halophFGD

Basic Information

Locus ID: Ag6G02827

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Description: Interconversion of serine and glycine

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr6	298838565	298841283	-	Ag6G02827

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
9.19	27,344.30 Da	35.96	90.16	-0.19

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
Pfam	PF00464	Serine hydroxymethyltransferase	1	201	8.2E-74	IPR039429
SUPERFAMILY	SSF53383	PLP-dependent transferases	1	247	1.19E-76	IPR015424
Gene3D	G3DSA:3.40.640.10	-	1	102	1.2E-40	IPR015421
Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1	103	249	2.0E-50	IPR015422
ProSitePatterns	PS00096	Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.	21	37	-	IPR019798

Gene Ontology

Molecular Function:

GO:0003824 (catalytic activity) GO:0030170 (pyridoxal phosphate binding)

KEGG Pathway

KO Term:

K00600 (glycine hydroxymethyltransferase [EC:2.1.2.1])

Pathway:

ko00260 (Glycine, serine and threonine metabolism) map00260 (Glycine, serine and threonine metabolism) ko00460 (Cyanoamino acid metabolism) map00460 (Cyanoamino acid metabolism) ko00630 (Glyoxylate and dicarboxylate metabolism) map00630 (Glyoxylate and dicarboxylate metabolism) ko00670 (One carbon pool by folate) map00670 (One carbon pool by folate) ko00680 (Methane metabolism) map00680 (Methane metabolism) ko01100 (Metabolic pathways) map01100 (Metabolic pathways) ko01110 (Biosynthesis of secondary metabolites) map01110 (Biosynthesis of secondary metabolites) ko01120 (Microbial metabolism in diverse environments) map01120 (Microbial metabolism in diverse environments) ko01200 (Carbon metabolism) map01200 (Carbon metabolism) ko01230 (Biosynthesis of amino acids) map01230 (Biosynthesis of amino acids) ko01523 (Antifolate resistance) map01523 (Antifolate resistance)

Module:

M00140 (C1-unit interconversion, prokaryotes) M00141 (C1-unit interconversion, eukaryotes) M00346 (Formaldehyde assimilation, serine pathway) M00532 (Photorespiration)

Reaction:

R00945 (5,10-Methylenetetrahydrofolate + Glycine + H2O <=> Tetrahydrofolate + L-Serine) R09099 (L-Serine + 5,6,7,8-Tetrahydromethanopterin <=> 5,10-Methylenetetrahydromethanopterin + Glycine + H2O)

Best hit

Source	Best Hit ID	Description
TAIR	AT1G22020.1	serine hydroxymethyltransferase 6. Encodes a putative serine hydroxymethyltransferase.
RefSeq	XP_017229598.1	PREDICTED: serine hydroxymethyltransferase 7-like [Daucus carota subsp. sativus]
Swiss-Prot	Q9LM59	Serine hydroxymethyltransferase 6 OS=Arabidopsis thaliana OX=3702 GN=SHM6 PE=1 SV=1
TrEMBL	A0A166GNP8	Serine hydroxymethyltransferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_001825 PE=3 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	53.311081	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	36.243843	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	48.331791	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	49.709194	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	48.644009	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	35.351284	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	40.991615	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	37.993984	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	33.437893	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	34.130737	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	36.972626	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	33.546333	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	34.454922	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	23.523476	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	31.92819	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	32.300602	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	28.63702	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	32.131931	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	42.636322	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	31.556208	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	27.766401	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	36.446571	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	30.523453	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	34.901405	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	40.602268	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	32.786392	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	27.936443	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	26.770611	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	26.145073	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	13.89863		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	11.256157		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	12.285296		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	31.601534		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	26.395864		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	24.980675		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	25.723949		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	17.52351		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	20.052853		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	28.981449	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	33.144157	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	33.083973	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	77.778503	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	37.46627	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	43.959152	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	45.039597	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	63.594593	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	26.978891	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	21.17622	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	20.963806	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	21.33147	Jinnan Shiqin	flower bud	early flowering period	early flowering period

Network

🔍 Co-expression Network

🔍 Protein-Protein Interaction Network

Orthology

Family	Species	Count	Orthologous Genes
Amaranthaceae	Chenopodium album	1	gene:ENSEOMG00000000970
Apiaceae	Apium graveolens	1	Ag6G02827
Arecaceae	Cocos nucifera	1	COCNU_01G020030
Brassicaceae	Brassica nigra	5	BniB01g013650.2N, BniB04g036870.2N, BniB06g058710.2N ... BniB06g058720.2N, BniB07g004560.2N
Casuarinaceae	Casuarina glauca	1	Cgl09G0209
Malvaceae	Hibiscus hamabo Siebold & Zucc.	3	nbisL1-mrna-12324, nbisL1-mrna-12360, nbisL1-mrna-1654
Plumbaginaceae	Limonium bicolor	1	Lb3G16609
Poaceae	Puccinellia tenuiflora	1	Pt_Chr0106080
Rhizophoraceae	Kandelia obovata	1	Maker00002798