Citrus Sinensis ID: 045019

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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-------25
Protein Sequence
MSTSARAQASHDPNPNLHKPEPKESVNLFSTVNVPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIREHKSENLATTNGTESALTPETASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSNADMDSSGSAAGSTKQKKPNIKAKTSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKIC
Secondary Structure (PSIPRED)
cccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccEEEEEEEcccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccccccccccHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHccccccccccccccccccccccccccccccHcccccEEcccccccccccccccccccccccccccccccccEEccccccccccccHHHHccccccccccccccEEEEEEEccccccccEEEEEEccccccEcccHHHHHHHHHcccccccccccccccccccccccccEEcccccccccccccccccccccccEEEEEEcccccccccccccccccHccHccHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
mstsaraqashdpnpnlhkpepkesvnlfstvnvppdplldsgffidaappatsgsnttttndqtskkrgtirehksenlattngtesaltpetasTRRLtateawlppgweiedrvrtsgatagtvdKYYFHVasgrrfrskKEVLYFLETGTkrkrrkensnadmdssgsaagstkqkkpnikaktsalnfdyfnspenvewvltdpsegswtpfigkvevpesvRQDWAAAFTdlttsnngskic
Flexible Loop (DISEMBL)
mstsaraqashdpnpnlhkpepKESVNLFSTVNVPPDPLLDSGFFIDAAppatsgsnttttndqtskkrgtirehksenlattngtesaltpetastrrltateawlppgweiedrvrtsgatagtvdkyyfhvasgrrfrskkevLYFLetgtkrkrrkensnadmdssgsaagstkqkkpnIKAKTSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAftdlttsnngskic
Low Complexity Region (SEG)
MSTSARAQASHDPNPNLHKPEPKESVNLFSTVNVPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIREHKSENLATTNGTESALTPETASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKEnsnadmdssgsaagsTKQKKPNIKAKTSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKIC
Disordered region (IsUnstruct)
****************************************************************************************************TATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE**************************************ALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTD***********
Disordered Region (DISOPRED)
*********************************************************************************************************WLPPGWEIEDRVRT**ATAGTVDKYYFHVASGRRFRSKKEVLYFLETGT*******************************************************S*GSWTPFIGKVEVPESVRQDWAAAFTDLTTS*******
Disordered Region (DISEMBL)
**************PNLHKPEPKESVNLFSTVNVPPDPLLDSGFFIDAAPPA*******************IREHKSENLATTNGTESALTPETASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKR***************************IKAKTSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKIC
Disordered Region (DISPRO)
**************PNLHKPEPKESVNLFSTVNVPPDPLLDSGFFIDAA******************************************************EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETG*********************************KTSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTS*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSTSARAQASHDPNPNLHKPEPKESVNLFSTVNVPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIREHKSENLATTNGTESALTPETASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSNADMDSSGSAAGSTKQKKPNIKAKTSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKIC
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	248	2.2.26 [Sep-21-2011]
Q9LTJ1	225	Methyl-CpG-binding domain	yes	no	0.858	0.946	0.395	1e-35
Q9SNC0	182	Methyl-CpG-binding domain	no	no	0.665	0.906	0.444	2e-31
Q9UBB5	411	Methyl-CpG-binding domain	yes	no	0.173	0.104	0.5	1e-05
Q9Z2E1	414	Methyl-CpG-binding domain	yes	no	0.173	0.103	0.5	1e-05

>sp|Q9LTJ1|MBD6_ARATH Methyl-CpG-binding domain-containing protein 6 OS=Arabidopsis thaliana GN=MBD6 PE=1 SV=1

 Score =  150 bits (378), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/220 (39%), Positives = 122/220 (55%), Gaps = 7/220 (3%)

Query: 33  NVPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIREHKSENLATTNGTESA-LT 91
           + PPDPLL SG FI +A   T  S+      Q         E  S  +   NGT+     
Sbjct: 8   DFPPDPLLASGAFISSAGDGTLDSSAKRRPIQGGIGISGSGE--SVRIGMANGTDQVNHQ 65

Query: 92  PETASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
            E+ S +R    + WLPPGW +ED++RTSGATAG+VDKYY+   +GR+FRS+ EVLY+LE
Sbjct: 66  TESKSRKRAAPGDNWLPPGWRVEDKIRTSGATAGSVDKYYYEPNTGRKFRSRTEVLYYLE 125

Query: 152 TGTKRK--RRKENSNADMDS-SGSAAGSTKQKKPNIKAKTSALNFDYFNSPENVEWVLTD 208
            GT ++  ++ EN+  + D   G  +    +           L+FD+ N P+ V W + +
Sbjct: 126 HGTSKRGTKKAENTYFNPDHFEGQGSNRVTRTATVPPPPPPPLDFDFKNPPDKVSWSMAN 185

Query: 209 PSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKIC 248
             E  W P IG V+V +SVR+DW+ AFT   TS N SK+ 
Sbjct: 186 AGEEGWIPNIGDVKVQDSVRRDWSTAFT-FITSRNPSKVS 224

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. May associate with histone deacetylase proteins (HDAC). Required for nucleolar dominance that consist in the silencing of rRNA genes inherited from one progenitor in genetic hybrids. Recruited to rRNA genes in a DRM2-dependent manner.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9SNC0|MBD5_ARATH Methyl-CpG-binding domain-containing protein 5 OS=Arabidopsis thaliana GN=MBD5 PE=1 SV=1

 Score =  135 bits (341), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 80/180 (44%), Positives = 101/180 (56%), Gaps = 15/180 (8%)

Query: 83  TNGTESALTP--------ETASTRRLT-ATEAWLPPGWEIEDRVRTSGATAGTVDKYYFH 133
           +NGT+ A  P        ++ S +R T   + WLPP W  E RVRTSG  AGTVDK+Y+ 
Sbjct: 2   SNGTDQAQPPPENPATPVDSKSRKRATPGDDNWLPPDWRTEIRVRTSGTKAGTVDKFYYE 61

Query: 134 VASGRRFRSKKEVLYFLETGT-KRKRRKENSNADMDSS-----GSAAGSTKQKKPNIKAK 187
             +GR+FRSK EVLY+LE GT K+K  K   N D  S      GSA   TK  K   +  
Sbjct: 62  PITGRKFRSKNEVLYYLEHGTPKKKSVKTAENGDSHSEHSEGRGSARRQTKSNKKVTEPP 121

Query: 188 TSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKI 247
              LNFD+ N PE V W   + SE +W PFIG  ++ ESV QDW   FT +T+ N G  +
Sbjct: 122 PKPLNFDFLNVPEKVTWTGINGSEEAWLPFIGDYKIQESVSQDWDRVFTLVTSQNAGKTM 181

Transcriptional regulator that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. In addition, binds specifically methylated m(5)CpNpN but not m(5)CpNpG (N is A, T or C). Plays probably a role in gene silencing.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 50.8 bits (120), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 31/44 (70%), Gaps = 1/44 (2%)

Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
           LPPGW+ E+ +R SG +AG  D YYF   SG++FRSK ++  +L
Sbjct: 155 LPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYL 197

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)

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

 Score = 50.4 bits (119), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 31/44 (70%), Gaps = 1/44 (2%)

Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
           LPPGW+ E+ +R SG +AG  D YYF   SG++FRSK ++  +L
Sbjct: 158 LPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYL 200

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)

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	248
297793491	233	hypothetical protein ARALYDRAFT_919168 [	0.814	0.866	0.403	3e-36
224106479	214	methyl binding domain protein [Populus t	0.645	0.747	0.509	1e-35
224059490	214	methyl binding domain protein [Populus t	0.806	0.934	0.411	4e-35
15238389	225	methyl-CPG-binding domain 6 protein [Ara	0.858	0.946	0.395	7e-34
255584216	234	DNA binding protein, putative [Ricinus c	0.745	0.790	0.446	3e-33
297815816	181	hypothetical protein ARALYDRAFT_485028 [	0.665	0.911	0.458	4e-30
15232591	182	methyl-CPG-binding domain protein 5 [Ara	0.665	0.906	0.444	1e-29
21554707	182	unknown [Arabidopsis thaliana]	0.665	0.906	0.444	1e-29
359478635	297	PREDICTED: methyl-CpG-binding domain-con	0.479	0.400	0.503	5e-28
297746071	135	unnamed protein product [Vitis vinifera]	0.479	0.881	0.503	1e-26

>gi|297793491|ref|XP_002864630.1| hypothetical protein ARALYDRAFT_919168 [Arabidopsis lyrata subsp. lyrata] gi|297310465|gb|EFH40889.1| hypothetical protein ARALYDRAFT_919168 [Arabidopsis lyrata subsp. lyrata]

 Score =  157 bits (398), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 92/228 (40%), Positives = 125/228 (54%), Gaps = 26/228 (11%)

Query: 33  NVPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKR------GTIREHKSENLATTNGT 86
           + PPDPLL SG FI +A   T         D +SK+R      G     +S  +   NGT
Sbjct: 8   DFPPDPLLASGAFISSAGDGTL--------DSSSKRRPIQGGIGVSGSGESVRIGMANGT 59

Query: 87  E--------SALTPETASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGR 138
           +        S+   E+ S +R    + WLPPGW +ED++RTSGATAG+VDKYY+   +GR
Sbjct: 60  DQVNPSPDSSSHQAESKSRKRAAPGDNWLPPGWRVEDKIRTSGATAGSVDKYYYEPNTGR 119

Query: 139 RFRSKKEVLYFLETGT-KRKRRKENSNADMDSS---GSAAGSTKQKKPNIKAKTSALNFD 194
           +FRS+ EVLY+LE GT KR   K+  N D  S    G  +   ++K          L+FD
Sbjct: 120 KFRSRTEVLYYLEHGTSKRGGTKKVENTDFLSDHFEGQGSNRARRKAKEPPPPPPPLDFD 179

Query: 195 YFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSN 242
           + N PE V W +    E +W P IG V+V +SVR+DW+ AFT +T  N
Sbjct: 180 FKNPPEKVSWSMAKAGEEAWIPIIGDVKVQDSVRRDWSTAFTFITNRN 227

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224106479|ref|XP_002314180.1| methyl binding domain protein [Populus trichocarpa] gi|222850588|gb|EEE88135.1| methyl binding domain protein [Populus trichocarpa]

 Score =  155 bits (393), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 84/165 (50%), Positives = 108/165 (65%), Gaps = 5/165 (3%)

Query: 85  GTESALTPETASTR--RLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRS 142
           G +  +TP  A  R    T   +WLPPGW +EDR+RTSGATAGTVDKYY   ASGR+FRS
Sbjct: 50  GNQQPVTPVRAKRRSSETTIETSWLPPGWVVEDRIRTSGATAGTVDKYYIDPASGRKFRS 109

Query: 143 KKEVLYFLETGTKRKRRKENSNADMDSSGSAAGSTKQKKPNIKAKTS-ALNFDYFNSPEN 201
           KK+V Y+LETGT +K+ K   N+D D+  ++AG+ K  K    A TS ALNFD FN P+ 
Sbjct: 110 KKDVQYYLETGTLKKKGKLTENSDADT--NSAGNLKVDKNKSGANTSFALNFDSFNVPDR 167

Query: 202 VEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSK 246
            EWVL +  E +W PFI   +VP   ++ W  AF  LTTS++G +
Sbjct: 168 TEWVLANAKEDTWIPFIDGKKVPLYDKEQWDFAFASLTTSSHGKR 212

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224059490|ref|XP_002299872.1| methyl binding domain protein [Populus trichocarpa] gi|118483055|gb|ABK93437.1| unknown [Populus trichocarpa] gi|222847130|gb|EEE84677.1| methyl binding domain protein [Populus trichocarpa]

 Score =  154 bits (388), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 97/236 (41%), Positives = 125/236 (52%), Gaps = 36/236 (15%)

Query: 15  PNLHKPEPKESVNLFSTVNVPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIRE 74
           P ++ P PK             DPLL +G  ID    +T+      TND+          
Sbjct: 11  PGMNPPGPKAD-----------DPLLQNGSSIDPNKHSTADETLNRTNDK---------- 49

Query: 75  HKSENLATTNGTESALTPETASTRRLTATE---AWLPPGWEIEDRVRTSGATAGTVDKYY 131
                     G +  +TP     RRL+ T    +WLPPGW +EDRVRTSGATAGT DKYY
Sbjct: 50  ----------GNQQPVTP-VREKRRLSETAVDTSWLPPGWVVEDRVRTSGATAGTRDKYY 98

Query: 132 FHVASGRRFRSKKEVLYFLETGTKRKRRKENSNADMDSSGSAAGSTKQKKPNIKAKTSAL 191
               SGRRFRSKK+V Y+LETGT +KR K   N D D++ SA  S   K  +      A 
Sbjct: 99  IEPVSGRRFRSKKDVQYYLETGTLKKRGKVAENVDADTN-SAENSKSSKNKSGANTNFAW 157

Query: 192 NFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKI 247
           NFD FN P+  EW LT+ +E +WTPFI   +VP   ++ W   F  LTTS++G ++
Sbjct: 158 NFDSFNVPDRTEWFLTEANEDTWTPFIDGKKVPLYDKEQWDFTFASLTTSSHGYRM 213

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15238389|ref|NP_200746.1| methyl-CPG-binding domain 6 protein [Arabidopsis thaliana] gi|75180469|sp|Q9LTJ1.1|MBD6_ARATH RecName: Full=Methyl-CpG-binding domain-containing protein 6; Short=AtMBD6; Short=MBD06; AltName: Full=Methyl-CpG-binding protein MBD6 gi|8885544|dbj|BAA97474.1| unnamed protein product [Arabidopsis thaliana] gi|28416643|gb|AAO42852.1| At5g59380 [Arabidopsis thaliana] gi|110743343|dbj|BAE99559.1| hypothetical protein [Arabidopsis thaliana] gi|332009795|gb|AED97178.1| methyl-CPG-binding domain 6 protein [Arabidopsis thaliana]

 Score =  150 bits (378), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 87/220 (39%), Positives = 122/220 (55%), Gaps = 7/220 (3%)

Query: 33  NVPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIREHKSENLATTNGTESA-LT 91
           + PPDPLL SG FI +A   T  S+      Q         E  S  +   NGT+     
Sbjct: 8   DFPPDPLLASGAFISSAGDGTLDSSAKRRPIQGGIGISGSGE--SVRIGMANGTDQVNHQ 65

Query: 92  PETASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
            E+ S +R    + WLPPGW +ED++RTSGATAG+VDKYY+   +GR+FRS+ EVLY+LE
Sbjct: 66  TESKSRKRAAPGDNWLPPGWRVEDKIRTSGATAGSVDKYYYEPNTGRKFRSRTEVLYYLE 125

Query: 152 TGTKRK--RRKENSNADMDS-SGSAAGSTKQKKPNIKAKTSALNFDYFNSPENVEWVLTD 208
            GT ++  ++ EN+  + D   G  +    +           L+FD+ N P+ V W + +
Sbjct: 126 HGTSKRGTKKAENTYFNPDHFEGQGSNRVTRTATVPPPPPPPLDFDFKNPPDKVSWSMAN 185

Query: 209 PSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKIC 248
             E  W P IG V+V +SVR+DW+ AFT   TS N SK+ 
Sbjct: 186 AGEEGWIPNIGDVKVQDSVRRDWSTAFT-FITSRNPSKVS 224

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255584216|ref|XP_002532846.1| DNA binding protein, putative [Ricinus communis] gi|223527383|gb|EEF29524.1| DNA binding protein, putative [Ricinus communis]

 Score =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 92/206 (44%), Positives = 115/206 (55%), Gaps = 21/206 (10%)

Query: 37  DPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIREHKSENLATTNGTESALTPETAS 96
           DPLL +G FIDA         TT   +  +        +  +      G E +      S
Sbjct: 30  DPLLRNGSFIDA---------TTIKPNIDNNVSNNNNNNNYQQQEANVGVEQSEATPLKS 80

Query: 97  TRRLTATEA---------WLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVL 147
            R++  T A         WLPPGW +EDRVR SGATAGTVDKYY    +GRRFRSKKEV 
Sbjct: 81  RRKVPVTMAPAPSADSANWLPPGWLVEDRVRASGATAGTVDKYYIEPVTGRRFRSKKEVQ 140

Query: 148 YFLETGTKR--KRRKENSNADMDSSGSAAGSTKQKKPNIKAKTSALNFDYFNSPENVEWV 205
           YFLETGTK+  KR  ENS  D++ + S  GS K KK +  AK    NFDY N P+ +EW 
Sbjct: 141 YFLETGTKKKTKRGMENSEGDVNFTES-PGSQKSKKASKNAKVQKRNFDYLNVPDRIEWA 199

Query: 206 LTDPSEGSWTPFIGKVEVPESVRQDW 231
           L D ++ +WTPF+G  +V E  RQ+W
Sbjct: 200 LIDANQDAWTPFLGGQKVAEYDRQNW 225

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297815816|ref|XP_002875791.1| hypothetical protein ARALYDRAFT_485028 [Arabidopsis lyrata subsp. lyrata] gi|297321629|gb|EFH52050.1| hypothetical protein ARALYDRAFT_485028 [Arabidopsis lyrata subsp. lyrata]

 Score =  137 bits (345), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 82/179 (45%), Positives = 103/179 (57%), Gaps = 14/179 (7%)

Query: 83  TNGTESALTP--------ETASTRRLT-ATEAWLPPGWEIEDRVRTSGATAGTVDKYYFH 133
           +NGT+ A  P        +  S +R T   + WLPP W  E RVRTSG  AGTVDK+Y+ 
Sbjct: 2   SNGTDQAQPPPENTATPVDLKSRKRATPGDDNWLPPDWRTEVRVRTSGTKAGTVDKFYYE 61

Query: 134 VASGRRFRSKKEVLYFLETGTKRKRRKENSNADMDSSGSAA-GST-KQKKPNIKAKT--- 188
             +GR+FRSK EVLY+LE G  +K  K+  N D  S  S   GS  +Q K N KA     
Sbjct: 62  PITGRKFRSKNEVLYYLEHGAPKKAVKKAENGDSLSEHSEGRGSIRRQTKSNKKANEPPP 121

Query: 189 SALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKI 247
             LNFD+ N PE V W   + SE +W PFIG  ++ ESV QDW  AFT +TT N G+ +
Sbjct: 122 KPLNFDFLNVPEKVTWTGINGSEEAWLPFIGDYKIQESVSQDWGRAFTLVTTQNAGTTM 180

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232591|ref|NP_190242.1| methyl-CPG-binding domain protein 5 [Arabidopsis thaliana] gi|75206905|sp|Q9SNC0.1|MBD5_ARATH RecName: Full=Methyl-CpG-binding domain-containing protein 5; Short=AtMBD5; Short=MBD05; AltName: Full=Methyl-CpG-binding protein MBD5 gi|6523061|emb|CAB62328.1| putative protein [Arabidopsis thaliana] gi|17380750|gb|AAL36205.1| unknown protein [Arabidopsis thaliana] gi|23296870|gb|AAN13191.1| unknown protein [Arabidopsis thaliana] gi|332644653|gb|AEE78174.1| methyl-CPG-binding domain protein 5 [Arabidopsis thaliana]

 Score =  135 bits (341), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/180 (44%), Positives = 101/180 (56%), Gaps = 15/180 (8%)

Query: 83  TNGTESALTP--------ETASTRRLT-ATEAWLPPGWEIEDRVRTSGATAGTVDKYYFH 133
           +NGT+ A  P        ++ S +R T   + WLPP W  E RVRTSG  AGTVDK+Y+ 
Sbjct: 2   SNGTDQAQPPPENPATPVDSKSRKRATPGDDNWLPPDWRTEIRVRTSGTKAGTVDKFYYE 61

Query: 134 VASGRRFRSKKEVLYFLETGT-KRKRRKENSNADMDSS-----GSAAGSTKQKKPNIKAK 187
             +GR+FRSK EVLY+LE GT K+K  K   N D  S      GSA   TK  K   +  
Sbjct: 62  PITGRKFRSKNEVLYYLEHGTPKKKSVKTAENGDSHSEHSEGRGSARRQTKSNKKVTEPP 121

Query: 188 TSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKI 247
              LNFD+ N PE V W   + SE +W PFIG  ++ ESV QDW   FT +T+ N G  +
Sbjct: 122 PKPLNFDFLNVPEKVTWTGINGSEEAWLPFIGDYKIQESVSQDWDRVFTLVTSQNAGKTM 181

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21554707|gb|AAM63666.1| unknown [Arabidopsis thaliana]

 Score =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/180 (44%), Positives = 101/180 (56%), Gaps = 15/180 (8%)

Query: 83  TNGTESALTP--------ETASTRRLT-ATEAWLPPGWEIEDRVRTSGATAGTVDKYYFH 133
           +NGT+ A  P        ++ S +R T   + WLPP W  E RVRTSG  AGTVDK+Y+ 
Sbjct: 2   SNGTDQAQPPPENPATPVDSKSRKRATPGDDNWLPPDWRTEIRVRTSGTKAGTVDKFYYE 61

Query: 134 VASGRRFRSKKEVLYFLETGT-KRKRRKENSNADMDSS-----GSAAGSTKQKKPNIKAK 187
             +GR+FRSK EVLY+LE GT K+K  K   N D  S      GSA   TK  K   +  
Sbjct: 62  PITGRKFRSKNEVLYYLEHGTPKKKSVKTAENGDSHSEHSEGRGSARRQTKSNKKVTEPP 121

Query: 188 TSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKI 247
              LNFD+ N PE V W   + SE +W PFIG  ++ ESV QDW   FT +T+ N G  +
Sbjct: 122 PKPLNFDFLNVPEKVTWTGINGSEETWLPFIGDYKIQESVSQDWDRVFTLVTSQNAGKTM 181

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478635|ref|XP_003632148.1| PREDICTED: methyl-CpG-binding domain-containing protein 6-like [Vitis vinifera]

 Score =  130 bits (327), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 68/135 (50%), Positives = 86/135 (63%), Gaps = 16/135 (11%)

Query: 104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENS 163
           E WLPPGW +E RVR+SGA+AG+ DKY+    +GRRFRSKKEV Y+LETG  RK+ K+N 
Sbjct: 169 EDWLPPGWIVEGRVRSSGASAGSRDKYFIEPITGRRFRSKKEVRYYLETGEVRKKPKKNP 228

Query: 164 NADMDSSGSAAGSTKQKKPNIKAKTSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEV 223
           +                 P    K+  LNF++ + P+ V+WV T  SEG WTPFI   EV
Sbjct: 229 D---------------NSPEKGTKSPPLNFNFEDVPDTVKWVRTGSSEG-WTPFINGQEV 272

Query: 224 PESVRQDWAAAFTDL 238
           PES ++DWAAAF  L
Sbjct: 273 PESSKRDWAAAFEFL 287

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297746071|emb|CBI16127.3| unnamed protein product [Vitis vinifera]

 Score =  125 bits (315), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 68/135 (50%), Positives = 86/135 (63%), Gaps = 16/135 (11%)

Query: 104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENS 163
           E WLPPGW +E RVR+SGA+AG+ DKY+    +GRRFRSKKEV Y+LETG  RK+ K+N 
Sbjct: 7   EDWLPPGWIVEGRVRSSGASAGSRDKYFIEPITGRRFRSKKEVRYYLETGEVRKKPKKNP 66

Query: 164 NADMDSSGSAAGSTKQKKPNIKAKTSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEV 223
           +                 P    K+  LNF++ + P+ V+WV T  SEG WTPFI   EV
Sbjct: 67  D---------------NSPEKGTKSPPLNFNFEDVPDTVKWVRTGSSEG-WTPFINGQEV 110

Query: 224 PESVRQDWAAAFTDL 238
           PES ++DWAAAF  L
Sbjct: 111 PESSKRDWAAAFEFL 125

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	248
TAIR|locus:2148308	225	MBD6 "methyl-CPG-binding domai	0.846	0.933	0.387	4e-35
TAIR|locus:2075135	182	MBD5 "methyl-CPG-binding domai	0.641	0.873	0.440	3.8e-30
UNIPROTKB|F1RPM5	360	MBD2 "Uncharacterized protein"	0.217	0.15	0.438	0.00023
UNIPROTKB|D4A986	380	D4A986 "Uncharacterized protei	0.217	0.142	0.438	0.00025
UNIPROTKB|Q9UBB5	411	MBD2 "Methyl-CpG-binding domai	0.217	0.131	0.438	0.00028
MGI|MGI:1333813	414	Mbd2 "methyl-CpG binding domai	0.217	0.130	0.438	0.00029

TAIR|locus:2148308 MBD6 "methyl-CPG-binding domain 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 380 (138.8 bits), Expect = 4.0e-35, P = 4.0e-35
 Identities = 84/217 (38%), Positives = 119/217 (54%)

Query:    35 PPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIREHKSENLATTNGTESAL-TPE 93
             PPDPLL SG FI +A   T  S+      Q     G     +S  +   NGT+      E
Sbjct:    10 PPDPLLASGAFISSAGDGTLDSSAKRRPIQGGI--GISGSGESVRIGMANGTDQVNHQTE 67

Query:    94 TASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETG 153
             + S +R    + WLPPGW +ED++RTSGATAG+VDKYY+   +GR+FRS+ EVLY+LE G
Sbjct:    68 SKSRKRAAPGDNWLPPGWRVEDKIRTSGATAGSVDKYYYEPNTGRKFRSRTEVLYYLEHG 127

Query:   154 TKRKRRKEXXXXXXXXXXXXXXXTKQ--KKPNIKAKTSA-LNFDYFNSPENVEWVLTDPS 210
             T ++  K+               + +  +   +       L+FD+ N P+ V W + +  
Sbjct:   128 TSKRGTKKAENTYFNPDHFEGQGSNRVTRTATVPPPPPPPLDFDFKNPPDKVSWSMANAG 187

Query:   211 EGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSKI 247
             E  W P IG V+V +SVR+DW+ AFT +T S N SK+
Sbjct:   188 EEGWIPNIGDVKVQDSVRRDWSTAFTFIT-SRNPSKV 223

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

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

GO:0008150 "biological_process" evidence=ND

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

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

GO:0005720 "nuclear heterochromatin" evidence=IDA

GO:0010370 "perinucleolar chromocenter" evidence=IDA

GO:0019899 "enzyme binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0043621 "protein self-association" evidence=IDA

GO:0005731 "nucleolus organizer region" evidence=IDA

TAIR|locus:2075135 MBD5 "methyl-CPG-binding domain protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 333 (122.3 bits), Expect = 3.8e-30, P = 3.8e-30
 Identities = 74/168 (44%), Positives = 92/168 (54%)

Query:    87 ESALTP-ETASTRRLT-ATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKK 144
             E+  TP ++ S +R T   + WLPP W  E RVRTSG  AGTVDK+Y+   +GR+FRSK 
Sbjct:    13 ENPATPVDSKSRKRATPGDDNWLPPDWRTEIRVRTSGTKAGTVDKFYYEPITGRKFRSKN 72

Query:   145 EVLYFLETGTKRKRR---KEXXXXXXXXXXXXXXXTKQKKPNIKAKT---SALNFDYFNS 198
             EVLY+LE GT +K+     E                +Q K N K        LNFD+ N 
Sbjct:    73 EVLYYLEHGTPKKKSVKTAENGDSHSEHSEGRGSARRQTKSNKKVTEPPPKPLNFDFLNV 132

Query:   199 PENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFTDLTTSNNGSK 246
             PE V W   + SE +W PFIG  ++ ESV QDW   FT L TS N  K
Sbjct:   133 PEKVTWTGINGSEEAWLPFIGDYKIQESVSQDWDRVFT-LVTSQNAGK 179

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

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

GO:0008150 "biological_process" evidence=ND

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

GO:0005720 "nuclear heterochromatin" evidence=IDA

GO:0010370 "perinucleolar chromocenter" evidence=IDA

GO:0019899 "enzyme binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0043621 "protein self-association" evidence=IDA

UNIPROTKB|F1RPM5 MBD2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 115 (45.5 bits), Expect = 0.00023, P = 0.00023
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query:    94 TASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
             T S +R+      LPPGW+ E+ +R SG +AG  D YYF   SG++FRSK ++  +L
Sbjct:    92 TESGKRMDCPA--LPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYL 145

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0043623 "cellular protein complex assembly" evidence=IEA

GO:0042711 "maternal behavior" evidence=IEA

GO:0042127 "regulation of cell proliferation" evidence=IEA

GO:0035197 "siRNA binding" evidence=IEA

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000792 "heterochromatin" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0000118 "histone deacetylase complex" evidence=IEA

UNIPROTKB|D4A986 D4A986 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 115 (45.5 bits), Expect = 0.00025, P = 0.00025
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query:    94 TASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
             T S +R+      LPPGW+ E+ +R SG +AG  D YYF   SG++FRSK ++  +L
Sbjct:   113 TESGKRMDCPA--LPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYL 166

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q9UBB5 MBD2 "Methyl-CpG-binding domain protein 2" [Homo sapiens (taxid:9606)]

 Score = 115 (45.5 bits), Expect = 0.00028, P = 0.00028
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query:    94 TASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
             T S +R+      LPPGW+ E+ +R SG +AG  D YYF   SG++FRSK ++  +L
Sbjct:   144 TESGKRMDCPA--LPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYL 197

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0000118 "histone deacetylase complex" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0000792 "heterochromatin" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IEA

GO:0035197 "siRNA binding" evidence=IEA

GO:0042127 "regulation of cell proliferation" evidence=IEA

GO:0042711 "maternal behavior" evidence=IEA

GO:0043623 "cellular protein complex assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0008327 "methyl-CpG binding" evidence=IDA;NAS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0019904 "protein domain specific binding" evidence=IPI

GO:0070742 "C2H2 zinc finger domain binding" evidence=IPI

GO:0003696 "satellite DNA binding" evidence=TAS

MGI|MGI:1333813 Mbd2 "methyl-CpG binding domain protein 2" [Mus musculus (taxid:10090)]

 Score = 115 (45.5 bits), Expect = 0.00029, P = 0.00029
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query:    94 TASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
             T S +R+      LPPGW+ E+ +R SG +AG  D YYF   SG++FRSK ++  +L
Sbjct:   147 TESGKRMDCPA--LPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYL 200


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        0.309   0.125   0.367    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      248       233   0.00086  113 3  11 23  0.38    34
                                                     32  0.43    36


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:  6
  No. of states in DFA:  598 (64 KB)
  Total size of DFA:  184 KB (2105 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:  21.88u 0.07s 21.95t   Elapsed:  00:00:03
  Total cpu time:  21.88u 0.07s 21.95t   Elapsed:  00:00:04
  Start:  Mon May 20 19:57:27 2013   End:  Mon May 20 19:57:31 2013

GO:0000118 "histone deacetylase complex" evidence=IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0000785 "chromatin" evidence=IDA

GO:0000792 "heterochromatin" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0003682 "chromatin binding" evidence=IDA

GO:0003729 "mRNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008327 "methyl-CpG binding" evidence=ISO;IDA

GO:0019904 "protein domain specific binding" evidence=ISO

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IGI

GO:0035197 "siRNA binding" evidence=IDA

GO:0042127 "regulation of cell proliferation" evidence=IGI

GO:0042711 "maternal behavior" evidence=IMP

GO:0043623 "cellular protein complex assembly" evidence=IMP

GO:0070742 "C2H2 zinc finger domain binding" evidence=ISO

---

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)
Q9LTJ1	MBD6_ARATH	No assigned EC number	0.3954	0.8588	0.9466	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

Your Input: scaffold_802568.1 annotation not avaliable (233 aa) (Arabidopsis lyrata)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	248
cd01396	77	cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and M	6e-11
pfam01429	75	pfam01429, MBD, Methyl-CpG binding domain	2e-10
cd00122	62	cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8	4e-09
smart00391	77	smart00391, MBD, Methyl-CpG binding domain	8e-06

>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 = 56.6 bits (137), Expect = 6e-11
 Identities = 22/51 (43%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTK 155
             LPPGW+ E   R SG +AG  D YY    +G++FRSK E+  +LE    
Sbjct: 5   PRLPPGWKRELVPRKSG-SAGKFDVYYIS-PTGKKFRSKVELARYLEKNGP 53

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|216497 pfam01429, MBD, Methyl-CpG binding domain

 Score = 55.1 bits (133), Expect = 2e-10
 Identities = 24/46 (52%), Positives = 34/46 (73%), Gaps = 1/46 (2%)

Query: 106 WLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
            LPPGW  E+R R SG++AG VD YY+   +G++FRSK E++ +LE
Sbjct: 9   PLPPGWRREERQRKSGSSAGKVDVYYYS-PTGKKFRSKSELIRYLE 53

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|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 = 51.2 bits (123), Expect = 4e-09
 Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 2/48 (4%)

Query: 104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
              LPPGW+ E  +R SG +AG  D YY+    G++ RSK EV  +LE
Sbjct: 3   RDPLPPGWKRELVIRKSG-SAGKGDVYYYS-PCGKKLRSKPEVARYLE 48

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|128673 smart00391, MBD, Methyl-CpG binding domain

 Score = 42.4 bits (100), Expect = 8e-06
 Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVL-YFLETGT 154
           LP GW  E + R SG +AG  D YY     G++ RSK E+  Y  + G 
Sbjct: 8   LPCGWRRETKQRKSGRSAGKFDVYYIS-PCGKKLRSKSELARYLHKNGD 55

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	248
cd01396	77	MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are me	99.74
PF01429	77	MBD: Methyl-CpG binding domain; InterPro: IPR00173	99.74
cd00122	62	MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and	99.69
smart00391	77	MBD Methyl-CpG binding domain. Methyl-CpG binding	99.68
KOG4161	272	consensus Methyl-CpG binding transcription regulat	99.53
cd01397	73	HAT_MBD Methyl-CpG binding domains (MBD) present i	99.48
cd01395	60	HMT_MBD Methyl-CpG binding domains (MBD) present i	98.5
PF00397	31	WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp	90.51

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

Probab=99.74  E-value=3e-18  Score=130.02  Aligned_cols=60  Identities=37%  Similarity=0.654  Sum_probs=55.0

Q ss_pred             CCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          103 TEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       103 ~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      .++.||+||+||+++|++| +++++|+|||+| +|++|||+.||++||+.......+.+||+
T Consensus         3 ~~~~lp~GW~r~~~~R~~g-s~~k~DvyY~sP-~Gkk~RS~~ev~~yL~~~~~~~~~~~~Fd   62 (77)
T cd01396           3 EDPRLPPGWKRELVPRKSG-SAGKFDVYYISP-TGKKFRSKVELARYLEKNGPTSLDLSDFD   62 (77)
T ss_pred             CCCCCCCCCEEEEEEecCC-CCCcceEEEECC-CCCEEECHHHHHHHHHhCCCCCCcHhHcc
Confidence            4667999999999999999 889999999999 89999999999999999876667778888

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.

>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=99.74  E-value=4.7e-18  Score=127.43  Aligned_cols=63  Identities=41%  Similarity=0.721  Sum_probs=54.7

Q ss_pred             ccCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCC-cccccccCCc
Q 045019          101 TATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGT-KRKRRKENSN  164 (248)
Q Consensus       101 ~~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~-~~~~~~en~~  164 (248)
                      .+.+.+||+||++|+++|++|.++|+.|+||++| +|++|||+.||.+||..+. ....+.++|+
T Consensus         5 ~~~~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP-~Gk~~RS~~eV~~yL~~~~~~~~l~~~~F~   68 (77)
T PF01429_consen    5 SPLDPPLPDGWKREVVVRKSGSSAGKKDVYYYSP-CGKRFRSKKEVVRYLKENPSEHDLKPENFS   68 (77)
T ss_dssp             ECEBTTSTTT-EEEEEESSSSTTTTSEEEEEEET-TSEEESSHHHHHHHHTTSS---SS-CTTBB
T ss_pred             ccccCCCCCCCEEEEEEecCCCcCCceEEEEECC-CCCEEeCHHHHHHHHHhCCCcccCCHhHCC
Confidence            4568899999999999999999999999999999 9999999999999999988 4666667776

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.

>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=99.69  E-value=4.7e-17  Score=117.67  Aligned_cols=58  Identities=41%  Similarity=0.662  Sum_probs=52.1

Q ss_pred             CCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       105 ~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      .+||.||+||+++|++| +.+++|+||++| +|++|||+.||++||........+.+||+
T Consensus         4 ~P~p~GW~R~~~~r~~g-~~~k~dv~Y~sP-~Gk~~Rs~~ev~~yL~~~~~~~l~~~~F~   61 (62)
T cd00122           4 DPLPPGWKRELVIRKSG-SAGKGDVYYYSP-CGKKLRSKPEVARYLEKTGPSSLDLENFS   61 (62)
T ss_pred             CCCCCCeEEEEEEcCCC-CCCcceEEEECC-CCceecCHHHHHHHHHhCCCCCCcHHHCC
Confidence            46799999999999999 789999999999 89999999999999999875556667775

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.

>smart00391 MBD Methyl-CpG binding domain

Probab=99.68  E-value=7.2e-17  Score=122.36  Aligned_cols=57  Identities=35%  Similarity=0.609  Sum_probs=55.0

Q ss_pred             CCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       107 LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      ||.||.|++++|++|.++|+.|+||++| +|++|||+.||.+||.+.....++.++|+
T Consensus         8 lp~GW~R~~~~r~~g~~~~~~dV~Y~sP-~GkklRs~~ev~~YL~~~~~~~~~~~~F~   64 (77)
T smart00391        8 LPCGWRRETKQRKSGRSAGKFDVYYISP-CGKKLRSKSELARYLHKNGDLSLDLECFD   64 (77)
T ss_pred             CCCCcEEEEEEecCCCCCCcccEEEECC-CCCeeeCHHHHHHHHHhCCCccccccccc
Confidence            9999999999999999999999999999 99999999999999999998888889888

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

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

Probab=99.53  E-value=1.2e-14  Score=131.91  Aligned_cols=148  Identities=24%  Similarity=0.387  Sum_probs=104.1

Q ss_pred             cccccccCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccc---------------
Q 045019           96 STRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRK---------------  160 (248)
Q Consensus        96 ~~~kl~~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~---------------  160 (248)
                      ..++ ..+|..||+||.+++++|++|.++|+.|+||++| +|++||||.++.+||+..+......               
T Consensus         9 ~~~~-~~~c~~lp~GW~~~~~~r~~~~~~g~~dv~~~sp-~g~~frsk~~l~~~~~~~~~~s~~~~v~~k~~~~~~~~~~   86 (272)
T KOG4161|consen    9 IAGK-RSDCPALPPGWTREEVQRSSGLSAGKSDVYYISP-SGKKFRSKPQLARYLGKVGDLSLFDFVTGKMSPSERQKNK   86 (272)
T ss_pred             cccC-cccCCCCCCCcchhhhcccCCCcccccceEEeCC-cccccccccHHHHHhccccccccCcccccccccccccccC
Confidence            3344 6789999999999999999999999999999999 8999999999999999544322211               


Q ss_pred             --cCCcc----------CCC-----------------CCCcCC-------------------------------------
Q 045019          161 --ENSNA----------DMD-----------------SSGSAA-------------------------------------  174 (248)
Q Consensus       161 --en~~~----------~~n-----------------~~~~s~-------------------------------------  174 (248)
                        +..+.          +.+                 .+..|.                                     
T Consensus        87 q~~~~~~~~~~k~~~r~~~~~~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql~~~~~~~~l~~~s~~~  166 (272)
T KOG4161|consen   87 QRKPEDPSKSNKRKGRGDLNLAIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQLFWLERLQDLEADSSRG  166 (272)
T ss_pred             CCCCCchhhhhccCCCcccccCCchhhhhccccccceeeccccchhhhhccccccccccccceEEEeccccccccccccc
Confidence              11111          000                 000000                                     


Q ss_pred             C----------CcCcCCCCcccc---------ccccccCCCCCCcceEEEEecCCCCCcccccCCcccC-hhhhhhHHH-
Q 045019          175 G----------STKQKKPNIKAK---------TSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVP-ESVRQDWAA-  233 (248)
Q Consensus       175 ~----------~~Ks~K~~k~~k---------~~~~nfD~~npP~KV~WVLsgp~~~~WtPfidds~Vp-es~K~~Ws~-  233 (248)
                      +          ++...+.-.++.         ..++.+++...|+.|.|....+..+.|.|++.+.+|+ +.++++|+. 
T Consensus       167 e~~d~~~l~~~~~g~~~~~~~~s~~~~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~  246 (272)
T KOG4161|consen  167 ESIDKLSLPKTPQGSGRSSAGESLLSSVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRV  246 (272)
T ss_pred             cccCccccCcCCCccCccccccccccccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccch
Confidence            0          000011001111         1156667788889999999998889999999999999 999999999 


Q ss_pred             ------HHHHhhhcCCCe
Q 045019          234 ------AFTDLTTSNNGS  245 (248)
Q Consensus       234 ------aF~~l~~~~~g~  245 (248)
                            .|..|+.++-..
T Consensus       247 ~~~r~~~~~~l~sd~~~~  264 (272)
T KOG4161|consen  247 KNVRRSLFSALTSDTLSK  264 (272)
T ss_pred             hhhhhccccchhhcCcch
Confidence                  777777765443

>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=99.48  E-value=5.1e-14  Score=107.16  Aligned_cols=58  Identities=26%  Similarity=0.394  Sum_probs=53.2

Q ss_pred             CCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       105 ~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      -.||.||+||+++|+.| +.++.|+||++| +|+||||+.||.+||........+.|||.
T Consensus         4 ~Pl~~GW~Re~vir~~~-~~~~~dV~Y~aP-cGKklRs~~ev~~yL~~~~~~~Lt~dnFs   61 (73)
T cd01397           4 VPLELGWRRETRIRGLG-GRIQGEVAYYAP-CGKKLRQYPEVIKYLSKNGISLLSRENFS   61 (73)
T ss_pred             CCCCCCceeEEEeccCC-CCccceEEEECC-CCcccccHHHHHHHHHhCCccCccHhHcc
Confidence            36899999999999998 779999999999 99999999999999998777777778887

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.

>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=98.50  E-value=1.8e-07  Score=69.12  Aligned_cols=55  Identities=20%  Similarity=0.126  Sum_probs=46.9

Q ss_pred             CCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          106 WLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       106 ~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      .|--||.|....|+.|.  -+.|++|.+| +|+++|+..||++||... ......|||.
T Consensus         5 Pll~gw~R~~~~~~~~~--~k~~V~Y~aP-CGr~Lr~~~EV~~YL~~t-~~~L~~d~Fs   59 (60)
T cd01395           5 PLLCGFQRMKYRARVGK--VKKHVIYKAP-CGRSLRNMSEVHRYLRET-CSFLTVDNFS   59 (60)
T ss_pred             ccccCeEEEEEeccCCC--cccceEEECC-cchhhhcHHHHHHHHHhc-cccceeeccc
Confidence            46789999998888773  5889999999 999999999999999988 5555557774

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.

>PF00397 WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet

Probab=90.51  E-value=0.28  Score=31.17  Aligned_cols=26  Identities=42%  Similarity=0.864  Sum_probs=17.7

Q ss_pred             CCCCceEEEEEccCCCCCCceeEEEeeCCCCCe
Q 045019          107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR  139 (248)
Q Consensus       107 LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK  139 (248)
                      ||+||.+....+ +|      ..||+...+|..
T Consensus         1 LP~gW~~~~~~~-~g------~~YY~N~~t~~s   26 (31)
T PF00397_consen    1 LPPGWEEYFDPD-SG------RPYYYNHETGES   26 (31)
T ss_dssp             SSTTEEEEEETT-TS------EEEEEETTTTEE
T ss_pred             CCcCCEEEEcCC-CC------CEEEEeCCCCCE
Confidence            899997443212 33      589999988753

This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.; GO: 0005515 protein binding; PDB: 2JXW_A 2DK1_A 2JOC_A 2JO9_A 1YIU_A 1O6W_A 2JMF_A 1TK7_A 2KYK_A 2L5F_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	248
2ky8_A	72	Solution Structure And Dynamic Analysis Of Chicken		2e-05

>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

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/44 (50%), Positives = 31/44 (70%), Gaps = 1/44 (2%)
Query: 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFL 150
           LPPGW+ E+ +R SG +AG  D YYF   SG++FRSK ++  +L
Sbjct: 13  LPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYL 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	248
2ky8_A	72	Methyl-CPG-binding domain protein 2; DNA binding d	9e-13
1d9n_A	75	Methyl-CPG-binding protein MBD1; PCM1, methylation	5e-11
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	1e-09
1ub1_A	133	MECP2, attachment region binding protein; chicken	5e-08

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

 Score = 61.1 bits (148), Expect = 9e-13
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 95  ASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETG 153
            S ++       LPPGW+ E+ +R SG +AG  D YYF   SG++FRSK ++  +L   
Sbjct: 1   GSDKQGRTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFS-PSGKKFRSKPQLARYLGNA 58

>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 = 56.1 bits (135), Expect = 5e-11
 Identities = 20/47 (42%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
             L PGW+  +  R SGAT G  D YY    +G R RSK E+  +L 
Sbjct: 9   PALGPGWKRREVFRKSGATCGRSDTYYQS-PTGDRIRSKVELTRYLG 54

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

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 94  TASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLET 152
               R     +  LP GW  + + R SG +AG  D Y  +   G+ FRSK E++ + E 
Sbjct: 11  IIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLIN-PQGKAFRSKVELIMYFEK 68

>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 = 49.5 bits (117), Expect = 5e-08
 Identities = 28/118 (23%), Positives = 49/118 (41%), Gaps = 4/118 (3%)

Query: 73  REHKSENLATTNGTESALTPETASTRRLTATEAW-LPPGWEIEDRVRTSGATAGTVDKYY 131
             H     A    + S     +    R    +   LP GW  + + R SG +AG  D Y 
Sbjct: 3   HHHHHHAPAVPEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYL 62

Query: 132 FHVASGRRFRSKKEVLYFLETGTKRKRRKENSNADMDSSGSAAGSTKQKKPNIKAKTS 189
            +   G+ FRSK E++ +           + ++ D   +G  + S ++++P  KAK+ 
Sbjct: 63  IN-PQGKAFRSKVELIAYF--EKVGDTSLDPNDFDFTVTGRGSPSRREQRPPKKAKSP 117

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	248
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	99.8
3vxv_A	69	Methyl-CPG-binding domain protein 4; methyl CPG bi	99.79
1ub1_A	133	MECP2, attachment region binding protein; chicken	99.78
2ky8_A	72	Methyl-CPG-binding domain protein 2; DNA binding d	99.78
1d9n_A	75	Methyl-CPG-binding protein MBD1; PCM1, methylation	99.77
1ymz_A	43	CC45; artificial protein, computational design, un	83.76
2jv4_A	54	Peptidyl-prolyl CIS/trans isomerase; ppiase domain	83.03
2ysh_A	40	GAS-7, growth-arrest-specific protein 7; WW domain	82.57
1wr3_A	36	Ubiquitin-protein ligase NEDD4-2; all-beta; NMR {M	82.54
2ysg_A	40	Syntaxin-binding protein 4; synip, STXBP4, WW doma	82.44
2law_A	38	Yorkie homolog; YAP, SMAD1, CDK, signal transducti	82.36
2ysf_A	40	E3 ubiquitin-protein ligase itchy homolog; AIP4, N	81.67
1wr4_A	36	Ubiquitin-protein ligase NEDD4-2; all-beta; NMR {M	81.65
1wr7_A	41	NEDD4-2; all-beta, ligase; NMR {Mus musculus}	81.35
1e0m_A	37	Wwprototype; SH3 prototype, protein design, de nov	80.04

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

Probab=99.80  E-value=8.2e-20  Score=143.92  Aligned_cols=63  Identities=29%  Similarity=0.512  Sum_probs=57.4

Q ss_pred             ccCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          101 TATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       101 ~~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      ...+++||+||++|+++|++|.++|++|+|||+| +|++|||+.||++||+.......+.++|+
T Consensus        18 ~~~~~~lP~GW~re~~~R~~G~s~gk~DvYY~sP-~GkkfRSk~ev~ryL~~~g~~~~~~~~Fd   80 (97)
T 3c2i_A           18 MYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINP-QGKAFRSKVELIMYFEKVGDTSLDPNDFD   80 (97)
T ss_dssp             CCCCTTSCTTCEEEEEECCSSTTTTCEEEEEECT-TSCEECSHHHHHHHHHHHTCCSSCTTTCC
T ss_pred             ccCCCCCCCCCEEEEEEecCCCCCCcceEEEECC-CCCEEECHHHHHHHHHHCCCCCCCHhhcc
Confidence            4678899999999999999999999999999999 89999999999999997665556778887

>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=99.79  E-value=1.7e-19  Score=133.82  Aligned_cols=61  Identities=33%  Similarity=0.512  Sum_probs=54.9

Q ss_pred             CCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          103 TEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       103 ~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      .|..||+||.||+++|++|.++|+.|+||++| +|+||||+.||++||+.......+.++|+
T Consensus         2 ~~~plp~GW~R~~~~R~~G~s~gk~DvyY~sP-~Gkk~RSk~ev~~yL~~~~~~~l~~~~Fd   62 (69)
T 3vxv_A            2 GHKPVPCGWERVVKQRLSGKTAGKFDVYFISP-QGLKFRSKRSLANYLLKNGETFLKPEDFN   62 (69)
T ss_dssp             --CCSCTTCEEEEEECCSSTTTTCEEEEEECT-TSCEECSHHHHHHHHHHHCCCCCCGGGSC
T ss_pred             CCCcCCCCCEEEEEEeccCCCCCcceEEEEcC-CCCEeeCHHHHHHHHHhCCCCCCCHHHcc
Confidence            46789999999999999999999999999999 89999999999999999876666778887

>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=99.78  E-value=5.6e-19  Score=145.92  Aligned_cols=62  Identities=29%  Similarity=0.513  Sum_probs=58.1

Q ss_pred             cCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          102 ATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       102 ~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      ..|++||+||+||+++|++|.++|++|+|||+| +|++|||+.||++||+.......+.++|+
T Consensus        33 ~~~~~LP~GWkRe~~~RksG~Sagk~DVYY~SP-~GKkfRSk~Ev~ryL~~~~~~~~~~e~Fd   94 (133)
T 1ub1_A           33 YDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINP-QGKAFRSKVELIAYFEKVGDTSLDPNDFD   94 (133)
T ss_dssp             SCCCCBTTBCEEEEEECCCSSSCCSEEEEEECT-TSCEESSHHHHHHHHTTSCCCSCCGGGCC
T ss_pred             cCCCCCCCCCEEEEEEecCCCCCCceeEEEECC-CCCeeeCHHHHHHHHHHCCccCCCHhHCc
Confidence            788999999999999999999999999999999 89999999999999998776667779998

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

Probab=99.78  E-value=3.8e-19  Score=132.79  Aligned_cols=59  Identities=37%  Similarity=0.679  Sum_probs=53.7

Q ss_pred             ccCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          101 TATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       101 ~~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      ..++++||+||.||+++|++|.++|+.|+|||+| +|++|||+.||++||..+    .+.++|+
T Consensus         7 ~~~~p~Lp~GW~R~~~~R~~g~s~~k~DvyY~sP-~Gkr~RS~~ev~~YL~~~----l~~~~Fd   65 (72)
T 2ky8_A            7 RTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSP-SGKKFRSKPQLARYLGNA----VDLSCFD   65 (72)
T ss_dssp             EEECSSSCTTCEEEEEECCSSTTTTCEEEEEECT-TCCEEESHHHHHHHHTTS----SCCTTCB
T ss_pred             cccCCCCCCCCEEEEEEecCCCCCCceEEEEECC-CCCEeEcHHHHHHHHhcC----CChhhcC
Confidence            4577899999999999999999999999999999 999999999999999883    5667776

>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=99.77  E-value=1.7e-19  Score=135.91  Aligned_cols=58  Identities=34%  Similarity=0.503  Sum_probs=52.9

Q ss_pred             cCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          102 ATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       102 ~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      ..|+.||+||+||+++|++|.++|+.|+|||+| +|++|||+.||++||+.    .++.++|+
T Consensus         6 ~~~p~LP~GW~Re~~~R~~g~s~gk~DvyY~sP-~Gkk~RS~~ev~ryL~~----~~~~~~Fd   63 (75)
T 1d9n_A            6 LDCPALGPGWKRREVFRKSGATCGRSDTYYQSP-TGDRIRSKVELTRYLGP----ACDLTLFD   63 (75)
T ss_dssp             EECTTTCSSCEEEECSSSSSCTTCCCCEEEECS-SSCEECSTHHHHHHHCT----TCCCTTCC
T ss_pred             ccCCCCCCCCEEEEEEecCCCCCCceEEEEECC-CCCeeecHHHHHHHhcc----CCCccccC
Confidence            468899999999999999999999999999999 99999999999999974    45667776

>1ymz_A CC45; artificial protein, computational design, unknown function; NMR {Synthetic} SCOP: k.22.1.1

Probab=83.76  E-value=1.2  Score=29.00  Aligned_cols=28  Identities=39%  Similarity=0.770  Sum_probs=17.7

Q ss_pred             CCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCC
Q 045019          103 TEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGR  138 (248)
Q Consensus       103 ~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGk  138 (248)
                      .+..||+||....  -.+|      .+||+.-.++.
T Consensus         5 ~~~~LP~gW~~~~--~~~G------r~YY~n~~T~~   32 (43)
T 1ymz_A            5 RSMPLPPGWERRT--DVEG------KVYYFNVRTLT   32 (43)
T ss_dssp             --CCCCSSEEEEE--CTTS------CEEEEETTTTE
T ss_pred             cCCCCCCCCEEEE--CCCC------CEEEEECCCCC
Confidence            3568999996652  2233      47899886664

>2jv4_A Peptidyl-prolyl CIS/trans isomerase; ppiase domain, WW domain group IV, rotamase; NMR {Emericella nidulans}

Probab=83.03  E-value=1.3  Score=30.87  Aligned_cols=40  Identities=23%  Similarity=0.521  Sum_probs=24.0

Q ss_pred             CCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCe------eecHHHHHHHH
Q 045019          104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR------FRSKKEVLYFL  150 (248)
Q Consensus       104 ~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK------FRSK~EV~rYL  150 (248)
                      ...||+||.... -+..|      -.||+...|+..      -....+|..|+
T Consensus         5 ~~~LP~GW~~~~-~~~~G------r~YY~N~~T~~sqWe~P~~~~~~~l~~~~   50 (54)
T 2jv4_A            5 NTGLPAGWEVRH-SNSKN------LPYYFNPATRESRWEPPADTDMETLKMYM   50 (54)
T ss_dssp             CCCCCSSCCEEE-CSSSS------CEEEEETTTTEEESSCCTTSCHHHHHHHH
T ss_pred             CCCCCCCcEEEE-ECCCC------CEEEEECCCCcEEecCCCCccHHHHHHHH
Confidence            357999997431 22233      479999877763      23445555554

>2ysh_A GAS-7, growth-arrest-specific protein 7; WW domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.22.1.1

Probab=82.57  E-value=1.9  Score=27.54  Aligned_cols=29  Identities=28%  Similarity=0.668  Sum_probs=18.8

Q ss_pred             CCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCe
Q 045019          103 TEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR  139 (248)
Q Consensus       103 ~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK  139 (248)
                      ....||+||....  -..|      .+||+...++..
T Consensus         4 ~~~~LP~gW~~~~--d~~G------r~YY~n~~T~~t   32 (40)
T 2ysh_A            4 GSSGLPPGWQSYL--SPQG------RRYYVNTTTNET   32 (40)
T ss_dssp             CCSSCCTTCEEEE--CTTS------CEEEECSSSCCE
T ss_pred             CCCCCCCCceEEE--CCCC------CEEEEECCCCCE
Confidence            3467999995442  2333      478998877654

>1wr3_A Ubiquitin-protein ligase NEDD4-2; all-beta; NMR {Mus musculus}

Probab=82.54  E-value=1.5  Score=27.42  Aligned_cols=27  Identities=33%  Similarity=0.656  Sum_probs=18.5

Q ss_pred             CCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCe
Q 045019          105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR  139 (248)
Q Consensus       105 ~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK  139 (248)
                      ..||+||....-  .+|      .+||++-.++..
T Consensus         3 ~~LP~GWe~~~d--~~G------~~Yy~n~~t~~t   29 (36)
T 1wr3_A            3 PPLPPGWEEKVD--NLG------RTYYVNHNNRST   29 (36)
T ss_dssp             SCSCTTEEEEEC--SSS------CEEEEETTTCCE
T ss_pred             CCCCCCCEEEEC--CCC------CEEEEECCCCCE
Confidence            469999976632  233      479998876653

>2ysg_A Syntaxin-binding protein 4; synip, STXBP4, WW domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.22.1.1

Probab=82.44  E-value=1.9  Score=27.81  Aligned_cols=27  Identities=30%  Similarity=0.557  Sum_probs=17.7

Q ss_pred             CCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCC
Q 045019          104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGR  138 (248)
Q Consensus       104 ~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGk  138 (248)
                      ...||+||.+..  -..|      -+|||+-.++.
T Consensus         5 ~~~LP~gWe~~~--~~~G------r~Yy~nh~t~~   31 (40)
T 2ysg_A            5 SSGLPYGWEEAY--TADG------IKYFINHVTQT   31 (40)
T ss_dssp             SSCCCTTEEEEE--CSSS------CEEEEESSSCC
T ss_pred             cCCCCCCcEEEE--cCCC------CEEEEECCCCc
Confidence            357999996553  2333      47999886554

>2law_A Yorkie homolog; YAP, SMAD1, CDK, signal transduction, signaling protein-TRAN complex; NMR {Homo sapiens}

Probab=82.36  E-value=1.2  Score=28.53  Aligned_cols=26  Identities=31%  Similarity=0.621  Sum_probs=18.3

Q ss_pred             CCCCCCceEEEEEccCCCCCCceeEEEeeCCCCC
Q 045019          105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGR  138 (248)
Q Consensus       105 ~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGk  138 (248)
                      ..||+||....-  .+|      .+|||+-.++.
T Consensus         5 ~~LP~gWe~~~~--~~G------~~Yy~nh~t~~   30 (38)
T 2law_A            5 GPLPDGWEQAMT--QDG------EIYYINHKNKT   30 (38)
T ss_dssp             CCCSSSCCEEEE--TTT------EEEEEETTTTE
T ss_pred             CCCCCCcEEEEC--CCC------CEEEEECCCCC
Confidence            469999977643  333      48999886654

>2ysf_A E3 ubiquitin-protein ligase itchy homolog; AIP4, NAPP1, WW domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: k.22.1.1

Probab=81.67  E-value=1.8  Score=27.97  Aligned_cols=27  Identities=26%  Similarity=0.536  Sum_probs=17.9

Q ss_pred             CCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCC
Q 045019          104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGR  138 (248)
Q Consensus       104 ~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGk  138 (248)
                      ...||+||.+.+-  .+|      -+|||+-.+..
T Consensus         5 ~~~LP~gWe~~~~--~~G------~~Yy~nh~t~~   31 (40)
T 2ysf_A            5 SSGLPEGWEMRFT--VDG------IPYFVDHNRRT   31 (40)
T ss_dssp             CCCCCSSEEEEEC--TTC------CEEEEETTTCC
T ss_pred             cCCCCcCcEEEEc--CCC------CEEEEECCCCc
Confidence            4579999976632  333      47898876543

>1wr4_A Ubiquitin-protein ligase NEDD4-2; all-beta; NMR {Mus musculus} PDB: 2lb2_A*

Probab=81.65  E-value=1.8  Score=26.70  Aligned_cols=27  Identities=30%  Similarity=0.613  Sum_probs=17.8

Q ss_pred             CCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCe
Q 045019          105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR  139 (248)
Q Consensus       105 ~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK  139 (248)
                      ..||+||...  ...+|      .+||+.-.++..
T Consensus         3 ~~LP~gWe~~--~d~~g------~~Yy~n~~t~~t   29 (36)
T 1wr4_A            3 PGLPSGWEER--KDAKG------RTYYVNHNNRTT   29 (36)
T ss_dssp             TTCCTTEEEE--ECSSS------CEEEEETTTTEE
T ss_pred             CCCCCCCEEE--ECCCC------CEEEEECCCCCE
Confidence            4799999665  22343      358998866543

>1wr7_A NEDD4-2; all-beta, ligase; NMR {Mus musculus}

Probab=81.35  E-value=1.7  Score=28.21  Aligned_cols=28  Identities=25%  Similarity=0.768  Sum_probs=18.9

Q ss_pred             CCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCe
Q 045019          104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR  139 (248)
Q Consensus       104 ~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK  139 (248)
                      ...||+||....-  .+|      -+|||+-.++..
T Consensus         6 ~~~LP~gWe~~~~--~~G------~~Yy~n~~t~~t   33 (41)
T 1wr7_A            6 QSFLPPGWEMRIA--PNG------RPFFIDHNTKTT   33 (41)
T ss_dssp             CCSSCTTEEEEEC--TTS------CEEEEETTTTEE
T ss_pred             cCCCCCCcEEEEc--CCC------CEEEEECCCCCe
Confidence            4579999976632  333      479998866543

>1e0m_A Wwprototype; SH3 prototype, protein design, de novo protein; NMR {} SCOP: k.22.1.1

Probab=80.04  E-value=2.2  Score=26.52  Aligned_cols=27  Identities=30%  Similarity=0.744  Sum_probs=17.8

Q ss_pred             CCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCe
Q 045019          105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR  139 (248)
Q Consensus       105 ~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK  139 (248)
                      ..||+||....  -.+|      -+||++-.++..
T Consensus         2 ~~LP~gW~~~~--~~~G------~~Yy~n~~t~~t   28 (37)
T 1e0m_A            2 MGLPPGWDEYK--THNG------KTYYYNHNTKTS   28 (37)
T ss_dssp             CCSCTTEEEEE--CSSC------CEEEEETTTTEE
T ss_pred             CCCCCCcEEEE--CCCC------CEEEEECCCCCe
Confidence            36999997653  2333      478988866654

---

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	248
d1ig4a_	75	d.10.1.3 (A:) Methylation-dependent transcriptiona	2e-11
d1qk9a_	92	d.10.1.3 (A:) Methyl-CpG-binding protein 2, MECP2	1e-10

>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 = 56.0 bits (135), Expect = 2e-11
 Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 106 WLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETG 153
            L PGW+  +  R SGAT G  D YY    +G R RSK E+  +L   
Sbjct: 10  ALGPGWKRREVFRKSGATCGRSDTYYQS-PTGDRIRSKVELTRYLGPA 56

>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 = 54.1 bits (130), Expect = 1e-10
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 94  TASTRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLE 151
               R     +  LP GW  + + R SG +AG  D Y  +   G+ FRSK E++ + E
Sbjct: 11  IIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLIN-PQGKAFRSKVELIAYFE 67

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	248
d1ig4a_	75	Methylation-dependent transcriptional repressor MB	99.77
d1qk9a_	92	Methyl-CpG-binding protein 2, MECP2 {Human (Homo s	99.76
d1pina1	34	Mitotic rotamase PIN1 {Human (Homo sapiens) [TaxId	87.1

>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=99.77  E-value=1.7e-19  Score=134.36  Aligned_cols=59  Identities=34%  Similarity=0.475  Sum_probs=53.1

Q ss_pred             ccCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019          101 TATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN  164 (248)
Q Consensus       101 ~~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~  164 (248)
                      .++|+.||+||+||+++|++|.++|+.|+|||+| +|++|||+.||.+||..    .++.++|+
T Consensus         5 ~~~~p~LP~GW~re~~~Rk~g~~~gk~DvyY~sP-~Gkk~RS~~ev~~yL~~----~l~~~~Fd   63 (75)
T d1ig4a_           5 WLDCPALGPGWKRREVFRKSGATCGRSDTYYQSP-TGDRIRSKVELTRYLGP----ACDLTLFD   63 (75)
T ss_dssp             EEECTTTCTTCEEEEECCCSSSSTTCCEEEEECS-SSCEECSHHHHHHHHCS----SSCCTTBC
T ss_pred             cccCCCCCCCcEEEEEEEcCCCCCCceeEEEECC-CCCEEeCHHHHHHHhcc----CCCcccee
Confidence            3567899999999999999999999999999999 89999999999999954    36667887

>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=99.76  E-value=3.8e-19  Score=136.53  Aligned_cols=64  Identities=28%  Similarity=0.482  Sum_probs=59.0

Q ss_pred             ccCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCcc
Q 045019          101 TATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSNA  165 (248)
Q Consensus       101 ~~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~~  165 (248)
                      ...++.||+||+||+++|++|.++|+.|+||++| +|++|||+.||.+||++......+.++|+-
T Consensus        18 ~~~dp~Lp~GW~r~~~~R~~g~~~gk~Dvyy~sP-~Gkk~RS~~eV~~yL~~~~~~~~~~~~FdF   81 (92)
T d1qk9a_          18 MYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINP-QGKAFRSKVELIAYFEKVGDTSLDPNDFDF   81 (92)
T ss_dssp             CSSBCCSSSSCEEEECCCCCSSSCSCCCEEEEET-TTEEESSHHHHHHHHHHHTCCSSCGGGCCC
T ss_pred             cccCCCCCCCCEEEEEEecCCCCCceeeEEEECC-CCCeeecHHHHHHHHHHCCCcccchhHeee
Confidence            4566789999999999999999999999999999 899999999999999998888888899983

>d1pina1 b.72.1.1 (A:6-39) Mitotic rotamase PIN1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: WW domain-like
superfamily: WW domain
family: WW domain
domain: Mitotic rotamase PIN1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.10  E-value=0.32  Score=29.57  Aligned_cols=27  Identities=37%  Similarity=0.727  Sum_probs=18.4

Q ss_pred             CCCCCceEEEEEccCCCCCCceeEEEeeCCCCCe
Q 045019          106 WLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR  139 (248)
Q Consensus       106 ~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK  139 (248)
                      .||+||...+ -..      ....||++..||..
T Consensus         1 ~LP~GW~~~~-d~~------~G~~YY~n~~T~~T   27 (34)
T d1pina1           1 KLPPGWEKRM-SRS------SGRVYYFNHITNAS   27 (34)
T ss_dssp             CCCTTEEEEE-CTT------SCCEEEEETTTCCE
T ss_pred             CcCCCcEEEE-CCC------CCCEEEEECCCCCE
Confidence            4999996653 122      33589999988764