 127
           QLV+YD   N  +E E +P   Q           P +     PS+GAFTVQCA CFKWRL
Sbjct: 23  QLVVYDLKGNDDTEEEVLPVQSQ-----------PLSSRTQCPSIGAFTVQCASCFKWRL 71

Query: 128 IPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPG 187
           +P+ +KYEEIRE +LENPF C+ AREW+PD+SCD P DI QDG+RLWAIDKPNI++PP G
Sbjct: 72  MPSMQKYEEIREQLLENPFFCDTAREWKPDISCDVPADIYQDGTRLWAIDKPNISRPPAG 131

Query: 188 WQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPK 247
           WQRLLRIRGEG T+FADVYY APSGKKLRS VE+QKY  ++ EY   GVK+SQFSFQIPK
Sbjct: 132 WQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNSEYIGEGVKLSQFSFQIPK 191

Query: 248 PLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPPVEAPIS 307
           PLQ++YVRKR  +   S D       +  +PL+W+SPD+   LQLG       P E+ ++
Sbjct: 192 PLQDDYVRKRPARLLDSIDNTNTPVAKEANPLAWISPDDHISLQLG------TPTESGLN 245

Query: 308 DPNPRPAKQARRAPKQMY 325
           + + +P+K+ + +   ++
Sbjct: 246 NSHYQPSKKKKTSTLSIF 263

Probable transcriptional regulator.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FZP6|MBD12_ARATH Putative methyl-CpG-binding domain protein 12 OS=Arabidopsis thaliana GN=MBD12 PE=3 SV=1

 Score =  147 bits (371), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 76/144 (52%), Positives = 92/144 (63%), Gaps = 11/144 (7%)

Query: 117 VQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRL--W 174
           VQC DC KWRLIP+ + Y  I+E  L+ PF C     W P++SC+ P    QDG+    W
Sbjct: 2   VQCTDCKKWRLIPSMQHYNIIKETQLQTPFVCGTTSGWTPNMSCNVP----QDGTTCDTW 57

Query: 175 AIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARA 234
               P+I   P GW R + IR E STKFADVYY  PSG++LRS  E+Q +   HPEY R 
Sbjct: 58  ----PSIPPIPTGWSRSVHIRSE-STKFADVYYFPPSGERLRSSAEVQSFLDNHPEYVRE 112

Query: 235 GVKMSQFSFQIPKPLQENYVRKRV 258
           GV  SQFSFQIPKPL +NYV+KR 
Sbjct: 113 GVNRSQFSFQIPKPLDDNYVKKRT 136

Probable transcriptional regulator.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LYB9|MBD4_ARATH Methyl-CpG-binding domain-containing protein 4 OS=Arabidopsis thaliana GN=MBD4 PE=2 SV=1

 Score =  116 bits (290), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 56/140 (40%), Positives = 87/140 (62%), Gaps = 8/140 (5%)

Query: 112 VGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGS 171
           +  +  QC +C KWR+I ++E+YE+IR  +LE+PF C+K    +  +SC++P DI  D S
Sbjct: 25  IDTYAAQCDNCHKWRVIDSQEEYEDIRSKMLEDPFNCQK----KQGMSCEEPADIDYDSS 80

Query: 172 RLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEY 231
           R W IDKP + + P G++R L +R + S    D YY  P+GKKLRS  EI  +   +PE+
Sbjct: 81  RTWVIDKPGLPKTPKGFKRSLVLRKDYSK--MDTYYFTPTGKKLRSRNEIAAFVEANPEF 138

Query: 232 ARAGVKMSQFSFQIPKPLQE 251
             A   +  F+F +PK +++
Sbjct: 139 RNA--PLGDFNFTVPKVMED 156

Transcriptional regulator that binds CpG, CpNpN and CpNpG (N is A, T, or C) islands in promoters regardless the DNA methylation status. Plays probably a role in gene silencing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q5XEN5|MBD1_ARATH Methyl-CpG-binding domain-containing protein 1 OS=Arabidopsis thaliana GN=MBD1 PE=2 SV=1

 Score =  115 bits (288), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 65/159 (40%), Positives = 91/159 (57%), Gaps = 13/159 (8%)

Query: 111 SVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDG 170
           S+  F VQC  C KWR I T+++YE+IR  V E+PF C K +E    VSC+D  D++ D 
Sbjct: 51  SIDVFAVQCEKCMKWRKIDTQDEYEDIRSRVQEDPFFC-KTKE---GVSCEDVGDLNYDS 106

Query: 171 SRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPE 230
           SR W IDKP + + P G++R L +R + S    D YY  P+GKKL+S  EI  +   + +
Sbjct: 107 SRTWVIDKPGLPRTPRGFKRSLILRKDYSK--MDAYYITPTGKKLKSRNEIAAFIDANQD 164

Query: 231 YARAGVKMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPK 269
           Y  A   +  F+F +PK ++E      VP    S  TPK
Sbjct: 165 YKYA--LLGDFNFTVPKVMEET-----VPSGILSDRTPK 196

Probable transcriptional regulator.

Arabidopsis thaliana (taxid: 3702)

>sp|Q4PSK1|MBD3_ARATH Methyl-CpG-binding domain-containing protein 3 OS=Arabidopsis thaliana GN=MBD3 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 67/136 (49%), Gaps = 16/136 (11%)

Query: 112 VGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGS 171
           + ++  QC  C K R I ++E YEEIR   LE  F C++         C++P D+  +  
Sbjct: 9   IDSYAAQCWKCLKVRSIESQEDYEEIRSKTLEKFFECKR---------CEEPGDMVMNFD 59

Query: 172 RL---WAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYE--APSGKKLRSMVEIQKYFL 226
            L   W  D+ +I + P G +R+L +R        DVYYE  AP  K+ +S+ E+  +  
Sbjct: 60  SLTMRWFQDEHSIPKTPQGLKRVLVVRTNCVK--VDVYYESLAPRRKRFKSIKEVATFIE 117

Query: 227 EHPEYARAGVKMSQFS 242
           +  E+    ++   F+
Sbjct: 118 DKEEFKDMTLEEVSFA 133

Probable transcriptional regulator.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9Z2E1|MBD2_MOUSE Methyl-CpG-binding domain protein 2 OS=Mus musculus GN=Mbd2 PE=2 SV=2

 Score = 46.2 bits (108), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 41/78 (52%), Gaps = 12/78 (15%)

Query: 185 PPGWQRLLRIRGEG-STKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
           PPGW++   IR  G S   +DVYY +PSGKK RS  ++ +Y           V +S F F
Sbjct: 159 PPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGN-------AVDLSSFDF 211

Query: 244 Q----IPKPLQENYVRKR 257
           +    +P  LQ+N  R R
Sbjct: 212 RTGKMMPSKLQKNKQRLR 229

Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemi-methylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. May enhance the activation of some unmethylated cAMP-responsive promoters (By similarity). Selectively represses transcription activity of methylated rRNA promoters.

Mus musculus (taxid: 10090)

>sp|Q9UBB5|MBD2_HUMAN Methyl-CpG-binding domain protein 2 OS=Homo sapiens GN=MBD2 PE=1 SV=1

 Score = 45.8 bits (107), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 41/78 (52%), Gaps = 12/78 (15%)

Query: 185 PPGWQRLLRIRGEG-STKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
           PPGW++   IR  G S   +DVYY +PSGKK RS  ++ +Y           V +S F F
Sbjct: 156 PPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNT-------VDLSSFDF 208

Query: 244 Q----IPKPLQENYVRKR 257
           +    +P  LQ+N  R R
Sbjct: 209 RTGKMMPSKLQKNKQRLR 226

Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemi-methylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. May enhance the activation of some unmethylated cAMP-responsive promoters.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	340
225468218	354	PREDICTED: methyl-CpG-binding domain-con	0.979	0.940	0.608	1e-109
224118772	343	methyl binding domain protein [Populus t	0.970	0.962	0.614	1e-108
224087333	328	methyl binding domain protein [Populus t	0.929	0.963	0.586	1e-103
356520885	309	PREDICTED: methyl-CpG-binding domain-con	0.829	0.912	0.604	2e-95
449465348	342	PREDICTED: methyl-CpG-binding domain-con	0.797	0.792	0.637	1e-94
356496785	312	PREDICTED: methyl-CpG-binding domain-con	0.873	0.951	0.564	4e-92
255570564	271	DNA binding protein, putative [Ricinus c	0.785	0.985	0.641	2e-91
449508228	268	PREDICTED: methyl-CpG-binding domain-con	0.614	0.779	0.704	4e-82
297805084	278	hypothetical protein ARALYDRAFT_915661 [	0.714	0.874	0.540	7e-75
15238478	272	methyl-CPG-binding domain protein 02 [Ar	0.708	0.886	0.538	8e-75

>gi|225468218|ref|XP_002263085.1| PREDICTED: methyl-CpG-binding domain-containing protein 2 [Vitis vinifera] gi|297736061|emb|CBI24099.3| unnamed protein product [Vitis vinifera]

 Score =  402 bits (1033), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 210/345 (60%), Positives = 238/345 (68%), Gaps = 12/345 (3%)

Query: 4   HSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPSSTSSSASEGQSDETVEGDDQING 63
           H GK   +  KE N+  GSSL   LD +L  PID+ SS          ++      +   
Sbjct: 3   HPGKIYRKANKEENDLTGSSLPRYLD-ALQVPIDLSSSEEEEEDFYAEEDDDNHSYE--- 58

Query: 64  DASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCF 123
           + S QLV+YDP AN  +E+EPVP+  QY    F  YS  N  SRVLPSVGAFTVQCA+CF
Sbjct: 59  NTSNQLVVYDPVANSATEVEPVPDPIQYRLPSFTGYSTTNAPSRVLPSVGAFTVQCANCF 118

Query: 124 KWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQ 183
           KWRLIPTKEKYEEIREH+LE PF CE AREWRP+VSCDDP DISQDGSRLWAIDKPNIAQ
Sbjct: 119 KWRLIPTKEKYEEIREHILEQPFVCETAREWRPNVSCDDPADISQDGSRLWAIDKPNIAQ 178

Query: 184 PPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
           PP GWQRLLRIRGEGSTKFADVYY APSGK+LRSMVE+QKY LEHPEY   GV +SQFSF
Sbjct: 179 PPAGWQRLLRIRGEGSTKFADVYYVAPSGKRLRSMVEVQKYLLEHPEYMVHGVTLSQFSF 238

Query: 244 QIPKPLQENYVRKRVPKAH-------TSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPA 296
           QIPKPLQENYVRKR  + +       TS    + LEP  V+PLSW  P    DLQL  P 
Sbjct: 239 QIPKPLQENYVRKRPARVNAGSYDDTTSSGMSRPLEPGEVNPLSWAGPAECIDLQLRTPG 298

Query: 297 LPAPPVEAPISDPNPRPAKQARRA-PKQMYSGSPISSDHKFRAEE 340
           L AP  EAP+ DP  RP KQARR  P+ MY  + + +  K + EE
Sbjct: 299 LSAPYFEAPVFDPVSRPTKQARRTLPRDMYDSNMVYNQQKVKVEE 343

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118772|ref|XP_002331442.1| methyl binding domain protein [Populus trichocarpa] gi|222873656|gb|EEF10787.1| methyl binding domain protein [Populus trichocarpa]

 Score =  399 bits (1025), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 210/342 (61%), Positives = 251/342 (73%), Gaps = 12/342 (3%)

Query: 1   MQSHSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPSSTSSSASEGQSDETVEGDDQ 60
           MQSH G+    ++KE ++  GS    +L+ SL EPI+V SS++   S+    +T + DDQ
Sbjct: 1   MQSHPGETFHVLKKEGDDCTGSRYTGHLNSSLQEPIEVSSSSNEDNSD----DTWDIDDQ 56

Query: 61  INGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCA 120
              D+SKQLVLYDP AN   EIEPVP+    +  PF RYS  N  SRVLPSVGAFTVQCA
Sbjct: 57  SIEDSSKQLVLYDPLANDAGEIEPVPQPI-LSHHPFRRYSDLNVPSRVLPSVGAFTVQCA 115

Query: 121 DCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPN 180
            CFKWRLIPTK+KYEE+REH+LE PF CE AREWRPD+SCDDPTDI QDGSRLWAIDKPN
Sbjct: 116 KCFKWRLIPTKQKYEELREHILEEPFFCETAREWRPDISCDDPTDIDQDGSRLWAIDKPN 175

Query: 181 IAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQ 240
           IAQPPPGWQRLLRIRGEGSTKFADVYY+APSGK+LRSMVEIQKY +EHPEY R G+ ++Q
Sbjct: 176 IAQPPPGWQRLLRIRGEGSTKFADVYYQAPSGKRLRSMVEIQKYLIEHPEYMRDGITLTQ 235

Query: 241 FSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPA-LPA 299
           FSFQIPKPLQENYVRK+ P+   S      LEP   +PL WV P + T+LQLGRPA LP 
Sbjct: 236 FSFQIPKPLQENYVRKKRPRLSAS-----CLEPGEANPLKWVGPGDCTELQLGRPAILPP 290

Query: 300 PPVEAPISDPNPRPAKQARRAP-KQMYSGSPISSDHKFRAEE 340
           P +++    P   P K+  R P KQ +  +P+ +  + + EE
Sbjct: 291 PLIQSSAYLPFYWPVKKKARTPSKQSHRTNPVCNLDEPKVEE 332

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224087333|ref|XP_002308125.1| methyl binding domain protein [Populus trichocarpa] gi|222854101|gb|EEE91648.1| methyl binding domain protein [Populus trichocarpa]

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 200/341 (58%), Positives = 239/341 (70%), Gaps = 25/341 (7%)

Query: 1   MQSHSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPSSTSSSASEGQSDETVEGDDQ 60
           MQS   +    V+KEA+    S    +L  +L EPI+V     SS++E  S +T + DD 
Sbjct: 1   MQSRPEETIRMVKKEADCCTDSCHTGHLQSTLQEPIEV-----SSSNEDNSHDTGDIDDP 55

Query: 61  INGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCA 120
              D+SKQLVLYDP  NG  +IEPVP+  Q+ R PF RYS PN  SRVLPSVG FTVQCA
Sbjct: 56  SIEDSSKQLVLYDPVTNGAGQIEPVPQPIQFQR-PFRRYSDPNVPSRVLPSVGTFTVQCA 114

Query: 121 DCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPN 180
            CFKWRLIPTK+KYEE+REH+LE PF CE AR WRPD+SCDDPTDI+QDGSRLWAIDKPN
Sbjct: 115 KCFKWRLIPTKKKYEELREHILEEPFFCETARGWRPDISCDDPTDITQDGSRLWAIDKPN 174

Query: 181 IAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQ 240
           IAQPPPGWQRLLRIRGEGS+KFADVYY++PSGK+LRSMVE+QKY +EHPEY   GV +SQ
Sbjct: 175 IAQPPPGWQRLLRIRGEGSSKFADVYYQSPSGKRLRSMVEVQKYLIEHPEYMTYGVTLSQ 234

Query: 241 FSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAP 300
           FSFQIPKPLQENYVRKR P    S D  + L+P            +FT+LQLGRPA  +P
Sbjct: 235 FSFQIPKPLQENYVRKRRPSISASCDYTRHLQP---------GEGDFTELQLGRPA--SP 283

Query: 301 PVEAPISDPNPRPAKQARRAPKQMY-SGSPISSDHKFRAEE 340
             + P+        K+A    KQ Y + +P+ +    + EE
Sbjct: 284 SFDRPVK-------KKAGTQSKQDYRTANPVCNQDGAKVEE 317

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356520885|ref|XP_003529090.1| PREDICTED: methyl-CpG-binding domain-containing protein 2-like [Glycine max]

 Score =  355 bits (910), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 180/298 (60%), Positives = 210/298 (70%), Gaps = 16/298 (5%)

Query: 4   HSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPSSTSSSASEGQSDETVEGDDQING 63
           H GK S+  + E  +  GSSL S    SL +PIDV SS+             + +D  N 
Sbjct: 2   HRGKFSLTPKNEVKDLTGSSLTSYKHSSLLDPIDVSSSSD------------DENDLPND 49

Query: 64  DASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCF 123
           D S QLVLYDP ANG + IE  P+  Q       R    ++  RVLPSVGAFTVQCA CF
Sbjct: 50  DVSNQLVLYDPVANGNNAIELAPDPLQCEHPLLPRSKPSHSVPRVLPSVGAFTVQCASCF 109

Query: 124 KWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQ 183
           KWRLIPTKEKYEEIREH+LE PF C+KAREWRP VSCDDP DISQDGSR+WAIDKPNIAQ
Sbjct: 110 KWRLIPTKEKYEEIREHILEQPFVCQKAREWRPHVSCDDPEDISQDGSRVWAIDKPNIAQ 169

Query: 184 PPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
           PP GW+RLLRIR EGS+KFAD+YY APSGK+LRSMVEIQK+ +EHPEY R GV +SQFSF
Sbjct: 170 PPAGWERLLRIRAEGSSKFADIYYIAPSGKRLRSMVEIQKFLMEHPEYTRDGVTLSQFSF 229

Query: 244 QIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPP 301
           QIP+PLQENYVRKR  +  +S++  + +E   VSPL+WV P+        R  LPAPP
Sbjct: 230 QIPRPLQENYVRKRPARLTSSYEVSEPVEHEQVSPLAWVDPEGHG----RRLGLPAPP 283

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465348|ref|XP_004150390.1| PREDICTED: methyl-CpG-binding domain-containing protein 2-like [Cucumis sativus]

 Score =  352 bits (903), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 174/273 (63%), Positives = 206/273 (75%), Gaps = 2/273 (0%)

Query: 60  QINGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQC 119
           Q N + S++LV+YDP+A+     +PV    +   +P   +  PN+ SRVLPSVGAFTVQC
Sbjct: 55  QSNDNPSRELVIYDPSADDGHANDPVSTPVKQQPSPVLGHLTPNS-SRVLPSVGAFTVQC 113

Query: 120 ADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKP 179
           A CFKWRLIPTKEKYEEIREH+LE PF CE AR WRPD+SCDDP DI+QDGSRLWAIDKP
Sbjct: 114 AGCFKWRLIPTKEKYEEIREHLLEKPFYCETARGWRPDISCDDPADITQDGSRLWAIDKP 173

Query: 180 NIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMS 239
           NIAQPPPGWQRLL IRGEGSTKFADVYY APSGKKLRSMV+IQKY +EHPEY   GV M+
Sbjct: 174 NIAQPPPGWQRLLHIRGEGSTKFADVYYTAPSGKKLRSMVDIQKYLIEHPEYQTEGVSMT 233

Query: 240 QFSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPA 299
           +FSFQIPKPL+E+YVRKR P  + S D  K LE   V P+SW  PD+ T LQLG+P L  
Sbjct: 234 RFSFQIPKPLREDYVRKRRPNMNASCDASK-LESGEVRPISWARPDDSTALQLGKPGLTE 292

Query: 300 PPVEAPISDPNPRPAKQARRAPKQMYSGSPISS 332
               +P+++P  RPAK+ +RA  Q    S ++S
Sbjct: 293 LLSTSPVNNPVTRPAKKVKRALAQEMRRSSLTS 325

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496785|ref|XP_003517246.1| PREDICTED: methyl-CpG-binding domain-containing protein 2-like [Glycine max]

 Score =  344 bits (882), Expect = 4e-92,   Method: Compositional matrix adjust.
 Identities = 180/319 (56%), Positives = 217/319 (68%), Gaps = 22/319 (6%)

Query: 4   HSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPSSTSSSASEGQSDETVEGDDQING 63
           + GK S+  + E  +  GSS  S    S  +PIDV SS+         DE    +D  N 
Sbjct: 2   YHGKFSLTPKNEVKDLTGSSFPSYKHSSQLDPIDVSSSSD--------DE----NDLPND 49

Query: 64  DASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCF 123
           D S QLVLYDP ANG + IE  P+  Q       R    ++  R LPSVG FTVQCA C 
Sbjct: 50  DVSNQLVLYDPVANGNNAIELAPDPLQCEPPLLPRSKPSHSVPRALPSVGVFTVQCASCL 109

Query: 124 KWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQ 183
           KWRLIPTKEKYEEIREH++E PF C+KAREWRPDVSCDDP DISQDGSR+WAIDKPNIAQ
Sbjct: 110 KWRLIPTKEKYEEIREHIIEQPFVCQKAREWRPDVSCDDPEDISQDGSRVWAIDKPNIAQ 169

Query: 184 PPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
           PP GW+RLLRIR EGS+KFAD+YY APSGK+LRSMVE+QK+ +EHPEY R GV +SQFSF
Sbjct: 170 PPAGWERLLRIRAEGSSKFADIYYIAPSGKRLRSMVEVQKFLMEHPEYTRDGVTLSQFSF 229

Query: 244 QIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPP-- 301
           QIP+PLQENYVRKR  +  +S++  + +E + VSPL+WV P+       GR  LP PP  
Sbjct: 230 QIPRPLQENYVRKRSARLTSSYEVSEPVEHQQVSPLAWVDPEGCG----GRLGLPPPPFM 285

Query: 302 ----VEAPISDPNPRPAKQ 316
               ++  I+    RPAK+
Sbjct: 286 GSHDLDTTINMSISRPAKR 304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255570564|ref|XP_002526239.1| DNA binding protein, putative [Ricinus communis] gi|223534433|gb|EEF36136.1| DNA binding protein, putative [Ricinus communis]

 Score =  342 bits (877), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 175/273 (64%), Positives = 207/273 (75%), Gaps = 6/273 (2%)

Query: 1   MQSHSGKASVRVEKEANEFLGSSLLSNLDESLHEPIDVPSSTSSSASEGQSDETVEGDDQ 60
           MQS  G+AS+ ++KEA ++  SS  +      H  +  P   SSS+ E  S ET + ++Q
Sbjct: 1   MQSPPGEASLSIKKEAIDYSSSSFAA------HSNLQSPVEVSSSSEEDNSHETEDANEQ 54

Query: 61  INGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCA 120
              +ASKQ+VLYDP ANG+ +IE VP+  Q    P  R  G    SRVLPSVGAFTVQCA
Sbjct: 55  STENASKQIVLYDPVANGSGQIEIVPQPLQCRPHPSARRPGFLMHSRVLPSVGAFTVQCA 114

Query: 121 DCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPN 180
            CFKWRLIPTKEKYEEIREH+LE PF CE AREWRPD+SC+DP DISQDGSRLWAIDKPN
Sbjct: 115 KCFKWRLIPTKEKYEEIREHILEQPFYCETAREWRPDISCNDPADISQDGSRLWAIDKPN 174

Query: 181 IAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQ 240
           IAQPP GWQRLLRIRGEGS+KFADVYY+APSGK+LRSMVEI++Y + +PEY + GVK+SQ
Sbjct: 175 IAQPPRGWQRLLRIRGEGSSKFADVYYQAPSGKRLRSMVEIERYLMANPEYVQNGVKLSQ 234

Query: 241 FSFQIPKPLQENYVRKRVPKAHTSHDTPKALEP 273
           FSFQIP+PLQENYVRKR  +   S D  + LEP
Sbjct: 235 FSFQIPRPLQENYVRKRPARLTASCDNIRPLEP 267

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449508228|ref|XP_004163256.1| PREDICTED: methyl-CpG-binding domain-containing protein 2-like, partial [Cucumis sativus]

 Score =  311 bits (796), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 148/210 (70%), Positives = 169/210 (80%), Gaps = 1/210 (0%)

Query: 60  QINGDASKQLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQC 119
           Q N + S++LV+YDP+A+     +PV    +   +P   +  PN+ SRVLPSVGAFTVQC
Sbjct: 55  QSNDNPSRELVIYDPSADDGHANDPVSTPVKQQPSPVLGHLTPNS-SRVLPSVGAFTVQC 113

Query: 120 ADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKP 179
           A CFKWRLIPTKEKYEEIREH+LE PF CE AR WRPD+SCDDP DI+QDGSRLWAIDKP
Sbjct: 114 AGCFKWRLIPTKEKYEEIREHLLEKPFYCETARGWRPDISCDDPADITQDGSRLWAIDKP 173

Query: 180 NIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMS 239
           NIAQPPPGWQRLL IRGEGSTKFADVYY APSGKKLRSMV+IQKY +EHPEY   GV M+
Sbjct: 174 NIAQPPPGWQRLLHIRGEGSTKFADVYYTAPSGKKLRSMVDIQKYLIEHPEYQTEGVSMT 233

Query: 240 QFSFQIPKPLQENYVRKRVPKAHTSHDTPK 269
           +FSFQIPKPL+E+YVRKR P  + S D  K
Sbjct: 234 RFSFQIPKPLREDYVRKRRPNMNASCDASK 263

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297805084|ref|XP_002870426.1| hypothetical protein ARALYDRAFT_915661 [Arabidopsis lyrata subsp. lyrata] gi|297316262|gb|EFH46685.1| hypothetical protein ARALYDRAFT_915661 [Arabidopsis lyrata subsp. lyrata]

 Score =  286 bits (733), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 141/261 (54%), Positives = 184/261 (70%), Gaps = 18/261 (6%)

Query: 68  QLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCFKWRL 127
           QLV+YD   N T E E +P   Q           P+++++  PS+GAFTVQCA CFKWRL
Sbjct: 30  QLVVYDLKGNDTEE-EVLPIQSQL----------PSSRTQC-PSIGAFTVQCASCFKWRL 77

Query: 128 IPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPG 187
           +P+ +KYEEIRE +LENPF CE AREW+PD+SCD P DI QDG+R+WAIDKPNI++PP G
Sbjct: 78  MPSMQKYEEIREQLLENPFFCETAREWKPDISCDVPADIYQDGTRVWAIDKPNISRPPAG 137

Query: 188 WQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPK 247
           WQRLLRIRGEG T+FADVYY APSGKKLRS VE+QKY  ++PEY   GVK+SQFSFQIPK
Sbjct: 138 WQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNPEYMSEGVKLSQFSFQIPK 197

Query: 248 PLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPPVEAPIS 307
           PLQ++YVRKR  +   S D       +  +PL+W+SPD+   LQLG       P E+ + 
Sbjct: 198 PLQDDYVRKRPARLVDSIDNTNTHVAKEANPLAWISPDDHIALQLG------TPTESGLY 251

Query: 308 DPNPRPAKQARRAPKQMYSGS 328
           + + +P+K+ + +   ++  +
Sbjct: 252 NSHDQPSKKRKTSKLSIFGAN 272

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15238478|ref|NP_198383.1| methyl-CPG-binding domain protein 02 [Arabidopsis thaliana] gi|42573507|ref|NP_974850.1| methyl-CPG-binding domain protein 02 [Arabidopsis thaliana] gi|334188017|ref|NP_001190421.1| methyl-CPG-binding domain protein 02 [Arabidopsis thaliana] gi|75154716|sp|Q8LA53.1|MBD2_ARATH RecName: Full=Methyl-CpG-binding domain-containing protein 2; Short=AtMBD2; Short=MBD02; AltName: Full=Methyl-CpG-binding protein MBD2 gi|21593605|gb|AAM65572.1| unknown [Arabidopsis thaliana] gi|107738396|gb|ABF83690.1| At5g35330 [Arabidopsis thaliana] gi|332006569|gb|AED93952.1| methyl-CPG-binding domain protein 02 [Arabidopsis thaliana] gi|332006570|gb|AED93953.1| methyl-CPG-binding domain protein 02 [Arabidopsis thaliana] gi|332006571|gb|AED93954.1| methyl-CPG-binding domain protein 02 [Arabidopsis thaliana]

 Score =  286 bits (733), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 139/258 (53%), Positives = 179/258 (69%), Gaps = 17/258 (6%)

Query: 68  QLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVGAFTVQCADCFKWRL 127
           QLV+YD   N  +E E +P   Q           P +     PS+GAFTVQCA CFKWRL
Sbjct: 23  QLVVYDLKGNDDTEEEVLPVQSQ-----------PLSSRTQCPSIGAFTVQCASCFKWRL 71

Query: 128 IPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPG 187
           +P+ +KYEEIRE +LENPF C+ AREW+PD+SCD P DI QDG+RLWAIDKPNI++PP G
Sbjct: 72  MPSMQKYEEIREQLLENPFFCDTAREWKPDISCDVPADIYQDGTRLWAIDKPNISRPPAG 131

Query: 188 WQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPK 247
           WQRLLRIRGEG T+FADVYY APSGKKLRS VE+QKY  ++ EY   GVK+SQFSFQIPK
Sbjct: 132 WQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNSEYIGEGVKLSQFSFQIPK 191

Query: 248 PLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALPAPPVEAPIS 307
           PLQ++YVRKR  +   S D       +  +PL+W+SPD+   LQLG       P E+ ++
Sbjct: 192 PLQDDYVRKRPARLLDSIDNTNTPVAKEANPLAWISPDDHISLQLG------TPTESGLN 245

Query: 308 DPNPRPAKQARRAPKQMY 325
           + + +P+K+ + +   ++
Sbjct: 246 NSHYQPSKKKKTSTLSIF 263

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	340
TAIR|locus:2182643	272	MBD02 "methyl-CPG-binding doma	0.770	0.963	0.517	4.8e-71
TAIR|locus:504954793	155	MBD12 "methyl-CPG-binding doma	0.388	0.851	0.531	6.5e-35
TAIR|locus:2099187	186	MBD4 "methyl-CPG-binding domai	0.432	0.790	0.382	3.5e-27
TAIR|locus:505006513	204	MBD1 "methyl-CPG-binding domai	0.429	0.715	0.408	1.4e-25
TAIR|locus:505006418	163	MBD3 "methyl-CPG-binding domai	0.402	0.840	0.303	2.7e-12
RGD|1305980	533	Mbd1 "methyl-CpG binding domai	0.376	0.240	0.301	0.00016
UNIPROTKB|H7C092	194	BAZ2B "Bromodomain adjacent to	0.188	0.329	0.432	0.00068

TAIR|locus:2182643 MBD02 "methyl-CPG-binding domain protein 02" [Arabidopsis thaliana (taxid:3702)]

 Score = 719 (258.2 bits), Expect = 4.8e-71, P = 4.8e-71
 Identities = 145/280 (51%), Positives = 188/280 (67%)

Query:    55 VEGDDQINGDASK-QLVLYDPTANGTSEIEPVPESFQYNRAPFGRYSGPNTQSRVLPSVG 113
             V+     N D  + QLV+YD   N  +E E +P   Q    P        TQ    PS+G
Sbjct:     9 VQRSSSPNEDRGENQLVVYDLKGNDDTEEEVLPVQSQ----PLSS----RTQC---PSIG 57

Query:   114 AFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRL 173
             AFTVQCA CFKWRL+P+ +KYEEIRE +LENPF C+ AREW+PD+SCD P DI QDG+RL
Sbjct:    58 AFTVQCASCFKWRLMPSMQKYEEIREQLLENPFFCDTAREWKPDISCDVPADIYQDGTRL 117

Query:   174 WAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYAR 233
             WAIDKPNI++PP GWQRLLRIRGEG T+FADVYY APSGKKLRS VE+QKY  ++ EY  
Sbjct:   118 WAIDKPNISRPPAGWQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNSEYIG 177

Query:   234 AGVKMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLG 293
              GVK+SQFSFQIPKPLQ++YVRKR  +   S D       +  +PL+W+SPD+   LQLG
Sbjct:   178 EGVKLSQFSFQIPKPLQDDYVRKRPARLLDSIDNTNTPVAKEANPLAWISPDDHISLQLG 237

Query:   294 RPALPAPPVEAPISDPNPRPAKQARRAPKQMYSGSPISSD 333
              P       E+ +++ + +P+K+ + +   ++  +   +D
Sbjct:   238 TPT------ESGLNNSHYQPSKKKKTSTLSIFGSNDELAD 271

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051747 "cytosine C-5 DNA demethylase activity" evidence=IDA

GO:0019899 "enzyme binding" evidence=IPI

TAIR|locus:504954793 MBD12 "methyl-CPG-binding domain 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 378 (138.1 bits), Expect = 6.5e-35, P = 6.5e-35
 Identities = 76/143 (53%), Positives = 92/143 (64%)

Query:   117 VQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRL--W 174
             VQC DC KWRLIP+ + Y  I+E  L+ PF C     W P++SC+ P    QDG+    W
Sbjct:     2 VQCTDCKKWRLIPSMQHYNIIKETQLQTPFVCGTTSGWTPNMSCNVP----QDGTTCDTW 57

Query:   175 AIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARA 234
                 P+I   P GW R + IR E STKFADVYY  PSG++LRS  E+Q +   HPEY R 
Sbjct:    58 ----PSIPPIPTGWSRSVHIRSE-STKFADVYYFPPSGERLRSSAEVQSFLDNHPEYVRE 112

Query:   235 GVKMSQFSFQIPKPLQENYVRKR 257
             GV  SQFSFQIPKPL +NYV+KR
Sbjct:   113 GVNRSQFSFQIPKPLDDNYVKKR 135

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008327 "methyl-CpG binding" evidence=ISS

TAIR|locus:2099187 MBD4 "methyl-CPG-binding domain 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 60/157 (38%), Positives = 94/157 (59%)

Query:    97 GRYSGPNTQSRVLPS--VGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREW 154
             G+ + P  +  V P   +  +  QC +C KWR+I ++E+YE+IR  +LE+PF C+K    
Sbjct:     8 GKPAKPKAKKDVAPGRLIDTYAAQCDNCHKWRVIDSQEEYEDIRSKMLEDPFNCQK---- 63

Query:   155 RPDVSCDDPTDISQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKK 214
             +  +SC++P DI  D SR W IDKP + + P G++R L +R + S    D YY  P+GKK
Sbjct:    64 KQGMSCEEPADIDYDSSRTWVIDKPGLPKTPKGFKRSLVLRKDYSKM--DTYYFTPTGKK 121

Query:   215 LRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQE 251
             LRS  EI  +   +PE+  A   +  F+F +PK +++
Sbjct:   122 LRSRNEIAAFVEANPEFRNA--PLGDFNFTVPKVMED 156

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008327 "methyl-CpG binding" evidence=ISS

GO:0051747 "cytosine C-5 DNA demethylase activity" evidence=IDA

TAIR|locus:505006513 MBD1 "methyl-CPG-binding domain 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 65/159 (40%), Positives = 91/159 (57%)

Query:   111 SVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDG 170
             S+  F VQC  C KWR I T+++YE+IR  V E+PF C K +E    VSC+D  D++ D 
Sbjct:    51 SIDVFAVQCEKCMKWRKIDTQDEYEDIRSRVQEDPFFC-KTKE---GVSCEDVGDLNYDS 106

Query:   171 SRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPE 230
             SR W IDKP + + P G++R L +R + S    D YY  P+GKKL+S  EI  +   + +
Sbjct:   107 SRTWVIDKPGLPRTPRGFKRSLILRKDYSKM--DAYYITPTGKKLKSRNEIAAFIDANQD 164

Query:   231 YARAGVKMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPK 269
             Y  A   +  F+F +PK ++E      VP    S  TPK
Sbjct:   165 YKYA--LLGDFNFTVPKVMEET-----VPSGILSDRTPK 196

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0008327 "methyl-CpG binding" evidence=ISS

GO:0051747 "cytosine C-5 DNA demethylase activity" evidence=IDA

TAIR|locus:505006418 MBD3 "methyl-CPG-binding domain 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 169 (64.5 bits), Expect = 2.7e-12, P = 2.7e-12
 Identities = 48/158 (30%), Positives = 81/158 (51%)

Query:   112 VGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGS 171
             + ++  QC  C K R I ++E YEEIR   LE  F C++         C++P D+  +  
Sbjct:     9 IDSYAAQCWKCLKVRSIESQEDYEEIRSKTLEKFFECKR---------CEEPGDMVMNFD 59

Query:   172 RL---WAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVYYE--APSGKKLRSMVEIQKYFL 226
              L   W  D+ +I + P G +R+L +R     K  DVYYE  AP  K+ +S+ E+  +  
Sbjct:    60 SLTMRWFQDEHSIPKTPQGLKRVLVVR-TNCVK-VDVYYESLAPRRKRFKSIKEVATFIE 117

Query:   227 EHPEYARAGVKMSQFSFQIPKPLQENYVRKRVPKAHTS 264
             +  E+    + + + SF  PK L+   ++K+   +H+S
Sbjct:   118 DKEEFK--DMTLEEVSFAAPKRLK---LKKKPVDSHSS 150

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008327 "methyl-CpG binding" evidence=ISS

RGD|1305980 Mbd1 "methyl-CpG binding domain protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 122 (48.0 bits), Expect = 0.00016, P = 0.00016
 Identities = 41/136 (30%), Positives = 60/136 (44%)

Query:   186 PGWQRLLRIRGEG-STKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQ 244
             PGW+R    R  G S   +D+YY +P+G+K+RS +E+ +Y     +      +       
Sbjct:    13 PGWKRREAFRKSGASCGRSDIYYRSPTGEKIRSKIELTRYLGPACDLTLFDFRQGILCHP 72

Query:   245 IPK--PLQENYVRKRV---P-KAHTSHDTPKALEPRAVSPLSWVSPDNFTDLQLGRPALP 298
             +PK  PL     +K+    P KA      P+  E R  +P         T L     + P
Sbjct:    73 VPKTHPLAVPSKKKKKTSKPAKAKKQQVGPQRSEVRKETPREGNKVAPATALLPVTASAP 132

Query:   299 APPVEAPISDPNPRPA 314
             AP V  P+S P P PA
Sbjct:   133 AP-VPVPVSAPAPAPA 147

GO:0000785 "chromatin" evidence=ISO

GO:0000792 "heterochromatin" evidence=IEA;ISO

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA;ISO

GO:0016607 "nuclear speck" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|H7C092 BAZ2B "Bromodomain adjacent to zinc finger domain protein 2B" [Homo sapiens (taxid:9606)]

 Score = 108 (43.1 bits), Expect = 0.00068, P = 0.00068
 Identities = 29/67 (43%), Positives = 35/67 (52%)

Query:   161 DDPTDISQDGS--RLWAIDKPNIAQPPP-GWQRLLRIRGEGSTKFADVYYEAPSGKKLRS 217
             DD +D SQ G+  R    D+  +  P   GWQR  RIR  G     +V Y AP GKKLR 
Sbjct:    57 DDESDDSQSGTSKRRRVTDERELRIPLEYGWQRETRIRNFGGRLQGEVAYYAPCGKKLRQ 116

Query:   218 MVEIQKY 224
               E+ KY
Sbjct:   117 YPEVIKY 123


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.313   0.132   0.399    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      340       328   0.00088  116 3  11 23  0.46    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  616 (65 KB)
  Total size of DFA:  249 KB (2134 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  32.89u 0.14s 33.03t   Elapsed:  00:00:01
  Total cpu time:  32.89u 0.14s 33.03t   Elapsed:  00:00:01
  Start:  Mon May 20 16:02:51 2013   End:  Mon May 20 16:02:52 2013

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8LA53	MBD2_ARATH	No assigned EC number	0.5387	0.7088	0.8860	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	340
cd01396	77	cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and M	1e-23
cd00122	62	cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8	3e-17
pfam07496	50	pfam07496, zf-CW, CW-type Zinc Finger	8e-12
pfam01429	75	pfam01429, MBD, Methyl-CpG binding domain	2e-10
smart00391	77	smart00391, MBD, Methyl-CpG binding domain	1e-09
cd01397	73	cd01397, HAT_MBD, Methyl-CpG binding domains (MBD)	2e-06
cd01395	60	cd01395, HMT_MBD, Methyl-CpG binding domains (MBD)	2e-05

>gnl|CDD|238690 cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD)

 Score = 92.1 bits (229), Expect = 1e-23
 Identities = 31/80 (38%), Positives = 43/80 (53%), Gaps = 3/80 (3%)

Query: 178 KPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVK 237
           KP   + PPGW+R L  R  GS    DVYY +P+GKK RS VE+ +Y  ++       + 
Sbjct: 1   KPEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGP---TSLD 57

Query: 238 MSQFSFQIPKPLQENYVRKR 257
           +S F F +PK L     R+ 
Sbjct: 58  LSDFDFTVPKKLGLGSPRRH 77

The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. Length = 77

>gnl|CDD|238069 cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD)

 Score = 74.3 bits (183), Expect = 3e-17
 Identities = 26/60 (43%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 184 PPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
            PPGW+R L IR  GS    DVYY +P GKKLRS  E+ +Y  +      + + +  FSF
Sbjct: 6   LPPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTG---PSSLDLENFSF 62

The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family. Length = 62

>gnl|CDD|219431 pfam07496, zf-CW, CW-type Zinc Finger

 Score = 59.0 bits (143), Expect = 8e-12
 Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 4/53 (7%)

Query: 115 FTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDIS 167
           + VQC  C KWR +P  E+YEEIR  + + P+ C          SCDDP +I 
Sbjct: 2   YWVQCDKCLKWRKLP--EEYEEIRSKLPD-PWFCSMNP-DPAYNSCDDPEEIE 50

This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found. Length = 50

>gnl|CDD|216497 pfam01429, MBD, Methyl-CpG binding domain

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 25/61 (40%), Positives = 37/61 (60%), Gaps = 6/61 (9%)

Query: 185 PPGWQRLLRIRGEGST--KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFS 242
           PPGW+R  R R  GS+  K  DVYY +P+GKK RS  E+ +Y  ++ + +   +K+  F 
Sbjct: 11  PPGWRREERQRKSGSSAGKV-DVYYYSPTGKKFRSKSELIRYLEKNGDTS---LKLEDFD 66

Query: 243 F 243
           F
Sbjct: 67  F 67

The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase. Length = 75

>gnl|CDD|128673 smart00391, MBD, Methyl-CpG binding domain

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 185 PPGWQRLLRIRGEGSTKF-ADVYYEAPSGKKLRSMVEIQKYFLE 227
           P GW+R  + R  G +    DVYY +P GKKLRS  E+ +Y  +
Sbjct: 9   PCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHK 52

Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain. Length = 77

>gnl|CDD|238691 cd01397, HAT_MBD, Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 187 GWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIP 246
           GW+R  RIRG G     +V Y AP GKKLR   E+ KY  ++     + +    FSF   
Sbjct: 9   GWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKN---GISLLSRENFSFSAR 65

Query: 247 KPLQENYV 254
            P+ + Y 
Sbjct: 66  APVGDFYE 73

The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog. Length = 73

>gnl|CDD|238689 cd01395, HMT_MBD, Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 187 GWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLE 227
           G+QR+      G  K   V Y+AP G+ LR+M E+ +Y  E
Sbjct: 9   GFQRMKYRARVGKVKKH-VIYKAPCGRSLRNMSEVHRYLRE 48

SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Length = 60

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	340
cd01396	77	MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are me	99.92
cd01397	73	HAT_MBD Methyl-CpG binding domains (MBD) present i	99.89
smart00391	77	MBD Methyl-CpG binding domain. Methyl-CpG binding	99.88
cd00122	62	MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and	99.84
PF01429	77	MBD: Methyl-CpG binding domain; InterPro: IPR00173	99.8
KOG4161	272	consensus Methyl-CpG binding transcription regulat	99.8
cd01395	60	HMT_MBD Methyl-CpG binding domains (MBD) present i	99.4
PF07496	50	zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zi	99.28
KOG4161	272	consensus Methyl-CpG binding transcription regulat	99.11

>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD)

Probab=99.92  E-value=2.1e-25  Score=175.41  Aligned_cols=76  Identities=41%  Similarity=0.725  Sum_probs=70.4

Q ss_pred             CCCCCCCCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCccccccc
Q 019505          178 KPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRK  256 (340)
Q Consensus       178 KpnIP~~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~yvkK  256 (340)
                      +++||.+|+||+|++++|++|+.+++||||++|+||||||++||++||..||.   .+|++++|||++++++++++.++
T Consensus         1 ~~~~~~lp~GW~r~~~~R~~gs~~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~~---~~~~~~~FdF~~~k~~~~~~~~~   76 (77)
T cd01396           1 KPEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGP---TSLDLSDFDFTVPKKLGLGSPRR   76 (77)
T ss_pred             CCCCCCCCCCCEEEEEEecCCCCCcceEEEECCCCCEEECHHHHHHHHHhCCC---CCCcHhHcccCCCcccccccCCC
Confidence            47899999999999999999977789999999999999999999999999985   47999999999999999988665

The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.

>cd01397 HAT_MBD Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity

Probab=99.89  E-value=9.1e-24  Score=166.22  Aligned_cols=69  Identities=36%  Similarity=0.562  Sum_probs=64.4

Q ss_pred             CCCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCccccc
Q 019505          183 QPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYV  254 (340)
Q Consensus       183 ~~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~yv  254 (340)
                      +++.||+|++|+|+.|++.++||||+|||||||||++||++||.+|+.   .+|+++||+|++..+++++|+
T Consensus         5 Pl~~GW~Re~vir~~~~~~~~dV~Y~aPcGKklRs~~ev~~yL~~~~~---~~Lt~dnFsF~~~~~vg~f~~   73 (73)
T cd01397           5 PLELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKNGI---SLLSRENFSFSARAPVGDFYE   73 (73)
T ss_pred             CCCCCceeEEEeccCCCCccceEEEECCCCcccccHHHHHHHHHhCCc---cCccHhHccccCCcccccccC
Confidence            457999999999999977899999999999999999999999999996   489999999999999999884

The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.

>smart00391 MBD Methyl-CpG binding domain

Probab=99.88  E-value=3.6e-23  Score=162.54  Aligned_cols=73  Identities=32%  Similarity=0.629  Sum_probs=66.1

Q ss_pred             cCCCCCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCcccc
Q 019505          177 DKPNIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENY  253 (340)
Q Consensus       177 DKpnIP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~y  253 (340)
                      +..++| +|+||+|++++|+.|.+ +++||||+|||||||||++||++||.+|+++   .+++++|||.+..++...+
T Consensus         2 ~~~~~P-lp~GW~R~~~~r~~g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~~~~~---~~~~~~F~F~~~~~~~~~~   75 (77)
T smart00391        2 DPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDL---SLDLECFDFNATVPVGPKF   75 (77)
T ss_pred             CcccCC-CCCCcEEEEEEecCCCCCCcccEEEECCCCCeeeCHHHHHHHHHhCCCc---ccccccccCcCCccccccc
Confidence            456788 99999999999999854 5899999999999999999999999999996   5899999999999988665

Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain

>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD)

Probab=99.84  E-value=2.5e-21  Score=145.19  Aligned_cols=61  Identities=43%  Similarity=0.748  Sum_probs=56.1

Q ss_pred             CCCCCCCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCccee
Q 019505          179 PNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF  243 (340)
Q Consensus       179 pnIP~~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdF  243 (340)
                      ..+|. |+||+|++++|+.|+..++||||++|+||+|||+.||++||.+|+.   .+|++++|||
T Consensus         2 l~~P~-p~GW~R~~~~r~~g~~~k~dv~Y~sP~Gk~~Rs~~ev~~yL~~~~~---~~l~~~~F~F   62 (62)
T cd00122           2 LRDPL-PPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGP---SSLDLENFSF   62 (62)
T ss_pred             CCCCC-CCCeEEEEEEcCCCCCCcceEEEECCCCceecCHHHHHHHHHhCCC---CCCcHHHCCC
Confidence            45777 9999999999999977789999999999999999999999999974   4799999999

The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.

>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer

Probab=99.80  E-value=4.1e-20  Score=143.75  Aligned_cols=69  Identities=36%  Similarity=0.627  Sum_probs=56.8

Q ss_pred             CCCCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCC
Q 019505          179 PNIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPL  249 (340)
Q Consensus       179 pnIP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~  249 (340)
                      +..+.+|+||+|++++|++|++ +++||||+||+|++|||+.||.+||..+++.  ..+++++|+|...+.+
T Consensus         6 ~~~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~~~--~~l~~~~F~F~~~~~~   75 (77)
T PF01429_consen    6 PLDPPLPDGWKREVVVRKSGSSAGKKDVYYYSPCGKRFRSKKEVVRYLKENPSE--HDLKPENFSFSKRLIM   75 (77)
T ss_dssp             CEBTTSTTT-EEEEEESSSSTTTTSEEEEEEETTSEEESSHHHHHHHHTTSS-----SS-CTTBBTTTTB--
T ss_pred             cccCCCCCCCEEEEEEecCCCcCCceEEEEECCCCCEEeCHHHHHHHHHhCCCc--ccCCHhHCCCCCCccc
Confidence            3456789999999999999976 6899999999999999999999999999853  3799999999987764

Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.

>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]

Probab=99.80  E-value=4.6e-20  Score=173.23  Aligned_cols=172  Identities=22%  Similarity=0.182  Sum_probs=151.8

Q ss_pred             CCCCccCCccceeeeecccccceeeeccHHHHHHHHhhhcCCCeeeccccccCCCCcCCCCCCCCCCCcceeeecCCCCC
Q 019505          103 NTQSRVLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIA  182 (340)
Q Consensus       103 ~~~~~~~~si~~yavQC~~C~KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP~Di~~d~sR~WaIDKpnIP  182 (340)
                      .+..+...+|.+|+++|..|++|+.|.+..+|+++|+.+.+++|+|.+.++    +.|++++|+.+++++.|.||+++++
T Consensus       100 ~~r~~~~~~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql----~~~~~~~~l~~~s~~~e~~d~~~l~  175 (272)
T KOG4161|consen  100 KGRGDLNLAIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQL----FWLERLQDLEADSSRGESIDKLSLP  175 (272)
T ss_pred             CCCcccccCCchhhhhccccccceeeccccchhhhhccccccccccccceE----EEeccccccccccccccccCccccC
Confidence            344566789999999999999999999999999999999999999999664    9999999999999999999999999


Q ss_pred             CCCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCcccccccCCCCCC
Q 019505          183 QPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRKRVPKAH  262 (340)
Q Consensus       183 ~~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~yvkKrp~~~~  262 (340)
                      .+|.||.|.+..++...  ..++||..|+|+++++.++++.++..|+.+-.....+++|.|+.+.++++.++.|+.+...
T Consensus       176 ~~~~g~~~~~~~~s~~~--~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~~~~r~~~  253 (272)
T KOG4161|consen  176 KTPQGSGRSSAGESLLS--SVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRVKNVRRSL  253 (272)
T ss_pred             cCCCccCcccccccccc--ccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccchhhhhhcc
Confidence            99999999997776544  4999999999999999999999999995433346799999999999999999999988888


Q ss_pred             CCCCCCCCCCCcccCCCc
Q 019505          263 TSHDTPKALEPRAVSPLS  280 (340)
Q Consensus       263 ~s~~~~~~l~~eEV~Pl~  280 (340)
                      .+.+++.-+..+++..+.
T Consensus       254 ~~~l~sd~~~~~~~~~~~  271 (272)
T KOG4161|consen  254 FSALTSDTLSKEAAKLQD  271 (272)
T ss_pred             ccchhhcCcchhhhcccc
Confidence            777766667776666554

>cd01395 HMT_MBD Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression

Probab=99.40  E-value=3.2e-13  Score=103.24  Aligned_cols=55  Identities=33%  Similarity=0.510  Sum_probs=48.8

Q ss_pred             CCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCccee
Q 019505          184 PPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF  243 (340)
Q Consensus       184 ~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdF  243 (340)
                      +-.||+|....|+.|+ -+.||+|.+||||+||+..||++||.++ .   +.|++++|+|
T Consensus         6 ll~gw~R~~~~~~~~~-~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t-~---~~L~~d~FsF   60 (60)
T cd01395           6 LLCGFQRMKYRARVGK-VKKHVIYKAPCGRSLRNMSEVHRYLRET-C---SFLTVDNFSF   60 (60)
T ss_pred             cccCeEEEEEeccCCC-cccceEEECCcchhhhcHHHHHHHHHhc-c---ccceeecccC
Confidence            3489999999998873 3688999999999999999999999999 3   3699999999

SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.

>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.28  E-value=8e-13  Score=96.33  Aligned_cols=49  Identities=41%  Similarity=0.882  Sum_probs=34.7

Q ss_pred             eeeecccccceeeeccHHHHHHHHhhhcCCCeeeccccccCCCCcCCCCCCCC
Q 019505          115 FTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDIS  167 (340)
Q Consensus       115 yavQC~~C~KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP~Di~  167 (340)
                      |+|||.+|.|||.||  .++..|++.+.+ +|+|.+.. |++..||+.|+|++
T Consensus         2 ~WVQCd~C~KWR~lp--~~~~~~~~~~~d-~W~C~~n~-~~~~~sC~~pee~e   50 (50)
T PF07496_consen    2 YWVQCDSCLKWRRLP--EEVDPIREELPD-PWYCSMNP-DPPFNSCDAPEEIE   50 (50)
T ss_dssp             EEEE-TTT--EEEE---CCHHCTSCCSST-T--GGGSS--CCC-STTS--SS-
T ss_pred             eEEECCCCCceeeCC--hhhCcccccCCC-eEEcCCCC-CCCCCCCCCcccCC
Confidence            799999999999999  778888888888 99999987 99999999999975

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.

>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]

Probab=99.11  E-value=6.7e-11  Score=111.73  Aligned_cols=66  Identities=35%  Similarity=0.571  Sum_probs=57.5

Q ss_pred             CCCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCccc
Q 019505          180 NIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQEN  252 (340)
Q Consensus       180 nIP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~  252 (340)
                      .+|.+|+||.|++++|++|.. ++.||||+||.||+|||+.+++.||+.+.       +++.|+|-+.+++...
T Consensus        15 ~c~~lp~GW~~~~~~r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~~-------~~s~~~~v~~k~~~~~   81 (272)
T KOG4161|consen   15 DCPALPPGWTREEVQRSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKVG-------DLSLFDFVTGKMSPSE   81 (272)
T ss_pred             cCCCCCCCcchhhhcccCCCcccccceEEeCCcccccccccHHHHHhcccc-------ccccCccccccccccc
Confidence            466789999999999999865 68999999999999999999999998754       5778888888877653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	340
2ky8_A	72	Methyl-CPG-binding domain protein 2; DNA binding d	2e-14
1ub1_A	133	MECP2, attachment region binding protein; chicken	4e-14
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	3e-13
1d9n_A	75	Methyl-CPG-binding protein MBD1; PCM1, methylation	3e-12

>2ky8_A Methyl-CPG-binding domain protein 2; DNA binding domain, transcription-DNA complex; HET: DNA 5CM TED; NMR {Gallus gallus} Length = 72

 Score = 66.5 bits (162), Expect = 2e-14
 Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 8/66 (12%)

Query: 183 QPPPGWQRLLRIRGEGSTK-FADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQF 241
             PPGW++   IR  G +   +DVYY +PSGKK RS  ++ +Y           V +S F
Sbjct: 12  ALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGN-------AVDLSCF 64

Query: 242 SFQIPK 247
            F+  K
Sbjct: 65  DFRTGK 70

>1ub1_A MECP2, attachment region binding protein; chicken methyl-CPG-binding protein 2 (cmecp2), MAR-binding protein (ARBP), spectroscopy; NMR {Gallus gallus} SCOP: d.10.1.3 Length = 133

 Score = 67.6 bits (164), Expect = 4e-14
 Identities = 30/125 (24%), Positives = 47/125 (37%), Gaps = 6/125 (4%)

Query: 159 SCDDPTDISQDGSRLWAIDKPNIAQP--PPGWQRLLRIRGEGSTK-FADVYYEAPSGKKL 215
           +  + +   +    +     P    P  P GW R L+ R  G +    DVY   P GK  
Sbjct: 11  AVPEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAF 70

Query: 216 RSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRA 275
           RS VE+  YF +  +     +  + F F +      +   +R PK   S  +P +   R 
Sbjct: 71  RSKVELIAYFEKVGDT---SLDPNDFDFTVTGRGSPSRREQRPPKKAKSPKSPGSGRGRG 127

Query: 276 VSPLS 280
               S
Sbjct: 128 RPKGS 132

>3c2i_A Methyl-CPG-binding protein 2; water mediated recognition; HET: DNA 5CM; 2.50A {Homo sapiens} PDB: 1qk9_A Length = 97

 Score = 64.0 bits (155), Expect = 3e-13
 Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 185 PPGWQRLLRIRGEGSTK-FADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
           P GW R L+ R  G +    DVY   P GK  RS VE+  YF +  +     +  + F F
Sbjct: 25  PEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEKVGDT---SLDPNDFDF 81

Query: 244 QIPKPLQENYVRKR 257
            +      +     
Sbjct: 82  TVTGRGSPSRHHHH 95

>1d9n_A Methyl-CPG-binding protein MBD1; PCM1, methylation, DNA binding domain, gene regulation; NMR {Homo sapiens} SCOP: d.10.1.3 PDB: 1ig4_A* Length = 75

 Score = 60.8 bits (147), Expect = 3e-12
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 185 PPGWQRLLRIRGEGSTK-FADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243
            PGW+R    R  G+T   +D YY++P+G ++RS VE+ +Y     +       ++ F F
Sbjct: 12  GPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACD-------LTLFDF 64

Query: 244 QIPK 247
           +   
Sbjct: 65  KQGI 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	340
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	99.89
3vxv_A	69	Methyl-CPG-binding domain protein 4; methyl CPG bi	99.89
2ky8_A	72	Methyl-CPG-binding domain protein 2; DNA binding d	99.87
1d9n_A	75	Methyl-CPG-binding protein MBD1; PCM1, methylation	99.87
1ub1_A	133	MECP2, attachment region binding protein; chicken	99.86
2l7p_A	100	Histone-lysine N-methyltransferase ASHH2; CW-domai	98.46
2e61_A	69	Zinc finger CW-type PWWP domain protein 1; ZF-CW d	97.72
4gut_A	776	Lysine-specific histone demethylase 1B; histone de	84.29

>3c2i_A Methyl-CPG-binding protein 2; water mediated recognition; HET: DNA 5CM; 2.50A {Homo sapiens} PDB: 1qk9_A

Probab=99.89  E-value=1.1e-23  Score=172.05  Aligned_cols=68  Identities=31%  Similarity=0.502  Sum_probs=61.0

Q ss_pred             CCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCcc
Q 019505          181 IAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQE  251 (340)
Q Consensus       181 IP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e  251 (340)
                      .|.+|+||+|++++|++|.+ +++||||+||+||||||++||++||++||++   +|++++|||++++++++
T Consensus        21 ~~~lP~GW~re~~~R~~G~s~gk~DvYY~sP~GkkfRSk~ev~ryL~~~g~~---~~~~~~FdF~~~~~~~~   89 (97)
T 3c2i_A           21 DPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEKVGDT---SLDPNDFDFTVTGRGSP   89 (97)
T ss_dssp             CTTSCTTCEEEEEECCSSTTTTCEEEEEECTTSCEECSHHHHHHHHHHHTCC---SSCTTTCCCCSSCC---
T ss_pred             CCCCCCCCEEEEEEecCCCCCCcceEEEECCCCCEEECHHHHHHHHHHCCCC---CCCHhhccccCCCcCcc
Confidence            46789999999999999965 6899999999999999999999999999986   69999999999999875

>3vxv_A Methyl-CPG-binding domain protein 4; methyl CPG binding domain, protein-DNA complex, versatIle BA recognition, hydrolase-DNA complex; HET: DNA 5CM; 2.00A {Mus musculus} PDB: 3vxx_A* 3vyb_A* 3vyq_A*

Probab=99.89  E-value=1.1e-23  Score=162.21  Aligned_cols=61  Identities=34%  Similarity=0.610  Sum_probs=57.2

Q ss_pred             CCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCC
Q 019505          183 QPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIP  246 (340)
Q Consensus       183 ~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstP  246 (340)
                      .+|+||+|++++|++|.+ ++.||||+||+||||||++||++||+.||++   +|++++|||++|
T Consensus         5 plp~GW~R~~~~R~~G~s~gk~DvyY~sP~Gkk~RSk~ev~~yL~~~~~~---~l~~~~FdF~~p   66 (69)
T 3vxv_A            5 PVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGET---FLKPEDFNFTVL   66 (69)
T ss_dssp             CSCTTCEEEEEECCSSTTTTCEEEEEECTTSCEECSHHHHHHHHHHHCCC---CCCGGGSCCCCC
T ss_pred             cCCCCCEEEEEEeccCCCCCcceEEEEcCCCCEeeCHHHHHHHHHhCCCC---CCCHHHcceeCC
Confidence            579999999999999965 5899999999999999999999999999996   699999999987

>2ky8_A Methyl-CPG-binding domain protein 2; DNA binding domain, transcription-DNA complex; HET: DNA 5CM TED; NMR {Gallus gallus}

Probab=99.87  E-value=7.3e-23  Score=158.61  Aligned_cols=63  Identities=38%  Similarity=0.678  Sum_probs=56.5

Q ss_pred             CCCCCCCCceEEEEEeccCC-CcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCC
Q 019505          180 NIAQPPPGWQRLLRIRGEGS-TKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPL  249 (340)
Q Consensus       180 nIP~~P~GWKRevViRksGs-t~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~  249 (340)
                      .+|.+|+||+|++++|++|. .+++||||++|+||||||++||++||..       +|++++|||++|++|
T Consensus         9 ~~p~Lp~GW~R~~~~R~~g~s~~k~DvyY~sP~Gkr~RS~~ev~~YL~~-------~l~~~~FdF~~~~~~   72 (72)
T 2ky8_A            9 DCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGN-------AVDLSCFDFRTGKMM   72 (72)
T ss_dssp             ECSSSCTTCEEEEEECCSSTTTTCEEEEEECTTCCEEESHHHHHHHHTT-------SSCCTTCBTTTTBC-
T ss_pred             cCCCCCCCCEEEEEEecCCCCCCceEEEEECCCCCEeEcHHHHHHHHhc-------CCChhhcCCCCCCcC
Confidence            35577999999999999985 4689999999999999999999999976       589999999999986

>1d9n_A Methyl-CPG-binding protein MBD1; PCM1, methylation, DNA binding domain, gene regulation; NMR {Homo sapiens} SCOP: d.10.1.3 PDB: 1ig4_A*

Probab=99.87  E-value=7.9e-23  Score=159.89  Aligned_cols=64  Identities=30%  Similarity=0.589  Sum_probs=58.2

Q ss_pred             CCCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCc
Q 019505          180 NIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQ  250 (340)
Q Consensus       180 nIP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~  250 (340)
                      .+|.+|+||+|++++|++|.+ +++||||+||+||||||++||++||+.       ++++++|||++++++.
T Consensus         7 ~~p~LP~GW~Re~~~R~~g~s~gk~DvyY~sP~Gkk~RS~~ev~ryL~~-------~~~~~~FdF~~gk~~~   71 (75)
T 1d9n_A            7 DCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGP-------ACDLTLFDFKQGILCY   71 (75)
T ss_dssp             ECTTTCSSCEEEECSSSSSCTTCCCCEEEECSSSCEECSTHHHHHHHCT-------TCCCTTCCTTTCCCCC
T ss_pred             cCCCCCCCCEEEEEEecCCCCCCceEEEEECCCCCeeecHHHHHHHhcc-------CCCccccCCCCCCccC
Confidence            456779999999999999966 689999999999999999999999963       5899999999999976

>1ub1_A MECP2, attachment region binding protein; chicken methyl-CPG-binding protein 2 (cmecp2), MAR-binding protein (ARBP), spectroscopy; NMR {Gallus gallus} SCOP: d.10.1.3

Probab=99.86  E-value=4.5e-22  Score=170.44  Aligned_cols=94  Identities=26%  Similarity=0.398  Sum_probs=74.6

Q ss_pred             CCCCCCCCcceeeecCCC----CCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcc
Q 019505          163 PTDISQDGSRLWAIDKPN----IAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVK  237 (340)
Q Consensus       163 P~Di~~d~sR~WaIDKpn----IP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLt  237 (340)
                      |+-.--.+.|.-+|+..+    .+.+|+||+|++++|++|.+ +++|||||||+||||||++||++||++|+++   +++
T Consensus        13 ~~~~~~~~~rr~vi~~~~~~~~~~~LP~GWkRe~~~RksG~Sagk~DVYY~SP~GKkfRSk~Ev~ryL~~~~~~---~~~   89 (133)
T 1ub1_A           13 PEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDT---SLD   89 (133)
T ss_dssp             CCCCSCCCCCCCCCCTTSCSSCCCCBTTBCEEEEEECCCSSSCCSEEEEEECTTSCEESSHHHHHHHHTTSCCC---SCC
T ss_pred             cccccCccCccceeeccccccCCCCCCCCCEEEEEEecCCCCCCceeEEEECCCCCeeeCHHHHHHHHHHCCcc---CCC
Confidence            333344556777775444    56789999999999999954 6899999999999999999999999999986   689


Q ss_pred             cCcceecC-CcCCcccccccCCC
Q 019505          238 MSQFSFQI-PKPLQENYVRKRVP  259 (340)
Q Consensus       238 Le~FdFst-PK~~~e~yvkKrp~  259 (340)
                      +++|||++ ++.+.....+|.+.
T Consensus        90 ~e~FdF~~~gk~~~s~R~~r~~k  112 (133)
T 1ub1_A           90 PNDFDFTVTGRGSPSRREQRPPK  112 (133)
T ss_dssp             GGGCCCCCCCCSCSSCCCCCCCC
T ss_pred             HhHCccccCCCCCCcccccCCCC
Confidence            99999995 56655455444443

>2l7p_A Histone-lysine N-methyltransferase ASHH2; CW-domain; NMR {Arabidopsis thaliana}

Probab=98.46  E-value=6.7e-08  Score=79.43  Aligned_cols=53  Identities=28%  Similarity=0.576  Sum_probs=39.2

Q ss_pred             ccceeeeecccccceeeeccHHHHHHHHhhhcCCCeeeccccccCCCCcCCCCCCCCC
Q 019505          111 SVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQ  168 (340)
Q Consensus       111 si~~yavQC~~C~KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP~Di~~  168 (340)
                      .++..+|||.+|.|||.+| .+.++.+.   ..+.|+|.+.- ...-.+|+.|+++.-
T Consensus        23 ~~~~~WVQCD~C~KWRrLP-~~~~~~~~---~pd~W~C~mN~-D~~~nsCs~PEE~~~   75 (100)
T 2l7p_A           23 STESAWVRCDDCFKWRRIP-ASVVGSID---ESSRWICMNNS-DKRFADCSKSQEMSN   75 (100)
T ss_dssp             SSSSEEEECTTTCCEEEEC-HHHHTTST---TSSCCCGGGSS-CSSSCSTTSCCSSCH
T ss_pred             CCCCeEEeeCCCCccccCC-hhHccccC---CCCCceeCCCC-CCCCCCCCCccCCCH
Confidence            4578999999999999999 44443332   35999999831 223389999998753

>2e61_A Zinc finger CW-type PWWP domain protein 1; ZF-CW domain, structural genomics, NPPSFA, national project protein structural and functional analyses; NMR {Homo sapiens} PDB: 2rr4_A*

Probab=97.72  E-value=9e-06  Score=62.68  Aligned_cols=52  Identities=25%  Similarity=0.434  Sum_probs=38.4

Q ss_pred             cceeeeecc--cccceeeeccHHHHHHHHhhhcCCCeeeccccccCCCCcCCCCCCCCCC
Q 019505          112 VGAFTVQCA--DCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQD  169 (340)
Q Consensus       112 i~~yavQC~--~C~KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP~Di~~d  169 (340)
                      ...++|||.  +|.|||.+|-....     ..+-+.|+|.+.- ..---+|+.|++..-|
T Consensus        14 ~~~~WVQCd~p~C~KWR~LP~~~~~-----~~lpd~W~C~mN~-d~~~~~Cs~pEE~~~~   67 (69)
T 2e61_A           14 QCLVWVQCSFPNCGKWRRLCGNIDP-----SVLPDNWSCDQNT-DVQYNRCDIPEETWTG   67 (69)
T ss_dssp             CCCCEEECSSTTTCCEEECCSSCCT-----TTSCTTCCGGGCS-CGGGCSSSSCCCCCCC
T ss_pred             CCCeEEEeCccccCcccCCcccccc-----ccCCCcCEeCCCC-CCccCCCCCCcccCCC
Confidence            458999999  99999999954322     2356899999842 3335689999887543

>4gut_A Lysine-specific histone demethylase 1B; histone demethylase; HET: FAD PGE; 2.00A {Homo sapiens} PDB: 4gur_A* 4gus_A* 4guu_A* 4fwe_A* 4fwf_A* 4fwj_A* 4gu1_A*

Probab=84.29  E-value=0.12  Score=53.68  Aligned_cols=48  Identities=23%  Similarity=0.645  Sum_probs=29.8

Q ss_pred             eeeeecc--cccceeeeccHHHHHHHHhhhcCCCeeecccccc--C--CCCcCCCCCC
Q 019505          114 AFTVQCA--DCFKWRLIPTKEKYEEIREHVLENPFTCEKAREW--R--PDVSCDDPTD  165 (340)
Q Consensus       114 ~yavQC~--~C~KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~w--r--p~~sCddP~D  165 (340)
                      -|++||.  .|.|||.+++.   +.|-..+ -+-|.|....--  +  -.=.|.-|+|
T Consensus        91 ~~~~~c~~~~c~~~~~~~~~---~~~~~~~-~~~~~c~~~~~~~~~~~~~~~~~~~~~  144 (776)
T 4gut_A           91 PYWVQCTKPECRKWRQLTKE---IQLTPQI-AKTYRCGMKPNTAIKPETSDHCSLPED  144 (776)
T ss_dssp             CCEEECCCTTTCCEEECCTT---CCCCHHH-HHHCCTTCCCC-------CCGGGSCCC
T ss_pred             cHhhhcCcccccchhhCCCc---CCCChhh-hheeeccCccCcccccccCCCCCCCcc
Confidence            5999999  99999999743   3333333 235899863210  1  1224677776

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	340
d1qk9a_	92	d.10.1.3 (A:) Methyl-CpG-binding protein 2, MECP2	2e-14
d1ig4a_	75	d.10.1.3 (A:) Methylation-dependent transcriptiona	1e-12

>d1qk9a_ d.10.1.3 (A:) Methyl-CpG-binding protein 2, MECP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 92

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain
superfamily: DNA-binding domain
family: Methyl-CpG-binding domain, MBD
domain: Methyl-CpG-binding protein 2, MECP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.1 bits (161), Expect = 2e-14
 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 183 QPPPGWQRLLRIRGEGSTK-FADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQF 241
             P GW R L+ R  G +    DVY   P GK  RS VE+  YF +  +     +  + F
Sbjct: 23  TLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDT---SLDPNDF 79

Query: 242 SFQIP 246
            F + 
Sbjct: 80  DFTVT 84

>d1ig4a_ d.10.1.3 (A:) Methylation-dependent transcriptional repressor MBD1/PCM1 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain
superfamily: DNA-binding domain
family: Methyl-CpG-binding domain, MBD
domain: Methylation-dependent transcriptional repressor MBD1/PCM1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.6 bits (147), Expect = 1e-12
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 8/68 (11%)

Query: 184 PPPGWQRLLRIRGEGSTK-FADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFS 242
             PGW+R    R  G+T   +D YY++P+G ++RS VE+ +Y             ++ F 
Sbjct: 11  LGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYL-------GPACDLTLFD 63

Query: 243 FQIPKPLQ 250
           F+      
Sbjct: 64  FKQGILCY 71

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	340
d1ig4a_	75	Methylation-dependent transcriptional repressor MB	99.85
d1qk9a_	92	Methyl-CpG-binding protein 2, MECP2 {Human (Homo s	99.83

>d1ig4a_ d.10.1.3 (A:) Methylation-dependent transcriptional repressor MBD1/PCM1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain
superfamily: DNA-binding domain
family: Methyl-CpG-binding domain, MBD
domain: Methylation-dependent transcriptional repressor MBD1/PCM1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.6e-22  Score=155.36  Aligned_cols=64  Identities=30%  Similarity=0.589  Sum_probs=56.8

Q ss_pred             CCCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCc
Q 019505          180 NIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQ  250 (340)
Q Consensus       180 nIP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~  250 (340)
                      .+|.+|+||+|++++|++|.+ +++||||+||+||||||+.||++||..       ++++++|||+++++.+
T Consensus         7 ~~p~LP~GW~re~~~Rk~g~~~gk~DvyY~sP~Gkk~RS~~ev~~yL~~-------~l~~~~FdF~tg~~~~   71 (75)
T d1ig4a_           7 DCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGP-------ACDLTLFDFKQGILCY   71 (75)
T ss_dssp             ECTTTCTTCEEEEECCCSSSSTTCCEEEEECSSSCEECSHHHHHHHHCS-------SSCCTTBCTTTCCBSC
T ss_pred             cCCCCCCCcEEEEEEEcCCCCCCceeEEEECCCCCEEeCHHHHHHHhcc-------CCCccceeccCCcEeC
Confidence            456779999999999999854 589999999999999999999999953       5899999999988754

>d1qk9a_ d.10.1.3 (A:) Methyl-CpG-binding protein 2, MECP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain
superfamily: DNA-binding domain
family: Methyl-CpG-binding domain, MBD
domain: Methyl-CpG-binding protein 2, MECP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=7e-22  Score=157.61  Aligned_cols=65  Identities=32%  Similarity=0.561  Sum_probs=58.0

Q ss_pred             CCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecC-CcC
Q 019505          181 IAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQI-PKP  248 (340)
Q Consensus       181 IP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFst-PK~  248 (340)
                      .|.+|+||+|++++|++|.+ +++||||++|+||||||+.||.+||.+|++.   +|++++|||++ ++.
T Consensus        21 dp~Lp~GW~r~~~~R~~g~~~gk~Dvyy~sP~Gkk~RS~~eV~~yL~~~~~~---~~~~~~FdF~~~~k~   87 (92)
T d1qk9a_          21 DPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDT---SLDPNDFDFTVTGRG   87 (92)
T ss_dssp             BCCSSSSCEEEECCCCCSSSCSCCCEEEEETTTEEESSHHHHHHHHHHHTCC---SSCGGGCCCCTTCCC
T ss_pred             CCCCCCCCEEEEEEecCCCCCceeeEEEECCCCCeeecHHHHHHHHHHCCCc---ccchhHeeeEeccCc
Confidence            35679999999999999954 5899999999999999999999999999985   79999999986 443