Citrus Sinensis ID: 042412

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70----
Protein Sequence
FLLSDYNYTMGKKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMKRFK
Secondary Structure (PSIPRED)
cccccccccccEEEEEEEEccccccEEEEEccccHHHHHHHHEEEEEcccEEEEEEccccccEEEEEccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEEEEcccccEEEEccccHHHcc
Coil and Loop (DISEMBL)
fllsdynytmgkKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLvlitfsptkrgrstkfcsmkrfk
Flexible Loop (DISEMBL)
fllsdynytmgkkieikkiadakarQVTYAKRKkslikkareisvacgidlvlitfsptkrgrstkfcsmkrfk
Low Complexity Region (SEG)
FLLSDYNYTMGkkieikkiadakaRQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMKRFK
Disordered region (IsUnstruct)
*****YNYTMGKKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFS*****************
Disordered Region (DISOPRED)
**************EIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC******
Disordered Region (DISEMBL)
FLLSDYNYTMGKKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMKRFK
Disordered Region (DISPRO)
************KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
FLLSDYNYTMGKKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMKRFK
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	74	2.2.26 [Sep-21-2011]
Q8RYD9	252	Protein TRANSPARENT TESTA	no	no	0.783	0.230	0.540	2e-10
Q9FVC1	240	MADS-box protein SVP OS=A	no	no	0.756	0.233	0.534	4e-09
Q944S9	224	MADS-box transcription fa	no	no	0.783	0.258	0.508	1e-08
Q03378	215	Floral homeotic protein G	N/A	no	0.783	0.269	0.475	1e-08
Q6VAM4	159	MADS-box transcription fa	no	no	0.702	0.327	0.528	2e-08
O04067	254	Agamous-like MADS-box pro	N/A	no	0.783	0.228	0.475	2e-08
P29384	250	Developmental protein SEP	no	no	0.783	0.232	0.475	3e-08
Q07474	212	Floral homeotic protein P	N/A	no	0.783	0.273	0.475	4e-08
Q9SAR1	248	MADS-box transcription fa	no	no	0.783	0.233	0.475	4e-08
O55087	349	Myocyte-specific enhancer	yes	no	0.675	0.143	0.52	5e-08

>sp|Q8RYD9|TT16_ARATH Protein TRANSPARENT TESTA 16 OS=Arabidopsis thaliana GN=TT16 PE=1 SV=1

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/61 (54%), Positives = 44/61 (72%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ KIEIKKI +  ARQVT++KR+  LIKK RE+S+ C   + LI FS T  G+ ++FC
Sbjct: 1  MGRGKIEIKKIENQTARQVTFSKRRTGLIKKTRELSILCDAHIGLIVFSAT--GKLSEFC 58

Query: 69 S 69
          S
Sbjct: 59 S 59

Transcription factor involved in the developmental regulation of the endothelium and in the accumulation of proanthocyanidins (PAs) or condensed tannins which give the seed its brown pigmentation after oxidation. Necessary for the normal activation of the BANYULS promoter in the endothelium body.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FVC1|SVP_ARATH MADS-box protein SVP OS=Arabidopsis thaliana GN=SVP PE=1 SV=1

 Score = 60.1 bits (144), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 31/58 (53%), Positives = 43/58 (74%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
          +KI+I+KI +A ARQVT++KR++ L KKA E+SV C  D+ LI FS T  G+  +FCS
Sbjct: 4  EKIQIRKIDNATARQVTFSKRRRGLFKKAEELSVLCDADVALIIFSST--GKLFEFCS 59

Transcription repressor that inhibit floral transition in the autonomous flowering pathway, independent of photoperiod and temperature. Acts in a dosage-dependent manner. Together with AGL24 and AP1, controls the identity of the floral meristem and regulates expression of class B, C and E genes.

Arabidopsis thaliana (taxid: 3702)

>sp|Q944S9|MAD16_ORYSJ MADS-box transcription factor 16 OS=Oryza sativa subsp. japonica GN=MADS16 PE=1 SV=2

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/61 (50%), Positives = 44/61 (72%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ KIEIK+I +A  RQVTY+KR+  ++KKARE++V C   + +I FS T  G+  +FC
Sbjct: 1  MGRGKIEIKRIENATNRQVTYSKRRTGIMKKARELTVLCDAQVAIIMFSST--GKYHEFC 58

Query: 69 S 69
          S
Sbjct: 59 S 59

Probable transcription factor involved in the development of floral organs. Required for normal development of lodicules and stamens (whorls 2 and 3). May function as an heterodimer with MADS4.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q03378|GLOB_ANTMA Floral homeotic protein GLOBOSA OS=Antirrhinum majus GN=GLO PE=1 SV=1

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 44/61 (72%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ KIEIK+I ++  RQVTY+KR+  ++KKA+EISV C   + +I F+ +  G+  +FC
Sbjct: 1  MGRGKIEIKRIENSSNRQVTYSKRRNGIMKKAKEISVLCDAHVSVIIFASS--GKMHEFC 58

Query: 69 S 69
          S
Sbjct: 59 S 59

Transcription factor involved in the genetic control of flower development. Acts in conjunction with DEFICIENS (defA).

Antirrhinum majus (taxid: 4151)

>sp|Q6VAM4|MAD23_ORYSJ MADS-box transcription factor 23 OS=Oryza sativa subsp. japonica GN=MADS23 PE=2 SV=1

 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 40/53 (75%), Gaps = 1/53 (1%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
          MG+ KIEIK+I +A +RQVT++KR+  L KKARE+S+ C  ++ L+ FS T R
Sbjct: 1  MGRGKIEIKRIDNATSRQVTFSKRRSGLFKKARELSILCDAEVGLLVFSSTSR 53

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|O04067|AGL9_SINAL Agamous-like MADS-box protein AGL9 homolog OS=Sinapis alba GN=AGL9 PE=2 SV=1

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 29/61 (47%), Positives = 43/61 (70%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ ++E+K+I +   RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FC
Sbjct: 1  MGRGRVELKRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFS--NRGKLYEFC 58

Query: 69 S 69
          S
Sbjct: 59 S 59

Probable transcription factor active in inflorescence development and floral organogenesis.

Sinapis alba (taxid: 3728)

>sp|P29384|SEP2_ARATH Developmental protein SEPALLATA 2 OS=Arabidopsis thaliana GN=SEP2 PE=1 SV=1

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 29/61 (47%), Positives = 43/61 (70%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ ++E+K+I +   RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FC
Sbjct: 1  MGRGRVELKRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVSLIVFS--NRGKLYEFC 58

Query: 69 S 69
          S
Sbjct: 59 S 59

Probable transcription factor. Functions with SEPALLATA1/AGL2 and SEPALLATA3/AGL9 to ensure proper development of petals, stamens and carpels and to prevent the indeterminate growth of the flower meristem. Forms an heterodimer via the K-box domain with AG, that could be involved in genes regulation during floral meristem development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q07474|MADS2_PETHY Floral homeotic protein PMADS 2 OS=Petunia hybrida GN=PMADS2 PE=2 SV=1

 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 43/61 (70%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ KIEIK+I ++  RQVTY+KR+  +IKKA+EI+V C   + LI F  +  G+  ++C
Sbjct: 1  MGRGKIEIKRIENSSNRQVTYSKRRNGIIKKAKEITVLCDAKVSLIIFGNS--GKMHEYC 58

Query: 69 S 69
          S
Sbjct: 59 S 59

Transcription factor involved in the genetic control of flower development.

Petunia hybrida (taxid: 4102)

>sp|Q9SAR1|MADS8_ORYSJ MADS-box transcription factor 8 OS=Oryza sativa subsp. japonica GN=MADS8 PE=1 SV=1

 Score = 56.6 bits (135), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/61 (47%), Positives = 43/61 (70%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ ++E+K+I +   RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FC
Sbjct: 1  MGRGRVELKRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFS--NRGKLYEFC 58

Query: 69 S 69
          S
Sbjct: 59 S 59

Probable transcription factor. May be involved in the control of flowering time.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|O55087|MEF2B_MOUSE Myocyte-specific enhancer factor 2B OS=Mus musculus GN=Mef2b PE=1 SV=1

 Score = 56.6 bits (135), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 26/50 (52%), Positives = 35/50 (70%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
          KKI+I +I D + RQVT+ KRK  L+KKA E+SV C  D+ LI F+  +R
Sbjct: 4  KKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCDIALIIFNSAQR 53

Transcriptional activator which binds specifically to the MEF2 element, 5'-YTA[AT](4)TAR-3', found in numerous muscle-specific genes. Activates transcription via this element. May be involved in muscle-specific and/or growth factor-related transcription.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	74
302142812	78	unnamed protein product [Vitis vinifera]	0.851	0.807	0.507	1e-11
284178626	426	MIKC* MADS-box transcription factor [Mar	0.851	0.147	0.530	2e-10
168034578	417	ppmads2 MIKC* MADS-domain protein PpMADS	0.783	0.139	0.573	2e-10
284178638	415	MIKC* MADS-box transcription factor [Fun	0.783	0.139	0.573	3e-10
284178654	416	MIKC* MADS-box transcription factor [Fun	0.783	0.139	0.573	3e-10
284178652	413	MIKC* MADS-box transcription factor [Fun	0.783	0.140	0.557	3e-10
168020149	416	MIKC MADS-domain protein PpMADS3 [Physco	0.783	0.139	0.557	5e-10
284178640	418	MIKC* MADS-box transcription factor [Fun	0.783	0.138	0.557	9e-10
168001060	410	MIKC MADS--domain protein PPMA8 [Physcom	0.783	0.141	0.540	1e-09
343160559	448	M14 protein [Ceratopteris richardii]	0.851	0.140	0.530	1e-09

>gi|302142812|emb|CBI20107.3| unnamed protein product [Vitis vinifera]

 Score = 73.6 bits (179), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/65 (50%), Positives = 49/65 (75%), Gaps = 2/65 (3%)

Query: 10 MGKKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
          MG+KIE++KI +   RQ+T++KRK SLI+KA EIS+ C +D+ L+T+SP+  GR  KFC+
Sbjct: 1  MGRKIEMRKIENTTRRQITFSKRKSSLIRKANEISILCDVDVALLTYSPS--GRLNKFCN 58

Query: 70 MKRFK 74
            R +
Sbjct: 59 RDRME 63

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|284178626|gb|ADB81895.1| MIKC* MADS-box transcription factor [Marchantia polymorpha]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/66 (53%), Positives = 47/66 (71%), Gaps = 3/66 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EIKKI +   RQVTY+KR+  LIKKA E+SV C ID+ +I FSP+  G+ T+FC
Sbjct: 1  MGRVKLEIKKIENPTNRQVTYSKRRNGLIKKAYELSVLCDIDIAVIMFSPS--GKLTQFC 58

Query: 69 SMKRFK 74
             R +
Sbjct: 59 KNDRIE 64

Source: Marchantia polymorpha

Species: Marchantia polymorpha

Genus: Marchantia

Family: Marchantiaceae

Order: Marchantiales

Class: Marchantiopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168034578|ref|XP_001769789.1| ppmads2 MIKC* MADS-domain protein PpMADS2 [Physcomitrella patens subsp. patens] gi|168034580|ref|XP_001769790.1| MIKC MADS-domain protein PpMADS2 [Physcomitrella patens subsp. patens] gi|42602137|gb|AAS21676.1| putative MADS-domain transcription factor [Physcomitrella patens] gi|162678898|gb|EDQ65351.1| ppmads2 MIKC* MADS-domain protein PpMADS2 [Physcomitrella patens subsp. patens] gi|162678899|gb|EDQ65352.1| MIKC MADS-domain protein PpMADS2 [Physcomitrella patens subsp. patens]

 Score = 69.7 bits (169), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/61 (57%), Positives = 46/61 (75%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EIKKI +   RQVTY+KR+  LIKKA E+SV C IDL LI FSP+  G+ T++C
Sbjct: 1  MGRVKLEIKKIENPTNRQVTYSKRRNGLIKKAYELSVLCDIDLALIMFSPS--GKLTQYC 58

Query: 69 S 69
          +
Sbjct: 59 N 59

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|284178638|gb|ADB81901.1| MIKC* MADS-box transcription factor [Funaria hygrometrica]

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/61 (57%), Positives = 46/61 (75%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EIKKI +   RQVTY+KR+  LIKKA E+SV C IDL LI FSP+  G+ T++C
Sbjct: 1  MGRVKLEIKKIENPTNRQVTYSKRRNGLIKKAYELSVLCDIDLALIMFSPS--GKLTQYC 58

Query: 69 S 69
          +
Sbjct: 59 N 59

Source: Funaria hygrometrica

Species: Funaria hygrometrica

Genus: Funaria

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|284178654|gb|ADB81909.1| MIKC* MADS-box transcription factor [Funaria hygrometrica]

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/61 (57%), Positives = 47/61 (77%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EIKKI ++  RQVTY+KR+  LIKKA E+SV C IDL LI FSP+  G+ T++C
Sbjct: 1  MGRVKLEIKKIENSTNRQVTYSKRRNGLIKKAYELSVLCDIDLALIMFSPS--GKLTQYC 58

Query: 69 S 69
          +
Sbjct: 59 N 59

Source: Funaria hygrometrica

Species: Funaria hygrometrica

Genus: Funaria

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|284178652|gb|ADB81908.1| MIKC* MADS-box transcription factor [Funaria hygrometrica]

 Score = 68.9 bits (167), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 34/61 (55%), Positives = 46/61 (75%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EIKKI +   RQVTY+KR+  LIKKA E+SV C IDL L+ FSP+  G+ T++C
Sbjct: 1  MGRVKLEIKKIENPTNRQVTYSKRRNGLIKKAYELSVLCDIDLALVMFSPS--GKLTQYC 58

Query: 69 S 69
          +
Sbjct: 59 N 59

Source: Funaria hygrometrica

Species: Funaria hygrometrica

Genus: Funaria

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168020149|ref|XP_001762606.1| MIKC MADS-domain protein PpMADS3 [Physcomitrella patens subsp. patens] gi|42602135|gb|AAS21675.1| putative MADS-domain transcription factor [Physcomitrella patens] gi|162686339|gb|EDQ72729.1| MIKC MADS-domain protein PpMADS3 [Physcomitrella patens subsp. patens]

 Score = 68.6 bits (166), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 34/61 (55%), Positives = 46/61 (75%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EIKKI +   RQVT++KR+  LIKKA E+SV C IDL LI FSP+  G+ T++C
Sbjct: 1  MGRVKLEIKKIENPTNRQVTFSKRRNGLIKKAYELSVLCDIDLALIMFSPS--GKLTQYC 58

Query: 69 S 69
          +
Sbjct: 59 N 59

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|284178640|gb|ADB81902.1| MIKC* MADS-box transcription factor [Funaria hygrometrica]

 Score = 67.8 bits (164), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 34/61 (55%), Positives = 46/61 (75%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EIKKI +   RQVT++KR+  LIKKA E+SV C IDL LI FSP+  G+ T++C
Sbjct: 1  MGRVKLEIKKIENPTNRQVTFSKRRNGLIKKAYELSVLCDIDLALIMFSPS--GKLTQYC 58

Query: 69 S 69
          +
Sbjct: 59 N 59

Source: Funaria hygrometrica

Species: Funaria hygrometrica

Genus: Funaria

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168001060|ref|XP_001753233.1| MIKC MADS--domain protein PPMA8 [Physcomitrella patens subsp. patens] gi|162695519|gb|EDQ81862.1| MIKC MADS--domain protein PPMA8 [Physcomitrella patens subsp. patens]

 Score = 67.4 bits (163), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 33/61 (54%), Positives = 46/61 (75%), Gaps = 3/61 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EIKKI +   RQVTY+KR+  L+KKA E+SV C IDL L+ FSP+  G+ T++C
Sbjct: 1  MGRVKLEIKKIENPTNRQVTYSKRRNGLMKKAYELSVLCDIDLALVMFSPS--GKLTQYC 58

Query: 69 S 69
          +
Sbjct: 59 N 59

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|343160559|emb|CAX33871.1| M14 protein [Ceratopteris richardii]

 Score = 67.4 bits (163), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/66 (53%), Positives = 45/66 (68%), Gaps = 3/66 (4%)

Query: 10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68
          MG+ K+EI+KI +   RQVTY+KR+  LIKKA E+SV C ID+ LI FSP+  GR   F 
Sbjct: 1  MGRVKLEIRKIENPTNRQVTYSKRRNGLIKKAYELSVLCDIDIALIMFSPS--GRLNHFS 58

Query: 69 SMKRFK 74
            KR +
Sbjct: 59 GKKRIE 64

Source: Ceratopteris richardii

Species: Ceratopteris richardii

Genus: Ceratopteris

Family: Pteridaceae

Order: Polypodiales

Class: Polypodiopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	74
TAIR|locus:2034949	389	AGL65 "AGAMOUS-like 65" [Arabi	0.554	0.105	0.604	1.7e-08
TAIR|locus:2029411	252	AGL67 "AGAMOUS-like 67" [Arabi	0.5	0.146	0.621	2.9e-07
TAIR|locus:2041233	240	SVP "AT2G22540" [Arabidopsis t	0.581	0.179	0.533	7.2e-07
TAIR|locus:2056760	386	AGL30 "AGAMOUS-like 30" [Arabi	0.608	0.116	0.489	9.5e-07
UNIPROTKB|O65874	247	MTF1 "MADS-box transcription f	0.581	0.174	0.533	1e-06
UNIPROTKB|Q03489	241	FBP2 "Agamous-like MADS-box pr	0.581	0.178	0.533	1.2e-06
UNIPROTKB|Q9ATF1	245	FBP9 "MADS-box transcription f	0.581	0.175	0.533	1.3e-06
UNIPROTKB|Q6EUV7	247	grcd2 "MADS domain protein" [G	0.581	0.174	0.533	1.3e-06
UNIPROTKB|D2T2F8	249	grcd4 "GRCD4 protein" [Gerbera	0.581	0.172	0.533	1.3e-06
UNIPROTKB|Q0J466	249	MADS7 "MADS-box transcription	0.581	0.172	0.533	1.3e-06

TAIR|locus:2034949 AGL65 "AGAMOUS-like 65" [Arabidopsis thaliana (taxid:3702)]

 Score = 136 (52.9 bits), Expect = 1.7e-08, P = 1.7e-08
 Identities = 26/43 (60%), Positives = 34/43 (79%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKF 67
             RQVTY KRK  ++KKA+E+S+ C ID+VL+ FSPT  GR+T F
Sbjct:    17 RQVTYTKRKNGILKKAKELSILCDIDIVLLMFSPT--GRATAF 57

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0009555 "pollen development" evidence=IGI

TAIR|locus:2029411 AGL67 "AGAMOUS-like 67" [Arabidopsis thaliana (taxid:3702)]

 Score = 121 (47.7 bits), Expect = 2.9e-07, P = 2.9e-07
 Identities = 23/37 (62%), Positives = 29/37 (78%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
             RQ+T++KRKK LIKKA E+S  C IDL L+ FSP+ R
Sbjct:    17 RQITFSKRKKGLIKKAYELSTLCDIDLALLMFSPSDR 53

GO:0003677 "DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

GO:0009686 "gibberellin biosynthetic process" evidence=RCA

GO:0009740 "gibberellic acid mediated signaling pathway" evidence=RCA

GO:0016114 "terpenoid biosynthetic process" evidence=RCA

TAIR|locus:2041233 SVP "AT2G22540" [Arabidopsis thaliana (taxid:3702)]

 Score = 117 (46.2 bits), Expect = 7.2e-07, P = 7.2e-07
 Identities = 24/45 (53%), Positives = 32/45 (71%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
             RQVT++KR++ L KKA E+SV C  D+ LI FS T  G+  +FCS
Sbjct:    17 RQVTFSKRRRGLFKKAEELSVLCDADVALIIFSST--GKLFEFCS 59

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;TAS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009910 "negative regulation of flower development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0048438 "floral whorl development" evidence=IGI

GO:0000900 "translation repressor activity, nucleic acid binding" evidence=IDA

GO:0009266 "response to temperature stimulus" evidence=IMP

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

GO:0010076 "maintenance of floral meristem identity" evidence=IGI

GO:0010582 "floral meristem determinacy" evidence=IGI

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0006944 "cellular membrane fusion" evidence=RCA

GO:0009556 "microsporogenesis" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

GO:0052543 "callose deposition in cell wall" evidence=RCA

TAIR|locus:2056760 AGL30 "AGAMOUS-like 30" [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 9.5e-07, P = 9.5e-07
 Identities = 23/47 (48%), Positives = 33/47 (70%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK 71
             RQ T+AKRK  ++KKA E+S+ C ID+VL+ FSPT  G++   C  +
Sbjct:    17 RQSTFAKRKNGILKKANELSILCDIDIVLLMFSPT--GKAAICCGTR 61

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0009555 "pollen development" evidence=IGI

GO:0010584 "pollen exine formation" evidence=RCA

UNIPROTKB|O65874 MTF1 "MADS-box transcription factor 1" [Pisum sativum (taxid:3888)]

 Score = 116 (45.9 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 24/45 (53%), Positives = 32/45 (71%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
             RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FCS
Sbjct:    17 RQVTFAKRRNGLLKKAYELSVLCDAEVALIVFS--NRGKLYEFCS 59

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=NAS

GO:0005634 "nucleus" evidence=IC

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

GO:0009888 "tissue development" evidence=NAS

UNIPROTKB|Q03489 FBP2 "Agamous-like MADS-box protein AGL9 homolog" [Petunia x hybrida (taxid:4102)]

 Score = 115 (45.5 bits), Expect = 1.2e-06, P = 1.2e-06
 Identities = 24/45 (53%), Positives = 32/45 (71%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
             RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FCS
Sbjct:    17 RQVTFAKRRNGLLKKAYELSVLCDAEVALIIFS--NRGKLYEFCS 59

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q9ATF1 FBP9 "MADS-box transcription factor FBP9" [Petunia x hybrida (taxid:4102)]

 Score = 115 (45.5 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 24/45 (53%), Positives = 32/45 (71%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
             RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FCS
Sbjct:    17 RQVTFAKRRNGLLKKAYELSVLCDAEVALIIFS--SRGKLYEFCS 59

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q6EUV7 grcd2 "MADS domain protein" [Gerbera hybrid cultivar (taxid:18101)]

 Score = 115 (45.5 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 24/45 (53%), Positives = 32/45 (71%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
             RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FCS
Sbjct:    17 RQVTFAKRRNGLLKKAYELSVLCDAEVALIIFS--NRGKLFEFCS 59

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|D2T2F8 grcd4 "GRCD4 protein" [Gerbera hybrid cultivar (taxid:18101)]

 Score = 115 (45.5 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 24/45 (53%), Positives = 32/45 (71%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
             RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FCS
Sbjct:    17 RQVTFAKRRNGLLKKAYELSVLCDAEVALIIFS--NRGKLYEFCS 59

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q0J466 MADS7 "MADS-box transcription factor 7" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 115 (45.5 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 24/45 (53%), Positives = 32/45 (71%)

Query:    25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
             RQVT+AKR+  L+KKA E+SV C  ++ LI FS   RG+  +FCS
Sbjct:    17 RQVTFAKRRNGLLKKAYELSVLCDAEVALIIFS--NRGKLYEFCS 59

GO:0005515 "protein binding" evidence=IPI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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: GSVIVG00027919001 SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (97 aa) (Vitis vinifera)

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	74
smart00432	59	smart00432, MADS, MADS domain	3e-16
cd00265	77	cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer fa	3e-16
cd00120	59	cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and	4e-15
cd00266	83	cd00266, MADS_SRF_like, SRF-like/Type I subfamily	1e-14
pfam00319	51	pfam00319, SRF-TF, SRF-type transcription factor (	1e-08
COG5068	412	COG5068, ARG80, Regulator of arginine metabolism a	9e-08

>gnl|CDD|197721 smart00432, MADS, MADS domain

 Score = 65.3 bits (160), Expect = 3e-16
 Identities = 29/58 (50%), Positives = 40/58 (68%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
          +KIEIK+I +   RQVT++KR+  L KKA E+SV C  ++ LI FSPT  G+  +F S
Sbjct: 3  RKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPT--GKLYEFAS 58

Length = 59

>gnl|CDD|238165 cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators

 Score = 65.7 bits (161), Expect = 3e-16
 Identities = 27/58 (46%), Positives = 40/58 (68%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
           KIEIK+I ++  RQVT++KR+  L+KKA E+SV C  ++ LI FS +  G+  +F S
Sbjct: 3  GKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSS--GKLYEFSS 58

Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. Length = 77

>gnl|CDD|238067 cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators

 Score = 62.1 bits (152), Expect = 4e-15
 Identities = 27/58 (46%), Positives = 40/58 (68%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
           KIEIK+I +  +RQVT++KR+  L KKA E+SV C  ++ +I FSP+  G+  +F S
Sbjct: 3  GKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPS--GKLYEFWS 58

Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. Length = 59

>gnl|CDD|238166 cd00266, MADS_SRF_like, SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators

 Score = 61.5 bits (150), Expect = 1e-14
 Identities = 23/52 (44%), Positives = 37/52 (71%)

Query: 10 MGKKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
            KKI+IK+I + K R VT++KR++ L KKA E+S  CG ++ +I +SP+ +
Sbjct: 1  GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGK 52

Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. Length = 83

>gnl|CDD|109379 pfam00319, SRF-TF, SRF-type transcription factor (DNA-binding and dimerisation domain)

 Score = 45.8 bits (109), Expect = 1e-08
 Identities = 19/43 (44%), Positives = 29/43 (67%)

Query: 17 KKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPT 59
          K+I +   RQVT++KR+  + KKA E+SV C  ++ +I FS T
Sbjct: 1  KRIENKSNRQVTFSKRRNGIFKKAHELSVLCDAEVAVIIFSST 43

Length = 51

>gnl|CDD|227400 COG5068, ARG80, Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]

 Score = 46.5 bits (110), Expect = 9e-08
 Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 11  GKKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSM 70
           G+KI I  I +   R VT++KRK  + KKA E+SV  G +++L+  S    G    F + 
Sbjct: 83  GRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISEN--GLVHTFTTP 140

Query: 71  K 71
           K
Sbjct: 141 K 141

Length = 412

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	74
KOG0014	195	consensus MADS box transcription factor [Transcrip	99.95
smart00432	59	MADS MADS domain.	99.95
cd00265	77	MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-li	99.95
cd00120	59	MADS MADS: MCM1, Agamous, Deficiens, and SRF (seru	99.94
cd00266	83	MADS_SRF_like SRF-like/Type I subfamily of MADS (M	99.93
PF00319	51	SRF-TF: SRF-type transcription factor (DNA-binding	99.93
KOG0015	338	consensus Regulator of arginine metabolism and rel	99.83
COG5068	412	ARG80 Regulator of arginine metabolism and related	99.48

>KOG0014 consensus MADS box transcription factor [Transcription]

Probab=99.95  E-value=1e-28  Score=167.05  Aligned_cols=60  Identities=48%  Similarity=0.837  Sum_probs=58.7

Q ss_pred             Ccc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412           10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus        10 mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      ||| ||+|++|+|+..|++||+||+.||||||+||||||||+||+|||+|+  |++|.|++++
T Consensus         1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~--~~~~~~~~~~   61 (195)
T KOG0014|consen    1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPS--GKLYEFGSSD   61 (195)
T ss_pred             CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCC--CCccccCCcc
Confidence            899 99999999999999999999999999999999999999999999999  9999999886

>smart00432 MADS MADS domain

Probab=99.95  E-value=3.2e-28  Score=142.66  Aligned_cols=58  Identities=52%  Similarity=0.854  Sum_probs=56.5

Q ss_pred             cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCC
Q 042412           11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSM   70 (74)
Q Consensus        11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~   70 (74)
                      || ||+|++|+|++.|++||+||+.||+|||+|||+||||+||+|||+|+  |.++.|.+|
T Consensus         1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~--g~~~~~~~p   59 (59)
T smart00432        1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPT--GKLYEFASP   59 (59)
T ss_pred             CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCC--CCeeeccCC
Confidence            78 99999999999999999999999999999999999999999999999  999999886

>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators

Probab=99.95  E-value=2.1e-28  Score=149.19  Aligned_cols=59  Identities=47%  Similarity=0.807  Sum_probs=57.8

Q ss_pred             cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412           11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus        11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      || ||+|++|+|++.|++||+||+.||||||.|||+|||++||+|||+|+  |++|.|++|+
T Consensus         1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~--gk~~~f~s~s   60 (77)
T cd00265           1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSS--GKLYEFSSPS   60 (77)
T ss_pred             CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCC--CceEEecCCC
Confidence            78 99999999999999999999999999999999999999999999999  9999999987

Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.

>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators

Probab=99.94  E-value=1.4e-27  Score=139.85  Aligned_cols=58  Identities=48%  Similarity=0.836  Sum_probs=56.1

Q ss_pred             cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCC
Q 042412           11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSM   70 (74)
Q Consensus        11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~   70 (74)
                      || ||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+  |.+++|+++
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~--g~~~~~~~~   59 (59)
T cd00120           1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPS--GKLYEFWSS   59 (59)
T ss_pred             CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCC--CCcccccCC
Confidence            68 99999999999999999999999999999999999999999999999  899999875

Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.

>cd00266 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators

Probab=99.93  E-value=1e-26  Score=143.31  Aligned_cols=59  Identities=42%  Similarity=0.786  Sum_probs=55.9

Q ss_pred             cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412           11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus        11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      || ||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+  |..+.|.+++
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~--~~~~~~~~~~   60 (83)
T cd00266           1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPS--GKLYVFWPSS   60 (83)
T ss_pred             CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCC--CCcceecCcH
Confidence            68 99999999999999999999999999999999999999999999999  7888887765

Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.

>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation

Probab=99.93  E-value=1.4e-26  Score=132.50  Aligned_cols=51  Identities=51%  Similarity=0.845  Sum_probs=46.9

Q ss_pred             EEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecC
Q 042412           17 KKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS   69 (74)
Q Consensus        17 k~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s   69 (74)
                      ++|+|+..|++||+||+.||+|||+|||+|||++||+|+|+|+  |++|+|+|
T Consensus         1 K~I~n~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~~iv~~~~--g~~~~f~s   51 (51)
T PF00319_consen    1 KRIENKSRRKVTFSKRKKGLFKKASELSTLCGVDVALIVFSPD--GKLYTFPS   51 (51)
T ss_dssp             S--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEEETT--SEEEEEES
T ss_pred             CCccchhHhHhHHHHHHhhhhhccceeeeecCCeEEEEEECCC--CCEEEecC
Confidence            5799999999999999999999999999999999999999999  99999997

SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....

>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]

Probab=99.83  E-value=4.4e-21  Score=141.76  Aligned_cols=68  Identities=34%  Similarity=0.468  Sum_probs=64.0

Q ss_pred             ccccccccCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412            2 LLSDYNYTMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus         2 ~~~~~k~~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      +...-|++.|| ||+|+||+|+-+|.+||+|||.|+||||+||++|+|.+|.|+|.++.  |.+|+|++|.
T Consensus        54 ~~~~~k~~~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEt--GhVyTFaTpK  122 (338)
T KOG0015|consen   54 QKDGGKKTTGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATPK  122 (338)
T ss_pred             ccCCCccccceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecC--cceEEecccc
Confidence            34556888999 99999999999999999999999999999999999999999999999  9999999885

>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]

Probab=99.48  E-value=3.4e-14  Score=108.19  Aligned_cols=61  Identities=36%  Similarity=0.518  Sum_probs=59.3

Q ss_pred             cCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412            9 TMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus         9 ~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      .||| |+.|.+|+|+.+|.+||.||+.|++|||+||++|+|.+|.+++.++.  |.++.|+.|+
T Consensus        80 ~~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~--g~v~tf~tp~  141 (412)
T COG5068          80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISEN--GLVHTFTTPK  141 (412)
T ss_pred             ccccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCC--CceeeecCCc
Confidence            6888 99999999999999999999999999999999999999999999999  9999999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	74
1tqe_P	93	Mechanism Of Recruitment Of Class Ii Histone Deacet		4e-04
1n6j_A	93	Structural Basis Of Sequence-Specific Recruitment O		4e-04
3mu6_A	71	Inhibiting The Binding Of Class Iia Histone Deacety		6e-04
1egw_A	77	Crystal Structure Of Mef2a Core Bound To Dna Length		6e-04
3kov_A	90	Structure Of Mef2a Bound To Dna Reveals A Completel		7e-04

>pdb|1TQE|P Chain P, Mechanism Of Recruitment Of Class Ii Histone Deacetylases By Myocyte Enhancer Factor-2 Length = 93

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 25/37 (67%)
Query: 25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
          RQVT+ KRK  L+KKA E+SV C  ++ LI F+   R
Sbjct: 17 RQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANR 53

>pdb|1N6J|A Chain A, Structural Basis Of Sequence-Specific Recruitment Of Histone Deacetylases By Myocyte Enhancer Factor-2 Length = 93

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 25/37 (67%)
Query: 25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
          RQVT+ KRK  L+KKA E+SV C  ++ LI F+   R
Sbjct: 16 RQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANR 52

>pdb|3MU6|A Chain A, Inhibiting The Binding Of Class Iia Histone Deacetylases To Myocyte Enhancer Factor-2 By Small Molecules Length = 71

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 26/37 (70%)
Query: 25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
          RQVT+ KRK  L+KKA E+SV C  ++ LI F+ + +
Sbjct: 16 RQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNK 52

>pdb|1EGW|A Chain A, Crystal Structure Of Mef2a Core Bound To Dna Length = 77

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 26/37 (70%)
Query: 25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
          RQVT+ KRK  L+KKA E+SV C  ++ LI F+ + +
Sbjct: 16 RQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNK 52

>pdb|3KOV|A Chain A, Structure Of Mef2a Bound To Dna Reveals A Completely Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND RECRUITS Transcription Co-Factors Length = 90

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 26/37 (70%)
Query: 25 RQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKR 61
          RQVT+ KRK  L+KKA E+SV C  ++ LI F+ + +
Sbjct: 16 RQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNK 52

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	74
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	2e-16
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	3e-16
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	4e-16
1hbx_A	92	SRF, serum response factor; gene regulation, trans	6e-16
1egw_A	77	MADS box transcription enhancer factor 2, polypept	8e-16

>1mnm_A Protein (MCM1 transcriptional regulator); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: d.88.1.1 Length = 100

 Score = 66.4 bits (162), Expect = 2e-16
 Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 9  TMG-KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKF 67
              +KIEIK I +   R VT++KRK  ++KKA E+SV  G  ++L+  S T  G    F
Sbjct: 15 QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSET--GLVYTF 72

Query: 68 CS 69
           +
Sbjct: 73 ST 74

>1k6o_B SRF, serum response factor; protein/DNA complex, transcription factor, combinatorial gene regulation, ETS proteins, MADS-box proteins; 3.19A {Homo sapiens} SCOP: d.88.1.1 Length = 103

 Score = 66.0 bits (161), Expect = 3e-16
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 9  TMG-KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKF 67
          T G  KI+++ I +   R  T++KRK  ++KKA E+S   G  ++L+  S T  G    F
Sbjct: 8  TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTF 65

Query: 68 CS 69
           +
Sbjct: 66 AT 67

>3p57_A Myocyte-specific enhancer factor 2A; protein-DNA complex, transcription factor, transcriptional activation, zinc finger; HET: DNA; 2.19A {Homo sapiens} PDB: 3kov_A* 1tqe_P 1n6j_A Length = 90

 Score = 65.1 bits (159), Expect = 4e-16
 Identities = 25/58 (43%), Positives = 37/58 (63%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
          KKI+I +I D + RQVT+ KRK  L+KKA E+SV C  ++ LI F+     +  ++ S
Sbjct: 3  KKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNS--SNKLFQYAS 58

>1hbx_A SRF, serum response factor; gene regulation, transcription complex; 3.15A {Homo sapiens} SCOP: d.88.1.1 PDB: 1srs_A* Length = 92

 Score = 64.8 bits (158), Expect = 6e-16
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 9  TMG-KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKF 67
          T G  KI+++ I +   R  T++KRK  ++KKA E+S   G  ++L+  S T  G    F
Sbjct: 9  TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTF 66

Query: 68 CS 69
           +
Sbjct: 67 AT 68

>1egw_A MADS box transcription enhancer factor 2, polypeptide A; MADS-box transcription factor, DNA/protein complex, transcription/DNA; HET: DNA; 1.50A {Homo sapiens} SCOP: d.88.1.1 PDB: 1c7u_A 3mu6_A* Length = 77

 Score = 64.0 bits (156), Expect = 8e-16
 Identities = 25/58 (43%), Positives = 38/58 (65%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
          KKI+I +I D + RQVT+ KRK  L+KKA E+SV C  ++ LI F+ +   +  ++ S
Sbjct: 3  KKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYAS 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	74
1hbx_A	92	SRF, serum response factor; gene regulation, trans	99.97
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	99.97
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	99.97
1egw_A	77	MADS box transcription enhancer factor 2, polypept	99.97
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	99.96

>1hbx_A SRF, serum response factor; gene regulation, transcription complex; 3.15A {Homo sapiens} SCOP: d.88.1.1 PDB: 1srs_A*

Probab=99.97  E-value=6.6e-33  Score=173.98  Aligned_cols=66  Identities=33%  Similarity=0.468  Sum_probs=62.5

Q ss_pred             ccccccCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412            4 SDYNYTMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus         4 ~~~k~~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      ...|++||| ||+|++|+|+.+|++||+||+.||||||+|||+||||+||||||+|+  |++|+|+||+
T Consensus         4 ~~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~V~livfs~~--gk~~~f~s~~   70 (92)
T 1hbx_A            4 KPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATRK   70 (92)
T ss_dssp             --CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTT--SCEEEEECGG
T ss_pred             CcCCCCCCcceEEEEEecChhHHHHHHHHhhhhHHHHHHHHHhhcCCceEEEEECCC--CCEEEecCCC
Confidence            356899999 99999999999999999999999999999999999999999999999  9999999985

>1k6o_B SRF, serum response factor; protein/DNA complex, transcription factor, combinatorial gene regulation, ETS proteins, MADS-box proteins; 3.19A {Homo sapiens} SCOP: d.88.1.1

Probab=99.97  E-value=1.8e-32  Score=174.97  Aligned_cols=66  Identities=33%  Similarity=0.468  Sum_probs=62.4

Q ss_pred             ccccccCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412            4 SDYNYTMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus         4 ~~~k~~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      ...|++||| ||+|++|+|+.+|++||+||+.||||||+|||+||||+||||||+|+  |++|.|+|++
T Consensus         3 ~~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~--gk~~~f~s~~   69 (103)
T 1k6o_B            3 KPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATRK   69 (103)
T ss_dssp             --CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECSS--SCEEEEECGG
T ss_pred             CCCCCCCCcceeEEEEecCchHHHHhHhHhhHhHHHHHHHHHhhhCCceEEEEEeCC--CCeeeecCcc
Confidence            356889999 99999999999999999999999999999999999999999999999  9999999985

>1mnm_A Protein (MCM1 transcriptional regulator); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: d.88.1.1

Probab=99.97  E-value=5.1e-32  Score=172.11  Aligned_cols=65  Identities=38%  Similarity=0.533  Sum_probs=60.1

Q ss_pred             cccccCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412            5 DYNYTMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus         5 ~~k~~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      ..+++||| ||+|++|+|+.+|++||+||+.||||||+|||+||||+||||||+|+  |++|.|+||+
T Consensus        11 ~~~~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~--gk~~~f~sps   76 (100)
T 1mnm_A           11 NNGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSET--GLVYTFSTPK   76 (100)
T ss_dssp             ----CCCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTT--CCEEEEECTT
T ss_pred             CCCCCCCccceeeEEecCcchhhhhhhHhhhhHHHHHHHHHHhcCCcEEEEEecCC--CCcceecCCC
Confidence            35789999 99999999999999999999999999999999999999999999999  9999999995

>1egw_A MADS box transcription enhancer factor 2, polypeptide A; MADS-box transcription factor, DNA/protein complex, transcription/DNA; HET: DNA; 1.50A {Homo sapiens} SCOP: d.88.1.1 PDB: 1c7u_A 3mu6_A*

Probab=99.97  E-value=2.9e-31  Score=161.74  Aligned_cols=59  Identities=42%  Similarity=0.724  Sum_probs=57.6

Q ss_pred             cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412           11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus        11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      || ||+|++|+|+.+|++||+||++||+|||+|||+||||+||||||+++  |++|.|+|++
T Consensus         1 GR~Ki~ik~I~n~~~R~vTfsKRr~GL~KKA~ELsvLCdaeV~livfs~~--gk~~~~~s~~   60 (77)
T 1egw_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYASTD   60 (77)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTT--CCEEEEESSC
T ss_pred             CCceeeeEEecCchHHHHHHHHhHHHHHHHHHHHhcccCCeEEEEEECCC--CCEeeCCCCC
Confidence            78 99999999999999999999999999999999999999999999999  9999999875

>3p57_A Myocyte-specific enhancer factor 2A; protein-DNA complex, transcription factor, transcriptional activation, zinc finger; HET: DNA; 2.19A {Homo sapiens} PDB: 3kov_A* 1tqe_P 1n6j_A

Probab=99.96  E-value=9.6e-31  Score=163.59  Aligned_cols=59  Identities=42%  Similarity=0.724  Sum_probs=57.6

Q ss_pred             cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412           11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus        11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      || ||+|++|+|+.+|++||+||+.||||||+|||+||||+||||||+|+  |++|+|+|++
T Consensus         1 GR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valiifs~~--gk~~~f~s~~   60 (90)
T 3p57_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYASTD   60 (90)
T ss_dssp             CCSCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTT--CCEEEEESSC
T ss_pred             CCCcceeEEecCchHHHHHHHHhhhhHHHHHHHHHhccCCceEEEEECCC--CCEEEeCCCC
Confidence            89 99999999999999999999999999999999999999999999999  9999999975

---

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	74
d1mnma_	85	d.88.1.1 (A:) MCM1 transcriptional regulator {Bake	8e-16
d1egwa_	71	d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {	9e-16
d1srsa_	84	d.88.1.1 (A:) Serum response factor (SRF) core {Hu	1e-15

>d1mnma_ d.88.1.1 (A:) MCM1 transcriptional regulator {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 85

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: MCM1 transcriptional regulator
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 63.2 bits (154), Expect = 8e-16
 Identities = 24/58 (41%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
          +KIEIK I +   R VT++KRK  ++KKA E+SV  G  ++L+  S T  G    F +
Sbjct: 5  RKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSET--GLVYTFST 60

>d1egwa_ d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: Myocyte enhancer factor Mef2a core
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.7 bits (153), Expect = 9e-16
 Identities = 25/58 (43%), Positives = 38/58 (65%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
          KKI+I +I D + RQVT+ KRK  L+KKA E+SV C  ++ LI F+ +   +  ++ S
Sbjct: 3  KKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYAS 58

>d1srsa_ d.88.1.1 (A:) Serum response factor (SRF) core {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: Serum response factor (SRF) core
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.8 bits (153), Expect = 1e-15
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 12 KKIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCS 69
           KI+++ I +   R  T++KRK  ++KKA E+S   G  ++L+  S T  G    F +
Sbjct: 5  VKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFAT 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	74
d1egwa_	71	Myocyte enhancer factor Mef2a core {Human (Homo sa	99.97
d1srsa_	84	Serum response factor (SRF) core {Human (Homo sapi	99.97
d1mnma_	85	MCM1 transcriptional regulator {Baker's yeast (Sac	99.96

>d1egwa_ d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: Myocyte enhancer factor Mef2a core
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2e-32  Score=163.44  Aligned_cols=59  Identities=42%  Similarity=0.724  Sum_probs=57.7

Q ss_pred             cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412           11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus        11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      || ||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+|+  |++|+|+||+
T Consensus         1 GR~Ki~ik~Ie~~~~R~vTFsKRk~GL~KKa~ELs~LC~~~valiv~s~~--gk~~~f~s~~   60 (71)
T d1egwa_           1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYASTD   60 (71)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTT--CCEEEEESSC
T ss_pred             CCccceEEeccCCchheeehhHhhhhHHHHHHHHhhccCCcEEEEEEcCC--CCEEEeeCCC
Confidence            89 99999999999999999999999999999999999999999999999  9999999985

>d1srsa_ d.88.1.1 (A:) Serum response factor (SRF) core {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: Serum response factor (SRF) core
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=9.9e-32  Score=164.87  Aligned_cols=61  Identities=36%  Similarity=0.538  Sum_probs=59.4

Q ss_pred             cCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412            9 TMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus         9 ~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      ++|| ||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+|+  |++|+|+||+
T Consensus         1 ~~GR~Ki~i~~Ie~~~~R~vTFsKRr~GL~KKa~ELs~Lc~~~v~liv~s~~--gk~~~f~s~~   62 (84)
T d1srsa_           1 TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATRK   62 (84)
T ss_dssp             CCCCCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTT--CCEEEEECGG
T ss_pred             CCCCceeeEEeecCcchhhhhhHHhhhhHHHHHHHHhcccCCcEEEEEEcCC--CCEEEeeCCC
Confidence            5899 99999999999999999999999999999999999999999999999  9999999986

>d1mnma_ d.88.1.1 (A:) MCM1 transcriptional regulator {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: MCM1 transcriptional regulator
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.96  E-value=1e-30  Score=160.57  Aligned_cols=60  Identities=42%  Similarity=0.581  Sum_probs=58.4

Q ss_pred             Ccc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412           10 MGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK   71 (74)
Q Consensus        10 mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~   71 (74)
                      .|| ||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+|+  |++|+|+||+
T Consensus         2 k~R~Ki~i~~I~~~~~R~vTFsKRr~GL~KKa~ELsvLc~a~vaviv~s~~--gk~~~f~sp~   62 (85)
T d1mnma_           2 KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSET--GLVYTFSTPK   62 (85)
T ss_dssp             CCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTT--CCEEEEECTT
T ss_pred             CCccceEEEEecCCchhhhhhHHHHhhHHHHHHHHhccCCCcEEEEEEcCC--CCEEeccCCC
Confidence            488 99999999999999999999999999999999999999999999999  9999999986