Basic Information
Locus ID:
gene_16634
Species & Taxonomic ID:
Mesembryanthemum crystallinum & 3544
Genome Assembly:
Koichi Toyokura Assembly
Description:
DNA ligase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| Super-Scaffold_4_Chr_5 | 3614522 | 3625303 | - | gene_16634 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.93 | 156,174.77 Da | 44.92 | 83.79 | -0.27 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd07969 | OBF_DNA_ligase_I | 1243 | 1387 | 2.443E-81 | - |
| CDD | cd07900 | Adenylation_DNA_ligase_I_Euk | 979 | 1238 | 3.90397E-92 | - |
| CDD | cd16273 | SNM1A-1C-like_MBL-fold | 62 | 210 | 1.3126E-68 | - |
| Pfam | PF04675 | DNA ligase N terminus | 745 | 921 | 1.7E-35 | IPR012308 |
| Pfam | PF07522 | DNA repair metallo-beta-lactamase | 289 | 386 | 1.3E-15 | IPR011084 |
| Pfam | PF04679 | ATP dependent DNA ligase C terminal region | 1261 | 1369 | 9.1E-20 | IPR012309 |
| Pfam | PF01068 | ATP dependent DNA ligase domain | 990 | 1235 | 4.2E-41 | IPR012310 |
| SUPERFAMILY | SSF117018 | ATP-dependent DNA ligase DNA-binding domain | 725 | 973 | 1.7E-71 | IPR036599 |
| SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 949 | 1237 | 7.67E-36 | - |
| SUPERFAMILY | SSF56281 | Metallo-hydrolase/oxidoreductase | 88 | 386 | 1.08E-30 | IPR036866 |
| SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 1243 | 1388 | 1.28E-40 | IPR012340 |
| Gene3D | G3DSA:2.40.50.140 | - | 1241 | 1396 | 4.6E-56 | - |
| Gene3D | G3DSA:3.30.1490.70 | - | 1150 | 1240 | 3.1E-19 | - |
| Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 990 | 1129 | 2.8E-39 | - |
| Gene3D | G3DSA:3.40.50.12650 | - | 213 | 369 | 6.1E-82 | - |
| Gene3D | G3DSA:1.10.3260.10 | - | 723 | 989 | 3.5E-92 | IPR036599 |
| Gene3D | G3DSA:3.60.15.10 | - | 67 | 386 | 6.1E-82 | IPR036866 |
| ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 1099 | 1273 | 30.633577 | IPR012310 |
| ProSitePatterns | PS00697 | ATP-dependent DNA ligase AMP-binding site. | 1014 | 1022 | - | IPR016059 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 687 | 701 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 500 | 528 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 687 | 706 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 542 | 581 | - | - |
Gene Ontology
Biological Process:
KEGG Pathway
Pathway:
Reaction:
R00381 (ATP + DNA(n) + 5'-Phospho-DNA(m) <=> AMP + Diphosphate + DNA(n+m))
R00382 (NAD+ + DNA(n) + 5'-Phospho-DNA(m) <=> AMP + Nicotinamide D-ribonucleotide + DNA(n+m))
R10822 (ADP + DNA(n) + 5'-Phospho-DNA(m) <=> AMP + Orthophosphate + DNA(n+m))
R10823 (GTP + DNA(n) + 5'-Phospho-DNA(m) <=> GMP + Diphosphate + DNA(n+m))
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G66730.1 | DNA LIGASE 6. Encodes a novel plant specific DNA ligase that is involved in seed germination and DNA repair. | 0 |
| RefSeq | XP_021862657.1 | DNA ligase 6 isoform X2 [Spinacia oleracea] | 0 |
| F4HPZ9 | DNA ligase 6 OS=Arabidopsis thaliana OX=3702 GN=LIG6 PE=2 SV=1 | 0 | |
| TrEMBL | A0A0K9RBV0 | DNA ligase OS=Spinacia oleracea OX=3562 GN=SOVF_088680 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| No sample metadata found. | |||||||
Network
No network data available for this species.
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg39833 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_16634 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah035542 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_2g027400 |
| Amaranthaceae | Salicornia bigelovii | 3 | Sbi_jg20899, Sbi_jg20901, Sbi_jg22882 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg16744 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00008435 |
| Amaranthaceae | Suaeda glauca | 3 | Sgl62191, Sgl62221, Sgl66753 |
| Amaranthaceae | Chenopodium album | 4 | gene:ENSEOMG00000018823, gene:ENSEOMG00000020288 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.2AG0018750, CQ.Regalona.r1.2BG0020440 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30191030 |
| Apiaceae | Apium graveolens | 1 | Ag5G00446 |
| Arecaceae | Cocos nucifera | 1 | COCNU_06G008000 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103705614 |
| Asparagaceae | Asparagus officinalis | 4 | AsparagusV1_01.2163.V1.1, AsparagusV1_04.1989.V1.1 ... |
| Asteraceae | Flaveria trinervia | 1 | Ftri18G06628 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT1G66730.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10018010m.g.v1.0 |
| Brassicaceae | Brassica nigra | 1 | BniB03g043990.2N |
| Casuarinaceae | Casuarina glauca | 1 | Cgl08G0663 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g10210 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0865s00004.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate02g36310 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG02.509 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00029645 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb2G15502, Lb6G29725 |
| Poaceae | Echinochloa crus-galli | 3 | AH02.2791, BH02.2921, CH02.3668 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1BG0079130, gene-QOZ80_1BG0079140 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0280850.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_054623 |
| Poaceae | Oryza coarctata | 2 | Oco01G017520, Oco02G017750 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g49180.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G235400 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0602385 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr02G012450, Chr03G013700, Chr08G013860 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G440100 |
| Poaceae | Triticum dicoccoides | 3 | gene_TRIDC2BG049630, gene_TRIDC3AG039520 ... |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G264800.1, TraesCS3B02G298100.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb156510_P003, Zm00001eb275110_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-12596 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g8446 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG05.760, evm.TU.LG25.564 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g19280 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_6_RagTag.1266 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-16235 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-12015 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-1091 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000011l.818 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00007581 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-13482 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-3984 |
| Salicaceae | Populus euphratica | 1 | populus_peu09595 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132622464 |
| Solanaceae | Solanum chilense | 1 | SOLCI003032800 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107011627 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_9842 |
| Tamaricaceae | Tamarix chinensis | 1 | TC08G0719 |