Citrus Sinensis ID: 022412

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------
Protein Sequence
MASSDSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENAPESTEETKEVEMKEAEKTEDNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEEETKQKTNRSAPEAEELKEKGAVNGSGEELNSVNQISRRWK
Secondary Structure (PSIPRED)
cccccccccccEEEcccccccccccccccccccccccEEEEEcccccccccHHHHHHHHHHccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccHHHHHHHHccccccccccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEccccccccEEEcccccccccccEEEEEcccccccccHHHHHHHHHHcccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccHHHcccccHHccccccccccHHHHHccccccccccccHccccccccccccccHHHcccHccccccHHHHccHHHccccccccccccccccccccccccccccccccHccccccccccccccccccHHccccccHHHHccccccccccccHHHccccccccccHHHccHHHHHHccc
Coil and Loop (DISEMBL)
massdsvkeeqvsfelpapfgwkkkivprkggtpkkseivftaptgeeisNKKQLEQYLkahpggpassefdwgtgetprrsarisekakispaadneppkkrgrkssaskkdgreaenapesteeTKEVEMKEAektednakvekeeDIVKesrdenevdqgpdtkteagpsgeakvgedankstdaeeskkteaepgnlketqdgtqadssgvtqdkagiegakneekvdqpqvetqkefgsgeqdkadpaaAEEETkqktnrsapeaeelkekgavngsgeelnsVNQISRRWK
Flexible Loop (DISEMBL)
massdsvkeeqvsfelpapfgwkkkivprkggtpkkseivftaptgeeisNKKQLEQYLKAHpggpassefdwgTGETPRRsarisekakispaadneppkkrgrkssaskkdgreaenapesteetkevemkeaektednakvekeedivkesrdenevdqgpdtkteagpsgeakvgedankstdaeeskkteaepgnlketqdgtqadssgvTQDKAGiegakneekvdqpqvetqkefgsgeqdkadpaaaeeetkqktnrsapeaeelkekgavngsgeelnsvnqisrrwk
Low Complexity Region (SEG)
MASSDSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPkkrgrkssaskkdgrEAENAPesteetkevemkeaekteDNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEEETKQKTNRSAPEAEELKEKGAVNGSGEELNSVNQISRRWK
Disordered region (IsUnstruct)
*******************FGWK**********************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
**************ELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGT******************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
************SFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDW***************************************************************************************************************************************************GIEG*************************************************************************
Disordered Region (DISPRO)
********EEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHP*****************************************************************************************************************************************************************************************************************************************K
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASSDSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENAPESTxxxxxxxxxxxxxxxxxxxxxxxxDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEEETKQKTNRSAPEAEELKEKGAVNGSGEELNSVNQISRRWK
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	297	2.2.26 [Sep-21-2011]
Q9LW00	254	Methyl-CpG-binding domain	yes	no	0.356	0.417	0.700	1e-36
Q9XI36	384	Methyl-CpG-binding domain	no	no	0.350	0.270	0.650	6e-35

>sp|Q9LW00|MBD11_ARATH Methyl-CpG-binding domain-containing protein 11 OS=Arabidopsis thaliana GN=MBD11 PE=1 SV=1

 Score =  153 bits (387), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 75/107 (70%), Positives = 83/107 (77%), Gaps = 1/107 (0%)

Query: 9   EEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPAS 68
           EE VS ELPAP  WKK   P K G+ KK+E+VF APTGEEISN+KQLEQYLK+HPG PA 
Sbjct: 5   EEVVSVELPAPSSWKKLFYPNKVGSVKKTEVVFVAPTGEEISNRKQLEQYLKSHPGNPAI 64

Query: 69  SEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGR-KSSASKKDG 114
           +EFDW T  TPRRSARISEK K +P+ D EPPKKRGR KS  SKKD 
Sbjct: 65  AEFDWTTSGTPRRSARISEKTKATPSPDKEPPKKRGRTKSPVSKKDA 111

Transcriptional regulator that binds DNA independently of its methylation status. Required during plant organogenesis and development.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9XI36|MBD10_ARATH Methyl-CpG-binding domain-containing protein 10 OS=Arabidopsis thaliana GN=MBD10 PE=1 SV=1

 Score =  148 bits (373), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 69/106 (65%), Positives = 83/106 (78%), Gaps = 2/106 (1%)

Query: 9   EEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPAS 68
           +E VS ELPAP  WKK   P++ GTP+K+EIVF APTGEEIS++KQLEQYLKAHPG P  
Sbjct: 5   DELVSIELPAPASWKKLFYPKRAGTPRKTEIVFVAPTGEEISSRKQLEQYLKAHPGNPVI 64

Query: 69  SEFDWGTGETPRRSARISEKAK-ISPAADNEPPKKRGRKSSASKKD 113
           SEF+W TGETPRRS+RIS+K K  +P  D EP  K+ R+SS +KKD
Sbjct: 65  SEFEWTTGETPRRSSRISQKVKATTPTPDKEPLLKK-RRSSLTKKD 109

Probable transcriptional regulator (By similarity). Required for nucleolar dominance that consist in the silencing of rRNA genes inherited from one progenitor in genetic hybrids.

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	297
225445563	311	PREDICTED: uncharacterized protein LOC10	0.959	0.916	0.525	6e-62
297738979	264	unnamed protein product [Vitis vinifera]	0.656	0.738	0.621	9e-54
147800964	663	hypothetical protein VITISV_001419 [Viti	0.858	0.384	0.52	2e-53
356517036	306	PREDICTED: uncharacterized protein LOC10	0.781	0.758	0.516	2e-48
449443071	312	PREDICTED: uncharacterized protein LOC10	0.744	0.708	0.492	1e-47
356516967	305	PREDICTED: uncharacterized protein LOC10	0.797	0.777	0.505	1e-46
363814368	292	uncharacterized protein LOC100801517 [Gl	0.808	0.821	0.492	2e-46
356508368	287	PREDICTED: uncharacterized protein LOC10	0.713	0.738	0.495	3e-46
358248950	306	uncharacterized protein LOC100813840 [Gl	0.895	0.869	0.444	1e-45
225442963	324	PREDICTED: uncharacterized protein LOC10	0.659	0.604	0.571	3e-44

>gi|225445563|ref|XP_002285323.1| PREDICTED: uncharacterized protein LOC100259445 [Vitis vinifera]

 Score =  243 bits (621), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 162/308 (52%), Positives = 207/308 (67%), Gaps = 23/308 (7%)

Query: 1   MASSDSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLK 60
           MASS   K+E VS ELPAP GWKKK +P++G TPKK+EI+FT+PTGEEI++K+QLEQYLK
Sbjct: 1   MASSVE-KDEVVSLELPAPPGWKKKFMPKRGLTPKKNEIIFTSPTGEEINSKRQLEQYLK 59

Query: 61  AHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENA 120
           +HPGGPA  EFDWGTGETPRRSARISEKAK +P  + EP KKR RKSSASKKD +E E  
Sbjct: 60  SHPGGPAIQEFDWGTGETPRRSARISEKAKATPPRELEPAKKRSRKSSASKKDNKETETI 119

Query: 121 PESTEETKEVEMKEAEKTEDNAKVEKEEDIVKESRDENEVDQGPD--TKTEAGPSGEAKV 178
           P+ T ETKEV M+EA+KTEDNA+ E ++D+V E+  E + D+  D  TKTE  P    +V
Sbjct: 120 PDET-ETKEVHMQEAKKTEDNAEAEIQKDVVNENLIETK-DKAEDVNTKTEEAPPEGTQV 177

Query: 179 GEDANKSTDAEESKKT-EAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVE 237
            +D     DAEE KK  E EPG           DS     +K   EG + +E VD+  V+
Sbjct: 178 EQDVKIPDDAEEGKKNAEKEPGE-------KGGDSEVAQNEKESTEGTEVQENVDEALVK 230

Query: 238 TQKEFGSGEQDKADPAAAEEE-------TKQKTNRSAPEAE-ELKEKGAVNGSGEELNSV 289
             K+ G GE DK D   A+E+        K+K NRSA E+E E+KEK + NG+  E +S+
Sbjct: 231 ADKDDGPGEHDKPDAVIADEKKPEVEGVEKEKENRSALESEGEIKEKESANGNNVEQHSL 290

Query: 290 --NQISRR 295
             ++IS++
Sbjct: 291 KDSEISKK 298

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738979|emb|CBI28224.3| unnamed protein product [Vitis vinifera]

 Score =  216 bits (550), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 125/201 (62%), Positives = 151/201 (75%), Gaps = 6/201 (2%)

Query: 1   MASSDSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLK 60
           MASS   K+E VS ELPAP GWKKK +P++G TPKK+EI+FT+PTGEEI++K+QLEQYLK
Sbjct: 1   MASSVE-KDEVVSLELPAPPGWKKKFMPKRGLTPKKNEIIFTSPTGEEINSKRQLEQYLK 59

Query: 61  AHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENA 120
           +HPGGPA  EFDWGTGETPRRSARISEKAK +P  + EP KKR RKSSASKKD +E E  
Sbjct: 60  SHPGGPAIQEFDWGTGETPRRSARISEKAKATPPRELEPAKKRSRKSSASKKDNKETETI 119

Query: 121 PESTEETKEVEMKEAEKTEDNAKVEKEEDIVKESRDENEVDQGPD--TKTEAGPSGEAKV 178
           P+ T ETKEV M+EA+KTEDNA+ E ++D+V E+  E + D+  D  TKTE  P    +V
Sbjct: 120 PDET-ETKEVHMQEAKKTEDNAEAEIQKDVVNENLIETK-DKAEDVNTKTEEAPPEGTQV 177

Query: 179 GEDANKSTDAEESKKT-EAEP 198
            +D     DAEE KK  E EP
Sbjct: 178 EQDVKIPDDAEEGKKNAEKEP 198

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147800964|emb|CAN75567.1| hypothetical protein VITISV_001419 [Vitis vinifera]

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 143/275 (52%), Positives = 184/275 (66%), Gaps = 20/275 (7%)

Query: 26  IVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETPRRSARI 85
            +P++G TPKK+EI+FT+PTGEEI++K+QLEQYLK+HPGGPA  EFDWGTGETPRRSARI
Sbjct: 377 FMPKRGLTPKKNEIIFTSPTGEEINSKRQLEQYLKSHPGGPAIQEFDWGTGETPRRSARI 436

Query: 86  SEKAKISPAADNEPPKKRGRKSSASKKDGREAENAPESTEETKEVEMKEAEKTEDNAKVE 145
           SEKAK +P  + EP KKR RKSSASKKD +E E  P+ T ETKEV M+EA+KTEDNA+ E
Sbjct: 437 SEKAKATPPRELEPAKKRSRKSSASKKDNKETETIPDET-ETKEVHMQEAKKTEDNAEAE 495

Query: 146 KEEDIVKESRDENEVDQGPD--TKTEAGPSGEAKVGEDANKSTDAEESKK-TEAEPGNLK 202
            ++D+V E+  E + D+  D  TKTE  P    +V +D     DAEE KK  E EPG   
Sbjct: 496 IQKDVVNENLIETK-DKAEDVNTKTEEAPXEGTQVEQDVKIPDDAEEGKKNAEKEPG--- 551

Query: 203 ETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEEE---- 258
             + G   DS     +K   EG + +E VD+  V+  K+ G GE DK D   A+E+    
Sbjct: 552 --EKG--GDSEVAQNEKESTEGTEVQENVDEALVKADKDDGPGEHDKPDAVIADEKKPEV 607

Query: 259 ---TKQKTNRSAPEAE-ELKEKGAVNGSGEELNSV 289
               K+K NRSA E+E E+KEK + NG+  E +S+
Sbjct: 608 EGVEKEKENRSALESEGEIKEKESANGNNVEQHSL 642

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517036|ref|XP_003527196.1| PREDICTED: uncharacterized protein LOC100814375 [Glycine max]

 Score =  198 bits (504), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 127/246 (51%), Positives = 170/246 (69%), Gaps = 14/246 (5%)

Query: 9   EEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPAS 68
           EE  S ELPAP GWKKK +P+K GTPKK+EIVFT+PTGEEI+++KQLE+YLKAHPGGPA 
Sbjct: 13  EETFSLELPAPPGWKKKFIPKKAGTPKKNEIVFTSPTGEEINSRKQLEKYLKAHPGGPAV 72

Query: 69  SEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENAPESTEETK 128
           SEFDWGTGETPRRS RISEKAK++P A++EPPKKR ++SSAS    ++  +  E  EETK
Sbjct: 73  SEFDWGTGETPRRSTRISEKAKVAPPAESEPPKKRTKRSSAS----QKETSLEEKEEETK 128

Query: 129 EVEMKEA-EKTEDNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTD 187
           E EM+EA + T+D+  +EKE+D VKE++D+  V+     K+    SGEAK  E+     +
Sbjct: 129 EAEMQEADDTTKDDNVIEKEKDFVKENQDDKSVENTDVNKS--AHSGEAKPVENVEVLIE 186

Query: 188 AEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQ 247
            E+S   + E   LK+  D  + + S   +D       K+EEK++ PQ ET++  G GEQ
Sbjct: 187 EEKSNAADGELPALKDKVDDKRTEGS---EDFL----RKDEEKIEHPQEETKEYRGFGEQ 239

Query: 248 DKADPA 253
           +K +  
Sbjct: 240 EKLETC 245

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443071|ref|XP_004139304.1| PREDICTED: uncharacterized protein LOC101219635 [Cucumis sativus]

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 123/250 (49%), Positives = 167/250 (66%), Gaps = 29/250 (11%)

Query: 1   MASS---DSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQ 57
           MA+S   D+V EE VS ELPAP GWKKK  P++G +P+K E++FT PTGEEI+NK++L+Q
Sbjct: 1   MAASVEKDTVNEEVVSVELPAPPGWKKKFFPKQGNSPRKHEVIFTTPTGEEINNKRKLDQ 60

Query: 58  YLKAHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREA 117
           YLKAHPGGPA++EFDWGTGETPRRSARISEKAK+SP  ++E PK+  +++S SKKD +E 
Sbjct: 61  YLKAHPGGPAAAEFDWGTGETPRRSARISEKAKVSPPMESEHPKR--KRTSVSKKDLKET 118

Query: 118 ENAPESTEETKEVEMKEAEKTEDNAKVEKEEDIVKESRDENEVDQGPDTKTEAG------ 171
           E  PE  EE KEV+  +A K E  A  E ++   KE++DE E      TK EA       
Sbjct: 119 EAEPEVMEEKKEVDNPDAGKDESMADAEVKDADKKENQDEKE------TKNEAAEAEPPK 172

Query: 172 PSGEAKVGEDA----NKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKN 227
           P  +   G +A    +K T+    +K+E   GNL E     + +SS +  ++  +EGAK+
Sbjct: 173 PDDQLNAGNEAEKQEHKITNESNQEKSE---GNLNE----KEPESSKLNLNE-NVEGAKH 224

Query: 228 EEKVDQPQVE 237
           EE +++PQVE
Sbjct: 225 EEMIEKPQVE 234

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516967|ref|XP_003527162.1| PREDICTED: uncharacterized protein LOC100796239 [Glycine max]

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 128/253 (50%), Positives = 166/253 (65%), Gaps = 16/253 (6%)

Query: 9   EEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPAS 68
           EE +S ELPAP GWKK+ +P+K GTPKK+EIVFTAPTGEEI+N+KQLE+YLKAHPGGPA 
Sbjct: 13  EETLSLELPAPPGWKKQFIPKKAGTPKKNEIVFTAPTGEEINNRKQLEKYLKAHPGGPAV 72

Query: 69  SEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENAPESTEETK 128
           SEFDWGTGETPRRS RISEKAK +P    EPPKKR ++SSAS+K+  +     E  EETK
Sbjct: 73  SEFDWGTGETPRRSTRISEKAKAAPPTQREPPKKRTKRSSASQKEISQE----EKEEETK 128

Query: 129 EVEMKEAEKTE--DNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKST 186
           E EM+EA+ T   DN  +EKE+ +V E+ D++  D   +  T  G   EAK GE+     
Sbjct: 129 EAEMQEADDTTKGDN-DIEKEKVVVNENHDKSVEDTDVNKSTRYGE--EAKAGENVEVPI 185

Query: 187 DAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGE 246
           + E+S   + E   LK+  D    + S V          K+EEK++QPQ ET++  G GE
Sbjct: 186 EEEKSNAADGELPALKDKADDKVTEGSEVFL-------RKDEEKIEQPQEETKEYSGFGE 238

Query: 247 QDKADPAAAEEET 259
            +K +     ++T
Sbjct: 239 PEKLETCTTADKT 251

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363814368|ref|NP_001242823.1| uncharacterized protein LOC100801517 [Glycine max] gi|255647122|gb|ACU24029.1| unknown [Glycine max]

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 130/264 (49%), Positives = 172/264 (65%), Gaps = 24/264 (9%)

Query: 1   MASS----DSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLE 56
           MASS        EE  S ELPAP GWKK+ +P+K GTPKK+EIVFTAPTGEEI+N+KQLE
Sbjct: 1   MASSVEKESGASEETFSLELPAPPGWKKQFIPKKAGTPKKNEIVFTAPTGEEINNRKQLE 60

Query: 57  QYLKAHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGRE 116
           +YLKAHPGGPA SEFDWGTGETPRRS RISEKAK +P  ++EPPK+R ++SSAS+K+  +
Sbjct: 61  KYLKAHPGGPAVSEFDWGTGETPRRSTRISEKAKATPPTESEPPKERTKRSSASQKETSQ 120

Query: 117 AENAPESTEETKEVEMKEA-EKTEDNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGE 175
                E  EETKE EM+E  + T+DN  +EKE+D+V E++D   V+     K+    SGE
Sbjct: 121 E----EKEEETKEAEMQEVDDTTKDNNDIEKEKDVVMENQDGKSVEDTDVNKSTH--SGE 174

Query: 176 AKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQ 235
           AK GE      + E+S   + E   LK+  D           DK  +   K+EEK++QPQ
Sbjct: 175 AKAGEYVEVPIEEEKSNAADGELPALKDKVD-----------DKVFLR--KDEEKIEQPQ 221

Query: 236 VETQKEFGSGEQDKADPAAAEEET 259
            ET++   +G  +K++     ++T
Sbjct: 222 EETKEYRRTGVPEKSETCTTADKT 245

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508368|ref|XP_003522929.1| PREDICTED: uncharacterized protein LOC100800976 [Glycine max]

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 121/244 (49%), Positives = 157/244 (64%), Gaps = 32/244 (13%)

Query: 9   EEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPAS 68
           EE  S ELPAP GWKK  +P+K GTPKK+EIVFTAPTGEEI+N+KQLE+YLKAHPGGPA 
Sbjct: 13  EETFSVELPAPPGWKKLFIPKKAGTPKKNEIVFTAPTGEEINNRKQLEKYLKAHPGGPAV 72

Query: 69  SEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENAPESTEETK 128
           SEFDWGTGETPRRS RISEKAK +P  ++EPPKKR ++SSAS+K+  + E   ++ E   
Sbjct: 73  SEFDWGTGETPRRSTRISEKAKAAPPIESEPPKKRTKRSSASQKETSQEEKEEKTKEAE- 131

Query: 129 EVEMKEAEK-TEDNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTD 187
              M+EA+  T+D+  +EKE+D+V E++D   V+     K+    SGEAK GE  N    
Sbjct: 132 ---MQEADYTTKDDNDIEKEKDVVMENQDVKSVEDTDVNKSTH--SGEAKAGE--NVEVP 184

Query: 188 AEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQ 247
            E+ K  E     L+                       K+EEK++QPQ ET++  GSGE 
Sbjct: 185 IEKDKGIEVSEVFLR-----------------------KDEEKIEQPQEETKEYRGSGEP 221

Query: 248 DKAD 251
           +K +
Sbjct: 222 EKLE 225

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248950|ref|NP_001239712.1| uncharacterized protein LOC100813840 [Glycine max] gi|255636226|gb|ACU18454.1| unknown [Glycine max]

 Score =  189 bits (481), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 135/304 (44%), Positives = 191/304 (62%), Gaps = 38/304 (12%)

Query: 8   KEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPA 67
           +EE  S ELPAP GWKK+ +P+K GTPKK+EIVFTA TGEEI N+KQLE+YLKAHPGGPA
Sbjct: 12  REETFSLELPAPPGWKKQFIPKKAGTPKKNEIVFTAATGEEIHNRKQLEKYLKAHPGGPA 71

Query: 68  SSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENAPESTEET 127
            SEFDWGTGETPRRS RISEKAK +P + +EPPKKR ++SSAS+K+     +  E  +E 
Sbjct: 72  VSEFDWGTGETPRRSTRISEKAKAAPPSVSEPPKKRTKRSSASQKET----SQEEKEQEI 127

Query: 128 KEVEMKEA-EKTEDNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKST 186
           KE EM+EA + T+D+  + KE+D+VKE++D+  V+   DT              D NKST
Sbjct: 128 KEAEMQEADDTTKDDNDIGKEKDVVKENQDDKCVE---DT--------------DVNKST 170

Query: 187 DA-EESKKTEAEPGNLKETQDGTQADSSGVTQ--DKAGIEGA-----KNEEKVDQPQVET 238
           ++ EE+K  E     + E  +    +   +    D  G EG+     K+E K++QPQ ET
Sbjct: 171 NSGEEAKAVENVEVPIDEKSNAADGELPALKDKVDDKGTEGSEVFLRKDEVKIEQPQEET 230

Query: 239 QKEFGSGEQDKADPAAAEEET-------KQKTNRSAPEAEELKEKGAVNGSGEELNSVNQ 291
           ++  GSGE +K++     ++T       K++  +S  E  E+ E       GEE + +++
Sbjct: 231 KEYRGSGEPEKSETCTTADKTVEVEGVDKEEHVKSTHEF-EVGEMEGTKVIGEEHHKLDE 289

Query: 292 ISRR 295
           I+++
Sbjct: 290 INKK 293

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442963|ref|XP_002267149.1| PREDICTED: uncharacterized protein LOC100249094 isoform 1 [Vitis vinifera]

 Score =  185 bits (469), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 124/217 (57%), Positives = 148/217 (68%), Gaps = 21/217 (9%)

Query: 1   MASSDSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLK 60
           MAS D V    VS ELPAP  WKK  +P+KG TP+K+EIVF APTGEEI+++KQLEQYLK
Sbjct: 1   MASQDEV----VSMELPAPPSWKKMFMPKKG-TPRKNEIVFIAPTGEEINSRKQLEQYLK 55

Query: 61  AHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENA 120
           +HPG PA SEFDWGTGETPRRSARISEKAK +P A++EPPKKRGRKSS SKKDG+E E A
Sbjct: 56  SHPGNPAISEFDWGTGETPRRSARISEKAKATPPAESEPPKKRGRKSSGSKKDGKETEAA 115

Query: 121 PESTEETKEVEMKEAEKTED-NAKVEKEEDIVKESRDEN------EVDQGPDTKT---EA 170
            E  E  KE+ M++A+ TE  NA   + ED+ KE + EN      E DQ  +      EA
Sbjct: 116 TEEQEGKKEISMQDADVTEKANA---ESEDVSKEIQVENGVKTVAEADQVKNLDVNMEEA 172

Query: 171 GPSGEAKVGEDANKSTDAEESK--KTEAEPGNLKETQ 205
           GP  EA  G+D    +D  +SK   TE E  N +E Q
Sbjct: 173 GPV-EAIDGKDEKIQSDTGDSKVAATETEVVNAEEAQ 208

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	297
TAIR|locus:2037863	384	MBD10 "methyl-CPG-binding doma	0.845	0.653	0.386	2.6e-38
TAIR|locus:2093197	254	MBD11 "methyl-CPG-binding doma	0.821	0.960	0.368	1.2e-33
TAIR|locus:504955937	734	AT2G22795 "AT2G22795" [Arabido	0.461	0.186	0.289	9.9e-07
ZFIN|ZDB-GENE-081015-2	1413	rpgrb "retinitis pigmentosa GT	0.936	0.196	0.206	2.2e-06
ZFIN|ZDB-GENE-070103-4	717	nefmb "neurofilament, medium p	0.515	0.213	0.257	4.5e-06
ZFIN|ZDB-GENE-050522-205	849	nefma "neurofilament, medium p	0.474	0.166	0.313	4.5e-06
TAIR|locus:2080823	895	AT3G51070 [Arabidopsis thalian	0.501	0.166	0.270	4.8e-06
DICTYBASE|DDB_G0291444	447	DDB_G0291444 [Dictyostelium di	0.818	0.543	0.191	6.7e-06
ZFIN|ZDB-GENE-041014-193	785	trdn "triadin" [Danio rerio (t	0.481	0.182	0.244	8.9e-06
UNIPROTKB|Q5JSK9	201	HMGN5 "High mobility group nuc	0.417	0.616	0.335	1.6e-05

TAIR|locus:2037863 MBD10 "methyl-CPG-binding domain 10" [Arabidopsis thaliana (taxid:3702)]

 Score = 410 (149.4 bits), Expect = 2.6e-38, P = 2.6e-38
 Identities = 104/269 (38%), Positives = 143/269 (53%)

Query:     9 EEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPAS 68
             +E VS ELPAP  WKK   P++ GTP+K+EIVF APTGEEIS++KQLEQYLKAHPG P  
Sbjct:     5 DELVSIELPAPASWKKLFYPKRAGTPRKTEIVFVAPTGEEISSRKQLEQYLKAHPGNPVI 64

Query:    69 SEFDWGTGETPRRSARISEKAKIS-PAADNEPPXXXXXXXXXXXXXXXEAENAPXXXXXX 127
             SEF+W TGETPRRS+RIS+K K + P  D EP                 AE         
Sbjct:    65 SEFEWTTGETPRRSSRISQKVKATTPTPDKEPLLKKRRSSLTKKDNKEAAEKNEEAAVKE 124

Query:   128 XXXXXXXXXXXXDNAKVEKEEDIVKESRD-ENEVDQGPDT----------KTEAGPSGEA 176
                           A+ EKE++ V E  + E E ++G  T          KTEAG  G+ 
Sbjct:   125 NMDVDKDGKTENAEAEKEKEKEGVTEIAEAEKENNEGEKTEAEKVNKEGEKTEAGKEGQT 184

Query:   177 KVGEDANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGI-EGAKNEEKVDQPQ 235
             ++ E A K  + E+++    E   +++ ++  + D+S + + KAG  EGA+   KV+  +
Sbjct:   185 EIAE-AEKEKEGEKAEAENKEAEVVRDKKESMEVDTSEL-EKKAGSGEGAEEPSKVEGLK 242

Query:   236 VETQKEFGS--GEQDKADPAAAEEETKQK 262
                 KE      E D  +   AEE+T+ K
Sbjct:   243 DTEMKEAQEVVTEAD-VEKKPAEEKTENK 270

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

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

GO:0008150 "biological_process" evidence=ND

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

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2093197 MBD11 "methyl-CPG-binding domain 11" [Arabidopsis thaliana (taxid:3702)]

 Score = 366 (133.9 bits), Expect = 1.2e-33, P = 1.2e-33
 Identities = 94/255 (36%), Positives = 124/255 (48%)

Query:     8 KEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPA 67
             +EE VS ELPAP  WKK   P K G+ KK+E+VF APTGEEISN+KQLEQYLK+HPG PA
Sbjct:     4 EEEVVSVELPAPSSWKKLFYPNKVGSVKKTEVVFVAPTGEEISNRKQLEQYLKSHPGNPA 63

Query:    68 SSEFDWGTGETPRRSARISEKAKISPAADNEPPXXXXXXXXXXXXXXXEAENAPXXXXXX 127
              +EFDW T  TPRRSARISEK K +P+ D EPP               E E +       
Sbjct:    64 IAEFDWTTSGTPRRSARISEKTKATPSPDKEPPKKRGRTKSPVSKKDAEGEKSEGGGEEN 123

Query:   128 XXXXXXXXXXXXDNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDAN---- 183
                           A+ E   D       E   D   +   E  P+  A V E+      
Sbjct:   124 SHVKDTEMNPPEGIAENENVTDKNGSGETERVNDAKENIVAEETPNA-APVQEEGESMKE 182

Query:   184 KSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFG 243
             K+ D+ + K  E +    KE   G+  + + V  +K  +E A +E+K  + +    +E G
Sbjct:   183 KALDSVDDKSKETD----KEKDTGS-IEKNSVDVEKKTVE-ASDEKKNSEAETRNHEENG 236

Query:   244 SGEQDKADPAAAEEE 258
                + +     AE E
Sbjct:   237 LTTEAEGKEKTAEGE 251

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

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

GO:0008150 "biological_process" evidence=ND

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

TAIR|locus:504955937 AT2G22795 "AT2G22795" [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 9.9e-07, P = 9.9e-07
 Identities = 44/152 (28%), Positives = 78/152 (51%)

Query:   140 DNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTDAEESKKTEAEPG 199
             D  K EKEE   +E  +E E +    TK     S + +  +  N+  + EE+   E    
Sbjct:   506 DETK-EKEESSSQEKTEEKETE----TKDNEESSSQEETKDKENEKIEKEEASSQEESKE 560

Query:   200 NLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEEET 259
             N  ET++  ++ S   T++K   E  K E++   PQ ET+++    E+ + + +A++EET
Sbjct:   561 NETETKEKEESSSQEETKEK---ENEKIEKEESAPQEETKEK--ENEKIEKEESASQEET 615

Query:   260 KQKTNRSAPEAEELKEKGAVNGSGEELNSVNQ 291
             K+K      E +E KE+ + N S E +N+ ++
Sbjct:   616 KEKET----ETKE-KEESSSNESQENVNTESE 642

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0005768 "endosome" evidence=IDA

GO:0005802 "trans-Golgi network" evidence=IDA

ZFIN|ZDB-GENE-081015-2 rpgrb "retinitis pigmentosa GTPase regulator b" [Danio rerio (taxid:7955)]

 Score = 141 (54.7 bits), Expect = 2.2e-06, P = 2.2e-06
 Identities = 60/290 (20%), Positives = 119/290 (41%)

Query:     2 ASSDSVKEEQVSFELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKA 61
             ASS+  +EE+ + +        ++   + G + K S    +    EE  N    +   K 
Sbjct:  1057 ASSEDEEEEEKNGDSAKASSEDEEEEEKSGSSVKAS----SEDEEEEEENGDSFKASSKE 1112

Query:    62 HPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPXXXXXXXXXXXXXXXEAENAP 121
               G  A++       E  +  +  ++  +     DNE                   +   
Sbjct:  1113 ESGDSANASNVNSEEEEQKSKSEATDDLESEEEEDNEDNEEEKSETSASTEDESNDDEDK 1172

Query:   122 XXXXXXXXXXXXXXXXXXDNAKVEKEEDIVKES-RDENEVDQGPDTKTEAGPSGEAKVGE 180
                                 ++  +E+D  +ES ++E+EV+   + + E G +   +  E
Sbjct:  1173 SETSQEEESGEESEGNSESRSERSEEDDEDEESEKEESEVESEAE-EDETGENTSEEDDE 1231

Query:   181 DANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDK-AGIEGAKNEEKVDQP-QVET 238
             +   S++ EE  ++EAE G  +E++   + +S   T DK    E ++NEE+ ++  +VE 
Sbjct:  1232 EQESSSEDEEKSESEAE-GEEEESEGDQEDESDEETSDKDEEEEESENEEEEEEESKVEE 1290

Query:   239 QKEFGSGEQDKADPAAAEEETKQKTNRSAPEA---EELKEKGAVNGSGEE 285
             ++E  + E++  +  A EEE  + T  +  E    E+ +E+   NG  EE
Sbjct:  1291 EEEESNEEEENEEEEAEEEEPGEDTEEAEDEEGEEEDTQEEEQENGDDEE 1340

GO:0060287 "epithelial cilium movement involved in determination of left/right asymmetry" evidence=IMP

GO:0060271 "cilium morphogenesis" evidence=IMP

GO:0010842 "retina layer formation" evidence=IMP

GO:0060041 "retina development in camera-type eye" evidence=IMP

GO:0007018 "microtubule-based movement" evidence=IMP

ZFIN|ZDB-GENE-070103-4 nefmb "neurofilament, medium polypeptide b" [Danio rerio (taxid:7955)]

 Score = 138 (53.6 bits), Expect = 4.5e-06, Sum P(2) = 4.5e-06
 Identities = 42/163 (25%), Positives = 81/163 (49%)

Query:   142 AKVEKEEDIVKESRDENEVDQGPDTKT--EAGPSGEAKVGEDANKSTDAE-ESKKTEAEP 198
             A+ E+EED   E  +E +V+   +T+   E  P+ E +  E   +  + + E K+ E E 
Sbjct:   484 AEEEEEEDEEGEEEEEPQVEVIEETELCGEKSPTSEKEGSEKEEEEDEGKGEEKEDEDEK 543

Query:   199 GNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEE- 257
              + K   +G + + SG  ++K    G + E+K +    E +KE   GE++K + +A EE 
Sbjct:   544 EDTKSEGEGEKKEESGGEEEKKEESGGEEEKKEESGGEEEKKEESGGEEEKKEESAGEEA 603

Query:   258 --ETKQKTNRSAPEAEELK----EKGAVNGSGEELNSVNQISR 294
               ++++   +S  E +E K    E+ A + + E+     Q+ +
Sbjct:   604 KADSEKDDKKSDTEEDEKKSPVSEEKAESPAEEKKQDEKQVDK 646

GO:0005198 "structural molecule activity" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005882 "intermediate filament" evidence=IEA

ZFIN|ZDB-GENE-050522-205 nefma "neurofilament, medium polypeptide a" [Danio rerio (taxid:7955)]

 Score = 136 (52.9 bits), Expect = 4.5e-06, P = 4.5e-06
 Identities = 47/150 (31%), Positives = 70/150 (46%)

Query:   142 AKVEKEEDIVKESRDENEVDQGPDTK-TEAGPSGEAKVGEDANKSTDAEE----SKKTEA 196
             A  E+EE+  KE  DE + ++    K  E    GE + GE+  K  +AEE    SK  EA
Sbjct:   504 APAEEEEEGEKEGGDEEQEEEEEAGKGDEEEEKGEEEEGEEEKKEEEAEEEAEESKAPEA 563

Query:   197 EPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDK-ADPAAA 255
             +     E  +  QA       ++ G E  + +   D+   + +KE    EQ K A+P AA
Sbjct:   564 KASPESEKAEEKQASGGEEEAEEEGDENQEGDAGSDKGSTD-EKEVEVKEQPKKAEPEAA 622

Query:   256 EEETKQKTNRSAPEAEELKEKGAVNGSGEE 285
             +E+ K K  +   EA+  KEK  V  +  E
Sbjct:   623 KEDKKGKEEKE--EAKSEKEKATVTETKAE 650

GO:0005882 "intermediate filament" evidence=IEA

GO:0005198 "structural molecule activity" evidence=IEA

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2080823 AT3G51070 [Arabidopsis thaliana (taxid:3702)]

 Score = 136 (52.9 bits), Expect = 4.8e-06, P = 4.8e-06
 Identities = 43/159 (27%), Positives = 69/159 (43%)

Query:   140 DNAKVEKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTDAEESKKTEAEPG 199
             D+A V+ E++  K +++++E         E   + + K+ E+  K    E     E+E G
Sbjct:    96 DDA-VKSEDEQRKSAKEKSETTSSKTQTQETQQNNDDKISEEKEKDNGKENQTVQESEEG 154

Query:   200 NLK------ETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPA 253
              +K      E +   Q D    TQ K G +G +  +  +QP VE   + G  EQD     
Sbjct:   155 QMKKVVKEFEKEQKQQRDEDAGTQPK-GTQGQEQGQGKEQPDVEQGNKQGQ-EQDSNTDV 212

Query:   254 AAEEETKQKTNRSAPEAEELK-EKGAVNGSGEELNSVNQ 291
                + TKQ+      + E  +  K   NG  EE NS N+
Sbjct:   213 TFTDATKQEQPMETGQGETSETSKNEENGQPEEQNSGNE 251

GO:0005794 "Golgi apparatus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

DICTYBASE|DDB_G0291444 DDB_G0291444 [Dictyostelium discoideum (taxid:44689)]

 Score = 131 (51.2 bits), Expect = 6.7e-06, P = 6.7e-06
 Identities = 49/256 (19%), Positives = 109/256 (42%)

Query:    47 EEISNKKQLEQYLKAHPGGPASSEFDWGTGETPR-RSARISEKAK-ISPAADNEPPXXXX 104
             EE S+KK   +   +     + SE D    E  + +  ++ +K +  S +++++      
Sbjct:    69 EEKSSKKHKVEKDSSDSSDSSDSESDSSDSEDEKEKEMKVDKKTEDSSSSSESDTESSSS 128

Query:   105 XXXXXXXXXXXEAENAPXXXXXXXXXXXXXXXXXXDNA---KVEKEEDIVKESRD--ENE 159
                        E++++                   +++   + E E++  KES D  ++E
Sbjct:   129 SESEDEKKKEKESDDSSSSESESDSSSSESESESSESSSSSESESEDEKKKESSDSSDSE 188

Query:   160 VDQGPDTKTEAGPSG--EAKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQA--DSSGV 215
              +     K E+  S   E++  + ++  ++ E+ KK E+   +  E++  + +  DSS  
Sbjct:   189 SEDEKKKKVESSDSSSSESESSDSSDSESEDEKKKKVESSDSSSSESESSSSSSSDSSDS 248

Query:   216 TQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEEETKQKTNRSAPEAEELKE 275
             +  ++  E  K  EK    +  ++ E    + +K D   +++E K K N+   E ++  E
Sbjct:   249 SDSESEDEKKKKVEKSSDKETSSESESEDSDDEK-DKKKSKKEDK-KENKKQEEKKKPIE 306

Query:   276 KGAVNGSGEELNSVNQ 291
             K +   S +E+  V Q
Sbjct:   307 KDSDEDSDDEMKVVEQ 322

GO:0044351 "macropinocytosis" evidence=RCA

ZFIN|ZDB-GENE-041014-193 trdn "triadin" [Danio rerio (taxid:7955)]

 Score = 133 (51.9 bits), Expect = 8.9e-06, P = 8.9e-06
 Identities = 36/147 (24%), Positives = 73/147 (49%)

Query:   140 DNAKVEKEE-DIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTDAEESKKTEAEP 198
             D  + E+EE D  +E  D  E ++  D + E     E ++ E+  +  D EE ++ E E 
Sbjct:   171 DEEEEEEEEMDTDEEEEDYEEEEEEYDEELEEEEEEEEELEEEEEEELDEEEEEELEKEE 230

Query:   199 GNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEEE 258
                KE ++  + +     +++ G++  + EE+ D+ + + +KE    E+D+ +  A EEE
Sbjct:   231 E--KELEEEEEDEEDEEEKEEPGVKVVEEEEE-DEEEAKEEKEKKKEEEDEEEAEAEEEE 287

Query:   259 TKQKTNRSAPEAEELKEKGAVNGSGEE 285
              ++     A + ++ +E GA     +E
Sbjct:   288 DEEAATEIAAKEKKKEEAGAKEEDEDE 314

GO:0016529 "sarcoplasmic reticulum" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q5JSK9 HMGN5 "High mobility group nucleosome-binding domain-containing protein 5" [Homo sapiens (taxid:9606)]

 Score = 120 (47.3 bits), Expect = 1.6e-05, P = 1.6e-05
 Identities = 45/134 (33%), Positives = 66/134 (49%)

Query:   145 EKEEDIVKESRDENEVDQGPDTKTEAGPSGEAKVGEDANKSTDAEESKKTEAEPGNLKET 204
             EKE   VKE   E+  ++G + K EA  + E K  E+ ++  D E+  + + E G  KE 
Sbjct:    74 EKEIVEVKEENIEDATEKGGEKK-EA-VAAEVK-NEEEDQKEDEEDQNEEKGEAG--KED 128

Query:   205 QDGTQADSSGVTQDKAGIE-GAKNEEKVDQPQVETQKEFGSGEQDKADPAAAEEETKQKT 263
             +D  + +  G  +DK G E G   +EK D  + E  K  G+GE  K      +EE  +K 
Sbjct:   129 KD-EKGEEDG-KEDKNGNEKGEDAKEKEDGKKGEDGK--GNGEDGKEKGEDEKEEEDRKE 184

Query:   264 NRSAPEAEELKEKG 277
                  E E+ KEKG
Sbjct:   185 TGDGKENEDGKEKG 198

GO:0000785 "chromatin" evidence=IEA

GO:0031492 "nucleosomal DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

---

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)
Q9LW00	MBD11_ARATH	No assigned EC number	0.7009	0.3569	0.4173	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	297
cd01396	77	cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and M	2e-13
cd00122	62	cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8	4e-13
pfam01429	75	pfam01429, MBD, Methyl-CpG binding domain	2e-12
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-04
smart00391	77	smart00391, MBD, Methyl-CpG binding domain	2e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	5e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.001
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.004

>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 = 63.9 bits (156), Expect = 2e-13
 Identities = 20/60 (33%), Positives = 37/60 (61%), Gaps = 1/60 (1%)

Query: 17 PAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHP-GGPASSEFDWGT 75
            P GWK+++VPRK G+  K ++ + +PTG++  +K +L +YL+ +       S+FD+  
Sbjct: 6  RLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTV 65

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

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

 Score = 62.7 bits (153), Expect = 4e-13
 Identities = 17/60 (28%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 15 ELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAH-PGGPASSEFDW 73
            P P GWK+++V RK G+  K ++ + +P G+++ +K ++ +YL+   P       F +
Sbjct: 3  RDPLPPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLENFSF 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|216497 pfam01429, MBD, Methyl-CpG binding domain

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 15 ELPAPFGWKKKIVPRKGGTPK-KSEIVFTAPTGEEISNKKQLEQYLKAHPGGPAS-SEFD 72
            P P GW+++   RK G+   K ++ + +PTG++  +K +L +YL+ +        +FD
Sbjct: 7  CPPLPPGWRREERQRKSGSSAGKVDVYYYSPTGKKFRSKSELIRYLEKNGDTSLKLEDFD 66

Query: 73 WGTGETPRR 81
          +       R
Sbjct: 67 FTVRSEVGR 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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 43.4 bits (102), Expect = 1e-04
 Identities = 57/243 (23%), Positives = 87/243 (35%), Gaps = 11/243 (4%)

Query: 45  TGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETPRRSARISEKAKISPAADNEPPKKRG 104
           TGEE     + E       GG A  E +  T         I  + K     + E   K  
Sbjct: 645 TGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEA 704

Query: 105 RKSSASKKDGREAENA--PESTEETKEVEMKE-AEKTEDNAKVE---KEEDIVKESRDEN 158
                ++ +  E E     E TE+  E+E  E  E+ ED  + E   K E   +  R E 
Sbjct: 705 DHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKET 764

Query: 159 EVDQGPDTKTEAGP-SGEAKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQ 217
           E +   + + +     GE + GED     D     K E E       +D  +  S     
Sbjct: 765 EHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQAD 824

Query: 218 DKAGIEGAKNEEKVDQPQVETQKEF----GSGEQDKADPAAAEEETKQKTNRSAPEAEEL 273
           D    +    +E   + Q E +++     G G  D  D    EEE +++      E EE 
Sbjct: 825 DTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEE 884

Query: 274 KEK 276
           +E+
Sbjct: 885 EEE 887

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 15 ELPAPFGWKKKIVPRKGGTPK-KSEIVFTAPTGEEISNKKQLEQYL 59
           LP P GW+++   RK G    K ++ + +P G+++ +K +L +YL
Sbjct: 5  RLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYL 50

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

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 41.5 bits (97), Expect = 5e-04
 Identities = 45/213 (21%), Positives = 77/213 (36%), Gaps = 32/213 (15%)

Query: 110 SKKDGREAENAPEST--------------EETKEVEMKEAEKTEDNAKVEKEEDIVKESR 155
           SK D  EAE+  E T               E    E ++  +TE   + E E +I  E +
Sbjct: 631 SKGDVAEAEHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERK 690

Query: 156 DENEVD-----QGPDTKTEAGPSGEAKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQA 210
            E E +     +  D K E         GE   + T+ E   +T  E G   E +   +A
Sbjct: 691 GEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEE-GEEVEDEGEGEA 749

Query: 211 DSSGVTQDKA--------GIEGAKNEEKVDQPQVETQKEF---GSGEQDKADPAAAEEET 259
           +     + +         G   A+ +E  D+ +++  ++    G    +       E E 
Sbjct: 750 EGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEA 809

Query: 260 KQKTNRSAPEAEELKEKGAVNGSGE-ELNSVNQ 291
            +K         +  +    + +GE ELN+ NQ
Sbjct: 810 GEKDEHEGQSETQADDTEVKDETGEQELNAENQ 842

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 40.4 bits (94), Expect = 0.001
 Identities = 31/169 (18%), Positives = 62/169 (36%), Gaps = 9/169 (5%)

Query: 113  DGREAENAPESTEETKEVEMKEAEKTEDNAKVEKEEDIVKESRDENEVDQGPDTKTEAGP 172
            + +  E +  + E     +  + +  ED  + EKE+    E    ++V    + + +   
Sbjct: 3920 EQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKED----EEEMSDDVGIDDEIQPDIQE 3975

Query: 173  SGEAKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAKNEEKVD 232
            +      E  N+  D  E  K + + G++ +  D    D     ++K   +  K+E   D
Sbjct: 3976 NNSQPPPE--NEDLDLPEDLKLDEKEGDVSKDSDLEDMDMEAADENKEEADAEKDEPMQD 4033

Query: 233  QPQVETQKEFGSGEQDKADPAAAEEETKQKTN---RSAPEAEELKEKGA 278
            +  +E         Q       AE++ K   +    +  E EE  E G 
Sbjct: 4034 EDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGV 4082

Length = 4600

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 48/222 (21%), Positives = 82/222 (36%), Gaps = 16/222 (7%)

Query: 77  ETPRRSARISEKAKISPAADNEPPKKRGRKSSASKKDGREAENAPE---------STEET 127
           E      R  E+ +    A+ E  ++ G ++    +   + EN  E           E  
Sbjct: 637 EAEHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGE 696

Query: 128 KEVEMKEAE---KTEDNAKVEKEEDIVKESRDENEVDQGPDTKTEAG-PSGEAKVGEDAN 183
            E+E KEA+   +TE      + E   + + DE E++ G + +       GEA+   +  
Sbjct: 697 GEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVE 756

Query: 184 KSTDAEESKKTEAEPGNLKETQD--GTQADSSGVTQDKAGIEGAKNEEKVDQPQVETQKE 241
              D +E++         KE +D    QA   G  +   G EG    E   +   + + E
Sbjct: 757 TEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHE 816

Query: 242 FGSGEQDKADPAAAEEETKQKTNRSAPEAEELKEKGAVNGSG 283
             S  Q        E   ++    +  EA++  EKG   G G
Sbjct: 817 GQSETQADDTEVKDETGEQELNAENQGEAKQ-DEKGVDGGGG 857

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 35/185 (18%), Positives = 70/185 (37%), Gaps = 18/185 (9%)

Query: 112  KDGREAENAPESTEETKEVE----MKEAEKTEDNAK-VEKEEDIVKESRDENEVDQGPDT 166
             +G  + + P+    + E+E    +      ED    + +++D+ + + +E+  +Q    
Sbjct: 3794 NNGFCSPDLPQEKSNSGELESGTGLGSGVGAEDITNTLNEDDDLEELANEEDTANQSDLD 3853

Query: 167  KTEAGPSGEAKVGEDANKSTDAEESKKTEAEPGNLKETQDGTQADSSGVTQDKAGIEGAK 226
            ++EA        G   +      E+  +E E  +L E  +    D S           + 
Sbjct: 3854 ESEARELESDMNGVTKDSVVSENENSDSEEENQDLDEEVNDIPEDLS----------NSL 3903

Query: 227  NEEKVDQPQVETQKEFGSGEQDKADPAAAEEETKQKTNRSAPEAEELKEKGAVNGSGEEL 286
            NE+  D+P  E   E    EQ   + +AA  E+   +     +A E K++       E  
Sbjct: 3904 NEKLWDEPNEEDLLE---TEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMS 3960

Query: 287  NSVNQ 291
            + V  
Sbjct: 3961 DDVGI 3965

Length = 4600

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	297
cd01396	77	MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are me	99.49
cd00122	62	MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and	99.32
smart00391	77	MBD Methyl-CpG binding domain. Methyl-CpG binding	99.14
PF01429	77	MBD: Methyl-CpG binding domain; InterPro: IPR00173	99.11
cd01397	73	HAT_MBD Methyl-CpG binding domains (MBD) present i	98.08
cd01395	60	HMT_MBD Methyl-CpG binding domains (MBD) present i	96.68
KOG4161	272	consensus Methyl-CpG binding transcription regulat	91.04

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

Probab=99.49  E-value=3.2e-14  Score=108.94  Aligned_cols=62  Identities=37%  Similarity=0.757  Sum_probs=58.0

Q ss_pred             ecc-CCCCCccccccCCCCCCCcceEEEecCCchhhcchHHHHHHHHhC-CCCCCccccccCCC
Q 022412           15 ELP-APFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAH-PGGPASSEFDWGTG   76 (297)
Q Consensus        15 eLP-AP~GWkKk~~pkkgGTPkK~eIvFvAPtGEEI~~krqLe~YLKah-pGgp~~seFdWgTg   76 (297)
                      ++| .|+||++.+.++++|+..+.+|.|++|+|..|+|+.+|.+||.+| ++++.+++|||+++
T Consensus         3 ~~~~lp~GW~r~~~~R~~gs~~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~~~~~~~~~FdF~~~   66 (77)
T cd01396           3 EDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTVP   66 (77)
T ss_pred             CCCCCCCCCEEEEEEecCCCCCcceEEEECCCCCEEECHHHHHHHHHhCCCCCCcHhHcccCCC
Confidence            455 789999999999999999999999999999999999999999999 55799999999985

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.

>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=99.32  E-value=1.6e-12  Score=94.56  Aligned_cols=60  Identities=28%  Similarity=0.687  Sum_probs=57.0

Q ss_pred             eeccCCCCCccccccCCCCCCCcceEEEecCCchhhcchHHHHHHHHhC-CCCCCcccccc
Q 022412           14 FELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAH-PGGPASSEFDW   73 (297)
Q Consensus        14 ~eLPAP~GWkKk~~pkkgGTPkK~eIvFvAPtGEEI~~krqLe~YLKah-pGgp~~seFdW   73 (297)
                      +.+|.|.||++.+..++.|+..+.+|.|++|+|..++|+.+|.+||..| +.++.++.|||
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 LRDPLPPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLENFSF   62 (62)
T ss_pred             CCCCCCCCeEEEEEEcCCCCCCcceEEEECCCCceecCHHHHHHHHHhCCCCCCcHHHCCC
Confidence            5789999999999999999999999999999999999999999999999 66799999997

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

>smart00391 MBD Methyl-CpG binding domain

Probab=99.14  E-value=5.2e-11  Score=91.20  Aligned_cols=64  Identities=27%  Similarity=0.606  Sum_probs=56.8

Q ss_pred             eeeccCCCCCccccccCCCC-CCCcceEEEecCCchhhcchHHHHHHHHhCCCC-CCccccccCCC
Q 022412           13 SFELPAPFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGG-PASSEFDWGTG   76 (297)
Q Consensus        13 s~eLPAP~GWkKk~~pkkgG-TPkK~eIvFvAPtGEEI~~krqLe~YLKahpGg-p~~seFdWgTg   76 (297)
                      .+.+|.|.||++.+..++.| +..+.+|+|++|+|..++|+.+|.+||.+|+.. ..+..|||+++
T Consensus         3 ~~~~Plp~GW~R~~~~r~~g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~~~~~~~~~~~F~F~~~   68 (77)
T smart00391        3 PLRLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNAT   68 (77)
T ss_pred             cccCCCCCCcEEEEEEecCCCCCCcccEEEECCCCCeeeCHHHHHHHHHhCCCcccccccccCcCC
Confidence            46899999999999988876 667999999999999999999999999999864 55678999875

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

>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=99.11  E-value=1e-10  Score=88.28  Aligned_cols=67  Identities=28%  Similarity=0.634  Sum_probs=58.2

Q ss_pred             eeeeeccCCCCCccccccCCCCCC-CcceEEEecCCchhhcchHHHHHHHHhCCC--CCCccccccCCCC
Q 022412           11 QVSFELPAPFGWKKKIVPRKGGTP-KKSEIVFTAPTGEEISNKKQLEQYLKAHPG--GPASSEFDWGTGE   77 (297)
Q Consensus        11 ~vs~eLPAP~GWkKk~~pkkgGTP-kK~eIvFvAPtGEEI~~krqLe~YLKahpG--gp~~seFdWgTge   77 (297)
                      ...+.+|-|.||++.+..++.|+. .+.+|.|++|+|..++|+.++.+||..+++  .+.+..|+|.+.-
T Consensus         4 ~~~~~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~~~~~l~~~~F~F~~~~   73 (77)
T PF01429_consen    4 ISPLDPPLPDGWKREVVVRKSGSSAGKKDVYYYSPCGKRFRSKKEVVRYLKENPSEHDLKPENFSFSKRL   73 (77)
T ss_dssp             SECEBTTSTTT-EEEEEESSSSTTTTSEEEEEEETTSEEESSHHHHHHHHTTSS---SS-CTTBBTTTTB
T ss_pred             cccccCCCCCCCEEEEEEecCCCcCCceEEEEECCCCCEEeCHHHHHHHHHhCCCcccCCHhHCCCCCCc
Confidence            455778999999999999998766 799999999999999999999999999998  9999999998763

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.

>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=98.08  E-value=4.8e-06  Score=64.65  Aligned_cols=62  Identities=19%  Similarity=0.475  Sum_probs=55.5

Q ss_pred             eeccCCCCCccccccCCCCCCCcceEEEecCCchhhcchHHHHHHHHhCC-CCCCccccccCC
Q 022412           14 FELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHP-GGPASSEFDWGT   75 (297)
Q Consensus        14 ~eLPAP~GWkKk~~pkkgGTPkK~eIvFvAPtGEEI~~krqLe~YLKahp-Ggp~~seFdWgT   75 (297)
                      +-+|-|.||++...-++.|.-.+.+|.|.||.|--+++.-++.+||..|+ .++.+..|+..+
T Consensus         2 ~r~Pl~~GW~Re~vir~~~~~~~~dV~Y~aPcGKklRs~~ev~~yL~~~~~~~Lt~dnFsF~~   64 (73)
T cd01397           2 LRVPLELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKNGISLLSRENFSFSA   64 (73)
T ss_pred             ccCCCCCCceeEEEeccCCCCccceEEEECCCCcccccHHHHHHHHHhCCccCccHhHccccC
Confidence            45788999999998888777789999999999999999999999999887 478899998865

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

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

Probab=96.68  E-value=0.0025  Score=48.04  Aligned_cols=58  Identities=19%  Similarity=0.410  Sum_probs=49.5

Q ss_pred             eeccCCCCCccccccCCCCCCCcceEEEecCCchhhcchHHHHHHHHhCCCCCCccccc
Q 022412           14 FELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFD   72 (297)
Q Consensus        14 ~eLPAP~GWkKk~~pkkgGTPkK~eIvFvAPtGEEI~~krqLe~YLKahpGgp~~seFd   72 (297)
                      +-+|--.||.+...-.+.| -.+..|+|-||.|.-++|-.++.+||..+.-.+.+..|+
T Consensus         2 L~~Pll~gw~R~~~~~~~~-~~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t~~~L~~d~Fs   59 (60)
T cd01395           2 LHTPLLCGFQRMKYRARVG-KVKKHVIYKAPCGRSLRNMSEVHRYLRETCSFLTVDNFS   59 (60)
T ss_pred             cccccccCeEEEEEeccCC-CcccceEEECCcchhhhcHHHHHHHHHhccccceeeccc
Confidence            4577779999998877766 457779999999999999999999999997677777775

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=91.04  E-value=0.2  Score=46.61  Aligned_cols=44  Identities=34%  Similarity=0.708  Sum_probs=39.3

Q ss_pred             CCCCccccccCCCCCC-CcceEEEecCCchhhcchHHHHHHHHhC
Q 022412           19 PFGWKKKIVPRKGGTP-KKSEIVFTAPTGEEISNKKQLEQYLKAH   62 (297)
Q Consensus        19 P~GWkKk~~pkkgGTP-kK~eIvFvAPtGEEI~~krqLe~YLKah   62 (297)
                      |+||++...++++|-+ -+.+|+|+.|.|--.+|+-+|-.||--.
T Consensus        20 p~GW~~~~~~r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~   64 (272)
T KOG4161|consen   20 PPGWTREEVQRSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKV   64 (272)
T ss_pred             CCCcchhhhcccCCCcccccceEEeCCcccccccccHHHHHhccc
Confidence            7999999999997644 5899999999999999999999999654

---

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	297
2ky8_A	72	Methyl-CPG-binding domain protein 2; DNA binding d	2e-08
1ub1_A	133	MECP2, attachment region binding protein; chicken	8e-08
1d9n_A	75	Methyl-CPG-binding protein MBD1; PCM1, methylation	3e-07
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	1e-06

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

 Score = 49.5 bits (118), Expect = 2e-08
 Identities = 26/71 (36%), Positives = 42/71 (59%), Gaps = 5/71 (7%)

Query: 9  EEQVSFELPA-PFGWKKKIVPRK-GGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGP 66
          ++Q   + PA P GWKK+ V RK G +  KS++ + +P+G++  +K QL +YL       
Sbjct: 3  DKQGRTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLG---NAV 59

Query: 67 ASSEFDWGTGE 77
            S FD+ TG+
Sbjct: 60 DLSCFDFRTGK 70

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

 Score = 49.5 bits (117), Expect = 8e-08
 Identities = 22/92 (23%), Positives = 33/92 (35%), Gaps = 3/92 (3%)

Query: 17  PAPFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSE-FDWG 74
             P GW +K+  RK G +  K ++    P G+   +K +L  Y +           FD+ 
Sbjct: 37  TLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFT 96

Query: 75  TGETPRRSARISEKAKISPAADNEPPKKRGRK 106
                  S R     K    +   P   RGR 
Sbjct: 97  VTGRGSPSRREQRPPK-KAKSPKSPGSGRGRG 127

>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 = 46.1 bits (109), Expect = 3e-07
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 19 PFGWKKKIVPRK-GGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGE 77
            GWK++ V RK G T  +S+  + +PTG+ I +K +L +YL         + FD+  G 
Sbjct: 12 GPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACD---LTLFDFKQGI 68

Query: 78 TPRRSAR 84
              + +
Sbjct: 69 LCYPAPK 75

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

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 17 PAPFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSE-FDWG 74
            P GW +K+  RK G +  K ++    P G+   +K +L  Y +           FD+ 
Sbjct: 23 TLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEKVGDTSLDPNDFDFT 82

Query: 75 TGETPRRS 82
                 S
Sbjct: 83 VTGRGSPS 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	297
1ub1_A	133	MECP2, attachment region binding protein; chicken	99.61
3c2i_A	97	Methyl-CPG-binding protein 2; water mediated recog	99.53
2ky8_A	72	Methyl-CPG-binding domain protein 2; DNA binding d	99.46
3vxv_A	69	Methyl-CPG-binding domain protein 4; methyl CPG bi	99.32
1d9n_A	75	Methyl-CPG-binding protein MBD1; PCM1, methylation	99.32

>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=99.61  E-value=8.1e-16  Score=128.56  Aligned_cols=82  Identities=27%  Similarity=0.508  Sum_probs=74.8

Q ss_pred             ccCCCCCccccccCCCC-CCCcceEEEecCCchhhcchHHHHHHHHhCCC-CCCccccccCC---CCCCcchhhhhcccc
Q 022412           16 LPAPFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYLKAHPG-GPASSEFDWGT---GETPRRSARISEKAK   90 (297)
Q Consensus        16 LPAP~GWkKk~~pkkgG-TPkK~eIvFvAPtGEEI~~krqLe~YLKahpG-gp~~seFdWgT---geTPRRSaRiseK~K   90 (297)
                      -+.|.||++.+..++.| +..+.||.|++|+|..|+|+.+|.+||..||+ ++.+++|||+.   +.++||+.|++.++|
T Consensus        36 ~~LP~GWkRe~~~RksG~Sagk~DVYY~SP~GKkfRSk~Ev~ryL~~~~~~~~~~e~FdF~~~gk~~~s~R~~r~~k~~k  115 (133)
T 1ub1_A           36 PTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSPSRREQRPPKKAK  115 (133)
T ss_dssp             CCBTTBCEEEEEECCCSSSCCSEEEEEECTTSCEESSHHHHHHHHTTSCCCSCCGGGCCCCCCCCSCSSCCCCCCCCCCC
T ss_pred             CCCCCCCEEEEEEecCCCCCCceeEEEECCCCCeeeCHHHHHHHHHHCCccCCCHhHCccccCCCCCCcccccCCCCCCC
Confidence            45789999999999988 88999999999999999999999999999998 79999999983   478999999999999


Q ss_pred             CCCCCCC
Q 022412           91 ISPAADN   97 (297)
Q Consensus        91 at~~~e~   97 (297)
                      +++++.+
T Consensus       116 ~~~~~~~  122 (133)
T 1ub1_A          116 SPKSPGS  122 (133)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9877654

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

Probab=99.53  E-value=4.7e-15  Score=118.21  Aligned_cols=69  Identities=23%  Similarity=0.455  Sum_probs=59.6

Q ss_pred             eccCCCCCccccccCCCC-CCCcceEEEecCCchhhcchHHHHHHHHhCCC-CCCccccccCCCCCCcchh
Q 022412           15 ELPAPFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYLKAHPG-GPASSEFDWGTGETPRRSA   83 (297)
Q Consensus        15 eLPAP~GWkKk~~pkkgG-TPkK~eIvFvAPtGEEI~~krqLe~YLKahpG-gp~~seFdWgTgeTPRRSa   83 (297)
                      .-|.|.||++.+.+++.| |..+.||.|++|+|..|+|+.+|.+||.+||. ++.+++|||+++.++++|.
T Consensus        21 ~~~lP~GW~re~~~R~~G~s~gk~DvYY~sP~GkkfRSk~ev~ryL~~~g~~~~~~~~FdF~~~~~~~~~~   91 (97)
T 3c2i_A           21 DPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEKVGDTSLDPNDFDFTVTGRGSPSR   91 (97)
T ss_dssp             CTTSCTTCEEEEEECCSSTTTTCEEEEEECTTSCEECSHHHHHHHHHHHTCCSSCTTTCCCCSSCC-----
T ss_pred             CCCCCCCCEEEEEEecCCCCCCcceEEEECCCCCEEECHHHHHHHHHHCCCCCCCHhhccccCCCcCcccc
Confidence            346889999999999987 67899999999999999999999999999987 6999999999999999874

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

Probab=99.46  E-value=4.4e-14  Score=106.41  Aligned_cols=62  Identities=40%  Similarity=0.699  Sum_probs=56.9

Q ss_pred             eeeccC-CCCCccccccCCCC-CCCcceEEEecCCchhhcchHHHHHHHHhCCCCCCccccccCCCC
Q 022412           13 SFELPA-PFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGE   77 (297)
Q Consensus        13 s~eLPA-P~GWkKk~~pkkgG-TPkK~eIvFvAPtGEEI~~krqLe~YLKahpGgp~~seFdWgTge   77 (297)
                      .+++|+ |.||++.+.+++.| ++.+.+|+|++|+|..|+|+.+|.+||..   ++.+++|||++|.
T Consensus         7 ~~~~p~Lp~GW~R~~~~R~~g~s~~k~DvyY~sP~Gkr~RS~~ev~~YL~~---~l~~~~FdF~~~~   70 (72)
T 2ky8_A            7 RTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGN---AVDLSCFDFRTGK   70 (72)
T ss_dssp             EEECSSSCTTCEEEEEECCSSTTTTCEEEEEECTTCCEEESHHHHHHHHTT---SSCCTTCBTTTTB
T ss_pred             cccCCCCCCCCEEEEEEecCCCCCCceEEEEECCCCCEeEcHHHHHHHHhc---CCChhhcCCCCCC
Confidence            467887 79999999999966 68999999999999999999999999988   6999999999985

>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=99.32  E-value=1.2e-12  Score=98.10  Aligned_cols=61  Identities=25%  Similarity=0.514  Sum_probs=56.2

Q ss_pred             ccCCCCCccccccCCCCC-CCcceEEEecCCchhhcchHHHHHHHHhCCC-CCCccccccCCC
Q 022412           16 LPAPFGWKKKIVPRKGGT-PKKSEIVFTAPTGEEISNKKQLEQYLKAHPG-GPASSEFDWGTG   76 (297)
Q Consensus        16 LPAP~GWkKk~~pkkgGT-PkK~eIvFvAPtGEEI~~krqLe~YLKahpG-gp~~seFdWgTg   76 (297)
                      -|.|.||++.+..++.|+ .-|.+|.|++|+|..|+|+.+|.+||..||. ++.+++|||.+.
T Consensus         4 ~plp~GW~R~~~~R~~G~s~gk~DvyY~sP~Gkk~RSk~ev~~yL~~~~~~~l~~~~FdF~~p   66 (69)
T 3vxv_A            4 KPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVL   66 (69)
T ss_dssp             CCSCTTCEEEEEECCSSTTTTCEEEEEECTTSCEECSHHHHHHHHHHHCCCCCCGGGSCCCCC
T ss_pred             CcCCCCCEEEEEEeccCCCCCcceEEEEcCCCCEeeCHHHHHHHHHhCCCCCCCHHHcceeCC
Confidence            488999999999998774 4688999999999999999999999999998 699999999875

>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=99.32  E-value=1.7e-12  Score=98.79  Aligned_cols=63  Identities=35%  Similarity=0.632  Sum_probs=56.7

Q ss_pred             eeeccC-CCCCccccccCCCCCC-CcceEEEecCCchhhcchHHHHHHHHhCCCCCCccccccCCCCC
Q 022412           13 SFELPA-PFGWKKKIVPRKGGTP-KKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGET   78 (297)
Q Consensus        13 s~eLPA-P~GWkKk~~pkkgGTP-kK~eIvFvAPtGEEI~~krqLe~YLKahpGgp~~seFdWgTgeT   78 (297)
                      +++.|. |.||++.+.+++.|+. .+.+|.|++|+|..|+|+.+|.+||.  + ++.++.|||++|.+
T Consensus         5 ~~~~p~LP~GW~Re~~~R~~g~s~gk~DvyY~sP~Gkk~RS~~ev~ryL~--~-~~~~~~FdF~~gk~   69 (75)
T 1d9n_A            5 WLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLG--P-ACDLTLFDFKQGIL   69 (75)
T ss_dssp             CEECTTTCSSCEEEECSSSSSCTTCCCCEEEECSSSCEECSTHHHHHHHC--T-TCCCTTCCTTTCCC
T ss_pred             cccCCCCCCCCEEEEEEecCCCCCCceEEEEECCCCCeeecHHHHHHHhc--c-CCCccccCCCCCCc
Confidence            456666 6999999999999876 79999999999999999999999996  3 79999999999976

---

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	297
d1ig4a_	75	d.10.1.3 (A:) Methylation-dependent transcriptiona	2e-11
d1qk9a_	92	d.10.1.3 (A:) Methyl-CpG-binding protein 2, MECP2	8e-09

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

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

 Score = 56.7 bits (137), Expect = 2e-11
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 15 ELPA-PFGWKKKIVPRK-GGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFD 72
          + PA   GWK++ V RK G T  +S+  + +PTG+ I +K +L +YL         + FD
Sbjct: 7  DCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYL---GPACDLTLFD 63

Query: 73 WGTGE 77
          +  G 
Sbjct: 64 FKQGI 68

>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 = 49.9 bits (119), Expect = 8e-09
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 7  VKEEQVSFELPA-PFGWKKKIVPRK-GGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPG 64
          +++    ++ P  P GW +K+  RK G +  K ++    P G+   +K +L  Y +    
Sbjct: 12 IRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGD 71

Query: 65 GPASSE-FDWGT 75
                 FD+  
Sbjct: 72 TSLDPNDFDFTV 83

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	297
d1ig4a_	75	Methylation-dependent transcriptional repressor MB	99.41
d1qk9a_	92	Methyl-CpG-binding protein 2, MECP2 {Human (Homo s	98.99

>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=99.41  E-value=1.3e-13  Score=103.44  Aligned_cols=64  Identities=33%  Similarity=0.556  Sum_probs=57.3

Q ss_pred             eeeeccC-CCCCccccccCCCCCC-CcceEEEecCCchhhcchHHHHHHHHhCCCCCCccccccCCCCC
Q 022412           12 VSFELPA-PFGWKKKIVPRKGGTP-KKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGET   78 (297)
Q Consensus        12 vs~eLPA-P~GWkKk~~pkkgGTP-kK~eIvFvAPtGEEI~~krqLe~YLKahpGgp~~seFdWgTgeT   78 (297)
                      .++++|+ |.||++.++.++.|+. .+.+|.|++|+|..|+|+.+|.+||   ++++.++.|||+||..
T Consensus         4 ~~~~~p~LP~GW~re~~~Rk~g~~~gk~DvyY~sP~Gkk~RS~~ev~~yL---~~~l~~~~FdF~tg~~   69 (75)
T d1ig4a_           4 DWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYL---GPACDLTLFDFKQGIL   69 (75)
T ss_dssp             CEEECTTTCTTCEEEEECCCSSSSTTCCEEEEECSSSCEECSHHHHHHHH---CSSSCCTTBCTTTCCB
T ss_pred             ccccCCCCCCCcEEEEEEEcCCCCCCceeEEEECCCCCEEeCHHHHHHHh---ccCCCccceeccCCcE
Confidence            5678897 8999999999998854 4889999999999999999999999   4679999999999864

>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=98.99  E-value=2e-10  Score=88.27  Aligned_cols=67  Identities=24%  Similarity=0.545  Sum_probs=58.2

Q ss_pred             cceeeeeccC-CCCCccccccCCCC-CCCcceEEEecCCchhhcchHHHHHHHHhCCC-CCCccccccCC
Q 022412            9 EEQVSFELPA-PFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYLKAHPG-GPASSEFDWGT   75 (297)
Q Consensus         9 ee~vs~eLPA-P~GWkKk~~pkkgG-TPkK~eIvFvAPtGEEI~~krqLe~YLKahpG-gp~~seFdWgT   75 (297)
                      +..+.++.|. |.||++.+..++.| +..+.+|.|++|+|..++|+.+|.+||..|++ +..+..||+..
T Consensus        14 ~~~~~~~dp~Lp~GW~r~~~~R~~g~~~gk~Dvyy~sP~Gkk~RS~~eV~~yL~~~~~~~~~~~~FdF~~   83 (92)
T d1qk9a_          14 DRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTV   83 (92)
T ss_dssp             CSSCCSSBCCSSSSCEEEECCCCCSSSCSCCCEEEEETTTEEESSHHHHHHHHHHHTCCSSCGGGCCCCT
T ss_pred             ccCccccCCCCCCCCEEEEEEecCCCCCceeeEEEECCCCCeeecHHHHHHHHHHCCCcccchhHeeeEe
Confidence            3445677786 89999999998887 46699999999999999999999999999985 58889999975