Citrus Sinensis ID: 040485

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110------
Protein Sequence
MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQEKMLKQMRRVKETQP
Secondary Structure (PSIPRED)
ccccccccccccEEEEEcccccccEEcccccccHHHHHHHHHHHccccEEEEEEccccccEEEcccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEEEEcccccEEEEccccHHHHHHHHHHHccccccccccccHHHHccHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFsqsgkpyiflhndnihPLVKAYRHARINELNQQHNDLLRQLDEEKEQEKMLKQMRRVKETQP
Flexible Loop (DISEMBL)
magkktkrrqkiemkkieneddrlitfskrrsgiYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQEKMLKQmrrvketqp
Low Complexity Region (SEG)
MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHARINELNQQHNDLLRqldeekeqekmlkqmRRVKETQP
Disordered region (IsUnstruct)
***********************LITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHARINEL********************************
Disordered Region (DISOPRED)
***********IEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHA******************************RV*****
Disordered Region (DISEMBL)
***********IEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKE****************
Disordered Region (DISPRO)
***********IEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHARINELN**HND***QLDEEKEQEKMLKQMRRVKET**
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxRRVKETQP
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	116	2.2.26 [Sep-21-2011]
Q9FKK2	299	Agamous-like MADS-box pro	no	no	0.913	0.354	0.4	3e-15
Q4PSU4	264	Agamous-like MADS-box pro	no	no	0.870	0.382	0.372	3e-14
Q8VWM8	259	MADS-box protein ZMM17 OS	N/A	no	0.879	0.393	0.367	5e-12
Q9S7Q7	196	MADS-box protein FLOWERIN	no	no	0.706	0.418	0.388	1e-11
Q38838	221	Agamous-like MADS-box pro	no	no	0.681	0.357	0.437	4e-11
Q2V0P1	272	MADS-box transcription fa	no	no	0.732	0.312	0.382	5e-11
Q9FPN7	196	Agamous-like MADS-box pro	no	no	0.655	0.387	0.421	8e-11
Q2QW53	270	MADS-box transcription fa	no	no	0.612	0.262	0.408	8e-11
Q39295	264	Agamous-like MADS-box pro	N/A	no	0.474	0.208	0.527	1e-10
Q8RYD9	252	Protein TRANSPARENT TESTA	no	no	0.706	0.325	0.433	1e-10

>sp|Q9FKK2|AGL62_ARATH Agamous-like MADS-box protein AGL62 OS=Arabidopsis thaliana GN=AGL62 PE=1 SV=1

 Score = 80.1 bits (196), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 50/125 (40%), Positives = 75/125 (60%), Gaps = 19/125 (15%)

Query: 4   KKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQS------ 57
           KK+K RQKIEM K++NE +  +TFSKRRSG++KKASE  TL  + +AIVVFS        
Sbjct: 3   KKSKGRQKIEMVKMKNESNLQVTFSKRRSGLFKKASELCTLCGAEVAIVVFSPGRKVFSF 62

Query: 58  GKPYI------FLHNDNIHP-------LVKAYRHARINELNQQHNDLLRQLDEEKEQEKM 104
           G P +      F++N+ + P       L +  R++ + +LN     +L QL+ EK++   
Sbjct: 63  GHPNVDSVIDRFINNNPLPPHQHNNMQLRETRRNSIVQDLNNHLTQVLSQLETEKKKYDE 122

Query: 105 LKQMR 109
           LK++R
Sbjct: 123 LKKIR 127

Probable transcription factor. Required for suppression of cellularization and promotion of nuclear proliferation during early endosperm development. The FERTILIZATION-INDEPENDENT SEED (FIS) polycomb complex is required for suppression of ALG62 expression at the end of the syncytial phase of endosperm development.
Arabidopsis thaliana (taxid: 3702)

>sp|Q4PSU4|AGL61_ARATH Agamous-like MADS-box protein AGL61 OS=Arabidopsis thaliana GN=AGL61 PE=1 SV=1

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/118 (37%), Positives = 68/118 (57%), Gaps = 17/118 (14%)

Query: 9   RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
           RQKI M KI+ E  R +TFSKRR+G++KKASE  TL  + I I+VFS + KP+ F H  +
Sbjct: 64  RQKIPMVKIKKESHRQVTFSKRRAGLFKKASELCTLCGAEIGIIVFSPAKKPFSFGH-PS 122

Query: 69  IHPLVKAY----------------RHARINELNQQHNDLLRQLDEEKEQEKMLKQMRR 110
           +  ++  Y                  A   ELN Q   +L +++EEK++ + +++MR+
Sbjct: 123 VESVLDRYVSRNNMSLAQSQQLQGSPAASCELNMQLTHILSEVEEEKKKGQAMEEMRK 180

Probable transcription factor. Controls central cell differentiation during female gametophyte development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8VWM8|M17_MAIZE MADS-box protein ZMM17 OS=Zea mays GN=M17 PE=2 SV=1

 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 39/106 (36%), Positives = 61/106 (57%), Gaps = 4/106 (3%)

Query: 9   RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLH-ND 67
           R KIE+K+IEN  +R +TFSKRR G+ KKA+E   L  + + +V+FS +GK + +     
Sbjct: 3   RGKIEIKRIENSTNRQVTFSKRRGGLLKKANELAVLCDARVGVVIFSSTGKMFEYCSPAC 62

Query: 68  NIHPLVKAYRHA---RINELNQQHNDLLRQLDEEKEQEKMLKQMRR 110
           ++  L++ Y+HA      E+N     LL     + E EK+   +RR
Sbjct: 63  SLRELIEQYQHATNSHFEEINHDQQILLEMTRMKNEMEKLETGIRR 108

Probable transcription factor.

Zea mays (taxid: 4577)

>sp|Q9S7Q7|FLC_ARATH MADS-box protein FLOWERING LOCUS C OS=Arabidopsis thaliana GN=FLC PE=2 SV=1

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 56/90 (62%), Gaps = 8/90 (8%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+K+E+K+IEN+  R +TFSKRR+G+ +KA +   L  +++A++V S SGK Y F   DN
Sbjct: 3  RKKLEIKRIENKSSRQVTFSKRRNGLIEKARQLSVLCDASVALLVVSASGKLYSFSSGDN 62

Query: 69 IHPLVKAYRHARINELNQQHNDLLRQLDEE 98
          +  ++  Y         +QH D L+ LD +
Sbjct: 63 LVKILDRY--------GKQHADDLKALDHQ 84

Putative transcription factor that seems to play a central role in the regulation of flowering time in the late-flowering phenotype by interacting with 'FRIGIDA', the autonomous and the vernalization flowering pathways. Inhibits flowering by repressing 'SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1'.

Arabidopsis thaliana (taxid: 3702)

>sp|Q38838|AGL14_ARATH Agamous-like MADS-box protein AGL14 OS=Arabidopsis thaliana GN=AGL14 PE=1 SV=2

 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 48/80 (60%), Gaps = 1/80 (1%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R K EMK+IEN   R +TFSKRR+G+ KKA E   L  + +A+++FS  GK Y F  + +
Sbjct: 3  RGKTEMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSSSSS 62

Query: 69 IHPLVKAYRHARINELNQQH 88
          I   V+ Y   RI +L   H
Sbjct: 63 IPKTVERY-QKRIQDLGSNH 81

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q2V0P1|MAD58_ORYSJ MADS-box transcription factor 58 OS=Oryza sativa subsp. japonica GN=MADS58 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 55/94 (58%), Gaps = 9/94 (9%)

Query: 3   GKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYI 62
            +K   R KIE+K+IEN  +R +TF KRRSG+ KKA E   L  + +A+VVFS  G+ Y 
Sbjct: 39  AEKIGSRGKIEIKRIENTTNRQVTFCKRRSGLLKKAYELSVLCDAEVALVVFSSRGRLYE 98

Query: 63  FLHNDNIHPLVKAYRHAR--------INELNQQH 88
           +  N+++   ++ Y+ A         + E+N QH
Sbjct: 99  Y-SNNSVKETIERYKKANSDTSNASTVAEINAQH 131

Probable transcription factor involved in the development of floral organs. Acts as a C-class protein in association with MADS3. Involved in the control of lodicule number (whorl 2), stamen specification (whorl 3), floral meristem determinacy and regulation of the carpel morphogenesis (whorl 4). Plays a more predominant role in floral meristem determinacy than MADS3.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9FPN7|AGL31_ARATH Agamous-like MADS-box protein AGL31 OS=Arabidopsis thaliana GN=AGL31 PE=2 SV=2

 Score = 65.9 bits (159), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 49/76 (64%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+K+E+K+IEN+  R +TFSKRR+G+ +KA +   L  S+IA++V S SGK Y     DN
Sbjct: 3  RKKVEIKRIENKSSRQVTFSKRRNGLIEKARQLSILCESSIAVLVVSGSGKLYKSASGDN 62

Query: 69 IHPLVKAYRHARINEL 84
          +  ++  Y     +EL
Sbjct: 63 MSKIIDRYEIHHADEL 78

Probable transcription factor that prevents vernalization by short periods of cold. Acts as a floral repressor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QW53|MAD13_ORYSJ MADS-box transcription factor 13 OS=Oryza sativa subsp. japonica GN=MADS13 PE=1 SV=2

 Score = 65.9 bits (159), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 46/71 (64%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R +IE+K+IEN   R +TF KRR+G+ KKA E   L  + +A++VFS  G+ Y + +N+N
Sbjct: 3  RGRIEIKRIENTTSRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYSNNNN 62

Query: 69 IHPLVKAYRHA 79
          +   +  Y+ A
Sbjct: 63 VKATIDRYKKA 73

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q39295|AGL15_BRANA Agamous-like MADS-box protein AGL15 OS=Brassica napus GN=AGL15 PE=3 SV=1

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 41/55 (74%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
          R KIE+K+IEN + R +TFSKRR+G+ KKA E   L  + +A++VFS+SGK + F
Sbjct: 3  RGKIEIKRIENANSRQVTFSKRRAGLLKKAHELSVLCDAEVAVIVFSKSGKLFEF 57

Probable transcription factor.

Brassica napus (taxid: 3708)

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

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 47/83 (56%), Gaps = 1/83 (1%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R KIE+KKIEN+  R +TFSKRR+G+ KK  E   L  + I ++VFS +GK   F    N
Sbjct: 3  RGKIEIKKIENQTARQVTFSKRRTGLIKKTRELSILCDAHIGLIVFSATGKLSEFCSEQN 62

Query: 69 IHP-LVKAYRHARINELNQQHND 90
            P L+  Y H     L   H+D
Sbjct: 63 RMPQLIDRYLHTNGLRLPDHHDD 85

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)

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	116
255557367	239	mads box protein, putative [Ricinus comm	0.905	0.439	0.608	8e-33
224077620	194	predicted protein [Populus trichocarpa]	0.991	0.592	0.537	4e-32
449505973	269	PREDICTED: agamous-like MADS-box protein	0.939	0.405	0.563	8e-32
449434264	260	PREDICTED: agamous-like MADS-box protein	0.939	0.419	0.580	1e-31
255557369	220	mads box protein, putative [Ricinus comm	0.965	0.509	0.569	2e-31
224054544	202	predicted protein [Populus trichocarpa]	0.956	0.549	0.573	7e-30
224104275	201	predicted protein [Populus trichocarpa]	0.913	0.527	0.508	1e-25
225462217	199	PREDICTED: agamous-like MADS-box protein	0.922	0.537	0.491	9e-24
225429161	214	PREDICTED: agamous-like MADS-box protein	0.991	0.537	0.424	8e-20
297736389	194	unnamed protein product [Vitis vinifera]	0.965	0.577	0.460	2e-18

>gi|255557367|ref|XP_002519714.1| mads box protein, putative [Ricinus communis] gi|223541131|gb|EEF42687.1| mads box protein, putative [Ricinus communis]

 Score =  144 bits (362), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 76/125 (60%), Positives = 88/125 (70%), Gaps = 20/125 (16%)

Query: 3   GKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYI 62
           GKKTK RQKIEMKKIENEDDRLITFSKRRSGIYKKASE VTLT + +A +V+S +GKP+ 
Sbjct: 7   GKKTKGRQKIEMKKIENEDDRLITFSKRRSGIYKKASELVTLTGAELAFLVYSPAGKPFS 66

Query: 63  FLH--------------------NDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQE 102
           F H                    N   HPL++A+R  RI ELNQQHN+LLRQL+ EKE+ 
Sbjct: 67  FAHPSMDAITNRFFGQGSADRNNNPTTHPLIEAHRLMRIEELNQQHNELLRQLEIEKEKG 126

Query: 103 KMLKQ 107
           K LKQ
Sbjct: 127 KQLKQ 131

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077620|ref|XP_002305331.1| predicted protein [Populus trichocarpa] gi|222848295|gb|EEE85842.1| predicted protein [Populus trichocarpa]

 Score =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 71/132 (53%), Positives = 93/132 (70%), Gaps = 17/132 (12%)

Query: 1   MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKP 60
           M GK+T+ RQKI +K+IENEDDRLITFSKRRSGIYKKASE VTL  + +A++VFS +GK 
Sbjct: 1   MEGKQTRGRQKIAIKRIENEDDRLITFSKRRSGIYKKASELVTLCGAEVAVLVFSPAGKA 60

Query: 61  YIFLH-----------------NDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQEK 103
           + F H                 NDN HPLV+A+R  RINELNQQHN+LL +++ E+++ K
Sbjct: 61  FSFGHPSIESVANRFLGQNIAPNDNTHPLVEAHRKVRINELNQQHNELLSEMEAERDRGK 120

Query: 104 MLKQMRRVKETQ 115
           +LK+    K +Q
Sbjct: 121 VLKEGTSEKSSQ 132

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449505973|ref|XP_004162618.1| PREDICTED: agamous-like MADS-box protein AGL61-like [Cucumis sativus]

 Score =  140 bits (354), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 75/133 (56%), Positives = 90/133 (67%), Gaps = 24/133 (18%)

Query: 4   KKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
           K+TK RQKIEMKKI NEDDRLITFSKRRSGIYKKASE  TL  + + +VVFS +GKP+ F
Sbjct: 15  KQTKGRQKIEMKKIVNEDDRLITFSKRRSGIYKKASELATLCGAEVGVVVFSPAGKPFSF 74

Query: 64  LH------------------------NDNIHPLVKAYRHARINELNQQHNDLLRQLDEEK 99
            H                        N+N HPLV+A+R  RINELNQQHN LL QLD EK
Sbjct: 75  AHPCIETIANKFLNGNKNNKGNNDDNNNNAHPLVEAHRRVRINELNQQHNQLLSQLDAEK 134

Query: 100 EQEKMLKQMRRVK 112
           E+ K L++++RV+
Sbjct: 135 EKGKALEKLKRVR 147

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434264|ref|XP_004134916.1| PREDICTED: agamous-like MADS-box protein AGL61-like [Cucumis sativus]

 Score =  140 bits (353), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 72/124 (58%), Positives = 86/124 (69%), Gaps = 15/124 (12%)

Query: 4   KKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
           K+TK RQKIEMKKI NEDDRLITFSKRRSGIYKKASE  TL  + + +VVFS +GKP+ F
Sbjct: 15  KQTKGRQKIEMKKIVNEDDRLITFSKRRSGIYKKASELATLCGAEVGVVVFSPAGKPFSF 74

Query: 64  LH---------------NDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQEKMLKQM 108
            H                    PLV+A+R  RINELNQQHN LL QLD EKE+ K L+++
Sbjct: 75  AHPCIETIANKFLNAAATTTTTPLVEAHRRVRINELNQQHNQLLSQLDAEKEKGKALEKL 134

Query: 109 RRVK 112
           +RV+
Sbjct: 135 KRVR 138

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255557369|ref|XP_002519715.1| mads box protein, putative [Ricinus communis] gi|223541132|gb|EEF42688.1| mads box protein, putative [Ricinus communis]

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 74/130 (56%), Positives = 92/130 (70%), Gaps = 18/130 (13%)

Query: 1   MAGKK-TKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGK 59
           MAGKK TK RQKI MK+IENE+DRLITFSKRRSGIYKKASE +TL  + + I+VFS +GK
Sbjct: 1   MAGKKQTKGRQKITMKRIENEEDRLITFSKRRSGIYKKASELITLCGAEVGILVFSPAGK 60

Query: 60  PYIFLH-----------------NDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQE 102
           P+ F H                 +DN HPLV+A+R  RINELN+Q+N+LL +L+ EKE+ 
Sbjct: 61  PFSFGHPSLESIANRFLGKNVPPSDNTHPLVEAHRKMRINELNKQYNELLNRLESEKERG 120

Query: 103 KMLKQMRRVK 112
            MLK+  R K
Sbjct: 121 SMLKKTIRGK 130

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224054544|ref|XP_002298313.1| predicted protein [Populus trichocarpa] gi|222845571|gb|EEE83118.1| predicted protein [Populus trichocarpa]

 Score =  134 bits (337), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 74/129 (57%), Positives = 88/129 (68%), Gaps = 18/129 (13%)

Query: 1   MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKP 60
           MA KKTK RQK+EMK+IEN+DDRLITFSKRRSGIYKKASE  TLT + IAI VFS +GKP
Sbjct: 1   MASKKTKGRQKVEMKRIENQDDRLITFSKRRSGIYKKASELATLTGAEIAIAVFSPAGKP 60

Query: 61  YIFLHN----------------DNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQEKM 104
           + F H                 D+ + LV+A+R  RI EL Q+HND+  QLDEEK  EK 
Sbjct: 61  FSFGHPSVESVINRFLEDPLDMDSTYHLVEAHRRMRIEELTQKHNDMQHQLDEEK--EKG 118

Query: 105 LKQMRRVKE 113
           LK   ++KE
Sbjct: 119 LKLKSKIKE 127

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224104275|ref|XP_002313380.1| predicted protein [Populus trichocarpa] gi|222849788|gb|EEE87335.1| predicted protein [Populus trichocarpa]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 62/122 (50%), Positives = 80/122 (65%), Gaps = 16/122 (13%)

Query: 1   MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKP 60
           M  KKT+ RQK+EMK+I NEDDRL+TFSKRRSGIYKK SE +TLT +  A +VFS  GKP
Sbjct: 1   MEAKKTRGRQKVEMKRIVNEDDRLVTFSKRRSGIYKKLSELITLTGTEAAFLVFSPGGKP 60

Query: 61  YIFLH----------------NDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQEKM 104
           + F H                 D  H LV+ YR ARI EL Q+++++ +QLD++KE+   
Sbjct: 61  FSFGHPSIENVLDRFLENPSNADGTHELVEEYRRARIEELTQKYDEMQQQLDDDKEKGSK 120

Query: 105 LK 106
           LK
Sbjct: 121 LK 122

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225462217|ref|XP_002269756.1| PREDICTED: agamous-like MADS-box protein AGL62-like [Vitis vinifera]

 Score =  114 bits (284), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 61/124 (49%), Positives = 84/124 (67%), Gaps = 17/124 (13%)

Query: 1   MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKP 60
           M  K+TK RQKIEMK+I NE+DRLITFSKRRSGIYKKASE  TL  + + ++VFS +GK 
Sbjct: 1   MEKKQTKGRQKIEMKRIPNEEDRLITFSKRRSGIYKKASELSTLCGAEVGVLVFSPAGKA 60

Query: 61  YIFLH-----------------NDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQEK 103
           + F                   NDN   LV+A+R  R+NEL+Q++++LL +++  KEQEK
Sbjct: 61  FSFGQPSIEKITNKVLYENPPPNDNTLNLVEAHRRFRLNELHQKYSELLSKMEVAKEQEK 120

Query: 104 MLKQ 107
           +L++
Sbjct: 121 ILRK 124

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429161|ref|XP_002270964.1| PREDICTED: agamous-like MADS-box protein AGL62 [Vitis vinifera] gi|147772544|emb|CAN63001.1| hypothetical protein VITISV_024203 [Vitis vinifera]

 Score =  100 bits (250), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 56/132 (42%), Positives = 81/132 (61%), Gaps = 17/132 (12%)

Query: 1   MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKP 60
           M  K +K RQKIE+ KI  ++   +TFSKRRSG++KKASE  TL  + +AI+VFS +GK 
Sbjct: 1   MVKKPSKGRQKIEISKIPKKNHLQVTFSKRRSGLFKKASELCTLCGANVAIIVFSPAGKV 60

Query: 61  YIFLHND---------NIHP--------LVKAYRHARINELNQQHNDLLRQLDEEKEQEK 103
           + F H D           +P        L++A+R+A + ELN Q   +L QL+ EK++ +
Sbjct: 61  FSFGHPDVESIVDRFFTCNPIPEPNGLHLIEAHRNASVRELNLQLTQVLNQLEAEKKRGE 120

Query: 104 MLKQMRRVKETQ 115
           +L QMRR  +TQ
Sbjct: 121 ILSQMRRASQTQ 132

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736389|emb|CBI25112.3| unnamed protein product [Vitis vinifera]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 53/115 (46%), Positives = 75/115 (65%), Gaps = 3/115 (2%)

Query: 1   MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKP 60
           M  K +K RQKIE+ KI  ++   +TFSKRRSG++KKASE  TL  + +AI+VFS +GK 
Sbjct: 1   MVKKPSKGRQKIEISKIPKKNHLQVTFSKRRSGLFKKASELCTLCGANVAIIVFSPAGKV 60

Query: 61  YIFLHNDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQEKMLKQMRRVKETQ 115
           + F H D +  +V   R   + ELN Q   +L QL+ EK++ ++L QMRR  +TQ
Sbjct: 61  FSFGHPD-VESIVD--RFFTVRELNLQLTQVLNQLEAEKKRGEILSQMRRASQTQ 112

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	116
TAIR|locus:2102990	207	AGL57 "AGAMOUS-like 57" [Arabi	0.543	0.304	0.571	1.2e-19
TAIR|locus:2115420	248	AT4G36590 [Arabidopsis thalian	0.75	0.350	0.444	6.9e-15
TAIR|locus:2175188	299	AGL62 "AGAMOUS-like 62" [Arabi	0.732	0.284	0.483	4.5e-14
TAIR|locus:2025386	247	AGL28 "AGAMOUS-like 28" [Arabi	0.698	0.327	0.511	1.3e-13
TAIR|locus:4010713489	185	AGL64 "AGAMOUS-like 64" [Arabi	0.543	0.340	0.539	4.4e-13
TAIR|locus:2206320	226	AGL23 "AGAMOUS-like 23" [Arabi	0.698	0.358	0.426	1.5e-12
TAIR|locus:2195798	217	AT1G17310 [Arabidopsis thalian	0.551	0.294	0.515	2.4e-12
TAIR|locus:2137070	221	AGL14 "AGAMOUS-like 14" [Arabi	0.698	0.366	0.440	2.4e-12
UNIPROTKB|Q43616	225	fbp7 "Floral binding protein n	0.655	0.337	0.428	6.4e-12
TAIR|locus:2165386	211	AGL72 "AGAMOUS-like 72" [Arabi	0.577	0.317	0.5	6.4e-12

TAIR|locus:2102990 AGL57 "AGAMOUS-like 57" [Arabidopsis thaliana (taxid:3702)]

 Score = 197 (74.4 bits), Expect = 1.2e-19, Sum P(2) = 1.2e-19
 Identities = 36/63 (57%), Positives = 48/63 (76%)

Query:     3 GKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYI 62
             G+KTK +QKIEMKK+EN  DR+ITFSKR++GI+KK +E V +    +A ++FSQ  KPY 
Sbjct:     9 GRKTKGKQKIEMKKVENYGDRMITFSKRKTGIFKKMNELVAMCDVEVAFLIFSQPKKPYT 68

Query:    63 FLH 65
             F H
Sbjct:    69 FAH 71

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

TAIR|locus:2115420 AT4G36590 [Arabidopsis thaliana (taxid:3702)]

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 40/90 (44%), Positives = 60/90 (66%)

Query:     4 KKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
             + TK RQKIEMKK+ENE +  +TFSKRR G++KKASE  TL+ + I ++VFS  GK + F
Sbjct:     3 RSTKGRQKIEMKKMENESNLQVTFSKRRFGLFKKASELCTLSGAEILLIVFSPGGKVFSF 62

Query:    64 LHNDNIHPLVKAYRHARINE--LNQQHNDL 91
              H  ++  L+  + +   N   ++ Q+N+L
Sbjct:    63 GH-PSVQELIHRFSNPNHNSAIVHHQNNNL 91

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:0005829 "cytosol" evidence=IDA

TAIR|locus:2175188 AGL62 "AGAMOUS-like 62" [Arabidopsis thaliana (taxid:3702)]

 Score = 183 (69.5 bits), Expect = 4.5e-14, P = 4.5e-14
 Identities = 43/89 (48%), Positives = 58/89 (65%)

Query:     4 KKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
             KK+K RQKIEM K++NE +  +TFSKRRSG++KKASE  TL  + +AIVVFS   K + F
Sbjct:     3 KKSKGRQKIEMVKMKNESNLQVTFSKRRSGLFKKASELCTLCGAEVAIVVFSPGRKVFSF 62

Query:    64 LHNDNIHPLVKAYRHARINELN-QQHNDL 91
              H  N+  ++   R    N L   QHN++
Sbjct:    63 GH-PNVDSVID--RFINNNPLPPHQHNNM 88

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0009960 "endosperm development" evidence=IMP

TAIR|locus:2025386 AGL28 "AGAMOUS-like 28" [Arabidopsis thaliana (taxid:3702)]

 Score = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 44/86 (51%), Positives = 53/86 (61%)

Query:     1 MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKP 60
             MA K   RR KIE+ K+ NE +  +TFSKRRSG++KK SE  TL  + IAI+VFS SGK 
Sbjct:     1 MARKNLGRR-KIELVKMTNESNLQVTFSKRRSGLFKKGSELCTLCDAEIAIIVFSPSGKA 59

Query:    61 YIFLH-NDNI---HPLVKAYRHARIN 82
             Y F H N N    H L +  RH   N
Sbjct:    60 YSFGHPNVNKLLDHSLGRVIRHNNTN 85

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

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

TAIR|locus:4010713489 AGL64 "AGAMOUS-like 64" [Arabidopsis thaliana (taxid:3702)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 34/63 (53%), Positives = 45/63 (71%)

Query:     1 MAGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKP 60
             M  KKTK +Q+I +KKIE ++DRL+T SKRR+GIY K SE   L  + +A + +S SGKP
Sbjct:     1 MKPKKTKGKQRINIKKIEKDEDRLVTLSKRRNGIYTKLSELSILCGAEVAFLGYSCSGKP 60

Query:    61 YIF 63
             Y F
Sbjct:    61 YTF 63

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

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

TAIR|locus:2206320 AGL23 "AGAMOUS-like 23" [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 35/82 (42%), Positives = 54/82 (65%)

Query:     4 KKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
             KKT  R+K+E+ K+  E +  +TFSKR++G++KKASEF TL  + IA++VFS +GK + F
Sbjct:     3 KKTLGRRKVEIVKMTKESNLQVTFSKRKAGLFKKASEFCTLCDAKIAMIVFSPAGKVFSF 62

Query:    64 LHNDNIHPLVKAYRHARINELN 85
              H  N+  L+  +R   +   N
Sbjct:    63 GH-PNVDVLLDHFRGCVVGHNN 83

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0009553 "embryo sac development" evidence=IMP

GO:0009658 "chloroplast organization" evidence=IMP

TAIR|locus:2195798 AT1G17310 [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 33/64 (51%), Positives = 45/64 (70%)

Query:     4 KKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
             K T+ RQKIE+KKIE E  R +TFSKRR G++KK++E   LT + IA++ FS+  + Y F
Sbjct:    44 KTTRGRQKIEIKKIEEETKRQVTFSKRRRGLFKKSAELSVLTGAKIAVITFSKCDRIYRF 103

Query:    64 LHND 67
              H D
Sbjct:   104 GHVD 107

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

TAIR|locus:2137070 AGL14 "AGAMOUS-like 14" [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 37/84 (44%), Positives = 51/84 (60%)

Query:     9 RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
             R K EMK+IEN   R +TFSKRR+G+ KKA E   L  + +A+++FS  GK Y F  + +
Sbjct:     3 RGKTEMKRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSSSSS 62

Query:    69 IHPLVKAYRHARINELNQQH--ND 90
             I   V+ Y+  RI +L   H  ND
Sbjct:    63 IPKTVERYQK-RIQDLGSNHKRND 85

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

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:0005515 "protein binding" evidence=IPI

GO:0010048 "vernalization response" evidence=RCA

GO:0043481 "anthocyanin accumulation in tissues in response to UV light" evidence=RCA

GO:0048440 "carpel development" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

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

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 33/77 (42%), Positives = 49/77 (63%)

Query:     9 RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
             R KIE+K+IEN  +R +TF KRR+G+ KKA E   L  + IA++VFS  G+ Y +  N+N
Sbjct:     3 RGKIEIKRIENNTNRQVTFCKRRNGLLKKAYELSVLCEAEIALIVFSTRGRVYEY-SNNN 61

Query:    69 IHPLVKAYRHARINELN 85
             I  ++  Y+ A +   N
Sbjct:    62 IRAIIDRYKKATVETSN 78

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2165386 AGL72 "AGAMOUS-like 72" [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 34/68 (50%), Positives = 45/68 (66%)

Query:     9 RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
             R KIE+KKIEN   R +TFSKRRSG++KKA E   L  + +A ++FSQ G+ Y F  +D 
Sbjct:     3 RGKIEIKKIENVTSRQVTFSKRRSGLFKKAHELSVLCDAQVAAMIFSQKGRLYEFASSD- 61

Query:    69 IHPLVKAY 76
             I   +K Y
Sbjct:    62 IRNTIKRY 69

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:0009909 "regulation of flower development" evidence=IMP

GO:0010048 "vernalization response" evidence=RCA

GO:0043481 "anthocyanin accumulation in tissues in response to UV light" evidence=RCA

GO:0048440 "carpel development" evidence=RCA

---

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: fgenesh4_pg.C_LG_IV001019 hypothetical protein (194 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	116
cd00120	59	cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and	1e-20
cd00265	77	cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer fa	1e-20
cd00266	83	cd00266, MADS_SRF_like, SRF-like/Type I subfamily	2e-19
smart00432	59	smart00432, MADS, MADS domain	3e-19
pfam00319	51	pfam00319, SRF-TF, SRF-type transcription factor (	2e-10
COG5068	412	COG5068, ARG80, Regulator of arginine metabolism a	1e-05

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

 Score = 77.9 bits (193), Expect = 1e-20
 Identities = 31/56 (55%), Positives = 42/56 (75%)

Query: 8  RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
           R KIE+K+IEN+  R +TFSKRR+G++KKASE   L  + +A++VFS SGK Y F
Sbjct: 1  GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEF 56

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|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 = 78.7 bits (195), Expect = 1e-20
 Identities = 29/61 (47%), Positives = 40/61 (65%)

Query: 8  RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHND 67
           R KIE+K+IEN  +R +TFSKRR+G+ KKA E   L  + +A+++FS SGK Y F    
Sbjct: 1  GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPS 60

Query: 68 N 68
           
Sbjct: 61 M 61

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|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 = 75.4 bits (186), Expect = 2e-19
 Identities = 30/69 (43%), Positives = 49/69 (71%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++K+IEN+  R +TFSKRR G++KKASE  TL  + +A++V+S SGK Y+F  +  
Sbjct: 2  RKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSE 61

Query: 69 IHPLVKAYR 77
          +  ++  + 
Sbjct: 62 VEGVISRFE 70

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|197721 smart00432, MADS, MADS domain

 Score = 74.1 bits (183), Expect = 3e-19
 Identities = 29/55 (52%), Positives = 43/55 (78%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
          R+KIE+K+IEN+ +R +TFSKRR+G++KKA E   L  + +A++VFS +GK Y F
Sbjct: 2  RRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEF 56

Length = 59

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

 Score = 51.6 bits (124), Expect = 2e-10
 Identities = 24/49 (48%), Positives = 37/49 (75%)

Query: 15 KKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
          K+IEN+ +R +TFSKRR+GI+KKA E   L  + +A+++FS +GK Y +
Sbjct: 1  KRIENKSNRQVTFSKRRNGIFKKAHELSVLCDAEVAVIIFSSTGKLYEY 49

Length = 51

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

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 22/55 (40%), Positives = 34/55 (61%)

Query: 9   RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
            +KI +  I N+  R +TFSKR+ GI KKA E   LT + + ++V S++G  + F
Sbjct: 83  GRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTF 137

Length = 412

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	116
cd00265	77	MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-li	99.96
KOG0014	195	consensus MADS box transcription factor [Transcrip	99.96
smart00432	59	MADS MADS domain.	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	99.91
KOG0015	338	consensus Regulator of arginine metabolism and rel	99.87
COG5068	412	ARG80 Regulator of arginine metabolism and related	99.5
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	83.72
PF09151	36	DUF1936: Domain of unknown function (DUF1936); Int	81.85

>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=99.96  E-value=1.8e-30  Score=169.54  Aligned_cols=71  Identities=42%  Similarity=0.716  Sum_probs=67.4

Q ss_pred             CccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCChhhHHhhhhh
Q 040485            8 RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHA   79 (116)
Q Consensus         8 gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~~~~~~~~~~   79 (116)
                      ||+||+|++|+|+..|++||+||+.||||||+|||+||||+||+|||||+|++|.|++|+. ..++++|...
T Consensus         1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~-~~vl~ry~~~   71 (77)
T cd00265           1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSM-EKIIERYQKT   71 (77)
T ss_pred             CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCH-HHHHHHHHhc
Confidence            8999999999999999999999999999999999999999999999999999999999986 7777888754

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.

>KOG0014 consensus MADS box transcription factor [Transcription]

Probab=99.96  E-value=4.5e-30  Score=189.35  Aligned_cols=72  Identities=49%  Similarity=0.763  Sum_probs=66.7

Q ss_pred             CCccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCC-ChhhHHhhhh
Q 040485            7 KRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN-IHPLVKAYRH   78 (116)
Q Consensus         7 ~gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~-~~~~~~~~~~   78 (116)
                      |||+||+|++|+|+..|+|||+|||.||||||+||||||||+||||||||+|++|.||+|+. ...++++|..
T Consensus         1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~   73 (195)
T KOG0014|consen    1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLN   73 (195)
T ss_pred             CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHh
Confidence            89999999999999999999999999999999999999999999999999999999999975 5556677743

>smart00432 MADS MADS domain

Probab=99.95  E-value=2.6e-29  Score=156.75  Aligned_cols=59  Identities=49%  Similarity=0.825  Sum_probs=58.1

Q ss_pred             CccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecC
Q 040485            8 RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHN   66 (116)
Q Consensus         8 gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~   66 (116)
                      ||+||+|++|+|+..|++||+||+.||||||+|||+||||+||+|||+|+|+++.|++|
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            89999999999999999999999999999999999999999999999999999999987

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

Probab=99.95  E-value=1.5e-28  Score=153.27  Aligned_cols=59  Identities=53%  Similarity=0.833  Sum_probs=57.8

Q ss_pred             CccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecC
Q 040485            8 RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHN   66 (116)
Q Consensus         8 gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~   66 (116)
                      ||+||+|++|+|+..|++||+||+.||||||+|||+||||+||+|||||+|+++.|++|
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            79999999999999999999999999999999999999999999999999999999886

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=2.7e-28  Score=161.24  Aligned_cols=71  Identities=42%  Similarity=0.772  Sum_probs=65.1

Q ss_pred             CccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCChhhHHhhhh
Q 040485            8 RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRH   78 (116)
Q Consensus         8 gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~~~~~~~~~   78 (116)
                      ||+||+|++|+|+.+|++||+||+.||||||+|||+||||+||+|||+|+|+.+.|++++....++++|..
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~   71 (83)
T cd00266           1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEV   71 (83)
T ss_pred             CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhh
Confidence            79999999999999999999999999999999999999999999999999999999888765556666643

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=99.91  E-value=4.4e-26  Score=138.38  Aligned_cols=51  Identities=51%  Similarity=0.820  Sum_probs=46.8

Q ss_pred             EEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeec
Q 040485           15 KKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLH   65 (116)
Q Consensus        15 ~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s   65 (116)
                      ++|+|+..|++||+||+.||||||+|||+||||+||+|||+|+|++|+|+|
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            479999999999999999999999999999999999999999999999986

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=6.9e-23  Score=161.35  Aligned_cols=65  Identities=48%  Similarity=0.681  Sum_probs=63.4

Q ss_pred             CCCCCCccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCC
Q 040485            3 GKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHND   67 (116)
Q Consensus         3 ~~~~~gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s   67 (116)
                      +|++.||+||+|+||+|+.+|++||||||.||||||+||++|+|.+|.|+|.|++|..|+|+.|-
T Consensus        58 ~k~~~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpK  122 (338)
T KOG0015|consen   58 GKKTTGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPK  122 (338)
T ss_pred             CccccceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEecccc
Confidence            68899999999999999999999999999999999999999999999999999999999999983

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

Probab=99.50  E-value=1.2e-14  Score=118.77  Aligned_cols=63  Identities=35%  Similarity=0.477  Sum_probs=61.0

Q ss_pred             CCCccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCC
Q 040485            6 TKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN   68 (116)
Q Consensus         6 ~~gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~   68 (116)
                      +||++||.|.+|+|+.+|.|||+||+.||+|||.||++|+|.+|.++|.+++|..+.|+.|+-
T Consensus        80 ~~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~  142 (412)
T COG5068          80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKL  142 (412)
T ss_pred             ccccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCcc
Confidence            689999999999999999999999999999999999999999999999999999999999953

>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []

Probab=83.72  E-value=4  Score=25.29  Aligned_cols=32  Identities=25%  Similarity=0.336  Sum_probs=24.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 040485           81 INELNQQHNDLLRQLDEEKEQEKMLKQMRRVK  112 (116)
Q Consensus        81 ~~~l~~~~~~L~~ql~~~k~~~~kL~~~~r~~  112 (116)
                      ...+++++..|+.+++.++.++++|+.+.+..
T Consensus        19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l   50 (80)
T PF04977_consen   19 YYQLNQEIAELQKEIEELKKENEELKEEIERL   50 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45667777888888888888888887777665

These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle

>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins

Probab=81.85  E-value=1.6  Score=23.96  Aligned_cols=28  Identities=14%  Similarity=0.207  Sum_probs=19.5

Q ss_pred             hhhhhcccceEEEeeeCCC--CceeeecCC
Q 040485           40 EFVTLTSSAIAIVVFSQSG--KPYIFLHND   67 (116)
Q Consensus        40 ELs~Lc~~~v~~vv~s~~g--~~~~~~s~s   67 (116)
                      .||.-||+-|.+.||+..|  +.|..+.|.
T Consensus         2 hlcpkcgvgvl~pvy~~kgeikvfrcsnpa   31 (36)
T PF09151_consen    2 HLCPKCGVGVLEPVYNQKGEIKVFRCSNPA   31 (36)
T ss_dssp             -B-TTTSSSBEEEEE-TTS-EEEEEES-TT
T ss_pred             ccCCccCceEEEEeecCCCcEEEEEcCCCc
Confidence            4788899999999999999  456655554

Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	116
1srs_A	92	Serum Response Factor (Srf) Core Complexed With Spe		5e-10
1k6o_B	103	Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dn		6e-10
1mnm_A	100	Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLE		9e-09
3mu6_A	71	Inhibiting The Binding Of Class Iia Histone Deacety		5e-07
3kov_A	90	Structure Of Mef2a Bound To Dna Reveals A Completel		5e-07
1egw_A	77	Crystal Structure Of Mef2a Core Bound To Dna Length		5e-07
1c7u_A	85	Complex Of The Dna Binding Core Domain Of The Trans		7e-07
1n6j_A	93	Structural Basis Of Sequence-Specific Recruitment O		3e-06
1tqe_P	93	Mechanism Of Recruitment Of Class Ii Histone Deacet		3e-06

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 48/73 (65%), Gaps = 1/73 (1%)
Query: 3  GKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYI 62
          GKKT+ R KI+M+ I+N+  R  TFSKR++GI KKA E  TLT + + ++V S++G  Y 
Sbjct: 6  GKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYT 65
Query: 63 FLHNDNIHPLVKA 75
          F     + P++ +
Sbjct: 66 F-ATRKLQPMITS 77

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 48/73 (65%), Gaps = 1/73 (1%)
Query: 3  GKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYI 62
          GKKT+ R KI+M+ I+N+  R  TFSKR++GI KKA E  TLT + + ++V S++G  Y 
Sbjct: 5  GKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYT 64
Query: 63 FLHNDNIHPLVKA 75
          F     + P++ +
Sbjct: 65 F-ATRKLQPMITS 76

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 39/57 (68%)
Query: 7  KRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIF 63
          K R+KIE+K IEN+  R +TFSKR+ GI KKA E   LT + + ++V S++G  Y F
Sbjct: 16 KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTF 72

>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 = 49.7 bits (117), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 41/66 (62%)
Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++ +I +E +R +TF+KR+ G+ KKA E   L    IA+++F+ S K + +   D 
Sbjct: 2  RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 69 IHPLVK 74
             L+K
Sbjct: 62 DKVLLK 67

>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 = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 41/66 (62%)
Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++ +I +E +R +TF+KR+ G+ KKA E   L    IA+++F+ S K + +   D 
Sbjct: 2  RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 69 IHPLVK 74
             L+K
Sbjct: 62 DKVLLK 67

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 41/66 (62%)
Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++ +I +E +R +TF+KR+ G+ KKA E   L    IA+++F+ S K + +   D 
Sbjct: 2  RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61
Query: 69 IHPLVK 74
             L+K
Sbjct: 62 DKVLLK 67

>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 = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 42/66 (63%)
Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++ +I +E +R +TF+KR+ G+ KKA E   L  + IA+++F+ S K + +   D 
Sbjct: 2  RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTDM 61
Query: 69 IHPLVK 74
             L+K
Sbjct: 62 DKVLLK 67

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 51/84 (60%), Gaps = 1/84 (1%)
Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++ +I ++ +R +TF+KR+ G+ KKA E   L    IA+++F+ + + + +   D 
Sbjct: 2  RKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDM 61
Query: 69 IHPLVKAYRHARINELNQQHNDLL 92
             L+K   ++  +E ++ + D+L
Sbjct: 62 DRVLLKYTEYSEPHE-SRTNTDIL 84

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 51/84 (60%), Gaps = 1/84 (1%)
Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++ +I ++ +R +TF+KR+ G+ KKA E   L    IA+++F+ + + + +   D 
Sbjct: 3  RKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDM 62
Query: 69 IHPLVKAYRHARINELNQQHNDLL 92
             L+K   ++  +E ++ + D+L
Sbjct: 63 DRVLLKYTEYSEPHE-SRTNTDIL 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	116
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	4e-23
1hbx_A	92	SRF, serum response factor; gene regulation, trans	2e-22
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	5e-21
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	3e-18
1egw_A	77	MADS box transcription enhancer factor 2, polypept	2e-16

>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 = 84.9 bits (210), Expect = 4e-23
 Identities = 34/100 (34%), Positives = 55/100 (55%), Gaps = 1/100 (1%)

Query: 2   AGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPY 61
            GKKT+ R KI+M+ I+N+  R  TFSKR++GI KKA E  TLT + + ++V S++G  Y
Sbjct: 4   PGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVY 63

Query: 62  IFLHNDNIHPLVKAYRHARINELNQQHNDLLRQLDEEKEQ 101
            F     + P++ +     + +      D   + D   +Q
Sbjct: 64  TFAT-RKLQPMITSETGKALIQTCLNSPDSPPRSDPTTDQ 102

>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 = 83.3 bits (206), Expect = 2e-22
 Identities = 32/89 (35%), Positives = 51/89 (57%), Gaps = 1/89 (1%)

Query: 2  AGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPY 61
           GKKT+ R KI+M+ I+N+  R  TFSKR++GI KKA E  TLT + + ++V S++G  Y
Sbjct: 5  PGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVY 64

Query: 62 IFLHNDNIHPLVKAYRHARINELNQQHND 90
           F     + P++ +     + +      D
Sbjct: 65 TFAT-RKLQPMITSETGKALIQTCLNSPD 92

>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 = 79.9 bits (197), Expect = 5e-21
 Identities = 31/89 (34%), Positives = 46/89 (51%), Gaps = 1/89 (1%)

Query: 2  AGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPY 61
             + K R+KIE+K IEN+  R +TFSKR+ GI KKA E   LT + + ++V S++G  Y
Sbjct: 11 NNGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVY 70

Query: 62 IFLHNDNIHPLVKAYRHARINELNQQHND 90
           F       P+V       + +      D
Sbjct: 71 TFST-PKFEPIVTQQEGRNLIQACLNAPD 98

>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 = 72.1 bits (177), Expect = 3e-18
 Identities = 24/90 (26%), Positives = 54/90 (60%), Gaps = 1/90 (1%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++ +I +E +R +TF+KR+ G+ KKA E   L    IA+++F+ S K + +  + +
Sbjct: 2  RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQY-ASTD 60

Query: 69 IHPLVKAYRHARINELNQQHNDLLRQLDEE 98
          +  ++  Y        ++ ++D++  L+++
Sbjct: 61 MDKVLLKYTEYNEPHESRTNSDIVEALNKK 90

>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 = 67.0 bits (164), Expect = 2e-16
 Identities = 25/75 (33%), Positives = 44/75 (58%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDN 68
          R+KI++ +I +E +R +TF+KR+ G+ KKA E   L    IA+++F+ S K + +   D 
Sbjct: 2  RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDM 61

Query: 69 IHPLVKAYRHARINE 83
             L+K   +   +E
Sbjct: 62 DKVLLKYTEYNEPHE 76

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	116
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	100.0
1hbx_A	92	SRF, serum response factor; gene regulation, trans	99.98
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	99.98
1egw_A	77	MADS box transcription enhancer factor 2, polypept	99.97
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	99.97

>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=100.00  E-value=2.9e-34  Score=194.44  Aligned_cols=83  Identities=37%  Similarity=0.505  Sum_probs=71.0

Q ss_pred             CCCCCCccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCChhhHHhhhhhhhH
Q 040485            3 GKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHARIN   82 (116)
Q Consensus         3 ~~~~~gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~~~~~~~~~~~~~   82 (116)
                      ++++|||+||+|++|+|+.+|++||+||+.||||||+||||||||+||||||||+|++|.|++|+.. .++++|..  ..
T Consensus        12 ~~~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~gk~~~f~sps~~-~il~r~~G--~~   88 (100)
T 1mnm_A           12 NGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFE-PIVTQQEG--RN   88 (100)
T ss_dssp             ---CCCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEECTTTT-HHHHSHHH--HH
T ss_pred             CCCCCCccceeeEEecCcchhhhhhhHhhhhHHHHHHHHHHhcCCcEEEEEecCCCCcceecCCCHH-HHHHHhhC--Cc
Confidence            5789999999999999999999999999999999999999999999999999999999999999754 55565543  55


Q ss_pred             HHHHHH
Q 040485           83 ELNQQH   88 (116)
Q Consensus        83 ~l~~~~   88 (116)
                      .|...+
T Consensus        89 lw~~cl   94 (100)
T 1mnm_A           89 LIQACL   94 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHhc
Confidence            565543

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

Probab=99.98  E-value=1.9e-34  Score=192.97  Aligned_cols=69  Identities=43%  Similarity=0.605  Sum_probs=65.3

Q ss_pred             CCCCCCCccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCCh
Q 040485            2 AGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIH   70 (116)
Q Consensus         2 ~~~~~~gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~   70 (116)
                      .+|++|||+||+|++|+|+.+|+|||+||+.||||||+||||||||+||||||||+|++|+|++|+...
T Consensus         5 ~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~V~livfs~~gk~~~f~s~~~~~   73 (92)
T 1hbx_A            5 PGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQP   73 (92)
T ss_dssp             -CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTTSCEEEEECGGGGG
T ss_pred             cCCCCCCcceEEEEEecChhHHHHHHHHhhhhHHHHHHHHHhhcCCceEEEEECCCCCEEEecCCCHHH
Confidence            478999999999999999999999999999999999999999999999999999999999999987543

>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=99.98  E-value=5.1e-34  Score=194.23  Aligned_cols=69  Identities=43%  Similarity=0.605  Sum_probs=65.2

Q ss_pred             CCCCCCCccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCCh
Q 040485            2 AGKKTKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIH   70 (116)
Q Consensus         2 ~~~~~~gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~   70 (116)
                      .+|++|||+||+|++|+|+.+|+|||+||+.||||||+||||||||+|||||||++|++|+|++|+...
T Consensus         4 ~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~gk~~~f~s~~~~~   72 (103)
T 1k6o_B            4 PGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQP   72 (103)
T ss_dssp             -CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECSSSCEEEEECGGGGG
T ss_pred             CCCCCCCcceeEEEEecCchHHHHhHhHhhHhHHHHHHHHHhhhCCceEEEEEeCCCCeeeecCccHHH
Confidence            378999999999999999999999999999999999999999999999999999999999999997543

>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=1.8e-33  Score=182.89  Aligned_cols=71  Identities=32%  Similarity=0.598  Sum_probs=66.5

Q ss_pred             CccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCChhhHHhhhhh
Q 040485            8 RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRHA   79 (116)
Q Consensus         8 gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~~~~~~~~~~   79 (116)
                      ||+||+|++|+|+.+|++||+||+.||||||+||||||||+|||||||++|++|+|++|+ ...++++|...
T Consensus         1 GR~Ki~ik~I~n~~~R~vTfsKRr~GL~KKA~ELsvLCdaeV~livfs~~gk~~~~~s~~-~~~il~ry~~~   71 (77)
T 1egw_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD-MDKVLLKYTEY   71 (77)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTCCEEEEESSC-HHHHHHHHHHC
T ss_pred             CCceeeeEEecCchHHHHHHHHhHHHHHHHHHHHhcccCCeEEEEEECCCCCEeeCCCCC-HHHHHHHHHhc
Confidence            899999999999999999999999999999999999999999999999999999999875 66677888653

>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=99.97  E-value=5.8e-33  Score=185.04  Aligned_cols=70  Identities=33%  Similarity=0.617  Sum_probs=65.8

Q ss_pred             CccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCChhhHHhhhh
Q 040485            8 RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRH   78 (116)
Q Consensus         8 gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~~~~~~~~~   78 (116)
                      ||+||+|++|+|+.+|+|||+||+.||||||+|||+||||+||||||||+|++|+|+||+ ...++++|+.
T Consensus         1 GR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valiifs~~gk~~~f~s~~-~~~il~rY~~   70 (90)
T 3p57_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD-MDKVLLKYTE   70 (90)
T ss_dssp             CCSCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEESSC-HHHHHHHHHH
T ss_pred             CCCcceeEEecCchHHHHHHHHhhhhHHHHHHHHHhccCCceEEEEECCCCCEEEeCCCC-HHHHHHHHHh
Confidence            899999999999999999999999999999999999999999999999999999999964 6667788864

---

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	116
d1srsa_	84	d.88.1.1 (A:) Serum response factor (SRF) core {Hu	6e-20
d1mnma_	85	d.88.1.1 (A:) MCM1 transcriptional regulator {Bake	9e-20
d1egwa_	71	d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {	1e-19

>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 = 75.2 bits (185), Expect = 6e-20
 Identities = 27/62 (43%), Positives = 40/62 (64%)

Query: 6  TKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLH 65
          T+ R KI+M+ I+N+  R  TFSKR++GI KKA E  TLT + + ++V S++G  Y F  
Sbjct: 1  TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 60

Query: 66 ND 67
            
Sbjct: 61 RK 62

>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 = 74.7 bits (184), Expect = 9e-20
 Identities = 28/61 (45%), Positives = 39/61 (63%)

Query: 7  KRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHN 66
          K R+KIE+K IEN+  R +TFSKR+ GI KKA E   LT + + ++V S++G  Y F   
Sbjct: 2  KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTP 61

Query: 67 D 67
           
Sbjct: 62 K 62

>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 = 74.3 bits (183), Expect = 1e-19
 Identities = 22/59 (37%), Positives = 38/59 (64%)

Query: 9  RQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHND 67
          R+KI++ +I +E +R +TF+KR+ G+ KKA E   L    IA+++F+ S K + +   D
Sbjct: 2  RKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	116
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	99.97
d1pvma3	36	Hypothetical protein Ta0289 C-terminal domain {Arc	82.02

>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=4.4e-34  Score=181.65  Aligned_cols=69  Identities=33%  Similarity=0.624  Sum_probs=64.8

Q ss_pred             CccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCChhhHHhhh
Q 040485            8 RRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYR   77 (116)
Q Consensus         8 gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~~~~~~~~   77 (116)
                      ||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||||+|++|+|+||+ ...++++|.
T Consensus         1 GR~Ki~ik~Ie~~~~R~vTFsKRk~GL~KKa~ELs~LC~~~valiv~s~~gk~~~f~s~~-~~~vl~ry~   69 (71)
T d1egwa_           1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD-MDKVLLKYT   69 (71)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTCCEEEEESSC-HHHHHHHHH
T ss_pred             CCccceEEeccCCchheeehhHhhhhHHHHHHHHhhccCCcEEEEEEcCCCCEEEeeCCC-HHHHHHHHh
Confidence            899999999999999999999999999999999999999999999999999999999986 555667764

>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=2.6e-33  Score=182.93  Aligned_cols=71  Identities=39%  Similarity=0.600  Sum_probs=65.1

Q ss_pred             CCCccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCChhhHHhhh
Q 040485            6 TKRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYR   77 (116)
Q Consensus         6 ~~gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~~~~~~~~   77 (116)
                      |+||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||||+|++|+|+||+. ..++++|.
T Consensus         1 ~~GR~Ki~i~~Ie~~~~R~vTFsKRr~GL~KKa~ELs~Lc~~~v~liv~s~~gk~~~f~s~~~-~~vi~~~~   71 (84)
T d1srsa_           1 TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKL-QPMITSET   71 (84)
T ss_dssp             CCCCCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTTCCEEEEECGGG-HHHHSSHH
T ss_pred             CCCCceeeEEeecCcchhhhhhHHhhhhHHHHHHHHhcccCCcEEEEEEcCCCCEEEeeCCCH-HHHHHHHH
Confidence            689999999999999999999999999999999999999999999999999999999999864 44445554

>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=99.97  E-value=1.6e-32  Score=179.65  Aligned_cols=71  Identities=42%  Similarity=0.631  Sum_probs=65.7

Q ss_pred             CCccccceEEeccCCCccccccccccchhhhhhhhhhhcccceEEEeeeCCCCceeeecCCCChhhHHhhhh
Q 040485            7 KRRQKIEMKKIENEDDRLITFSKRRSGIYKKASEFVTLTSSAIAIVVFSQSGKPYIFLHNDNIHPLVKAYRH   78 (116)
Q Consensus         7 ~gR~ki~i~~I~~~~~R~~tf~KR~~Gl~KKa~ELs~Lc~~~v~~vv~s~~g~~~~~~s~s~~~~~~~~~~~   78 (116)
                      +||+||+|++|+|+..|++||+||+.||||||+|||+||||+||||||||+|++|+|++|+ ...++++|..
T Consensus         2 k~R~Ki~i~~I~~~~~R~vTFsKRr~GL~KKa~ELsvLc~a~vaviv~s~~gk~~~f~sp~-v~~vl~r~~~   72 (85)
T d1mnma_           2 KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPK-FEPIVTQQEG   72 (85)
T ss_dssp             CCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEECTT-TTHHHHSHHH
T ss_pred             CCccceEEEEecCCchhhhhhHHHHhhHHHHHHHHhccCCCcEEEEEEcCCCCEEeccCCC-HHHHHHHHhc
Confidence            5999999999999999999999999999999999999999999999999999999999987 4445566654

>d1pvma3 g.41.13.1 (A:143-178) Hypothetical protein Ta0289 C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Hypothetical protein Ta0289 C-terminal domain
family: Hypothetical protein Ta0289 C-terminal domain
domain: Hypothetical protein Ta0289 C-terminal domain
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=82.02  E-value=0.48  Score=23.96  Aligned_cols=28  Identities=11%  Similarity=0.195  Sum_probs=22.3

Q ss_pred             hhhhhcccceEEEeeeCCC--CceeeecCC
Q 040485           40 EFVTLTSSAIAIVVFSQSG--KPYIFLHND   67 (116)
Q Consensus        40 ELs~Lc~~~v~~vv~s~~g--~~~~~~s~s   67 (116)
                      .||.-||+-|.+.||+..|  +.|..+.|.
T Consensus         2 hlcpkcgvgvl~pvy~~kgeikvfrcsnpa   31 (36)
T d1pvma3           2 HLCPKCGVGVLEPVYNEKGEIKVFRCSNPA   31 (36)
T ss_dssp             CBCTTTSSSBEEEEECTTSCEEEEEESCTT
T ss_pred             ccCCccCceEEEEeecCCCcEEEEEcCCCc
Confidence            3678899999999999999  556666664