Citrus Sinensis ID: 038783

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70------
Protein Sequence
MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEEEEEEccccccEEEEEEccccHHHHcEEEEEEEccEEEEEEEcccccEEEEccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEcccccEEEEEcc
Coil and Loop (DISEMBL)
mefpkqnpesssqskkigrgkiEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSsrgrlyeyann
Flexible Loop (DISEMBL)
mefpkqnpesssqskkigrgkieikrienttnrqvtfcKRRNGLLKKAYELSVLCDAEVALIvfssrgrlyeyann
Low Complexity Region (SEG)
MEFPKQNPESSSQSkkigrgkieikrieNTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN
Disordered region (IsUnstruct)
**********************EIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEY***
Disordered Region (DISOPRED)
***********************IKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEY***
Disordered Region (DISEMBL)
******************RGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN
Disordered Region (DISPRO)
********************KIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN
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	76	2.2.26 [Sep-21-2011]
Q40885	242	Floral homeotic protein A	N/A	no	1.0	0.314	0.842	2e-30
P29385	246	Agamous-like MADS-box pro	yes	no	0.894	0.276	0.897	4e-30
Q43585	248	Floral homeotic protein A	N/A	no	1.0	0.306	0.828	4e-30
Q40872	242	Floral homeotic protein A	N/A	no	1.0	0.314	0.815	1e-29
P29381	248	Agamous-like MADS-box pro	no	no	0.828	0.254	0.936	1e-29
Q40168	248	Floral homeotic protein A	N/A	no	1.0	0.306	0.802	2e-29
Q01540	252	Floral homeotic protein A	N/A	no	0.868	0.261	0.924	2e-29
Q40704	236	MADS-box transcription fa	yes	no	0.789	0.254	0.983	3e-29
P17839	252	Floral homeotic protein A	no	no	0.868	0.261	0.924	5e-29
Q38836	230	Agamous-like MADS-box pro	no	no	0.789	0.260	0.95	2e-28

>sp|Q40885|AG_PETHY Floral homeotic protein AGAMOUS OS=Petunia hybrida GN=AG1 PE=1 SV=1

 Score =  130 bits (327), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 64/76 (84%), Positives = 66/76 (86%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEF        S  +K+GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFQSDLTREISPQRKLGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFSSRGRLYEYANN
Sbjct: 61 LIVFSSRGRLYEYANN 76

Probable transcription factor involved in regulating genes that determines stamen and carpel development in wild-type flowers.
Petunia hybrida (taxid: 4102)

>sp|P29385|AGL5_ARATH Agamous-like MADS-box protein AGL5 OS=Arabidopsis thaliana GN=AGL5 PE=1 SV=1

 Score =  129 bits (325), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 61/68 (89%), Positives = 65/68 (95%)

Query: 9  ESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRG 68
          E +  SKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVAL++FS+RG
Sbjct: 8  EVAESSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALVIFSTRG 67

Query: 69 RLYEYANN 76
          RLYEYANN
Sbjct: 68 RLYEYANN 75

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q43585|AG_TOBAC Floral homeotic protein AGAMOUS OS=Nicotiana tabacum GN=AG1 PE=2 SV=1

 Score =  129 bits (325), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 63/76 (82%), Positives = 66/76 (86%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          M+F        S  +K+GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MDFQSDLTREISPQRKLGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFSSRGRLYEYANN
Sbjct: 61 LIVFSSRGRLYEYANN 76

Probable transcription factor involved in regulating genes that determines stamen and carpel development in wild-type flowers.

Nicotiana tabacum (taxid: 4097)

>sp|Q40872|AG_PANGI Floral homeotic protein AGAMOUS OS=Panax ginseng GN=AG2 PE=2 SV=1

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 66/76 (86%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          M F      + S  +K+GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MSFYDDQSGNLSPQRKLGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFS+RGRLYEYANN
Sbjct: 61 LIVFSTRGRLYEYANN 76

Probable transcription factor involved in regulating genes that determines stamen and carpel development in wild-type flowers.

Panax ginseng (taxid: 4054)

>sp|P29381|AGL1_ARATH Agamous-like MADS-box protein AGL1 OS=Arabidopsis thaliana GN=AGL1 PE=1 SV=1

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 59/63 (93%), Positives = 63/63 (100%)

Query: 14 SKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEY 73
          SKK+GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVAL++FS+RGRLYEY
Sbjct: 13 SKKLGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALVIFSTRGRLYEY 72

Query: 74 ANN 76
          ANN
Sbjct: 73 ANN 75

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q40168|AG_SOLLC Floral homeotic protein AGAMOUS OS=Solanum lycopersicum GN=AG1 PE=2 SV=1

 Score =  127 bits (320), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 61/76 (80%), Positives = 66/76 (86%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          M+F        S  +K+GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MDFQSDLTREISPQRKLGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60

Query: 61 LIVFSSRGRLYEYANN 76
          L+VFS+RGRLYEYANN
Sbjct: 61 LVVFSNRGRLYEYANN 76

Probable transcription factor involved in regulating genes that determines stamen and carpel development in wild-type flowers.

Solanum lycopersicum (taxid: 4081)

>sp|Q01540|AG_BRANA Floral homeotic protein AGAMOUS OS=Brassica napus GN=AG1 PE=2 SV=1

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 61/66 (92%), Positives = 63/66 (95%)

Query: 11 SSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRL 70
          SS  +K GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRL
Sbjct: 11 SSPQRKAGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRL 70

Query: 71 YEYANN 76
          YEY+NN
Sbjct: 71 YEYSNN 76

Probable transcription factor involved in regulating genes that determines stamen and carpel development in wild-type flowers.

Brassica napus (taxid: 3708)

>sp|Q40704|MADS3_ORYSJ MADS-box transcription factor 3 OS=Oryza sativa subsp. japonica GN=MADS3 PE=2 SV=1

 Score =  126 bits (317), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 59/60 (98%), Positives = 60/60 (100%)

Query: 17 IGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
          +GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN
Sbjct: 1  MGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 60

Probable transcription factor involved in the development of floral organs. Acts as C-class protein in association with MADS58. Involved in the control of lodicule number (whorl 2), stamen specification (whorl 3) and floral meristem determinacy (whorl 4), but not in the regulation of carpel morphogenesis. Plays a more predominant role in controlling lodicule development and in specifying stamen identity than MADS58.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P17839|AG_ARATH Floral homeotic protein AGAMOUS OS=Arabidopsis thaliana GN=AG PE=1 SV=2

 Score =  126 bits (316), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 61/66 (92%), Positives = 63/66 (95%)

Query: 11 SSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRL 70
          SS  +K GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRL
Sbjct: 11 SSPLRKSGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRL 70

Query: 71 YEYANN 76
          YEY+NN
Sbjct: 71 YEYSNN 76

Probable transcription factor involved in the control of organ identity during the early development of flowers. Is required for normal development of stamens and carpels in the wild-type flower. Plays a role in maintaining the determinacy of the floral meristem. Acts as C class cadastral protein by repressing the A class floral homeotic genes like APETALA1. Forms an heterodimer via the K-box domain with either SEPALATTA1/AGL2, SEPALATTA2/AGL4, SEPALLATA3/AGL9 or AGL6 that could be involved in genes regulation during floral meristem development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q38836|AGL11_ARATH Agamous-like MADS-box protein AGL11 OS=Arabidopsis thaliana GN=AGL11 PE=1 SV=1

 Score =  124 bits (311), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 57/60 (95%), Positives = 60/60 (100%)

Query: 17 IGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
          +GRGKIEIKRIEN+TNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFS+RGRLYEYANN
Sbjct: 1  MGRGKIEIKRIENSTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSTRGRLYEYANN 60

Probable transcription factor.

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	76
116078101	257	MADS-box protein [Citrus unshiu]	1.0	0.295	1.0	4e-37
110559304	244	SHATTERPROOF-like [Prunus persica] gi|15	0.986	0.307	0.934	2e-33
390979684	246	transcription factor MADS5 [Prunus avium	0.986	0.304	0.934	2e-33
295854727	246	mutant SHATTERPROOF-like protein [Prunus	0.986	0.304	0.934	2e-33
295854725	246	SHATTERPROOF-like protein [Prunus serrul	0.986	0.304	0.934	2e-33
336093333	244	SHATTERPPOOF-like protein [Prunus trilob	0.986	0.307	0.934	2e-33
33308109	242	AGAMOUS-like protein [Malus x domestica]	0.986	0.309	0.934	2e-33
427192297	242	transcription factor [Pyrus pyrifolia]	0.986	0.309	0.934	3e-33
122938399	234	MADS-box protein MADS7 [Gossypium hirsut	0.986	0.320	0.934	6e-33
354683684	241	AGAMOUS-like protein [Mangifera indica]	0.986	0.311	0.921	7e-33

>gi|116078101|dbj|BAF34914.1| MADS-box protein [Citrus unshiu]

 Score =  158 bits (399), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 76/76 (100%), Positives = 76/76 (100%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 11 MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 70

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFSSRGRLYEYANN
Sbjct: 71 LIVFSSRGRLYEYANN 86

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|110559304|gb|ABG75908.1| SHATTERPROOF-like [Prunus persica] gi|156081602|gb|ABU48614.1| SHATTERPROOF-like protein [Prunus persica] gi|219664385|gb|ACL31234.1| PLENA-like MADS-box protein [Prunus persica]

 Score =  146 bits (368), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP Q PESSSQ +KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPNQAPESSSQ-RKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFS+RGRLYEYANN
Sbjct: 60 LIVFSTRGRLYEYANN 75

Source: Prunus persica

Species: Prunus persica

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|390979684|gb|AFM30905.1| transcription factor MADS5 [Prunus avium]

 Score =  146 bits (368), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP Q PESSSQ +KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPNQAPESSSQ-RKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFS+RGRLYEYANN
Sbjct: 60 LIVFSTRGRLYEYANN 75

Source: Prunus avium

Species: Prunus avium

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|295854727|gb|ADG45820.1| mutant SHATTERPROOF-like protein [Prunus serrulata var. lannesiana]

 Score =  146 bits (368), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP Q PESSSQ +KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPNQAPESSSQ-RKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFS+RGRLYEYANN
Sbjct: 60 LIVFSTRGRLYEYANN 75

Source: Prunus serrulata var. lannesiana

Species: Prunus serrulata

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|295854725|gb|ADG45819.1| SHATTERPROOF-like protein [Prunus serrulata var. lannesiana]

 Score =  146 bits (368), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP Q PESSSQ +KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPNQAPESSSQ-RKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFS+RGRLYEYANN
Sbjct: 60 LIVFSTRGRLYEYANN 75

Source: Prunus serrulata var. lannesiana

Species: Prunus serrulata

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|336093333|gb|AEI01160.1| SHATTERPPOOF-like protein [Prunus triloba]

 Score =  146 bits (368), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP Q PESSSQ +KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPNQAPESSSQ-RKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFS+RGRLYEYANN
Sbjct: 60 LIVFSTRGRLYEYANN 75

Source: Prunus triloba

Species: Prunus triloba

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|33308109|gb|AAQ03090.1| AGAMOUS-like protein [Malus x domestica]

 Score =  146 bits (368), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP Q PESSSQ KK+GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPNQAPESSSQ-KKLGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFS+RGRLYEYANN
Sbjct: 60 LIVFSNRGRLYEYANN 75

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|427192297|dbj|BAM71400.1| transcription factor [Pyrus pyrifolia]

 Score =  145 bits (367), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP Q PESSSQ KK+GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPNQAPESSSQ-KKLGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFS+RGRLYEYANN
Sbjct: 60 LIVFSNRGRLYEYANN 75

Source: Pyrus pyrifolia

Species: Pyrus pyrifolia

Genus: Pyrus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|122938399|gb|ABM69045.1| MADS-box protein MADS7 [Gossypium hirsutum]

 Score =  144 bits (364), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP  +PESSSQ KK+GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPNLDPESSSQ-KKMGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          LIVFSSRGRLYEYANN
Sbjct: 60 LIVFSSRGRLYEYANN 75

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|354683684|gb|AER34989.1| AGAMOUS-like protein [Mangifera indica]

 Score =  144 bits (363), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 70/76 (92%), Positives = 71/76 (93%), Gaps = 1/76 (1%)

Query: 1  MEFPKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
          MEFP Q PESSS  KK GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct: 1  MEFPSQEPESSSH-KKTGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query: 61 LIVFSSRGRLYEYANN 76
          L+VFSSRGRLYEYANN
Sbjct: 60 LVVFSSRGRLYEYANN 75

Source: Mangifera indica

Species: Mangifera indica

Genus: Mangifera

Family: Anacardiaceae

Order: Sapindales

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	76
UNIPROTKB|Q9ZS29	246	GAGA2 "MADS-box protein, GAGA2	0.986	0.304	0.710	1.5e-21
UNIPROTKB|Q9ZS30	264	gaga1 "MADS-box protein, GAGA1	0.986	0.284	0.697	4.9e-21
UNIPROTKB|Q40885	242	AG1 "Floral homeotic protein A	0.631	0.198	1.0	6.3e-21
TAIR|locus:2140578	256	STK "AT4G09960" [Arabidopsis t	0.631	0.187	0.958	3.5e-20
UNIPROTKB|Q2QW53	270	MADS13 "MADS-box transcription	0.631	0.177	0.958	4.4e-20
UNIPROTKB|Q40882	228	fbp11 "Fbp11 protein" [Petunia	0.631	0.210	0.916	1.2e-19
UNIPROTKB|Q43616	225	fbp7 "Floral binding protein n	0.631	0.213	0.875	6.5e-19
UNIPROTKB|Q9ATF1	245	FBP9 "MADS-box transcription f	0.618	0.191	0.829	2.9e-16
UNIPROTKB|Q6EU39	250	MADS6 "MADS-box transcription	0.618	0.188	0.829	3.7e-16
UNIPROTKB|Q7XUN2	249	MADS17 "MADS-box transcription	0.618	0.188	0.829	3.7e-16

UNIPROTKB|Q9ZS29 GAGA2 "MADS-box protein, GAGA2" [Gerbera hybrid cultivar (taxid:18101)]

 Score = 252 (93.8 bits), Expect = 1.5e-21, P = 1.5e-21
 Identities = 54/76 (71%), Positives = 55/76 (72%)

Query:     1 MEFPKQNPESSSQSXXXXXXXXXXXXXXNTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
             M FP  + E S Q               NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct:     1 MSFPNDSGEMSPQRKLGRGKIEIKRIE-NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 59

Query:    61 LIVFSSRGRLYEYANN 76
             LIVFSSRGRLYEYANN
Sbjct:    60 LIVFSSRGRLYEYANN 75

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q9ZS30 gaga1 "MADS-box protein, GAGA1" [Gerbera hybrid cultivar (taxid:18101)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 53/76 (69%), Positives = 54/76 (71%)

Query:     1 MEFPKQNPESSSQSXXXXXXXXXXXXXXNTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 60
             M FP    + S Q               NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA
Sbjct:    18 MSFPDDTGDMSPQRKMGKGKIEIKRIE-NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVA 76

Query:    61 LIVFSSRGRLYEYANN 76
             LIVFSSRGRLYEYANN
Sbjct:    77 LIVFSSRGRLYEYANN 92

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q40885 AG1 "Floral homeotic protein AGAMOUS" [Petunia x hybrida (taxid:4102)]

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 48/48 (100%), Positives = 48/48 (100%)

Query:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
             NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN
Sbjct:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2140578 STK "AT4G09960" [Arabidopsis thaliana (taxid:3702)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 46/48 (95%), Positives = 48/48 (100%)

Query:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
             N+TNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFS+RGRLYEYANN
Sbjct:    39 NSTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSTRGRLYEYANN 86

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

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0048440 "carpel development" evidence=IMP

GO:0048481 "ovule development" evidence=IGI;RCA;IMP

GO:0048316 "seed development" evidence=IGI

GO:0080155 "regulation of double fertilization forming a zygote and endosperm" evidence=IGI

GO:0009827 "plant-type cell wall modification" evidence=RCA

GO:0009860 "pollen tube growth" evidence=RCA

GO:0009886 "post-embryonic morphogenesis" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0048441 "petal development" evidence=RCA

GO:0048443 "stamen development" evidence=RCA

GO:0048507 "meristem development" evidence=RCA

UNIPROTKB|Q2QW53 MADS13 "MADS-box transcription factor 13" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 46/48 (95%), Positives = 48/48 (100%)

Query:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
             NTT+RQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEY+NN
Sbjct:    13 NTTSRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYSNN 60

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

GO:0005515 "protein binding" evidence=IPI

GO:0048283 "indeterminate inflorescence morphogenesis" evidence=IMP

GO:0048481 "ovule development" evidence=IMP

UNIPROTKB|Q40882 fbp11 "Fbp11 protein" [Petunia x hybrida (taxid:4102)]

 Score = 234 (87.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 44/48 (91%), Positives = 47/48 (97%)

Query:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
             N TNRQVTFCKRRNGLLKKAYELSVLCDAE+ALIVFS+RGR+YEYANN
Sbjct:    13 NNTNRQVTFCKRRNGLLKKAYELSVLCDAEIALIVFSTRGRVYEYANN 60

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q43616 fbp7 "Floral binding protein number 7" [Petunia x hybrida (taxid:4102)]

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 42/48 (87%), Positives = 47/48 (97%)

Query:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
             N TNRQVTFCKRRNGLLKKAYELSVLC+AE+ALIVFS+RGR+YEY+NN
Sbjct:    13 NNTNRQVTFCKRRNGLLKKAYELSVLCEAEIALIVFSTRGRVYEYSNN 60

GO:0005515 "protein binding" evidence=IPI

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

 Score = 202 (76.2 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 39/47 (82%), Positives = 43/47 (91%)

Query:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
             N  NRQVTF KRRNGLLKKAYELSVLCDAEVALI+FSSRG+LYE+ +
Sbjct:    13 NKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSSRGKLYEFCS 59

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q6EU39 MADS6 "MADS-box transcription factor 6" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 39/47 (82%), Positives = 43/47 (91%)

Query:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
             N  NRQVTF KRRNGLLKKAYELSVLCDAEVALI+FSSRG+LYE+ +
Sbjct:    13 NKINRQVTFSKRRNGLLKKAYELSVLCDAEVALIIFSSRGKLYEFGS 59

GO:0005515 "protein binding" evidence=IPI

GO:0010022 "meristem determinacy" evidence=IMP

GO:0010093 "specification of floral organ identity" evidence=IMP

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

UNIPROTKB|Q7XUN2 MADS17 "MADS-box transcription factor 17" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 39/47 (82%), Positives = 43/47 (91%)

Query:    29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
             N  NRQVTF KRRNGLLKKAYELSVLCDAEVALI+FSSRG+LYE+ +
Sbjct:    13 NKINRQVTFSKRRNGLLKKAYELSVLCDAEVALIIFSSRGKLYEFGS 59

GO:0010093 "specification of floral organ identity" evidence=IMP

---

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)
P29385	AGL5_ARATH	No assigned EC number	0.8970	0.8947	0.2764	yes	no
Q40704	MADS3_ORYSJ	No assigned EC number	0.9833	0.7894	0.2542	yes	no
Q01540	AG_BRANA	No assigned EC number	0.9242	0.8684	0.2619	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: PTAG2 SubName- Full=AGAMOUS homolog; (238 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	76
cd00265	77	cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer fa	2e-39
smart00432	59	smart00432, MADS, MADS domain	5e-34
cd00120	59	cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and	4e-32
cd00266	83	cd00266, MADS_SRF_like, SRF-like/Type I subfamily	2e-26
pfam00319	51	pfam00319, SRF-TF, SRF-type transcription factor (	3e-25
COG5068	412	COG5068, ARG80, Regulator of arginine metabolism a	3e-12

>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 =  124 bits (313), Expect = 2e-39
 Identities = 49/59 (83%), Positives = 56/59 (94%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
          GRGKIEIKRIEN+TNRQVTF KRRNGLLKKA+ELSVLCDAEVALI+FSS G+LYE+++ 
Sbjct: 1  GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSP 59

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|197721 smart00432, MADS, MADS domain

 Score =  109 bits (276), Expect = 5e-34
 Identities = 48/57 (84%), Positives = 51/57 (89%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 74
          GR KIEIKRIEN TNRQVTF KRRNGL KKA+ELSVLCDAEVALIVFS  G+LYE+A
Sbjct: 1  GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFA 57

Length = 59

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

 Score =  105 bits (264), Expect = 4e-32
 Identities = 46/57 (80%), Positives = 50/57 (87%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 74
          GRGKIEIKRIEN T+RQVTF KRRNGL KKA ELSVLCDAEVA+IVFS  G+LYE+ 
Sbjct: 1  GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFW 57

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 = 91.6 bits (228), Expect = 2e-26
 Identities = 37/57 (64%), Positives = 42/57 (73%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 74
          GR KI+IKRIEN   R VTF KRR GL KKA ELS LC AEVA+IV+S  G+LY + 
Sbjct: 1  GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFW 57

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 = 87.8 bits (218), Expect = 3e-25
 Identities = 39/51 (76%), Positives = 47/51 (92%)

Query: 25 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          KRIEN +NRQVTF KRRNG+ KKA+ELSVLCDAEVA+I+FSS G+LYEY++
Sbjct: 1  KRIENKSNRQVTFSKRRNGIFKKAHELSVLCDAEVAVIIFSSTGKLYEYSS 51

Length = 51

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

 Score = 59.6 bits (144), Expect = 3e-12
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 6   QNPESSSQSK-KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVF 64
           Q      +    +   KI I  I N T R VTF KR++G+ KKA+ELSVL   EV L+V 
Sbjct: 69  QTKAQLQKFLISVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVI 128

Query: 65  SSRGRLYEYA 74
           S  G ++ + 
Sbjct: 129 SENGLVHTFT 138

Length = 412

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	76
smart00432	59	MADS MADS domain.	99.96
KOG0014	195	consensus MADS box transcription factor [Transcrip	99.96
cd00265	77	MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-li	99.95
cd00120	59	MADS MADS: MCM1, Agamous, Deficiens, and SRF (seru	99.95
cd00266	83	MADS_SRF_like SRF-like/Type I subfamily of MADS (M	99.94
PF00319	51	SRF-TF: SRF-type transcription factor (DNA-binding	99.92
KOG0015	338	consensus Regulator of arginine metabolism and rel	99.87
COG5068	412	ARG80 Regulator of arginine metabolism and related	99.56
PF13540	30	RCC1_2: Regulator of chromosome condensation (RCC1	83.43

>smart00432 MADS MADS domain

Probab=99.96  E-value=1.4e-29  Score=151.15  Aligned_cols=59  Identities=81%  Similarity=1.157  Sum_probs=58.1

Q ss_pred             cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ||+||+|++|+|++.|++||+||+.||+|||+|||+||||+||+|||+|+|++|+|++|
T Consensus         1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~p   59 (59)
T smart00432        1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP   59 (59)
T ss_pred             CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccCC
Confidence            89999999999999999999999999999999999999999999999999999999986

>KOG0014 consensus MADS box transcription factor [Transcription]

Probab=99.96  E-value=9.1e-30  Score=174.27  Aligned_cols=60  Identities=73%  Similarity=1.158  Sum_probs=58.8

Q ss_pred             ccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           17 IGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        17 mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      |||+||+|++|+|+..|++||+||+.||||||+||||||||+||+|||+|+|++|.|+++
T Consensus         1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~   60 (195)
T KOG0014|consen    1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSS   60 (195)
T ss_pred             CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCc
Confidence            899999999999999999999999999999999999999999999999999999999874

>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=3.8e-29  Score=155.11  Aligned_cols=59  Identities=83%  Similarity=1.220  Sum_probs=57.9

Q ss_pred             cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ||+||+|++|+|+..|++||+||+.||||||.|||+||||+||+|||+|+|++|+|+++
T Consensus         1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~   59 (77)
T cd00265           1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSP   59 (77)
T ss_pred             CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCC
Confidence            89999999999999999999999999999999999999999999999999999999985

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=99.95  E-value=1.3e-28  Score=146.95  Aligned_cols=59  Identities=78%  Similarity=1.149  Sum_probs=57.8

Q ss_pred             cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+|++++|+++
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~~   59 (59)
T cd00120           1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWSS   59 (59)
T ss_pred             CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccCC
Confidence            79999999999999999999999999999999999999999999999999999999975

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=99.94  E-value=2e-27  Score=148.94  Aligned_cols=59  Identities=63%  Similarity=0.947  Sum_probs=57.2

Q ss_pred             cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+|+.++|+++
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~   59 (83)
T cd00266           1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPS   59 (83)
T ss_pred             CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCc
Confidence            79999999999999999999999999999999999999999999999999999999864

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=99.92  E-value=4.7e-27  Score=137.03  Aligned_cols=51  Identities=61%  Similarity=1.001  Sum_probs=47.0

Q ss_pred             EEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccC
Q 038783           25 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN   75 (76)
Q Consensus        25 k~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s   75 (76)
                      ++|+|+..|++||+||+.||+|||+|||+|||++||||||+|+|++|+|+|
T Consensus         1 K~I~n~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~~iv~~~~g~~~~f~s   51 (51)
T PF00319_consen    1 KRIENKSRRKVTFSKRKKGLFKKASELSTLCGVDVALIVFSPDGKLYTFPS   51 (51)
T ss_dssp             S--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEEETTSEEEEEES
T ss_pred             CCccchhHhHhHHHHHHhhhhhccceeeeecCCeEEEEEECCCCCEEEecC
Confidence            579999999999999999999999999999999999999999999999987

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=99.87  E-value=6.3e-23  Score=154.65  Aligned_cols=69  Identities=43%  Similarity=0.683  Sum_probs=65.0

Q ss_pred             CCCCcccccccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783            8 PESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus         8 ~~~~~~~k~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ......+++.||+||+|+||+|+..|.+||+|||.||||||+||++|+|.+|.|+|.+++|.+|+|+++
T Consensus        53 ~~~~~~k~~~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTp  121 (338)
T KOG0015|consen   53 SQKDGGKKTTGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATP  121 (338)
T ss_pred             cccCCCccccceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccc
Confidence            335567888999999999999999999999999999999999999999999999999999999999985

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

Probab=99.56  E-value=2.5e-15  Score=116.65  Aligned_cols=61  Identities=44%  Similarity=0.635  Sum_probs=59.5

Q ss_pred             cccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           16 KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        16 ~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      .|||++|.|.+|+|+.+|.+||.||+.||+|||.||++|+|.+|.++|.+++|.+|+|+++
T Consensus        80 ~~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp  140 (412)
T COG5068          80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTP  140 (412)
T ss_pred             ccccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCC
Confidence            6889999999999999999999999999999999999999999999999999999999975

>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B

Probab=83.43  E-value=1.2  Score=22.51  Aligned_cols=24  Identities=21%  Similarity=0.466  Sum_probs=16.8

Q ss_pred             ccccCceEEEEEEcCCCcEEEccCC
Q 038783           52 SVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        52 s~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ++-||....+++.+ +|++|.|+.+
T Consensus         3 ~ia~G~~ht~al~~-~g~v~~wG~n   26 (30)
T PF13540_consen    3 QIACGGYHTCALTS-DGEVYCWGDN   26 (30)
T ss_dssp             EEEEESSEEEEEE--TTEEEEEE--
T ss_pred             EEEecCCEEEEEEc-CCCEEEEcCC
Confidence            46678787777765 6999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	76
1tqe_P	93	Mechanism Of Recruitment Of Class Ii Histone Deacet		3e-13
1n6j_A	93	Structural Basis Of Sequence-Specific Recruitment O		4e-13
3kov_A	90	Structure Of Mef2a Bound To Dna Reveals A Completel		5e-13
1c7u_A	85	Complex Of The Dna Binding Core Domain Of The Trans		6e-13
1egw_A	77	Crystal Structure Of Mef2a Core Bound To Dna Length		7e-13
3mu6_A	71	Inhibiting The Binding Of Class Iia Histone Deacety		7e-13
1mnm_A	100	Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLE		4e-08
1k6o_B	103	Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dn		7e-07
1srs_A	92	Serum Response Factor (Srf) Core Complexed With Spe		9e-07

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 39/44 (88%)
Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  RL++YA+
Sbjct: 16 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAS 59

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 39/44 (88%)
Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  RL++YA+
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAS 58

>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 = 69.3 bits (168), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 30/43 (69%), Positives = 38/43 (88%)
Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 74
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYA 57

>pdb|1C7U|A Chain A, Complex Of The Dna Binding Core Domain Of The Transcription Factor Mef2a With A 20mer Oligonucleotide Length = 85

Iteration: 1
 Score = 68.9 bits (167), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 30/44 (68%), Positives = 39/44 (88%)
Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          NRQVTF KR+ GL+KKAYELSVL DAE+ALI+F+S  +L++YA+
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYAS 58

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 30/44 (68%), Positives = 39/44 (88%)
Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA+
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAS 58

>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 = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 30/45 (66%), Positives = 39/45 (86%)
Query: 32 NRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
          NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA+ 
Sbjct: 15 NRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59

>pdb|1MNM|A Chain A, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX Crystal Structure Length = 100

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 33/46 (71%)
Query: 29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 74
          N T R VTF KR++G++KKA+ELSVL   +V L+V S  G +Y ++
Sbjct: 28 NKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFS 73

>pdb|1K6O|B Chain B, Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dna Complex Length = 103

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 29/47 (61%)
Query: 29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          N   R  TF KR+ G++KKAYELS L   +V L+V S  G +Y +A 
Sbjct: 21 NKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 67

>pdb|1SRS|A Chain A, Serum Response Factor (Srf) Core Complexed With Specific Sre Dna Length = 92

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 29/47 (61%)
Query: 29 NTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          N   R  TF KR+ G++KKAYELS L   +V L+V S  G +Y +A 
Sbjct: 22 NKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	76
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	4e-38
1hbx_A	92	SRF, serum response factor; gene regulation, trans	9e-38
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	1e-37
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	3e-37
1egw_A	77	MADS box transcription enhancer factor 2, polypept	6e-37

>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 =  121 bits (304), Expect = 4e-38
 Identities = 31/73 (42%), Positives = 46/73 (63%)

Query: 4  PKQNPESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIV 63
            +    ++  ++  R KIEIK IEN T R VTF KR++G++KKA+ELSVL   +V L+V
Sbjct: 3  DIEEGTPTNNGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLV 62

Query: 64 FSSRGRLYEYANN 76
           S  G +Y ++  
Sbjct: 63 VSETGLVYTFSTP 75

>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 =  119 bits (301), Expect = 9e-38
 Identities = 28/67 (41%), Positives = 40/67 (59%)

Query: 10 SSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGR 69
          +    K  GR KI+++ I+N   R  TF KR+ G++KKAYELS L   +V L+V S  G 
Sbjct: 3  AKPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGH 62

Query: 70 LYEYANN 76
          +Y +A  
Sbjct: 63 VYTFATR 69

>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 =  119 bits (300), Expect = 1e-37
 Identities = 37/59 (62%), Positives = 48/59 (81%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
          GR KI+I RI +  NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA+ 
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59

>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 =  119 bits (299), Expect = 3e-37
 Identities = 28/67 (41%), Positives = 40/67 (59%)

Query: 10 SSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGR 69
          +    K  GR KI+++ I+N   R  TF KR+ G++KKAYELS L   +V L+V S  G 
Sbjct: 2  AKPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGH 61

Query: 70 LYEYANN 76
          +Y +A  
Sbjct: 62 VYTFATR 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 =  117 bits (295), Expect = 6e-37
 Identities = 37/59 (62%), Positives = 48/59 (81%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
          GR KI+I RI +  NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA+ 
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	76
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=5.3e-34  Score=182.41  Aligned_cols=67  Identities=42%  Similarity=0.665  Sum_probs=62.8

Q ss_pred             CCcccccccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           10 SSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        10 ~~~~~k~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      +..++++|||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+++|++|+|+|+
T Consensus         3 ~~~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~V~livfs~~gk~~~f~s~   69 (92)
T 1hbx_A            3 AKPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATR   69 (92)
T ss_dssp             ---CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTTSCEEEEECG
T ss_pred             cCcCCCCCCcceEEEEEecChhHHHHHHHHhhhhHHHHHHHHHhhcCCceEEEEECCCCCEEEecCC
Confidence            4567899999999999999999999999999999999999999999999999999999999999985

>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=1.9e-33  Score=182.92  Aligned_cols=66  Identities=42%  Similarity=0.669  Sum_probs=62.6

Q ss_pred             CcccccccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           11 SSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        11 ~~~~k~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ..++++|||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+++|++|+|+|+
T Consensus         3 ~~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~gk~~~f~s~   68 (103)
T 1k6o_B            3 KPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATR   68 (103)
T ss_dssp             --CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECSSSCEEEEECG
T ss_pred             CCCCCCCCcceeEEEEecCchHHHHhHhHhhHhHHHHHHHHHhhhCCceEEEEEeCCCCeeeecCc
Confidence            457899999999999999999999999999999999999999999999999999999999999985

>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=2.5e-33  Score=181.60  Aligned_cols=67  Identities=46%  Similarity=0.732  Sum_probs=60.3

Q ss_pred             CCcccccccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           10 SSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        10 ~~~~~k~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      +...+++|||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+++|++|+|+||
T Consensus         9 ~~~~~~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~gk~~~f~sp   75 (100)
T 1mnm_A            9 PTNNGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTP   75 (100)
T ss_dssp             ------CCCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEECT
T ss_pred             cCCCCCCCCccceeeEEecCcchhhhhhhHhhhhHHHHHHHHHHhcCCcEEEEEecCCCCcceecCC
Confidence            4457899999999999999999999999999999999999999999999999999999999999986

>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=4.6e-32  Score=168.33  Aligned_cols=59  Identities=63%  Similarity=1.030  Sum_probs=57.9

Q ss_pred             cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ||+||+|++|+|+..|++||+||+.||+|||+|||+||||+||||||+++|++|+|+|+
T Consensus         1 GR~Ki~ik~I~n~~~R~vTfsKRr~GL~KKA~ELsvLCdaeV~livfs~~gk~~~~~s~   59 (77)
T 1egw_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST   59 (77)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTCCEEEEESS
T ss_pred             CCceeeeEEecCchHHHHHHHHhHHHHHHHHHHHhcccCCeEEEEEECCCCCEeeCCCC
Confidence            89999999999999999999999999999999999999999999999999999999975

>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=1.6e-31  Score=170.30  Aligned_cols=59  Identities=63%  Similarity=1.030  Sum_probs=58.0

Q ss_pred             cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+++|++|+|+|+
T Consensus         1 GR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valiifs~~gk~~~f~s~   59 (90)
T 3p57_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST   59 (90)
T ss_dssp             CCSCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEESS
T ss_pred             CCCcceeEEecCchHHHHHHHHhhhhHHHHHHHHHhccCCceEEEEECCCCCEEEeCCC
Confidence            89999999999999999999999999999999999999999999999999999999985

---

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	76
d1egwa_	71	d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {	3e-31
d1srsa_	84	d.88.1.1 (A:) Serum response factor (SRF) core {Hu	1e-30
d1mnma_	85	d.88.1.1 (A:) MCM1 transcriptional regulator {Bake	1e-29

>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 =  102 bits (255), Expect = 3e-31
 Identities = 37/59 (62%), Positives = 48/59 (81%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76
          GR KI+I RI +  NRQVTF KR+ GL+KKAYELSVLCD E+ALI+F+S  +L++YA+ 
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST 59

>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 =  100 bits (251), Expect = 1e-30
 Identities = 27/58 (46%), Positives = 38/58 (65%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
          GR KI+++ I+N   R  TF KR+ G++KKAYELS L   +V L+V S  G +Y +A 
Sbjct: 3  GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 60

>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 = 98.2 bits (245), Expect = 1e-29
 Identities = 31/58 (53%), Positives = 41/58 (70%)

Query: 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75
           R KIEIK IEN T R VTF KR++G++KKA+ELSVL   +V L+V S  G +Y ++ 
Sbjct: 3  ERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFST 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	76
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=4.8e-33  Score=169.26  Aligned_cols=59  Identities=63%  Similarity=1.030  Sum_probs=58.1

Q ss_pred             cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ||+||+|++|+|+..|++||+||+.||||||.|||+||||+||||||+|+|++|+|+||
T Consensus         1 GR~Ki~ik~Ie~~~~R~vTFsKRk~GL~KKa~ELs~LC~~~valiv~s~~gk~~~f~s~   59 (71)
T d1egwa_           1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST   59 (71)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTCCEEEEESS
T ss_pred             CCccceEEeccCCchheeehhHhhhhHHHHHHHHhhccCCcEEEEEEcCCCCEEEeeCC
Confidence            89999999999999999999999999999999999999999999999999999999986

>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=1.1e-32  Score=172.51  Aligned_cols=61  Identities=44%  Similarity=0.709  Sum_probs=59.6

Q ss_pred             cccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           16 KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        16 ~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ++||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+|+|++|+|+||
T Consensus         1 ~~GR~Ki~i~~Ie~~~~R~vTFsKRr~GL~KKa~ELs~Lc~~~v~liv~s~~gk~~~f~s~   61 (84)
T d1srsa_           1 TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATR   61 (84)
T ss_dssp             CCCCCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTTCCEEEEECG
T ss_pred             CCCCceeeEEeecCcchhhhhhHHhhhhHHHHHHHHhcccCCcEEEEEEcCCCCEEEeeCC
Confidence            5899999999999999999999999999999999999999999999999999999999985

>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=5.6e-32  Score=169.37  Aligned_cols=61  Identities=51%  Similarity=0.774  Sum_probs=59.4

Q ss_pred             cccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783           16 KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN   76 (76)
Q Consensus        16 ~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~   76 (76)
                      ..||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||+|+|++|+|+||
T Consensus         1 ~k~R~Ki~i~~I~~~~~R~vTFsKRr~GL~KKa~ELsvLc~a~vaviv~s~~gk~~~f~sp   61 (85)
T d1mnma_           1 QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTP   61 (85)
T ss_dssp             CCCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEECT
T ss_pred             CCCccceEEEEecCCchhhhhhHHHHhhHHHHHHHHhccCCCcEEEEEEcCCCCEEeccCC
Confidence            3699999999999999999999999999999999999999999999999999999999986