Citrus Sinensis ID: 029175

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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-------
Protein Sequence
MEDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGDGTARDEGSVAMH
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccEEEEEccccccEEEEccHHHHHHHHHHcccccEEEccccccccccccccccccccEEEEccccccccccccEEEEEEccccccEEEEEEcccccccccHHHHHHHHHHcccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccEEEEEEHHHcccEEEcccHHHHHHHHHHHcccccEcccccccccccccccccccccEEEEEcccccccccccEEEEEEEcccccEEEEEEcccccEcccHHHHHHHHHHccccccccccccccccccccHcccccccEEccccccccccccccccccEccccccccccEccc
Coil and Loop (DISEMBL)
MEDKQETLKtaskkprgggepirsIDTYAAQCEKCFKWRVINSSEEYEEIRCKIaeipfvcdrkpgvscedpadieydasrvwvidrpgipktpggfkrsLVLRkdfskmdayyitptgkklRTLNEVAGFlaanpeysdvslsdftfsvpkvmddtipedvvkkgsassdakrkpktskgvvgdgtardegsvamh
Flexible Loop (DISEMBL)
medkqetlktaskkprgggepirsIDTYAAQCEKCFKWRVINSSEEYEEIRCKIaeipfvcdrkpgVSCEDPAdieydasrvwvidrpgipktpggfkrslvlrkdfskMDAYyitptgkklrTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDvvkkgsassdakrkpktskgvvgdgtardegsvamh
Low Complexity Region (SEG)
MEDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGDGTARDEGSVAMH
Disordered region (IsUnstruct)
***********************SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM*******************************************
Disordered Region (DISOPRED)
**************************TYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSV***********************************************
Disordered Region (DISEMBL)
*******************EPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPED***********************DGTAR********
Disordered Region (DISPRO)
*********************IRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDV***********************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGDGTARDEGSVAMH
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	197	2.2.26 [Sep-21-2011]
Q9LYB9	186	Methyl-CpG-binding domain	yes	no	0.715	0.758	0.687	4e-56
Q5XEN5	204	Methyl-CpG-binding domain	no	no	0.852	0.823	0.551	3e-53
Q8LA53	272	Methyl-CpG-binding domain	no	no	0.827	0.599	0.4	9e-30
Q4PSK1	163	Methyl-CpG-binding domain	no	no	0.609	0.736	0.430	1e-21
Q9FZP6	155	Putative methyl-CpG-bindi	no	no	0.619	0.787	0.377	1e-16

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

 Score =  217 bits (553), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 97/141 (68%), Positives = 117/141 (82%)

Query: 21  PIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDAS 80
           P R IDTYAAQC+ C KWRVI+S EEYE+IR K+ E PF C +K G+SCE+PADI+YD+S
Sbjct: 21  PGRLIDTYAAQCDNCHKWRVIDSQEEYEDIRSKMLEDPFNCQKKQGMSCEEPADIDYDSS 80

Query: 81  RVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSD 140
           R WVID+PG+PKTP GFKRSLVLRKD+SKMD YY TPTGKKLR+ NE+A F+ ANPE+ +
Sbjct: 81  RTWVIDKPGLPKTPKGFKRSLVLRKDYSKMDTYYFTPTGKKLRSRNEIAAFVEANPEFRN 140

Query: 141 VSLSDFTFSVPKVMDDTIPED 161
             L DF F+VPKVM+DT+P D
Sbjct: 141 APLGDFNFTVPKVMEDTVPPD 161

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 =  207 bits (527), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 97/176 (55%), Positives = 125/176 (71%), Gaps = 8/176 (4%)

Query: 10  TASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSC 69
           T  K  +  G P RSID +A QCEKC KWR I++ +EYE+IR ++ E PF C  K GVSC
Sbjct: 37  TTIKVQKKAGTPGRSIDVFAVQCEKCMKWRKIDTQDEYEDIRSRVQEDPFFCKTKEGVSC 96

Query: 70  EDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVA 129
           ED  D+ YD+SR WVID+PG+P+TP GFKRSL+LRKD+SKMDAYYITPTGKKL++ NE+A
Sbjct: 97  EDVGDLNYDSSRTWVIDKPGLPRTPRGFKRSLILRKDYSKMDAYYITPTGKKLKSRNEIA 156

Query: 130 GFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGD 185
            F+ AN +Y    L DF F+VPKVM++T+P  ++        + R PK S+ V  D
Sbjct: 157 AFIDANQDYKYALLGDFNFTVPKVMEETVPSGIL--------SDRTPKPSRKVTID 204

Probable transcriptional regulator.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  129 bits (325), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 70/175 (40%), Positives = 99/175 (56%), Gaps = 12/175 (6%)

Query: 2   EDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVC 61
           +D +E +     +P        SI  +  QC  CFKWR++ S ++YEEIR ++ E PF C
Sbjct: 33  DDTEEEVLPVQSQPLSSRTQCPSIGAFTVQCASCFKWRLMPSMQKYEEIREQLLENPFFC 92

Query: 62  DR----KPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSK--MDAYYI 115
           D     KP +SC+ PADI  D +R+W ID+P I + P G++R L +R +      D YY+
Sbjct: 93  DTAREWKPDISCDVPADIYQDGTRLWAIDKPNISRPPAGWQRLLRIRGEGGTRFADVYYV 152

Query: 116 TPTGKKLRTLNEVAGFLAANPEY--SDVSLSDFTFSVPKVMDDTIPEDVVKKGSA 168
            P+GKKLR+  EV  +L  N EY    V LS F+F +PK + D    D V+K  A
Sbjct: 153 APSGKKLRSTVEVQKYLNDNSEYIGEGVKLSQFSFQIPKPLQD----DYVRKRPA 203

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 =  103 bits (256), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 56/130 (43%), Positives = 78/130 (60%), Gaps = 10/130 (7%)

Query: 25  IDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPAD--IEYDASRV 82
           ID+YAAQC KC K R I S E+YEEIR K  E  F C R     CE+P D  + +D+  +
Sbjct: 9   IDSYAAQCWKCLKVRSIESQEDYEEIRSKTLEKFFECKR-----CEEPGDMVMNFDSLTM 63

Query: 83  -WVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYY--ITPTGKKLRTLNEVAGFLAANPEYS 139
            W  D   IPKTP G KR LV+R +  K+D YY  + P  K+ +++ EVA F+    E+ 
Sbjct: 64  RWFQDEHSIPKTPQGLKRVLVVRTNCVKVDVYYESLAPRRKRFKSIKEVATFIEDKEEFK 123

Query: 140 DVSLSDFTFS 149
           D++L + +F+
Sbjct: 124 DMTLEEVSFA 133

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 = 86.7 bits (213), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 51/135 (37%), Positives = 70/135 (51%), Gaps = 13/135 (9%)

Query: 30  AQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR----KPGVSCEDPADIEYDASRVWVI 85
            QC  C KWR+I S + Y  I+    + PFVC       P +SC  P D        W  
Sbjct: 2   VQCTDCKKWRLIPSMQHYNIIKETQLQTPFVCGTTSGWTPNMSCNVPQD--GTTCDTW-- 57

Query: 86  DRPGIPKTPGGFKRSLVLRKDFSKM-DAYYITPTGKKLRTLNEVAGFLAANPEY--SDVS 142
             P IP  P G+ RS+ +R + +K  D YY  P+G++LR+  EV  FL  +PEY    V+
Sbjct: 58  --PSIPPIPTGWSRSVHIRSESTKFADVYYFPPSGERLRSSAEVQSFLDNHPEYVREGVN 115

Query: 143 LSDFTFSVPKVMDDT 157
            S F+F +PK +DD 
Sbjct: 116 RSQFSFQIPKPLDDN 130

Probable transcriptional regulator.

Arabidopsis thaliana (taxid: 3702)

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	197
224128656	182	methyl binding domain protein [Populus t	0.868	0.939	0.712	1e-67
224117174	182	methyl binding domain protein [Populus t	0.868	0.939	0.695	4e-66
255567630	160	DNA binding protein, putative [Ricinus c	0.771	0.95	0.745	2e-59
297799740	176	hypothetical protein ARALYDRAFT_914336 [	0.868	0.971	0.570	4e-55
15229373	186	methyl-CPG-binding domain 4 protein [Ara	0.715	0.758	0.687	2e-54
356535711	193	PREDICTED: methyl-CpG-binding domain-con	0.868	0.886	0.606	2e-54
297817640	182	methyl-CpG-binding domain 4 [Arabidopsis	0.756	0.818	0.666	3e-54
358248398	177	uncharacterized protein LOC100802350 [Gl	0.868	0.966	0.595	4e-54
388511439	180	unknown [Lotus japonicus]	0.766	0.838	0.655	1e-53
388503158	176	unknown [Lotus japonicus]	0.766	0.857	0.642	5e-53

>gi|224128656|ref|XP_002320386.1| methyl binding domain protein [Populus trichocarpa] gi|118485542|gb|ABK94623.1| unknown [Populus trichocarpa] gi|222861159|gb|EEE98701.1| methyl binding domain protein [Populus trichocarpa]

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 124/174 (71%), Positives = 145/174 (83%), Gaps = 3/174 (1%)

Query: 2   EDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVC 61
           E   ET KT+SK PR     +RSIDTYAAQC+KC KWRVI + EEYEEIR K+ E PFVC
Sbjct: 5   ERSPETPKTSSKNPRVA---VRSIDTYAAQCDKCLKWRVIATEEEYEEIRSKMEESPFVC 61

Query: 62  DRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKK 121
           +RKPGVSC+DPADIEY+A+R WVIDRPGIPKTP GFKRSLVLR+DFSKMDAYYITPTGKK
Sbjct: 62  NRKPGVSCDDPADIEYNATRTWVIDRPGIPKTPEGFKRSLVLRRDFSKMDAYYITPTGKK 121

Query: 122 LRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRK 175
           LRT NE+A F+ ANP+Y DV+LSDF F+ PKVM+DTIPED V+K S+S +  ++
Sbjct: 122 LRTRNEIAAFIDANPKYKDVNLSDFNFTSPKVMEDTIPEDAVRKVSSSGNGNKR 175

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224117174|ref|XP_002331766.1| methyl binding domain protein [Populus trichocarpa] gi|224117178|ref|XP_002331767.1| hypothetical protein POPTRDRAFT_585558 [Populus trichocarpa] gi|222874359|gb|EEF11490.1| methyl binding domain protein [Populus trichocarpa] gi|222874360|gb|EEF11491.1| hypothetical protein POPTRDRAFT_585558 [Populus trichocarpa]

 Score =  256 bits (653), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 121/174 (69%), Positives = 143/174 (82%), Gaps = 3/174 (1%)

Query: 2   EDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVC 61
           E   ET KT+ K PR     +RSIDTYAAQC+KC KWRVI + EEYEEIR K+ E P+VC
Sbjct: 5   ERSPETPKTSPKNPRVA---VRSIDTYAAQCDKCLKWRVIPTEEEYEEIRSKMEENPYVC 61

Query: 62  DRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKK 121
           DRKPGVSC+DPADIEY+A+R WVIDRPG+PKTP GFKRSLVLR+DFSKMDAYYITPTGKK
Sbjct: 62  DRKPGVSCDDPADIEYNATRTWVIDRPGVPKTPEGFKRSLVLRRDFSKMDAYYITPTGKK 121

Query: 122 LRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRK 175
           LRT NE+A F+ ANP+Y DV+LS F F+ PKVM+DTIPED V+K  +S++  +K
Sbjct: 122 LRTRNEIAAFIEANPKYKDVNLSAFNFTSPKVMEDTIPEDAVRKVPSSANGNKK 175

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255567630|ref|XP_002524794.1| DNA binding protein, putative [Ricinus communis] gi|223535978|gb|EEF37637.1| DNA binding protein, putative [Ricinus communis]

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 114/153 (74%), Positives = 133/153 (86%), Gaps = 1/153 (0%)

Query: 22  IRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASR 81
           +RS+DTYAAQCEKC KWRVI + EEYEEIR KI E PF C+RKPG+SCEDPADIE DASR
Sbjct: 1   MRSVDTYAAQCEKCMKWRVIETEEEYEEIRSKIVENPFYCNRKPGISCEDPADIECDASR 60

Query: 82  VWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDV 141
            WVID+PG+PKTPGGFKRSLVLR+DFSKMDAYYITPTGKKLRT NE+A FL ANP+Y  V
Sbjct: 61  TWVIDKPGLPKTPGGFKRSLVLRRDFSKMDAYYITPTGKKLRTRNEIAAFLEANPKYKGV 120

Query: 142 SLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKR 174
           S+ DF F+ PKVM++T+PED VKK +AS+ +K+
Sbjct: 121 SIEDFNFTSPKVMEETVPED-VKKATASASSKK 152

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799740|ref|XP_002867754.1| hypothetical protein ARALYDRAFT_914336 [Arabidopsis lyrata subsp. lyrata] gi|297313590|gb|EFH44013.1| hypothetical protein ARALYDRAFT_914336 [Arabidopsis lyrata subsp. lyrata]

 Score =  219 bits (559), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 105/184 (57%), Positives = 135/184 (73%), Gaps = 13/184 (7%)

Query: 1   MEDKQETLKTASKKP---RGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEI 57
           M+D+ +T K A  KP   +  G P RSID +A QCEKC KWR I + +EYEEIR +I E 
Sbjct: 1   MDDQSQTEKLA--KPILKKKAGTPGRSIDVFAVQCEKCLKWRQIGTQDEYEEIRSRIQED 58

Query: 58  PFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITP 117
           P+VC++K G+SCED  D+ YD+SR WVID+PG+PKTP GFKRSL+LRKD+SKMDAYYITP
Sbjct: 59  PYVCEKKEGISCEDAGDLNYDSSRTWVIDKPGLPKTPRGFKRSLILRKDYSKMDAYYITP 118

Query: 118 TGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPK 177
           TGKKL++ NE+A F+ AN +Y    L DF F+VPKVM++T+P  ++        + R PK
Sbjct: 119 TGKKLKSRNEIAAFIDANQDYKYALLGDFNFTVPKVMEETVPNGII--------SDRTPK 170

Query: 178 TSKG 181
           TSKG
Sbjct: 171 TSKG 174

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15229373|ref|NP_191862.1| methyl-CPG-binding domain 4 protein [Arabidopsis thaliana] gi|75181050|sp|Q9LYB9.1|MBD4_ARATH RecName: Full=Methyl-CpG-binding domain-containing protein 4; Short=AtMBD4; Short=MBD04; AltName: Full=Methyl-CpG-binding protein MBD4 gi|7573432|emb|CAB87748.1| putative protein [Arabidopsis thaliana] gi|34365655|gb|AAQ65139.1| At3g63030 [Arabidopsis thaliana] gi|51971397|dbj|BAD44363.1| unknown protein [Arabidopsis thaliana] gi|332646905|gb|AEE80426.1| methyl-CPG-binding domain 4 protein [Arabidopsis thaliana]

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 97/141 (68%), Positives = 117/141 (82%)

Query: 21  PIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDAS 80
           P R IDTYAAQC+ C KWRVI+S EEYE+IR K+ E PF C +K G+SCE+PADI+YD+S
Sbjct: 21  PGRLIDTYAAQCDNCHKWRVIDSQEEYEDIRSKMLEDPFNCQKKQGMSCEEPADIDYDSS 80

Query: 81  RVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSD 140
           R WVID+PG+PKTP GFKRSLVLRKD+SKMD YY TPTGKKLR+ NE+A F+ ANPE+ +
Sbjct: 81  RTWVIDKPGLPKTPKGFKRSLVLRKDYSKMDTYYFTPTGKKLRSRNEIAAFVEANPEFRN 140

Query: 141 VSLSDFTFSVPKVMDDTIPED 161
             L DF F+VPKVM+DT+P D
Sbjct: 141 APLGDFNFTVPKVMEDTVPPD 161

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535711|ref|XP_003536387.1| PREDICTED: methyl-CpG-binding domain-containing protein 4-like [Glycine max]

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 105/173 (60%), Positives = 127/173 (73%), Gaps = 2/173 (1%)

Query: 1   MEDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFV 60
           M+  QE  KT S   R   +   S+D YAAQC+ C KWR I++ EE+EEIR K+AE PF+
Sbjct: 17  MKGGQEISKTPSSSKRTLSQG--SVDIYAAQCKNCLKWREIDTQEEFEEIRSKVAEEPFL 74

Query: 61  CDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGK 120
           C RK   SC++P DI+YD+SR WVID+P +PKTP GFKRSLVLRKD+SK+DAYYITP GK
Sbjct: 75  CSRKANSSCDEPGDIKYDSSRTWVIDKPNLPKTPQGFKRSLVLRKDYSKLDAYYITPAGK 134

Query: 121 KLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAK 173
           KLRT NE+A FL  NPE+  VS SDF FS PK+M DTIPE V +K SA+   K
Sbjct: 135 KLRTRNEIAAFLKDNPEFKGVSASDFDFSSPKIMQDTIPEVVEQKDSANKKVK 187

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297817640|ref|XP_002876703.1| methyl-CpG-binding domain 4 [Arabidopsis lyrata subsp. lyrata] gi|297322541|gb|EFH52962.1| methyl-CpG-binding domain 4 [Arabidopsis lyrata subsp. lyrata]

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 100/150 (66%), Positives = 121/150 (80%), Gaps = 1/150 (0%)

Query: 21  PIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDAS 80
           P R IDTYAAQCE C KWRVI+S EEYE+IR K+ E PF C +K G+SCE+PAD++YD+S
Sbjct: 20  PGRLIDTYAAQCENCHKWRVIDSQEEYEDIRSKMLEDPFNCQKKQGMSCEEPADLDYDSS 79

Query: 81  RVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSD 140
           R WVID+PG+PKTP GF+RSLVLRKD+SKMD YY TPTGKKLR+ NE+A F+ ANPE+ +
Sbjct: 80  RTWVIDKPGLPKTPQGFRRSLVLRKDYSKMDTYYFTPTGKKLRSRNEIAAFVEANPEFKN 139

Query: 141 VSLSDFTFSVPKVMDDTIPEDVVKKGSASS 170
             L DF F+VPKVM+DT+P  V K GS  S
Sbjct: 140 APLGDFNFTVPKVMEDTVPP-VPKLGSPIS 168

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248398|ref|NP_001239875.1| uncharacterized protein LOC100802350 [Glycine max] gi|255641529|gb|ACU21038.1| unknown [Glycine max]

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 103/173 (59%), Positives = 126/173 (72%), Gaps = 2/173 (1%)

Query: 1   MEDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFV 60
           M+  QE  KT S   R   +   S+D YAAQC+ C KWR I++ EE+EEIR K+ E PF+
Sbjct: 1   MKSGQEISKTPSSSKRTLSQG--SVDIYAAQCKNCLKWREIDTQEEFEEIRSKVTEEPFL 58

Query: 61  CDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGK 120
           C RK   SC++P DIEYD++R WVID+P +PKTP GFKRSLVLRKD+SK+DAYYITP GK
Sbjct: 59  CSRKANSSCDEPGDIEYDSTRTWVIDKPNLPKTPQGFKRSLVLRKDYSKLDAYYITPAGK 118

Query: 121 KLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAK 173
           KLRT NE+A FL  NPE+  VS SDF FS PK+M DTIPE + +K SA+   K
Sbjct: 119 KLRTRNEIAAFLKDNPEFKGVSASDFDFSSPKIMQDTIPEIIEQKDSANKKVK 171

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388511439|gb|AFK43781.1| unknown [Lotus japonicus]

 Score =  215 bits (547), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 99/151 (65%), Positives = 118/151 (78%)

Query: 24  SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVW 83
           SID YAAQC KC KWRVI++ +E+EEIR K+++ PF C RK   SC+DPADIEYD+SR W
Sbjct: 25  SIDVYAAQCIKCLKWRVIDTQQEFEEIRHKVSQEPFDCSRKANCSCDDPADIEYDSSRTW 84

Query: 84  VIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 143
           VID+P +PKTP GFKRSLVLRKD+SK+DAYYITPTGKKLRT NE A FL  +PE   +S 
Sbjct: 85  VIDKPNLPKTPEGFKRSLVLRKDYSKLDAYYITPTGKKLRTRNEAAAFLKDHPELQGISA 144

Query: 144 SDFTFSVPKVMDDTIPEDVVKKGSASSDAKR 174
            DF FS PK+M DTIPE V +K SA+   K+
Sbjct: 145 QDFDFSCPKIMQDTIPEIVEQKDSANKKVKK 175

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388503158|gb|AFK39645.1| unknown [Lotus japonicus]

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 97/151 (64%), Positives = 117/151 (77%)

Query: 24  SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVW 83
           S+D YA QC KC KWRV+++ EE+EE R K  E PF C RK   SC+DPADIEYD+SR W
Sbjct: 24  SVDIYATQCIKCLKWRVVDTQEEFEEFRQKANEEPFDCSRKANCSCDDPADIEYDSSRTW 83

Query: 84  VIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 143
           VID+P +PKTP GF+RSLVLRKD+SK+DAYYITPTGKKLRT NE+A FL  +PE+  +S 
Sbjct: 84  VIDKPNVPKTPQGFRRSLVLRKDYSKLDAYYITPTGKKLRTRNEIAAFLKEHPEFEGISA 143

Query: 144 SDFTFSVPKVMDDTIPEDVVKKGSASSDAKR 174
            DF FS PKVM +TIPE + +K SAS  AK+
Sbjct: 144 QDFDFSSPKVMHETIPEGLEQKASASKIAKK 174

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

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	197
TAIR|locus:2099187	186	MBD4 "methyl-CPG-binding domai	0.842	0.892	0.628	2.9e-55
TAIR|locus:505006513	204	MBD1 "methyl-CPG-binding domai	0.852	0.823	0.562	1.1e-50
TAIR|locus:2182643	272	MBD02 "methyl-CPG-binding doma	0.827	0.599	0.4	1.3e-29
TAIR|locus:505006418	163	MBD3 "methyl-CPG-binding domai	0.624	0.754	0.436	6.1e-23
TAIR|locus:504954793	155	MBD12 "methyl-CPG-binding doma	0.695	0.883	0.375	4.6e-18

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

 Score = 570 (205.7 bits), Expect = 2.9e-55, P = 2.9e-55
 Identities = 105/167 (62%), Positives = 130/167 (77%)

Query:     1 MEDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFV 60
             M++++E  K A  K +    P R IDTYAAQC+ C KWRVI+S EEYE+IR K+ E PF 
Sbjct:     1 MKEEEEIGKPAKPKAKKDVAPGRLIDTYAAQCDNCHKWRVIDSQEEYEDIRSKMLEDPFN 60

Query:    61 CDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGK 120
             C +K G+SCE+PADI+YD+SR WVID+PG+PKTP GFKRSLVLRKD+SKMD YY TPTGK
Sbjct:    61 CQKKQGMSCEEPADIDYDSSRTWVIDKPGLPKTPKGFKRSLVLRKDYSKMDTYYFTPTGK 120

Query:   121 KLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGS 167
             KLR+ NE+A F+ ANPE+ +  L DF F+VPKVM+DT+P D  K GS
Sbjct:   121 KLRSRNEIAAFVEANPEFRNAPLGDFNFTVPKVMEDTVPPDP-KLGS 166

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 = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 99/176 (56%), Positives = 126/176 (71%)

Query:    10 TASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSC 69
             T  K  +  G P RSID +A QCEKC KWR I++ +EYE+IR ++ E PF C  K GVSC
Sbjct:    37 TTIKVQKKAGTPGRSIDVFAVQCEKCMKWRKIDTQDEYEDIRSRVQEDPFFCKTKEGVSC 96

Query:    70 EDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVA 129
             ED  D+ YD+SR WVID+PG+P+TP GFKRSL+LRKD+SKMDAYYITPTGKKL++ NE+A
Sbjct:    97 EDVGDLNYDSSRTWVIDKPGLPRTPRGFKRSLILRKDYSKMDAYYITPTGKKLKSRNEIA 156

Query:   130 GFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGD 185
              F+ AN +Y    L DF F+VPKVM++T+P  ++      SD  R PK S+ V  D
Sbjct:   157 AFIDANQDYKYALLGDFNFTVPKVMEETVPSGIL------SD--RTPKPSRKVTID 204

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

 Score = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 70/175 (40%), Positives = 99/175 (56%)

Query:     2 EDKQETLKTASKKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVC 61
             +D +E +     +P        SI  +  QC  CFKWR++ S ++YEEIR ++ E PF C
Sbjct:    33 DDTEEEVLPVQSQPLSSRTQCPSIGAFTVQCASCFKWRLMPSMQKYEEIREQLLENPFFC 92

Query:    62 DR----KPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKM--DAYYI 115
             D     KP +SC+ PADI  D +R+W ID+P I + P G++R L +R +      D YY+
Sbjct:    93 DTAREWKPDISCDVPADIYQDGTRLWAIDKPNISRPPAGWQRLLRIRGEGGTRFADVYYV 152

Query:   116 TPTGKKLRTLNEVAGFLAANPEY--SDVSLSDFTFSVPKVMDDTIPEDVVKKGSA 168
              P+GKKLR+  EV  +L  N EY    V LS F+F +PK + D    D V+K  A
Sbjct:   153 APSGKKLRSTVEVQKYLNDNSEYIGEGVKLSQFSFQIPKPLQD----DYVRKRPA 203

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

 Score = 265 (98.3 bits), Expect = 6.1e-23, P = 6.1e-23
 Identities = 58/133 (43%), Positives = 80/133 (60%)

Query:    25 IDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADI--EYDASRV 82
             ID+YAAQC KC K R I S E+YEEIR K  E  F C R     CE+P D+   +D+  +
Sbjct:     9 IDSYAAQCWKCLKVRSIESQEDYEEIRSKTLEKFFECKR-----CEEPGDMVMNFDSLTM 63

Query:    83 -WVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYY--ITPTGKKLRTLNEVAGFLAANPEYS 139
              W  D   IPKTP G KR LV+R +  K+D YY  + P  K+ +++ EVA F+    E+ 
Sbjct:    64 RWFQDEHSIPKTPQGLKRVLVVRTNCVKVDVYYESLAPRRKRFKSIKEVATFIEDKEEFK 123

Query:   140 DVSLSDFTFSVPK 152
             D++L + +F+ PK
Sbjct:   124 DMTLEEVSFAAPK 136

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

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

 Score = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 59/157 (37%), Positives = 82/157 (52%)

Query:    31 QCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRK----PGVSCEDPADIEYDASRVWVID 86
             QC  C KWR+I S + Y  I+    + PFVC       P +SC  P D        W   
Sbjct:     3 QCTDCKKWRLIPSMQHYNIIKETQLQTPFVCGTTSGWTPNMSCNVPQD--GTTCDTW--- 57

Query:    87 RPGIPKTPGGFKRSLVLRKDFSKM-DAYYITPTGKKLRTLNEVAGFLAANPEY--SDVSL 143
              P IP  P G+ RS+ +R + +K  D YY  P+G++LR+  EV  FL  +PEY    V+ 
Sbjct:    58 -PSIPPIPTGWSRSVHIRSESTKFADVYYFPPSGERLRSSAEVQSFLDNHPEYVREGVNR 116

Query:   144 SDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSK 180
             S F+F +PK +DD    + VKK   +   KR+ K+SK
Sbjct:   117 SQFSFQIPKPLDD----NYVKK--RTRPVKRR-KSSK 146


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        0.314   0.133   0.392    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      197       197   0.00082  111 3  11 23  0.39    33
                                                     31  0.44    35


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:  5
  No. of states in DFA:  579 (62 KB)
  Total size of DFA:  169 KB (2100 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:  18.54u 0.18s 18.72t   Elapsed:  00:00:01
  Total cpu time:  18.54u 0.18s 18.72t   Elapsed:  00:00:01
  Start:  Fri May 10 08:57:29 2013   End:  Fri May 10 08:57:30 2013

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

---

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)
Q9LYB9	MBD4_ARATH	No assigned EC number	0.6879	0.7157	0.7580	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	197
cd01396	77	cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and M	5e-17
pfam01429	75	pfam01429, MBD, Methyl-CpG binding domain	2e-13
smart00391	77	smart00391, MBD, Methyl-CpG binding domain	3e-12
cd00122	62	cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8	4e-11
pfam07496	50	pfam07496, zf-CW, CW-type Zinc Finger	9e-11
cd01397	73	cd01397, HAT_MBD, Methyl-CpG binding domains (MBD)	0.003

>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 = 71.6 bits (176), Expect = 5e-17
 Identities = 35/75 (46%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 87  RPGIPKTPGGFKRSLVLRKDFS--KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLS 144
           +P  P+ P G+KR LV RK  S  K D YYI+PTGKK R+  E+A +L  N   + + LS
Sbjct: 1   KPEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGP-TSLDLS 59

Query: 145 DFTFSVPKVMDDTIP 159
           DF F+VPK +    P
Sbjct: 60  DFDFTVPKKLGLGSP 74

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 = 62.0 bits (151), Expect = 2e-13
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 85  IDRPGIPKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDV 141
             R   P  P G++R    RK      K+D YY +PTGKK R+ +E+  +L  N + S +
Sbjct: 2   RKREDCPPLPPGWRREERQRKSGSSAGKVDVYYYSPTGKKFRSKSELIRYLEKNGDTS-L 60

Query: 142 SLSDFTFSVPKVMDD 156
            L DF F+V   +  
Sbjct: 61  KLEDFDFTVRSEVGR 75

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 = 59.3 bits (144), Expect = 3e-12
 Identities = 28/74 (37%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 85  IDRPGIPKTPGGFKRSLVLRKDFS---KMDAYYITPTGKKLRTLNEVAGFLAANPEYS-D 140
            D   +P  P G++R    RK      K D YYI+P GKKLR+ +E+A +L  N + S D
Sbjct: 1   GDPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLD 59

Query: 141 VSLSDFTFSVPKVM 154
           +   DF  +VP   
Sbjct: 60  LECFDFNATVPVGP 73

Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain. 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 = 55.8 bits (135), Expect = 4e-11
 Identities = 27/57 (47%), Positives = 35/57 (61%), Gaps = 3/57 (5%)

Query: 94  PGGFKRSLVLRKDFS--KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF 148
           P G+KR LV+RK  S  K D YY +P GKKLR+  EVA +L      S + L +F+F
Sbjct: 7   PPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGP-SSLDLENFSF 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 = 54.7 bits (132), Expect = 9e-11
 Identities = 24/53 (45%), Positives = 31/53 (58%), Gaps = 6/53 (11%)

Query: 27 TYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR---KPGVSCEDPADIE 76
           Y  QC+KC KWR +   EEYEEIR K+ + P+ C         SC+DP +IE
Sbjct: 1  DYWVQCDKCLKWRKL--PEEYEEIRSKLPD-PWFCSMNPDPAYNSCDDPEEIE 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|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 = 35.1 bits (81), Expect = 0.003
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 4/63 (6%)

Query: 94  PGGFKRSLVLRKDFSKM--DAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVP 151
             G++R   +R    ++  +  Y  P GKKLR   EV  +L+ N   S +S  +F+FS  
Sbjct: 7   ELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKN-GISLLSRENFSFS-A 64

Query: 152 KVM 154
           +  
Sbjct: 65  RAP 67

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	197
cd01396	77	MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are me	99.92
smart00391	77	MBD Methyl-CpG binding domain. Methyl-CpG binding	99.9
cd01397	73	HAT_MBD Methyl-CpG binding domains (MBD) present i	99.88
cd00122	62	MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and	99.87
PF01429	77	MBD: Methyl-CpG binding domain; InterPro: IPR00173	99.84
KOG4161	272	consensus Methyl-CpG binding transcription regulat	99.76
cd01395	60	HMT_MBD Methyl-CpG binding domains (MBD) present i	99.52
KOG4161	272	consensus Methyl-CpG binding transcription regulat	99.25
PF07496	50	zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zi	99.17

>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=9.3e-26  Score=166.20  Aligned_cols=72  Identities=47%  Similarity=0.758  Sum_probs=66.8

Q ss_pred             CCCCCCCCCceEEEEEcccC--CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccCCCCCC
Q 029175           88 PGIPKTPGGFKRSLVLRKDF--SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPE  160 (197)
Q Consensus        88 p~iP~~P~GWkRevv~R~~g--sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~~~~p~  160 (197)
                      +++|.+|+||+|++++|++|  +++||||++|+|++|||++||++||+.||.. +|++++|||++++++.++++.
T Consensus         2 ~~~~~lp~GW~r~~~~R~~gs~~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~~~-~~~~~~FdF~~~k~~~~~~~~   75 (77)
T cd01396           2 PEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGPT-SLDLSDFDFTVPKKLGLGSPR   75 (77)
T ss_pred             CCCCCCCCCCEEEEEEecCCCCCcceEEEECCCCCEEECHHHHHHHHHhCCCC-CCcHhHcccCCCcccccccCC
Confidence            57888999999999999997  5899999999999999999999999999854 899999999999999988765

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.

>smart00391 MBD Methyl-CpG binding domain

Probab=99.90  E-value=2.7e-24  Score=158.27  Aligned_cols=69  Identities=36%  Similarity=0.618  Sum_probs=63.4

Q ss_pred             cCCCCCCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccCC
Q 029175           86 DRPGIPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD  156 (197)
Q Consensus        86 Dkp~iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~~  156 (197)
                      ++.++| +|+||+|++++|++|   +++||||+||+||+|||++||++||.+|+++ .+++++|||.+..++..
T Consensus         2 ~~~~~P-lp~GW~R~~~~r~~g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~~~~~-~~~~~~F~F~~~~~~~~   73 (77)
T smart00391        2 DPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDL-SLDLECFDFNATVPVGP   73 (77)
T ss_pred             CcccCC-CCCCcEEEEEEecCCCCCCcccEEEECCCCCeeeCHHHHHHHHHhCCCc-ccccccccCcCCccccc
Confidence            456788 899999999999998   4899999999999999999999999999997 78999999999988765

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

>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=99.88  E-value=3.1e-23  Score=152.72  Aligned_cols=63  Identities=30%  Similarity=0.392  Sum_probs=58.7

Q ss_pred             CCCCceEEEEEcccCC--cceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccCC
Q 029175           93 TPGGFKRSLVLRKDFS--KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD  156 (197)
Q Consensus        93 ~P~GWkRevv~R~~gs--K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~~  156 (197)
                      +|+||+|++|+|+.++  ++|||||+||||||||++||++||..|+.. +|+++||+|+++.++.+
T Consensus         6 l~~GW~Re~vir~~~~~~~~dV~Y~aPcGKklRs~~ev~~yL~~~~~~-~Lt~dnFsF~~~~~vg~   70 (73)
T cd01397           6 LELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKNGIS-LLSRENFSFSARAPVGD   70 (73)
T ss_pred             CCCCceeEEEeccCCCCccceEEEECCCCcccccHHHHHHHHHhCCcc-CccHhHccccCCccccc
Confidence            4899999999999884  699999999999999999999999999975 89999999999988776

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.

>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=99.87  E-value=2.4e-22  Score=141.21  Aligned_cols=59  Identities=44%  Similarity=0.695  Sum_probs=54.1

Q ss_pred             CCCCCCCCCceEEEEEcccC--CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCcee
Q 029175           88 PGIPKTPGGFKRSLVLRKDF--SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF  148 (197)
Q Consensus        88 p~iP~~P~GWkRevv~R~~g--sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF  148 (197)
                      ..+|. |+||+|++++|++|  +++||||++|+|++|||+.||++||.+|+.. +|++++|||
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-PPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPS-SLDLENFSF   62 (62)
T ss_pred             CCCCC-CCCeEEEEEEcCCCCCCcceEEEECCCCceecCHHHHHHHHHhCCCC-CCcHHHCCC
Confidence            35666 99999999999997  5899999999999999999999999999853 899999998

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=99.84  E-value=2.7e-21  Score=140.97  Aligned_cols=64  Identities=41%  Similarity=0.742  Sum_probs=53.4

Q ss_pred             CCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCccc
Q 029175           91 PKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM  154 (197)
Q Consensus        91 P~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~  154 (197)
                      +.+|+||+|++++|++|   ++.||||+||+|++|||+.||.+||..++....|++++|+|.....+
T Consensus         9 ~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~~~~~l~~~~F~F~~~~~~   75 (77)
T PF01429_consen    9 PPLPDGWKREVVVRKSGSSAGKKDVYYYSPCGKRFRSKKEVVRYLKENPSEHDLKPENFSFSKRLIM   75 (77)
T ss_dssp             TTSTTT-EEEEEESSSSTTTTSEEEEEEETTSEEESSHHHHHHHHTTSS---SS-CTTBBTTTTB--
T ss_pred             CCCCCCCEEEEEEecCCCcCCceEEEEECCCCCEEeCHHHHHHHHHhCCCcccCCHhHCCCCCCccc
Confidence            45699999999999998   47999999999999999999999999999544899999999988764

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=99.76  E-value=4.3e-19  Score=156.30  Aligned_cols=144  Identities=31%  Similarity=0.296  Sum_probs=132.6

Q ss_pred             CCccccceeeeecccccceeeeccHHHHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCCCCCCCCCceE
Q 029175           20 EPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKR   99 (197)
Q Consensus        20 ~~~~~i~~ya~QC~~C~KwR~i~t~e~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~iP~~P~GWkR   99 (197)
                      .....|.+|++||..|++|+.|.++.+|+++|+.+.+++|+|..+..+.|++++|+++++.+.|.||.++++.+|.||.|
T Consensus       104 ~~~~~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql~~~~~~~~l~~~s~~~e~~d~~~l~~~~~g~~~  183 (272)
T KOG4161|consen  104 DLNLAIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQLFWLERLQDLEADSSRGESIDKLSLPKTPQGSGR  183 (272)
T ss_pred             ccccCCchhhhhccccccceeeccccchhhhhccccccccccccceEEEeccccccccccccccccCccccCcCCCccCc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcccCCcceEEEECCCCCcccchHHHHHhhhhCC--CCCCCCcCCceeeCCcccCCCCCCcce
Q 029175          100 SLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANP--EYSDVSLSDFTFSVPKVMDDTIPEDVV  163 (197)
Q Consensus       100 evv~R~~gsK~DVYY~SP~GKKlRSk~EV~ryL~~np--e~~~l~le~FsF~~pk~~~~~~p~~~~  163 (197)
                      .+..+......++||.+|+++.+++.++++.++..|+  ++....+.+|.|+.+.++.+...-..+
T Consensus       184 ~~~~~s~~~~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~~~~  249 (272)
T KOG4161|consen  184 SSAGESLLSSVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRVKNV  249 (272)
T ss_pred             cccccccccccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccchhhh
Confidence            9999988889999999999999999999999999994  444578999999999888886654333

>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=99.52  E-value=1.1e-14  Score=103.98  Aligned_cols=53  Identities=28%  Similarity=0.456  Sum_probs=49.0

Q ss_pred             CCCceEEEEEcccCC-cceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCcee
Q 029175           94 PGGFKRSLVLRKDFS-KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF  148 (197)
Q Consensus        94 P~GWkRevv~R~~gs-K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF  148 (197)
                      -.||+|....|+.|+ |.||+|.+||||+||++.||++||.++ . ..|++++|+|
T Consensus         7 l~gw~R~~~~~~~~~~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t-~-~~L~~d~FsF   60 (60)
T cd01395           7 LCGFQRMKYRARVGKVKKHVIYKAPCGRSLRNMSEVHRYLRET-C-SFLTVDNFSF   60 (60)
T ss_pred             ccCeEEEEEeccCCCcccceEEECCcchhhhcHHHHHHHHHhc-c-ccceeecccC
Confidence            699999999998765 899999999999999999999999999 3 3799999998

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.

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

Probab=99.25  E-value=4.8e-12  Score=111.85  Aligned_cols=71  Identities=35%  Similarity=0.510  Sum_probs=58.0

Q ss_pred             CcceeeecCCCCCCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccC
Q 029175           79 ASRVWVIDRPGIPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMD  155 (197)
Q Consensus        79 ~sr~W~iDkp~iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~  155 (197)
                      .+.+|  |++.   +|+||.|++++|..|   ++.||||+||.|++|||+.+++.||+.+     .+.+.|+|...+++.
T Consensus        10 ~~~~~--~c~~---lp~GW~~~~~~r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~-----~~~s~~~~v~~k~~~   79 (272)
T KOG4161|consen   10 AGKRS--DCPA---LPPGWTREEVQRSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKV-----GDLSLFDFVTGKMSP   79 (272)
T ss_pred             ccCcc--cCCC---CCCCcchhhhcccCCCcccccceEEeCCcccccccccHHHHHhccc-----cccccCccccccccc
Confidence            34444  5554   499999999999987   4899999999999999999999999994     467888888887766


Q ss_pred             CCCC
Q 029175          156 DTIP  159 (197)
Q Consensus       156 ~~~p  159 (197)
                      ....
T Consensus        80 ~~~~   83 (272)
T KOG4161|consen   80 SERQ   83 (272)
T ss_pred             cccc
Confidence            6333

>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=99.17  E-value=4.5e-12  Score=86.36  Aligned_cols=46  Identities=41%  Similarity=0.954  Sum_probs=32.1

Q ss_pred             eeeecccccceeeeccHHHHHHHHhHhcCCCeeecc---CCCCCCCCCCCcc
Q 029175           28 YAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR---KPGVSCEDPADIE   76 (197)
Q Consensus        28 ya~QC~~C~KwR~i~t~e~yEeiR~~~~~~pf~C~~---~~~~sC~dP~Di~   76 (197)
                      |.|||..|.|||.||  .++..|++.+.+ +|+|..   .+..||+.|+|++
T Consensus         2 ~WVQCd~C~KWR~lp--~~~~~~~~~~~d-~W~C~~n~~~~~~sC~~pee~e   50 (50)
T PF07496_consen    2 YWVQCDSCLKWRRLP--EEVDPIREELPD-PWYCSMNPDPPFNSCDAPEEIE   50 (50)
T ss_dssp             EEEE-TTT--EEEE---CCHHCTSCCSST-T--GGGSS-CCC-STTS--SS-
T ss_pred             eEEECCCCCceeeCC--hhhCcccccCCC-eEEcCCCCCCCCCCCCCcccCC
Confidence            789999999999999  788888888877 999998   6689999999985

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.

---

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	197
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	1e-13
1ub1_A	133	MECP2, attachment region binding protein; chicken	2e-12
2ky8_A	72	Methyl-CPG-binding domain protein 2; DNA binding d	2e-12
1d9n_A	75	Methyl-CPG-binding protein MBD1; PCM1, methylation	8e-11

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

 Score = 62.8 bits (152), Expect = 1e-13
 Identities = 23/81 (28%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 81  RVWVIDRPGI---PKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAA 134
           R  + DR  +   P  P G+ R L  RK      K D Y I P GK  R+  E+  +   
Sbjct: 9   RSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEK 68

Query: 135 NPEYSDVSLSDFTFSVPKVMD 155
             +   +  +DF F+V     
Sbjct: 69  VGDT-SLDPNDFDFTVTGRGS 88

>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 = 61.1 bits (147), Expect = 2e-12
 Identities = 26/106 (24%), Positives = 40/106 (37%), Gaps = 7/106 (6%)

Query: 81  RVWVIDRPGI---PKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAA 134
           R  + DR  +   P  P G+ R L  RK      K D Y I P GK  R+  E+  +   
Sbjct: 23  RSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEK 82

Query: 135 NPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSK 180
             +   +  +DF F+V      +  E    K + S  +    +   
Sbjct: 83  VGDT-SLDPNDFDFTVTGRGSPSRREQRPPKKAKSPKSPGSGRGRG 127

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

 Score = 58.8 bits (142), Expect = 2e-12
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 8/71 (11%)

Query: 87  RPGIPKTPGGFKRSLVLRKDFS---KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 143
           R   P  P G+K+  V+RK      K D YY +P+GKK R+  ++A +L    +     L
Sbjct: 7   RTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNAVD-----L 61

Query: 144 SDFTFSVPKVM 154
           S F F   K+M
Sbjct: 62  SCFDFRTGKMM 72

>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 = 55.0 bits (132), Expect = 8e-11
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 8/72 (11%)

Query: 86  DRPGIPKTPGGFKRSLVLRK---DFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVS 142
           D    P    G+KR  V RK      + D YY +PTG ++R+  E+  +L          
Sbjct: 4   DWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLG-----PACD 58

Query: 143 LSDFTFSVPKVM 154
           L+ F F    + 
Sbjct: 59  LTLFDFKQGILC 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	197
1ub1_A	133	MECP2, attachment region binding protein; chicken	99.94
3vxv_A	69	Methyl-CPG-binding domain protein 4; methyl CPG bi	99.91
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	99.91
2ky8_A	72	Methyl-CPG-binding domain protein 2; DNA binding d	99.9
1d9n_A	75	Methyl-CPG-binding protein MBD1; PCM1, methylation	99.89
2l7p_A	100	Histone-lysine N-methyltransferase ASHH2; CW-domai	98.52
2e61_A	69	Zinc finger CW-type PWWP domain protein 1; ZF-CW d	97.88
4gut_A	776	Lysine-specific histone demethylase 1B; histone de	89.57

>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=99.94  E-value=4.8e-27  Score=188.43  Aligned_cols=113  Identities=29%  Similarity=0.453  Sum_probs=89.1

Q ss_pred             CCCcccCCcceeeecCCC----CCCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcC
Q 029175           72 PADIEYDASRVWVIDRPG----IPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLS  144 (197)
Q Consensus        72 P~Di~~d~sr~W~iDkp~----iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le  144 (197)
                      |+.-.....|+.||+..+    .|.+|+||+|++++|++|   +++|||||||+||+|||++||++||++|+++ +|+++
T Consensus        13 ~~~~~~~~~rr~vi~~~~~~~~~~~LP~GWkRe~~~RksG~Sagk~DVYY~SP~GKkfRSk~Ev~ryL~~~~~~-~~~~e   91 (133)
T 1ub1_A           13 PEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDT-SLDPN   91 (133)
T ss_dssp             CCCCSCCCCCCCCCCTTSCSSCCCCBTTBCEEEEEECCCSSSCCSEEEEEECTTSCEESSHHHHHHHHTTSCCC-SCCGG
T ss_pred             cccccCccCccceeeccccccCCCCCCCCCEEEEEEecCCCCCCceeEEEECCCCCeeeCHHHHHHHHHHCCcc-CCCHh
Confidence            333444456787886555    355799999999999998   5899999999999999999999999999997 89999


Q ss_pred             CceeeCCcccCCCCCCcceeccCCCcccccCCCccCCCC-CCCCcCCCCcc
Q 029175          145 DFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVV-GDGTARDEGSV  194 (197)
Q Consensus       145 ~FsF~~pk~~~~~~p~~~~~k~~~~~~~~kk~k~~k~~~-g~~~~~~~~~~  194 (197)
                      +|||++...   .+++....+      ..++.|+.+..+ |+|++|++||.
T Consensus        92 ~FdF~~~gk---~~~s~R~~r------~~k~~k~~~~~~~~~~~~~~~~~~  133 (133)
T 1ub1_A           92 DFDFTVTGR---GSPSRREQR------PPKKAKSPKSPGSGRGRGRPKGSG  133 (133)
T ss_dssp             GCCCCCCCC---SCSSCCCCC------CCCCCCCCCCCCCCCCCCCCCCCC
T ss_pred             HCccccCCC---CCCcccccC------CCCCCCCCCCCCCCCCCCCCCCCC
Confidence            999996422   234444422      356778877766 99999999984

>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=99.91  E-value=5.1e-25  Score=158.86  Aligned_cols=58  Identities=34%  Similarity=0.578  Sum_probs=55.3

Q ss_pred             CCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCC
Q 029175           93 TPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVP  151 (197)
Q Consensus        93 ~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~p  151 (197)
                      +|+||+|++++|++|   +|.||||+||+||||||++||++||+.||++ +|++++|||++|
T Consensus         6 lp~GW~R~~~~R~~G~s~gk~DvyY~sP~Gkk~RSk~ev~~yL~~~~~~-~l~~~~FdF~~p   66 (69)
T 3vxv_A            6 VPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGET-FLKPEDFNFTVL   66 (69)
T ss_dssp             SCTTCEEEEEECCSSTTTTCEEEEEECTTSCEECSHHHHHHHHHHHCCC-CCCGGGSCCCCC
T ss_pred             CCCCCEEEEEEeccCCCCCcceEEEEcCCCCEeeCHHHHHHHHHhCCCC-CCCHHHcceeCC
Confidence            599999999999987   4899999999999999999999999999998 899999999987

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

Probab=99.91  E-value=7.3e-25  Score=167.71  Aligned_cols=75  Identities=31%  Similarity=0.465  Sum_probs=59.7

Q ss_pred             ceeeecCCC----CCCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcc
Q 029175           81 RVWVIDRPG----IPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKV  153 (197)
Q Consensus        81 r~W~iDkp~----iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~  153 (197)
                      |+.+|+..+    .|.+|+||+|++++|++|   +++|||||||+||+|||++||++||+.||++ +|++++|||+++++
T Consensus         8 rr~~i~~~~~~~~~~~lP~GW~re~~~R~~G~s~gk~DvYY~sP~GkkfRSk~ev~ryL~~~g~~-~~~~~~FdF~~~~~   86 (97)
T 3c2i_A            8 RRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEKVGDT-SLDPNDFDFTVTGR   86 (97)
T ss_dssp             -------CCCCCCCTTSCTTCEEEEEECCSSTTTTCEEEEEECTTSCEECSHHHHHHHHHHHTCC-SSCTTTCCCCSSCC
T ss_pred             cceeEecCCcccCCCCCCCCCEEEEEEecCCCCCCcceEEEECCCCCEEECHHHHHHHHHHCCCC-CCCHhhccccCCCc
Confidence            444554433    256799999999999997   4899999999999999999999999999998 89999999999988


Q ss_pred             cCC
Q 029175          154 MDD  156 (197)
Q Consensus       154 ~~~  156 (197)
                      +++
T Consensus        87 ~~~   89 (97)
T 3c2i_A           87 GSP   89 (97)
T ss_dssp             ---
T ss_pred             Ccc
Confidence            665

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

Probab=99.90  E-value=2.7e-24  Score=156.09  Aligned_cols=60  Identities=42%  Similarity=0.712  Sum_probs=55.0

Q ss_pred             CCCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCccc
Q 029175           90 IPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM  154 (197)
Q Consensus        90 iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~  154 (197)
                      +|.+|+||+|++++|++|   +++||||++|+|++|||++||++||+.     +|++++|||.++++|
T Consensus        10 ~p~Lp~GW~R~~~~R~~g~s~~k~DvyY~sP~Gkr~RS~~ev~~YL~~-----~l~~~~FdF~~~~~~   72 (72)
T 2ky8_A           10 CPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGN-----AVDLSCFDFRTGKMM   72 (72)
T ss_dssp             CSSSCTTCEEEEEECCSSTTTTCEEEEEECTTCCEEESHHHHHHHHTT-----SSCCTTCBTTTTBC-
T ss_pred             CCCCCCCCEEEEEEecCCCCCCceEEEEECCCCCEeEcHHHHHHHHhc-----CCChhhcCCCCCCcC
Confidence            456699999999999988   589999999999999999999999998     789999999999875

>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=99.89  E-value=5.4e-24  Score=155.90  Aligned_cols=62  Identities=31%  Similarity=0.512  Sum_probs=56.3

Q ss_pred             CCCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccCC
Q 029175           90 IPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD  156 (197)
Q Consensus        90 iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~~  156 (197)
                      .|.+|+||+|++++|++|   +++|||||||+||+|||++||++||+.     ++++++|||++++++.-
T Consensus         8 ~p~LP~GW~Re~~~R~~g~s~gk~DvyY~sP~Gkk~RS~~ev~ryL~~-----~~~~~~FdF~~gk~~~~   72 (75)
T 1d9n_A            8 CPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGP-----ACDLTLFDFKQGILCYP   72 (75)
T ss_dssp             CTTTCSSCEEEECSSSSSCTTCCCCEEEECSSSCEECSTHHHHHHHCT-----TCCCTTCCTTTCCCCCS
T ss_pred             CCCCCCCCEEEEEEecCCCCCCceEEEEECCCCCeeecHHHHHHHhcc-----CCCccccCCCCCCccCC
Confidence            355599999999999998   589999999999999999999999975     78999999999998654

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

Probab=98.52  E-value=3.7e-08  Score=75.62  Aligned_cols=49  Identities=22%  Similarity=0.627  Sum_probs=39.3

Q ss_pred             ccceeeeecccccceeeeccHHHHHHHHhHhcCCCeeeccCCC---CCCCCCCCcc
Q 029175           24 SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPG---VSCEDPADIE   76 (197)
Q Consensus        24 ~i~~ya~QC~~C~KwR~i~t~e~yEeiR~~~~~~pf~C~~~~~---~sC~dP~Di~   76 (197)
                      .++.+.|||.+|+|||.+| .+.++++.   ..++|+|...++   .+|+.|+++.
T Consensus        23 ~~~~~WVQCD~C~KWRrLP-~~~~~~~~---~pd~W~C~mN~D~~~nsCs~PEE~~   74 (100)
T 2l7p_A           23 STESAWVRCDDCFKWRRIP-ASVVGSID---ESSRWICMNNSDKRFADCSKSQEMS   74 (100)
T ss_dssp             SSSSEEEECTTTCCEEEEC-HHHHTTST---TSSCCCGGGSSCSSSCSTTSCCSSC
T ss_pred             CCCCeEEeeCCCCccccCC-hhHccccC---CCCCceeCCCCCCCCCCCCCccCCC
Confidence            4578899999999999999 44444332   359999999776   8999999985

>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=97.88  E-value=6.2e-06  Score=59.23  Aligned_cols=50  Identities=20%  Similarity=0.334  Sum_probs=38.2

Q ss_pred             ccccceeeeecc--cccceeeeccHHHHHHHHhHhcCCCeeeccCC---CCCCCCCCCcc
Q 029175           22 IRSIDTYAAQCE--KCFKWRVINSSEEYEEIRCKIAEIPFVCDRKP---GVSCEDPADIE   76 (197)
Q Consensus        22 ~~~i~~ya~QC~--~C~KwR~i~t~e~yEeiR~~~~~~pf~C~~~~---~~sC~dP~Di~   76 (197)
                      ......+.|||.  .|.|||.+|-....     ..+-+.|+|.-.+   -.+|+.|++..
T Consensus        11 ~~~~~~~WVQCd~p~C~KWR~LP~~~~~-----~~lpd~W~C~mN~d~~~~~Cs~pEE~~   65 (69)
T 2e61_A           11 GFGQCLVWVQCSFPNCGKWRRLCGNIDP-----SVLPDNWSCDQNTDVQYNRCDIPEETW   65 (69)
T ss_dssp             SCCCCCCEEECSSTTTCCEEECCSSCCT-----TTSCTTCCGGGCSCGGGCSSSSCCCCC
T ss_pred             CCCCCCeEEEeCccccCcccCCcccccc-----ccCCCcCEeCCCCCCccCCCCCCcccC
Confidence            345578899999  99999999954322     2356899999765   46899999875

>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=89.57  E-value=0.027  Score=54.50  Aligned_cols=62  Identities=27%  Similarity=0.574  Sum_probs=40.0

Q ss_pred             eeeeecc--cccceeeeccHHHHHHHHhHhcCCCeeeccCC--------CCCCCCCCCcccCC-cceeeecCCCCCC
Q 029175           27 TYAAQCE--KCFKWRVINSSEEYEEIRCKIAEIPFVCDRKP--------GVSCEDPADIEYDA-SRVWVIDRPGIPK   92 (197)
Q Consensus        27 ~ya~QC~--~C~KwR~i~t~e~yEeiR~~~~~~pf~C~~~~--------~~sC~dP~Di~~d~-sr~W~iDkp~iP~   92 (197)
                      -|.+||.  .|.|||.+++.   +.|-..+ -+-|.|...+        .-.|..|+|.---. +..|-+....+|+
T Consensus        91 ~~~~~c~~~~c~~~~~~~~~---~~~~~~~-~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (776)
T 4gut_A           91 PYWVQCTKPECRKWRQLTKE---IQLTPQI-AKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPP  163 (776)
T ss_dssp             CCEEECCCTTTCCEEECCTT---CCCCHHH-HHHCCTTCCCC-------CCGGGSCCCHHHHHTTSTTTTTTCCSCC
T ss_pred             cHhhhcCcccccchhhCCCc---CCCChhh-hheeeccCccCcccccccCCCCCCCcccchhhccchHHHHhhcCCH
Confidence            6899999  99999999744   2332332 2458898654        45688899963222 4455555555543

---

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	197
d1qk9a_	92	d.10.1.3 (A:) Methyl-CpG-binding protein 2, MECP2	2e-13
d1ig4a_	75	d.10.1.3 (A:) Methylation-dependent transcriptiona	6e-11

>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 = 61.5 bits (149), Expect = 2e-13
 Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 87  RPGIPKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 143
               P  P G+ R L  RK      K D Y I P GK  R+  E+  +     +   +  
Sbjct: 18  MYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDT-SLDP 76

Query: 144 SDFTFSVPKVMD 155
           +DF F+V     
Sbjct: 77  NDFDFTVTGRGS 88

>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 = 54.0 bits (130), Expect = 6e-11
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 8/67 (11%)

Query: 90  IPKTPGGFKRSLVLRK---DFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDF 146
            P    G+KR  V RK      + D YY +PTG ++R+  E+  +L          L+ F
Sbjct: 8   CPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLG-----PACDLTLF 62

Query: 147 TFSVPKV 153
            F    +
Sbjct: 63  DFKQGIL 69

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	197
d1ig4a_	75	Methylation-dependent transcriptional repressor MB	99.88
d1qk9a_	92	Methyl-CpG-binding protein 2, MECP2 {Human (Homo s	99.86

>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=99.88  E-value=1e-23  Score=152.85  Aligned_cols=61  Identities=31%  Similarity=0.527  Sum_probs=54.9

Q ss_pred             CCCCCCCceEEEEEcccCC---cceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccC
Q 029175           90 IPKTPGGFKRSLVLRKDFS---KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMD  155 (197)
Q Consensus        90 iP~~P~GWkRevv~R~~gs---K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~  155 (197)
                      +|.+|.||+|++++|++|.   +.|||||||+||+|||++||++||..     +|++++|||+++++.+
T Consensus         8 ~p~LP~GW~re~~~Rk~g~~~gk~DvyY~sP~Gkk~RS~~ev~~yL~~-----~l~~~~FdF~tg~~~~   71 (75)
T d1ig4a_           8 CPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGP-----ACDLTLFDFKQGILCY   71 (75)
T ss_dssp             CTTTCTTCEEEEECCCSSSSTTCCEEEEECSSSCEECSHHHHHHHHCS-----SSCCTTBCTTTCCBSC
T ss_pred             CCCCCCCcEEEEEEEcCCCCCCceeEEEECCCCCEEeCHHHHHHHhcc-----CCCccceeccCCcEeC
Confidence            4556999999999999873   79999999999999999999999965     7899999999998844

>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=99.86  E-value=3.5e-23  Score=154.72  Aligned_cols=59  Identities=34%  Similarity=0.604  Sum_probs=55.1

Q ss_pred             CCCCCCceEEEEEcccCC---cceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeC
Q 029175           91 PKTPGGFKRSLVLRKDFS---KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSV  150 (197)
Q Consensus        91 P~~P~GWkRevv~R~~gs---K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~  150 (197)
                      |.+|+||+|++++|++|.   ++||||++|+||+|||++||.+||..|++. +|++++|||++
T Consensus        22 p~Lp~GW~r~~~~R~~g~~~gk~Dvyy~sP~Gkk~RS~~eV~~yL~~~~~~-~~~~~~FdF~~   83 (92)
T d1qk9a_          22 PTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDT-SLDPNDFDFTV   83 (92)
T ss_dssp             CCSSSSCEEEECCCCCSSSCSCCCEEEEETTTEEESSHHHHHHHHHHHTCC-SSCGGGCCCCT
T ss_pred             CCCCCCCEEEEEEecCCCCCceeeEEEECCCCCeeecHHHHHHHHHHCCCc-ccchhHeeeEe
Confidence            456999999999999873   799999999999999999999999999987 89999999986