halophFGD

Basic Information

Locus ID: BniB04g037180.2N

Species & Taxonomic ID: Brassica nigra & 3710

Genome Assembly: N100

Description: Interconversion of serine and glycine

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
B4	19825934	19827998	+	BniB04g037180.2N

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
7.21	66,090.23 Da	50.39	73.51	-0.40

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
CDD	cd00378	SHMT	140	550	0.0	IPR001085
Pfam	PF00464	Serine hydroxymethyltransferase	138	542	9.5E-169	IPR039429
SUPERFAMILY	SSF53383	PLP-dependent transferases	127	593	1.13E-165	IPR015424
Gene3D	G3DSA:3.40.640.10	-	167	447	3.1E-192	IPR015421
Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1	142	591	3.1E-192	IPR015422
ProSitePatterns	PS00096	Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.	362	378	-	IPR019798
Hamap	MF_00051	Serine hydroxymethyltransferase [glyA].	137	592	39.77232	IPR001085
MobiDBLite	mobidb-lite	consensus disorder prediction	1	33	-	-

Gene Ontology

Biological Process:

GO:0019264 (glycine biosynthetic process from serine) GO:0035999 (tetrahydrofolate interconversion)

Molecular Function:

GO:0003824 (catalytic activity) GO:0004372 (glycine hydroxymethyltransferase 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_018438808.1	PREDICTED: serine hydroxymethyltransferase 6 [Raphanus sativus]
Swiss-Prot	Q9LM59	Serine hydroxymethyltransferase 6 OS=Arabidopsis thaliana OX=3702 GN=SHM6 PE=1 SV=1
TrEMBL	A0A8X7V5Z9	Uncharacterized protein OS=Brassica carinata OX=52824 GN=Bca52824_032220 PE=4 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
No sample metadata found.

Network

🔍 Protein-Protein Interaction Network

Orthology

Family	Species	Count	Orthologous Genes
Acanthaceae	Avicennia marina	3	jg1286, jg26404, jg30084
Aizoaceae	Mesembryanthemum crystallinum	2	gene_19313, gene_24838
Amaranthaceae	Atriplex hortensis	1	Ah025164
Amaranthaceae	Beta vulgaris	1	BVRB_6g143730
Amaranthaceae	Salicornia bigelovii	2	Sbi_jg41930, Sbi_jg48201
Amaranthaceae	Salicornia europaea	1	Seu_jg27550
Amaranthaceae	Suaeda aralocaspica	1	GOSA_00021971
Amaranthaceae	Chenopodium album	1	gene:ENSEOMG00000026959
Amaranthaceae	Chenopodium quinoa	2	CQ.Regalona.r1.6AG0011740, CQ.Regalona.r1.6BG0012560
Anacardiaceae	Pistacia vera	1	pistato.v30040380
Apiaceae	Apium graveolens	1	Ag1G00709
Arecaceae	Cocos nucifera	2	COCNU_02G011180, COCNU_15G002830
Arecaceae	Phoenix dactylifera	3	gene-LOC103701327, gene-LOC103702634, gene-LOC103719953
Asparagaceae	Asparagus officinalis	2	AsparagusV1_02.668.V1.1, AsparagusV1_09.690.V1.1
Asteraceae	Flaveria trinervia	2	Ftri15G12832, Ftri4G20388
Brassicaceae	Arabidopsis thaliana	2	AT1G22020.1, AT1G36370.1
Brassicaceae	Eutrema salsugineum	2	Thhalv10003888m.g.v1.0, Thhalv10007136m.g.v1.0
Brassicaceae	Schrenkiella parvula	2	Sp1g19530.v2.2, Sp1g30960.v2.2
Brassicaceae	Brassica nigra	3	BniB03g020050.2N, BniB04g037180.2N, BniB07g014550.2N
Casuarinaceae	Casuarina equisetifolia	2	Ceq09G0176, Ceq09G1911
Casuarinaceae	Casuarina glauca	1	Cgl09G2085
Cymodoceaceae	Cymodocea nodosa	2	gene.Cymno07g01800, gene.Cymno08g07320
Hydrocharitaceae	Thalassia testudinum	3	gene.Thate01g13400, gene.Thate03g19860, gene.Thate05g13340
Malvaceae	Hibiscus hamabo Siebold & Zucc.	2	nbisL1-mrna-1655, nbisL1-mrna-5234
Nitrariaceae	Nitraria sibirica	2	evm.TU.LG06.986, evm.TU.LG08.755
Plantaginaceae	Plantago ovata	1	Pov_00002002
Plumbaginaceae	Limonium bicolor	1	Lb3G16625
Poaceae	Echinochloa crus-galli	3	AH02.4041, BH02.4053, CH02.4083
Poaceae	Eleusine coracana subsp. coracana	2	gene-QOZ80_1AG0041610, gene-QOZ80_1BG0091620
Poaceae	Hordeum vulgare	1	HORVU.MOREX.r3.3HG0298480.1
Poaceae	Lolium multiflorum	1	gene-QYE76_056890
Poaceae	Oryza coarctata	4	Oco01G026240, Oco02G027220, Oco09G010300, Oco10G010400
Poaceae	Oryza sativa	2	LOC_Os01g65410.1, LOC_Os05g35440.1
Poaceae	Paspalum vaginatum	1	gene-BS78_03G353200
Poaceae	Puccinellia tenuiflora	1	Pt_Chr0601240
Poaceae	Sporobolus alterniflorus	4	Chr02G003360, Chr05G029880, Chr08G021020, Chr23G013160
Poaceae	Thinopyrum elongatum	1	Tel3E01G613900
Poaceae	Triticum dicoccoides	2	gene_TRIDC3AG055130, gene_TRIDC3BG061710
Poaceae	Triticum aestivum	3	TraesCS3A02G385600.1, TraesCS3B02G417800.1 ... TraesCS3D02G378700.1
Poaceae	Zea mays	3	Zm00001eb090070_P001, Zm00001eb146170_P002 ... Zm00001eb366470_P002
Poaceae	Zoysia japonica	1	nbis-gene-11224
Poaceae	Zoysia macrostachya	2	Zma_g11647, Zma_g9107
Portulacaceae	Portulaca oleracea	2	evm.TU.LG02.1996, evm.TU.LG23.251
Posidoniaceae	Posidonia oceanica	2	gene.Posoc01g01960, gene.Posoc05g19240
Rhizophoraceae	Bruguiera sexangula	2	evm.TU.Scaffold_7_RagTag.1044, evm.TU.Scaffold_8_RagTag.692
Rhizophoraceae	Carallia pectinifolia	2	nbisL1-mrna-18799, nbisL1-mrna-9543
Rhizophoraceae	Ceriops tagal	2	nbisL1-mrna-14178, nbisL1-mrna-15118
Rhizophoraceae	Ceriops zippeliana	2	nbisL1-mrna-18241, nbisL1-mrna-6866
Rhizophoraceae	Kandelia candel	2	evm.TU.utg000002l.792, evm.TU.utg000018l.550
Rhizophoraceae	Kandelia obovata	1	Maker00010457
Rhizophoraceae	Rhizophora apiculata	2	nbisL1-mrna-2962, nbisL1-mrna-8181
Rhizophoraceae	Rhizophora mangle	2	nbisL1-mrna-20356, nbisL1-mrna-9898
Salicaceae	Populus euphratica	3	populus_peu02510, populus_peu14672, populus_peu32341
Solanaceae	Lycium barbarum	2	gene-LOC132598683, gene-LOC132606362
Solanaceae	Solanum chilense	1	SOLCI002907200
Solanaceae	Solanum pennellii	1	gene-LOC107007833
Tamaricaceae	Reaumuria soongarica	1	STRG.23054_chr05_-
Tamaricaceae	Tamarix chinensis	2	TC01G3684, TC04G0031
Zosteraceae	Zostera marina	1	Zosma04g23460.v3.1