Citrus Sinensis ID: 029286

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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
MEDKQETLKTASKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGDGTARDEGSVAMH
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccEEEEEccccccEEEEccHHHHHHHHHHHccccEEEccccccccccccccccccccEEEEccccccccccccEEEEEEccccccEEEEEEcccccccccHHHHHHHHHHccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccEEEEEEEHHHcccEEEcccHHHHHHHHHHHcccccEcccccccccccccccccccccEEEEEcccccccccccEEEEEEEcccccEEEEEEcccccEcccHHHHHHHHHHccccccccHHccccccccccHcccccccEEccccccccccccccccccEccccccccccEccc
Coil and Loop (DISEMBL)
MEDKQETlktaskprgggepirsIDTYAAQCEKCFKWRVINSSEEYEEIRCKIaeipfvcdrkpgvscedpadieydasrvwvidrpgipktpggfkrsLVLRkdfskmdayyitptgkklRTLNEVAGFlaanpeysdvslsdftfsvpkvmddtipedvvkkgsassdakrkpktskgvvgdgtardegsvamh
Flexible Loop (DISEMBL)
medkqetlktaskprgggepirsIDTYAAQCEKCFKWRVINSSEEYEEIRCKIaeipfvcdrkpgVSCEDPAdieydasrvwvidrpgipktpggfkrslvlrkdfskMDAYyitptgkklrTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDvvkkgsassdakrkpktskgvvgdgtardegsvamh
Low Complexity Region (SEG)
MEDKQETLKTASKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGDGTARDEGSVAMH
Disordered region (IsUnstruct)
**********************SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM*******************************************
Disordered Region (DISOPRED)
*************************TYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFK*SLV**KDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSV***********************************************
Disordered Region (DISEMBL)
******************EPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPED***********************DGTAR********
Disordered Region (DISPRO)
********************IRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDV***********************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEDKQETLKTASKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGDGTARDEGSVAMH
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	196	2.2.26 [Sep-21-2011]
Q9LYB9	186	Methyl-CpG-binding domain	yes	no	0.719	0.758	0.687	4e-56
Q5XEN5	204	Methyl-CpG-binding domain	no	no	0.826	0.794	0.558	5e-53
Q8LA53	272	Methyl-CpG-binding domain	no	no	0.816	0.588	0.412	2e-30
Q4PSK1	163	Methyl-CpG-binding domain	no	no	0.612	0.736	0.430	1e-21
Q9FZP6	155	Putative methyl-CpG-bindi	no	no	0.622	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 (552), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 97/141 (68%), Positives = 117/141 (82%)

Query: 20  PIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDAS 79
           P R IDTYAAQC+ C KWRVI+S EEYE+IR K+ E PF C +K G+SCE+PADI+YD+S
Sbjct: 21  PGRLIDTYAAQCDNCHKWRVIDSQEEYEDIRSKMLEDPFNCQKKQGMSCEEPADIDYDSS 80

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

Query: 140 VSLSDFTFSVPKVMDDTIPED 160
             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 (526), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 95/170 (55%), Positives = 123/170 (72%), Gaps = 8/170 (4%)

Query: 15  RGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADI 74
           +  G P RSID +A QCEKC KWR I++ +EYE+IR ++ E PF C  K GVSCED  D+
Sbjct: 43  KKAGTPGRSIDVFAVQCEKCMKWRKIDTQDEYEDIRSRVQEDPFFCKTKEGVSCEDVGDL 102

Query: 75  EYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAAN 134
            YD+SR WVID+PG+P+TP GFKRSL+LRKD+SKMDAYYITPTGKKL++ NE+A F+ AN
Sbjct: 103 NYDSSRTWVIDKPGLPRTPRGFKRSLILRKDYSKMDAYYITPTGKKLKSRNEIAAFIDAN 162

Query: 135 PEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGD 184
            +Y    L DF F+VPKVM++T+P  ++        + R PK S+ V  D
Sbjct: 163 QDYKYALLGDFNFTVPKVMEETVPSGIL--------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 =  132 bits (331), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 71/172 (41%), Positives = 99/172 (57%), Gaps = 12/172 (6%)

Query: 4   KQETLKTASKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR- 62
           ++E L   S+P        SI  +  QC  CFKWR++ S ++YEEIR ++ E PF CD  
Sbjct: 36  EEEVLPVQSQPLSSRTQCPSIGAFTVQCASCFKWRLMPSMQKYEEIREQLLENPFFCDTA 95

Query: 63  ---KPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSK--MDAYYITPT 117
              KP +SC+ PADI  D +R+W ID+P I + P G++R L +R +      D YY+ P+
Sbjct: 96  REWKPDISCDVPADIYQDGTRLWAIDKPNISRPPAGWQRLLRIRGEGGTRFADVYYVAPS 155

Query: 118 GKKLRTLNEVAGFLAANPEY--SDVSLSDFTFSVPKVMDDTIPEDVVKKGSA 167
           GKKLR+  EV  +L  N EY    V LS F+F +PK + D    D V+K  A
Sbjct: 156 GKKLRSTVEVQKYLNDNSEYIGEGVKLSQFSFQIPKPLQD----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 =  102 bits (255), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 56/130 (43%), Positives = 78/130 (60%), Gaps = 10/130 (7%)

Query: 24  IDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPAD--IEYDASRV 81
           ID+YAAQC KC K R I S E+YEEIR K  E  F C R     CE+P D  + +D+  +
Sbjct: 9   IDSYAAQCWKCLKVRSIESQEDYEEIRSKTLEKFFECKR-----CEEPGDMVMNFDSLTM 63

Query: 82  -WVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYY--ITPTGKKLRTLNEVAGFLAANPEYS 138
            W  D   IPKTP G KR LV+R +  K+D YY  + P  K+ +++ EVA F+    E+ 
Sbjct: 64  RWFQDEHSIPKTPQGLKRVLVVRTNCVKVDVYYESLAPRRKRFKSIKEVATFIEDKEEFK 123

Query: 139 DVSLSDFTFS 148
           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 = 86.3 bits (212), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 51/135 (37%), Positives = 70/135 (51%), Gaps = 13/135 (9%)

Query: 29  AQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR----KPGVSCEDPADIEYDASRVWVI 84
            QC  C KWR+I S + Y  I+    + PFVC       P +SC  P D        W  
Sbjct: 2   VQCTDCKKWRLIPSMQHYNIIKETQLQTPFVCGTTSGWTPNMSCNVPQD--GTTCDTW-- 57

Query: 85  DRPGIPKTPGGFKRSLVLRKDFSKM-DAYYITPTGKKLRTLNEVAGFLAANPEY--SDVS 141
             P IP  P G+ RS+ +R + +K  D YY  P+G++LR+  EV  FL  +PEY    V+
Sbjct: 58  --PSIPPIPTGWSRSVHIRSESTKFADVYYFPPSGERLRSSAEVQSFLDNHPEYVREGVN 115

Query: 142 LSDFTFSVPKVMDDT 156
            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	196
224128656	182	methyl binding domain protein [Populus t	0.867	0.934	0.712	3e-66
224117174	182	methyl binding domain protein [Populus t	0.872	0.939	0.687	8e-65
255567630	160	DNA binding protein, putative [Ricinus c	0.775	0.95	0.745	2e-59
297799740	176	hypothetical protein ARALYDRAFT_914336 [	0.872	0.971	0.573	3e-55
15229373	186	methyl-CPG-binding domain 4 protein [Ara	0.719	0.758	0.687	2e-54
297817640	182	methyl-CpG-binding domain 4 [Arabidopsis	0.760	0.818	0.666	3e-54
356535711	193	PREDICTED: methyl-CpG-binding domain-con	0.765	0.777	0.653	7e-54
388511439	180	unknown [Lotus japonicus]	0.770	0.838	0.655	9e-54
225436873	179	PREDICTED: methyl-CpG-binding domain-con	0.897	0.983	0.573	2e-53
358248398	177	uncharacterized protein LOC100802350 [Gl	0.765	0.847	0.64	2e-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 =  256 bits (655), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 124/174 (71%), Positives = 145/174 (83%), Gaps = 4/174 (2%)

Query: 2   EDKQETLKTASK-PRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVC 60
           E   ET KT+SK PR     +RSIDTYAAQC+KC KWRVI + EEYEEIR K+ E PFVC
Sbjct: 5   ERSPETPKTSSKNPRVA---VRSIDTYAAQCDKCLKWRVIATEEEYEEIRSKMEESPFVC 61

Query: 61  DRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKK 120
           +RKPGVSC+DPADIEY+A+R WVIDRPGIPKTP GFKRSLVLR+DFSKMDAYYITPTGKK
Sbjct: 62  NRKPGVSCDDPADIEYNATRTWVIDRPGIPKTPEGFKRSLVLRRDFSKMDAYYITPTGKK 121

Query: 121 LRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRK 174
           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 =  251 bits (642), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 119/173 (68%), Positives = 142/173 (82%), Gaps = 2/173 (1%)

Query: 2   EDKQETLKTASKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCD 61
           E   ET KT+  P+     +RSIDTYAAQC+KC KWRVI + EEYEEIR K+ E P+VCD
Sbjct: 5   ERSPETPKTS--PKNPRVAVRSIDTYAAQCDKCLKWRVIPTEEEYEEIRSKMEENPYVCD 62

Query: 62  RKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKL 121
           RKPGVSC+DPADIEY+A+R WVIDRPG+PKTP GFKRSLVLR+DFSKMDAYYITPTGKKL
Sbjct: 63  RKPGVSCDDPADIEYNATRTWVIDRPGVPKTPEGFKRSLVLRRDFSKMDAYYITPTGKKL 122

Query: 122 RTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRK 174
           RT NE+A F+ ANP+Y DV+LS F F+ PKVM+DTIPED V+K  +S++  +K
Sbjct: 123 RTRNEIAAFIEANPKYKDVNLSAFNFTSPKVMEDTIPEDAVRKVPSSANGNKK 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: 21  IRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASR 80
           +RS+DTYAAQCEKC KWRVI + EEYEEIR KI E PF C+RKPG+SCEDPADIE DASR
Sbjct: 1   MRSVDTYAAQCEKCMKWRVIETEEEYEEIRSKIVENPFYCNRKPGISCEDPADIECDASR 60

Query: 81  VWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDV 140
            WVID+PG+PKTPGGFKRSLVLR+DFSKMDAYYITPTGKKLRT NE+A FL ANP+Y  V
Sbjct: 61  TWVIDKPGLPKTPGGFKRSLVLRRDFSKMDAYYITPTGKKLRTRNEIAAFLEANPKYKGV 120

Query: 141 SLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKR 173
           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 =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 105/183 (57%), Positives = 135/183 (73%), Gaps = 12/183 (6%)

Query: 1   MEDKQETLKTASKP---RGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIP 57
           M+D+ +T K A KP   +  G P RSID +A QCEKC KWR I + +EYEEIR +I E P
Sbjct: 1   MDDQSQTEKLA-KPILKKKAGTPGRSIDVFAVQCEKCLKWRQIGTQDEYEEIRSRIQEDP 59

Query: 58  FVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPT 117
           +VC++K G+SCED  D+ YD+SR WVID+PG+PKTP GFKRSL+LRKD+SKMDAYYITPT
Sbjct: 60  YVCEKKEGISCEDAGDLNYDSSRTWVIDKPGLPKTPRGFKRSLILRKDYSKMDAYYITPT 119

Query: 118 GKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKT 177
           GKKL++ NE+A F+ AN +Y    L DF F+VPKVM++T+P  ++        + R PKT
Sbjct: 120 GKKLKSRNEIAAFIDANQDYKYALLGDFNFTVPKVMEETVPNGII--------SDRTPKT 171

Query: 178 SKG 180
           SKG
Sbjct: 172 SKG 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 (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 97/141 (68%), Positives = 117/141 (82%)

Query: 20  PIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDAS 79
           P R IDTYAAQC+ C KWRVI+S EEYE+IR K+ E PF C +K G+SCE+PADI+YD+S
Sbjct: 21  PGRLIDTYAAQCDNCHKWRVIDSQEEYEDIRSKMLEDPFNCQKKQGMSCEEPADIDYDSS 80

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

Query: 140 VSLSDFTFSVPKVMDDTIPED 160
             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|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: 20  PIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDAS 79
           P R IDTYAAQCE C KWRVI+S EEYE+IR K+ E PF C +K G+SCE+PAD++YD+S
Sbjct: 20  PGRLIDTYAAQCENCHKWRVIDSQEEYEDIRSKMLEDPFNCQKKQGMSCEEPADLDYDSS 79

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

Query: 140 VSLSDFTFSVPKVMDDTIPEDVVKKGSASS 169
             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|356535711|ref|XP_003536387.1| PREDICTED: methyl-CpG-binding domain-containing protein 4-like [Glycine max]

 Score =  215 bits (548), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 98/150 (65%), Positives = 118/150 (78%)

Query: 23  SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVW 82
           S+D YAAQC+ C KWR I++ EE+EEIR K+AE PF+C RK   SC++P DI+YD+SR W
Sbjct: 38  SVDIYAAQCKNCLKWREIDTQEEFEEIRSKVAEEPFLCSRKANSSCDEPGDIKYDSSRTW 97

Query: 83  VIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 142
           VID+P +PKTP GFKRSLVLRKD+SK+DAYYITP GKKLRT NE+A FL  NPE+  VS 
Sbjct: 98  VIDKPNLPKTPQGFKRSLVLRKDYSKLDAYYITPAGKKLRTRNEIAAFLKDNPEFKGVSA 157

Query: 143 SDFTFSVPKVMDDTIPEDVVKKGSASSDAK 172
           SDF FS PK+M DTIPE V +K SA+   K
Sbjct: 158 SDFDFSSPKIMQDTIPEVVEQKDSANKKVK 187

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 = 9e-54,   Method: Compositional matrix adjust.
 Identities = 99/151 (65%), Positives = 118/151 (78%)

Query: 23  SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVW 82
           SID YAAQC KC KWRVI++ +E+EEIR K+++ PF C RK   SC+DPADIEYD+SR W
Sbjct: 25  SIDVYAAQCIKCLKWRVIDTQQEFEEIRHKVSQEPFDCSRKANCSCDDPADIEYDSSRTW 84

Query: 83  VIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 142
           VID+P +PKTP GFKRSLVLRKD+SK+DAYYITPTGKKLRT NE A FL  +PE   +S 
Sbjct: 85  VIDKPNLPKTPEGFKRSLVLRKDYSKLDAYYITPTGKKLRTRNEAAAFLKDHPELQGISA 144

Query: 143 SDFTFSVPKVMDDTIPEDVVKKGSASSDAKR 173
            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|225436873|ref|XP_002273070.1| PREDICTED: methyl-CpG-binding domain-containing protein 4-like isoform 1 [Vitis vinifera]

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 101/176 (57%), Positives = 124/176 (70%)

Query: 5   QETLKTASKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKP 64
           Q   KT  K R       SI  YA QCE C KWR+I++ EEYEEIR +  E PFVC +K 
Sbjct: 2   QPMEKTKGKKRKSALVRSSIGAYAVQCEACLKWRLIDTEEEYEEIRSRFIEEPFVCSKKA 61

Query: 65  GVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTL 124
            VSCEDP DIEYDA+R W  D+P +PKTP GF+R LVLRKDFSKMDAYYITPTGKK+R L
Sbjct: 62  DVSCEDPTDIEYDATRTWAADKPNVPKTPKGFQRDLVLRKDFSKMDAYYITPTGKKVRAL 121

Query: 125 NEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKG 180
           +E+A +L++NP+  D+S SDF F VPK+M DTIP  + +K S S   K++ K+  G
Sbjct: 122 SEIAAYLSSNPDCKDLSPSDFNFMVPKIMADTIPAHIERKVSTSGSNKKRKKSENG 177

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 96/150 (64%), Positives = 117/150 (78%)

Query: 23  SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVW 82
           S+D YAAQC+ C KWR I++ EE+EEIR K+ E PF+C RK   SC++P DIEYD++R W
Sbjct: 22  SVDIYAAQCKNCLKWREIDTQEEFEEIRSKVTEEPFLCSRKANSSCDEPGDIEYDSTRTW 81

Query: 83  VIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 142
           VID+P +PKTP GFKRSLVLRKD+SK+DAYYITP GKKLRT NE+A FL  NPE+  VS 
Sbjct: 82  VIDKPNLPKTPQGFKRSLVLRKDYSKLDAYYITPAGKKLRTRNEIAAFLKDNPEFKGVSA 141

Query: 143 SDFTFSVPKVMDDTIPEDVVKKGSASSDAK 172
           SDF FS PK+M DTIPE + +K SA+   K
Sbjct: 142 SDFDFSSPKIMQDTIPEIIEQKDSANKKVK 171

Source: Glycine max

Species: Glycine max

Genus: Glycine

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	196
TAIR|locus:2099187	186	MBD4 "methyl-CPG-binding domai	0.836	0.881	0.630	1.3e-54
TAIR|locus:505006513	204	MBD1 "methyl-CPG-binding domai	0.852	0.818	0.561	1.7e-50
TAIR|locus:2182643	272	MBD02 "methyl-CPG-binding doma	0.826	0.595	0.408	4.9e-30
TAIR|locus:505006418	163	MBD3 "methyl-CPG-binding domai	0.627	0.754	0.436	6.1e-23
TAIR|locus:504954793	155	MBD12 "methyl-CPG-binding doma	0.698	0.883	0.375	4.6e-18

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

 Score = 564 (203.6 bits), Expect = 1.3e-54, P = 1.3e-54
 Identities = 106/168 (63%), Positives = 132/168 (78%)

Query:     1 MEDKQETLKTASKPRGGGE--PIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPF 58
             M++++E  K A KP+   +  P R IDTYAAQC+ C KWRVI+S EEYE+IR K+ E PF
Sbjct:     1 MKEEEEIGKPA-KPKAKKDVAPGRLIDTYAAQCDNCHKWRVIDSQEEYEDIRSKMLEDPF 59

Query:    59 VCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTG 118
              C +K G+SCE+PADI+YD+SR WVID+PG+PKTP GFKRSLVLRKD+SKMD YY TPTG
Sbjct:    60 NCQKKQGMSCEEPADIDYDSSRTWVIDKPGLPKTPKGFKRSLVLRKDYSKMDTYYFTPTG 119

Query:   119 KKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGS 166
             KKLR+ NE+A F+ ANPE+ +  L DF F+VPKVM+DT+P D  K GS
Sbjct:   120 KKLRSRNEIAAFVEANPEFRNAPLGDFNFTVPKVMEDTVPPDP-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 = 525 (189.9 bits), Expect = 1.7e-50, P = 1.7e-50
 Identities = 100/178 (56%), Positives = 127/178 (71%)

Query:     7 TLKTASKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGV 66
             T+K   K    G P RSID +A QCEKC KWR I++ +EYE+IR ++ E PF C  K GV
Sbjct:    38 TIKVQKK---AGTPGRSIDVFAVQCEKCMKWRKIDTQDEYEDIRSRVQEDPFFCKTKEGV 94

Query:    67 SCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTGKKLRTLNE 126
             SCED  D+ YD+SR WVID+PG+P+TP GFKRSL+LRKD+SKMDAYYITPTGKKL++ NE
Sbjct:    95 SCEDVGDLNYDSSRTWVIDKPGLPRTPRGFKRSLILRKDYSKMDAYYITPTGKKLKSRNE 154

Query:   127 VAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVVGD 184
             +A F+ AN +Y    L DF F+VPKVM++T+P  ++      SD  R PK S+ V  D
Sbjct:   155 IAAFIDANQDYKYALLGDFNFTVPKVMEETVPSGIL------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 = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 71/174 (40%), Positives = 100/174 (57%)

Query:     2 EDKQETLKTASKPRGGGEPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCD 61
             + ++E L   S+P        SI  +  QC  CFKWR++ S ++YEEIR ++ E PF CD
Sbjct:    34 DTEEEVLPVQSQPLSSRTQCPSIGAFTVQCASCFKWRLMPSMQKYEEIREQLLENPFFCD 93

Query:    62 R----KPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKM--DAYYIT 115
                  KP +SC+ PADI  D +R+W ID+P I + P G++R L +R +      D YY+ 
Sbjct:    94 TAREWKPDISCDVPADIYQDGTRLWAIDKPNISRPPAGWQRLLRIRGEGGTRFADVYYVA 153

Query:   116 PTGKKLRTLNEVAGFLAANPEY--SDVSLSDFTFSVPKVMDDTIPEDVVKKGSA 167
             P+GKKLR+  EV  +L  N EY    V LS F+F +PK + D    D V+K  A
Sbjct:   154 PSGKKLRSTVEVQKYLNDNSEYIGEGVKLSQFSFQIPKPLQD----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:    24 IDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADI--EYDASRV 81
             ID+YAAQC KC K R I S E+YEEIR K  E  F C R     CE+P D+   +D+  +
Sbjct:     9 IDSYAAQCWKCLKVRSIESQEDYEEIRSKTLEKFFECKR-----CEEPGDMVMNFDSLTM 63

Query:    82 -WVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYY--ITPTGKKLRTLNEVAGFLAANPEYS 138
              W  D   IPKTP G KR LV+R +  K+D YY  + P  K+ +++ EVA F+    E+ 
Sbjct:    64 RWFQDEHSIPKTPQGLKRVLVVRTNCVKVDVYYESLAPRRKRFKSIKEVATFIEDKEEFK 123

Query:   139 DVSLSDFTFSVPK 151
             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:    30 QCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRK----PGVSCEDPADIEYDASRVWVID 85
             QC  C KWR+I S + Y  I+    + PFVC       P +SC  P D        W   
Sbjct:     3 QCTDCKKWRLIPSMQHYNIIKETQLQTPFVCGTTSGWTPNMSCNVPQD--GTTCDTW--- 57

Query:    86 RPGIPKTPGGFKRSLVLRKDFSKM-DAYYITPTGKKLRTLNEVAGFLAANPEY--SDVSL 142
              P IP  P G+ RS+ +R + +K  D YY  P+G++LR+  EV  FL  +PEY    V+ 
Sbjct:    58 -PSIPPIPTGWSRSVHIRSESTKFADVYYFPPSGERLRSSAEVQSFLDNHPEYVREGVNR 116

Query:   143 SDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSK 179
             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   0.393    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      196       196   0.00080  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:  578 (61 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:  17.46u 0.10s 17.56t   Elapsed:  00:00:01
  Total cpu time:  17.46u 0.10s 17.56t   Elapsed:  00:00:01
  Start:  Fri May 10 13:30:41 2013   End:  Fri May 10 13:30:42 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	0.7193	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

Your Input: MBD903 SubName- Full=Putative uncharacterized protein; (183 aa) (Populus trichocarpa)

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	196
cd01396	77	cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and M	4e-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	3e-11
pfam07496	50	pfam07496, zf-CW, CW-type Zinc Finger	8e-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 = 72.0 bits (177), Expect = 4e-17
 Identities = 35/75 (46%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 86  RPGIPKTPGGFKRSLVLRKDFS--KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLS 143
           +P  P+ P G+KR LV RK  S  K D YYI+PTGKK R+  E+A +L  N   + + LS
Sbjct: 1   KPEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGP-TSLDLS 59

Query: 144 DFTFSVPKVMDDTIP 158
           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 = 62.4 bits (152), Expect = 2e-13
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 84  IDRPGIPKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDV 140
             R   P  P G++R    RK      K+D YY +PTGKK R+ +E+  +L  N + S +
Sbjct: 2   RKREDCPPLPPGWRREERQRKSGSSAGKVDVYYYSPTGKKFRSKSELIRYLEKNGDTS-L 60

Query: 141 SLSDFTFSVPKVMDD 155
            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: 84  IDRPGIPKTPGGFKRSLVLRKDFS---KMDAYYITPTGKKLRTLNEVAGFLAANPEYS-D 139
            D   +P  P G++R    RK      K D YYI+P GKKLR+ +E+A +L  N + S D
Sbjct: 1   GDPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLD 59

Query: 140 VSLSDFTFSVPKVM 153
           +   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 = 56.2 bits (136), Expect = 3e-11
 Identities = 27/57 (47%), Positives = 35/57 (61%), Gaps = 3/57 (5%)

Query: 93  PGGFKRSLVLRKDFS--KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF 147
           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 = 8e-11
 Identities = 24/53 (45%), Positives = 31/53 (58%), Gaps = 6/53 (11%)

Query: 26 TYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR---KPGVSCEDPADIE 75
           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: 93  PGGFKRSLVLRKDFSKM--DAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVP 150
             G++R   +R    ++  +  Y  P GKKLR   EV  +L+ N   S +S  +F+FS  
Sbjct: 7   ELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKN-GISLLSRENFSFS-A 64

Query: 151 KVM 153
           +  
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	196
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	99.78
cd01395	60	HMT_MBD Methyl-CpG binding domains (MBD) present i	99.53
KOG4161	272	consensus Methyl-CpG binding transcription regulat	99.29
PF07496	50	zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zi	99.18

>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=1.7e-25  Score=164.65  Aligned_cols=72  Identities=47%  Similarity=0.758  Sum_probs=66.6

Q ss_pred             CCCCCCCCCceEEEEEcccC--CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCCCCCC
Q 029286           87 PGIPKTPGGFKRSLVLRKDF--SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPE  159 (196)
Q Consensus        87 p~iP~~P~GWkRevv~R~~g--sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~~ip~  159 (196)
                      +++|.+|+||+|++++|++|  +++||||++|+|++|||++||++||+.||.. +|++++|||++++++.++++.
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 899999999999999987765

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=3.1e-24  Score=157.82  Aligned_cols=69  Identities=36%  Similarity=0.618  Sum_probs=63.3

Q ss_pred             cCCCCCCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286           85 DRPGIPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD  155 (196)
Q Consensus        85 Dkp~iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~  155 (196)
                      ++..+| +|+||+|++++|++|   +++||||+||+||+|||++||++||.+|+++ .+++++|||.+..++..
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   5899999999999999999999999999997 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=4.7e-23  Score=151.72  Aligned_cols=63  Identities=30%  Similarity=0.392  Sum_probs=58.6

Q ss_pred             CCCCceEEEEEcccCC--cceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286           92 TPGGFKRSLVLRKDFS--KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD  155 (196)
Q Consensus        92 ~P~GWkRevv~R~~gs--K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~  155 (196)
                      +|.||+|++|+|+.++  ++||||++||||||||++||++||..|+.. +|+++||+|+++.++.+
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  799999999999999999999999999975 89999999999988765

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=2.3e-22  Score=141.20  Aligned_cols=59  Identities=44%  Similarity=0.695  Sum_probs=54.1

Q ss_pred             CCCCCCCCCceEEEEEcccC--CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeee
Q 029286           87 PGIPKTPGGFKRSLVLRKDF--SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF  147 (196)
Q Consensus        87 p~iP~~P~GWkRevv~R~~g--sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F  147 (196)
                      ..+|. |+||+|++++|++|  +++||||++|+|++|||+.||++||..|+.. +|++++|||
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  5899999999999999999999999999843 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=2.4e-21  Score=141.06  Aligned_cols=64  Identities=41%  Similarity=0.742  Sum_probs=53.5

Q ss_pred             CCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCccc
Q 029286           90 PKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM  153 (196)
Q Consensus        90 P~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~  153 (196)
                      +.+|+||+|++++|++|   ++.||||+||+|++|||+.||.+||..++....|++++|+|.....+
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   47999999999999999999999999999644899999999988764

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=99.78  E-value=1.2e-19  Score=159.73  Aligned_cols=145  Identities=30%  Similarity=0.300  Sum_probs=133.5

Q ss_pred             CCccccchhhhccccccceeeeccHHHHHHHHhhhcCCCeeeccCCCCCcCCCCCcccCCcceeeecCCCCCCCCCCceE
Q 029286           19 EPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKR   98 (196)
Q Consensus        19 ~~~~~i~~yavQC~~C~KwR~ipt~e~yEeir~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~iP~~P~GWkR   98 (196)
                      ....+|.+|++||..|++|+.|.++.+|+++|+.+.++||+|..+..+.|++++|+++++++.|.||.++++.+|.||.|
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            44569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcccCCcceEEEECCCCCccccHHHHHHhhhhCC--CCCCCCcCCeeeeCCcccCCCCCCcccc
Q 029286           99 SLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANP--EYSDVSLSDFTFSVPKVMDDTIPEDVVK  163 (196)
Q Consensus        99 evv~R~~gsK~DVYY~SP~GKKlRSk~EV~ryL~~np--e~~~l~le~F~F~~pk~~~~~ip~~~~~  163 (196)
                      .+..+......++||.+|+|+.+++..+++.++..|+  ++....+.+|.|+.+.++.+.+.-.-++
T Consensus       184 ~~~~~s~~~~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~~~~r  250 (272)
T KOG4161|consen  184 SSAGESLLSSVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRVKNVR  250 (272)
T ss_pred             cccccccccccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccchhhhh
Confidence            9999988889999999999999999999999999994  4446789999999998888866543333

>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=99.53  E-value=1e-14  Score=104.08  Aligned_cols=53  Identities=28%  Similarity=0.456  Sum_probs=48.9

Q ss_pred             CCCceEEEEEcccCC-cceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeee
Q 029286           93 PGGFKRSLVLRKDFS-KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF  147 (196)
Q Consensus        93 P~GWkRevv~R~~gs-K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F  147 (196)
                      -.||+|....|+.|+ |.||+|.+||||+||++.||++||..+ . ..|++++|+|
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=99.29  E-value=2.3e-12  Score=113.75  Aligned_cols=63  Identities=38%  Similarity=0.609  Sum_probs=54.8

Q ss_pred             cCCCCCCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286           85 DRPGIPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD  155 (196)
Q Consensus        85 Dkp~iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~  155 (196)
                      |++.|   |+||.|++++|++|   ++.||||+||.|++|||+.+++.||+.+     .+.+.|+|-..+++..
T Consensus        15 ~c~~l---p~GW~~~~~~r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~-----~~~s~~~~v~~k~~~~   80 (272)
T KOG4161|consen   15 DCPAL---PPGWTREEVQRSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKV-----GDLSLFDFVTGKMSPS   80 (272)
T ss_pred             cCCCC---CCCcchhhhcccCCCcccccceEEeCCcccccccccHHHHHhccc-----cccccCcccccccccc
Confidence            55545   99999999999987   5899999999999999999999999994     4678888888877665

>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=99.18  E-value=2.8e-12  Score=87.35  Aligned_cols=46  Identities=41%  Similarity=0.954  Sum_probs=32.4

Q ss_pred             hhhccccccceeeeccHHHHHHHHhhhcCCCeeecc---CCCCCcCCCCCcc
Q 029286           27 YAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR---KPGVSCEDPADIE   75 (196)
Q Consensus        27 yavQC~~C~KwR~ipt~e~yEeir~~~~~~pf~C~~---~~~~sC~dP~Di~   75 (196)
                      |.|||..|.|||.||  .++..|++.+.+ +|+|..   .+..||+.|+|++
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            689999999999999  888888888888 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	196
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	1e-13
1ub1_A	133	MECP2, attachment region binding protein; chicken	1e-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	7e-11

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

 Score = 63.2 bits (153), Expect = 1e-13
 Identities = 23/81 (28%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 80  RVWVIDRPGI---PKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAA 133
           R  + DR  +   P  P G+ R L  RK      K D Y I P GK  R+  E+  +   
Sbjct: 9   RSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEK 68

Query: 134 NPEYSDVSLSDFTFSVPKVMD 154
             +   +  +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 = 61.4 bits (148), Expect = 1e-12
 Identities = 26/106 (24%), Positives = 40/106 (37%), Gaps = 7/106 (6%)

Query: 80  RVWVIDRPGI---PKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAA 133
           R  + DR  +   P  P G+ R L  RK      K D Y I P GK  R+  E+  +   
Sbjct: 23  RSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEK 82

Query: 134 NPEYSDVSLSDFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSK 179
             +   +  +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 = 59.2 bits (143), Expect = 2e-12
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 8/71 (11%)

Query: 86  RPGIPKTPGGFKRSLVLRKDFS---KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 142
           R   P  P G+K+  V+RK      K D YY +P+GKK R+  ++A +L    +     L
Sbjct: 7   RTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNAVD-----L 61

Query: 143 SDFTFSVPKVM 153
           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 = 7e-11
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 8/72 (11%)

Query: 85  DRPGIPKTPGGFKRSLVLRK---DFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVS 141
           D    P    G+KR  V RK      + D YY +PTG ++R+  E+  +L          
Sbjct: 4   DWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLG-----PACD 58

Query: 142 LSDFTFSVPKVM 153
           L+ F F    + 
Sbjct: 59  LTLFDFKQGILC 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	196
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	97.8
4gut_A	776	Lysine-specific histone demethylase 1B; histone de	90.85

>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=2.9e-27  Score=189.54  Aligned_cols=113  Identities=29%  Similarity=0.457  Sum_probs=89.4

Q ss_pred             CCCcccCCcceeeecCCC----CCCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcC
Q 029286           71 PADIEYDASRVWVIDRPG----IPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLS  143 (196)
Q Consensus        71 P~Di~~d~sr~W~iDkp~----iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le  143 (196)
                      |+.......|+.||+...    .|.+|+||+|++++|++|   +++|||||||+||+|||++||++||+.|+++ +|+++
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            444444566887886555    355799999999999998   5899999999999999999999999999997 89999


Q ss_pred             CeeeeCCcccCCCCCCcccccCCCCccccCCCCccCCCC-CCCCcCCCCcc
Q 029286          144 DFTFSVPKVMDDTIPEDVVKKGSASSDAKRKPKTSKGVV-GDGTARDEGSV  193 (196)
Q Consensus       144 ~F~F~~pk~~~~~ip~~~~~k~~~~~~~~kk~~~~k~~~-g~~~~~~~~~~  193 (196)
                      +|||++...   .+++    ++.+  +..++.|+.+..+ |+|++|++||.
T Consensus        92 ~FdF~~~gk---~~~s----~R~~--r~~k~~k~~~~~~~~~~~~~~~~~~  133 (133)
T 1ub1_A           92 DFDFTVTGR---GSPS----RREQ--RPPKKAKSPKSPGSGRGRGRPKGSG  133 (133)
T ss_dssp             GCCCCCCCC---SCSS----CCCC--CCCCCCCCCCCCCCCCCCCCCCCCC
T ss_pred             HCccccCCC---CCCc----cccc--CCCCCCCCCCCCCCCCCCCCCCCCC
Confidence            999996422   2233    2333  4467778877777 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=3.4e-25  Score=159.66  Aligned_cols=59  Identities=34%  Similarity=0.565  Sum_probs=55.7

Q ss_pred             CCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCC
Q 029286           91 KTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVP  150 (196)
Q Consensus        91 ~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~p  150 (196)
                      .+|+||+|++++|++|   +|.||||+||+||||||++||++||+.||++ +|++++|||++|
T Consensus         5 plp~GW~R~~~~R~~G~s~gk~DvyY~sP~Gkk~RSk~ev~~yL~~~~~~-~l~~~~FdF~~p   66 (69)
T 3vxv_A            5 PVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGET-FLKPEDFNFTVL   66 (69)
T ss_dssp             CSCTTCEEEEEECCSSTTTTCEEEEEECTTSCEECSHHHHHHHHHHHCCC-CCCGGGSCCCCC
T ss_pred             cCCCCCEEEEEEeccCCCCCcceEEEEcCCCCEeeCHHHHHHHHHhCCCC-CCCHHHcceeCC
Confidence            3599999999999987   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=6e-25  Score=168.07  Aligned_cols=65  Identities=31%  Similarity=0.497  Sum_probs=58.7

Q ss_pred             CCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286           90 PKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD  155 (196)
Q Consensus        90 P~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~  155 (196)
                      |.+|+||+|++++|++|   +++|||||||+||+|||++||++||+.||++ +|++++|||++++++.+
T Consensus        22 ~~lP~GW~re~~~R~~G~s~gk~DvYY~sP~GkkfRSk~ev~ryL~~~g~~-~~~~~~FdF~~~~~~~~   89 (97)
T 3c2i_A           22 PTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEKVGDT-SLDPNDFDFTVTGRGSP   89 (97)
T ss_dssp             TTSCTTCEEEEEECCSSTTTTCEEEEEECTTSCEECSHHHHHHHHHHHTCC-SSCTTTCCCCSSCC---
T ss_pred             CCCCCCCEEEEEEecCCCCCCcceEEEECCCCCEEECHHHHHHHHHHCCCC-CCCHhhccccCCCcCcc
Confidence            56799999999999997   5899999999999999999999999999998 89999999999988665

>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=2e-24  Score=156.63  Aligned_cols=60  Identities=42%  Similarity=0.712  Sum_probs=55.0

Q ss_pred             CCCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCccc
Q 029286           89 IPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM  153 (196)
Q Consensus        89 iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~  153 (196)
                      +|.+|+||+|++++|++|   +++||||++|+|++|||++||++||..     +|++++|||.++++|
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   589999999999999999999999988     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=3.9e-24  Score=156.52  Aligned_cols=62  Identities=31%  Similarity=0.512  Sum_probs=56.3

Q ss_pred             CCCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286           89 IPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD  155 (196)
Q Consensus        89 iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~  155 (196)
                      .|.+|+||+|++++|++|   +++|||||||+||+|||++||++||+.     ++++++|||++++++.-
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            345599999999999998   589999999999999999999999975     78999999999998654

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

Probab=98.52  E-value=2.6e-08  Score=76.38  Aligned_cols=49  Identities=22%  Similarity=0.627  Sum_probs=39.3

Q ss_pred             ccchhhhccccccceeeeccHHHHHHHHhhhcCCCeeeccCCC---CCcCCCCCcc
Q 029286           23 SIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPG---VSCEDPADIE   75 (196)
Q Consensus        23 ~i~~yavQC~~C~KwR~ipt~e~yEeir~~~~~~pf~C~~~~~---~sC~dP~Di~   75 (196)
                      .++.+.|||.+|+|||.+| .+.++.+.   ..+.|+|...++   .+|+.|+++.
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 44443332   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=97.80  E-value=6.4e-06  Score=59.14  Aligned_cols=50  Identities=20%  Similarity=0.334  Sum_probs=38.2

Q ss_pred             ccccchhhhccc--cccceeeeccHHHHHHHHhhhcCCCeeeccCC---CCCcCCCCCcc
Q 029286           21 IRSIDTYAAQCE--KCFKWRVINSSEEYEEIRCKIAEIPFVCDRKP---GVSCEDPADIE   75 (196)
Q Consensus        21 ~~~i~~yavQC~--~C~KwR~ipt~e~yEeir~~~~~~pf~C~~~~---~~sC~dP~Di~   75 (196)
                      ......+.|||.  .|.|||.+|-....     ..+-+.|+|.-.+   -.+|+.|++..
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            345568899999  99999999954322     2356899999755   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=90.85  E-value=0.016  Score=55.97  Aligned_cols=62  Identities=29%  Similarity=0.587  Sum_probs=39.8

Q ss_pred             hhhhccc--cccceeeeccHHHHHHHHhhhcCCCeeeccCC--------CCCcCCCCCcccCC-cceeeecCCCCCC
Q 029286           26 TYAAQCE--KCFKWRVINSSEEYEEIRCKIAEIPFVCDRKP--------GVSCEDPADIEYDA-SRVWVIDRPGIPK   91 (196)
Q Consensus        26 ~yavQC~--~C~KwR~ipt~e~yEeir~~~~~~pf~C~~~~--------~~sC~dP~Di~~d~-sr~W~iDkp~iP~   91 (196)
                      -|.+||.  .|.|||.+|+.   +.|-..+. +-|.|...+        +-.|..|+|.---. +..|-+-...+|+
T Consensus        91 ~~~~~c~~~~c~~~~~~~~~---~~~~~~~~-~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (776)
T 4gut_A           91 PYWVQCTKPECRKWRQLTKE---IQLTPQIA-KTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPP  163 (776)
T ss_dssp             CCEEECCCTTTCCEEECCTT---CCCCHHHH-HHCCTTCCCC-------CCGGGSCCCHHHHHTTSTTTTTTCCSCC
T ss_pred             cHhhhcCcccccchhhCCCc---CCCChhhh-heeeccCccCcccccccCCCCCCCcccchhhccchHHHHhhcCCH
Confidence            5889999  99999999744   33333332 348898754        44688899963222 4555555555543

---

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	196
d1qk9a_	92	d.10.1.3 (A:) Methyl-CpG-binding protein 2, MECP2	1e-13
d1ig4a_	75	d.10.1.3 (A:) Methylation-dependent transcriptiona	5e-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 = 1e-13
 Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 86  RPGIPKTPGGFKRSLVLRKD---FSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSL 142
               P  P G+ R L  RK      K D Y I P GK  R+  E+  +     +   +  
Sbjct: 18  MYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDT-SLDP 76

Query: 143 SDFTFSVPKVMD 154
           +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 = 54.4 bits (131), Expect = 5e-11
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 8/67 (11%)

Query: 89  IPKTPGGFKRSLVLRK---DFSKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDF 145
            P    G+KR  V RK      + D YY +PTG ++R+  E+  +L          L+ F
Sbjct: 8   CPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLG-----PACDLTLF 62

Query: 146 TFSVPKV 152
            F    +
Sbjct: 63  DFKQGIL 69

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	196
d1ig4a_	75	Methylation-dependent transcriptional repressor MB	99.89
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=99.89  E-value=6.6e-24  Score=153.80  Aligned_cols=61  Identities=31%  Similarity=0.524  Sum_probs=54.8

Q ss_pred             CCCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccC
Q 029286           89 IPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMD  154 (196)
Q Consensus        89 iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~  154 (196)
                      +|.+|+||+|++++|++|   ++.|||||||+||+|||++||++||..     +|++++|||+++++.+
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            455699999999999987   379999999999999999999999965     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=2.8e-23  Score=155.10  Aligned_cols=59  Identities=34%  Similarity=0.607  Sum_probs=55.0

Q ss_pred             CCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeC
Q 029286           90 PKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSV  149 (196)
Q Consensus        90 P~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~  149 (196)
                      |.+|+||+|++++|++|   +++||||++|+||+|||++||++||..|++. +|++++|||++
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            45699999999999987   3799999999999999999999999999987 89999999986