Basic Information
Locus ID:
Ag5G02859
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
2-isopropylmalate synthase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr5 | 316634821 | 316642025 | + | Ag5G02859 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.06 | 65,783.62 Da | 34.91 | 95.80 | -0.05 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd07940 | DRE_TIM_IPMS | 67 | 346 | 1.74813E-180 | - |
| Pfam | PF08502 | LeuA allosteric (dimerisation) domain | 444 | 588 | 2.4E-34 | IPR013709 |
| Pfam | PF00682 | HMGL-like | 65 | 344 | 7.8E-96 | IPR000891 |
| SUPERFAMILY | SSF51569 | Aldolase | 61 | 362 | 3.3E-92 | - |
| SUPERFAMILY | SSF110921 | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 473 | 587 | 1.57E-16 | IPR036230 |
| Gene3D | G3DSA:3.30.160.270 | - | 470 | 588 | 7.5E-23 | IPR036230 |
| Gene3D | G3DSA:1.10.238.260 | - | 352 | 466 | 6.0E-36 | - |
| Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 60 | 350 | 8.4E-102 | IPR013785 |
| SMART | SM00917 | LeuA_dimer_2 | 443 | 588 | 2.2E-27 | IPR013709 |
| TIGRFAM | TIGR00973 | leuA_bact: 2-isopropylmalate synthase | 65 | 585 | 4.1E-200 | IPR005671 |
| ProSiteProfiles | PS50991 | Pyruvate carboxyltransferase domain. | 65 | 338 | 43.073479 | IPR000891 |
| ProSitePatterns | PS00815 | Alpha-isopropylmalate and homocitrate synthases signature 1. | 72 | 88 | - | IPR002034 |
| Hamap | MF_01025 | 2-isopropylmalate synthase [leuA]. | 62 | 597 | 39.927513 | IPR005671 |
Gene Ontology
Biological Process:
KEGG Pathway
Pathway:
ko00290 (Valine, leucine and isoleucine biosynthesis)
map00290 (Valine, leucine and isoleucine biosynthesis)
ko00620 (Pyruvate metabolism)
map00620 (Pyruvate metabolism)
ko01100 (Metabolic pathways)
map01100 (Metabolic pathways)
ko01110 (Biosynthesis of secondary metabolites)
map01110 (Biosynthesis of secondary metabolites)
ko01210 (2-Oxocarboxylic acid metabolism)
map01210 (2-Oxocarboxylic acid metabolism)
ko01230 (Biosynthesis of amino acids)
map01230 (Biosynthesis of amino acids)
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G74040.1 | 2-isopropylmalate synthase 1. Encodes an active Arabidopsis isopropylmalate synthase IPMS2. Involved in leucine biosynthesis. Do not participate in the chain elongation of glucosinolates. Expressed constitutively throughout the plant. Loss of IPMS2 can be compensated by a second isopropylmalate synthase gene IPMS1 (At1g18500). | 0 |
| RefSeq | XP_017219050.1 | PREDICTED: 2-isopropylmalate synthase A-like [Daucus carota subsp. sativus] | 0 |
| O04974 | 2-isopropylmalate synthase B OS=Solanum pennellii OX=28526 GN=IPMSB PE=2 SV=1 | 0 | |
| TrEMBL | A0A164SX13 | Pyruvate carboxyltransferase domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_023912 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 37.515892 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 26.915178 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 18.809101 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 19.262302 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 19.228918 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 16.468781 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 18.26676 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 12.378093 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 51.834541 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 51.156826 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 54.669197 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 56.94257 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 50.207672 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 49.625294 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 14.069509 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 20.526764 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 19.294876 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 29.967945 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 30.997936 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 28.662191 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 25.82136 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 22.175383 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 25.721712 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 25.900728 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 29.762243 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 33.263321 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 30.780943 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 31.928223 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 34.693859 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 5.096605 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 10.408381 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 9.387407 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 26.544054 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 21.783417 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 21.404266 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 16.995335 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 11.938165 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 12.530777 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 60.410431 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 30.01697 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 29.314573 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 13.98312 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 14.256325 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 44.598236 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 24.316355 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 21.980036 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 20.2679 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 32.936607 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 31.538467 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 33.633217 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg10976, jg10977, jg5907 |
| Aizoaceae | Mesembryanthemum crystallinum | 2 | gene_15767, gene_19447 |
| Amaranthaceae | Atriplex hortensis | 2 | Ah019627, Ah019628 |
| Amaranthaceae | Beta vulgaris | 2 | BVRB_3g058810, BVRB_3g058820 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg38490, Sbi_jg6594 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg15332 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00006427, GOSA_00006428 |
| Amaranthaceae | Suaeda glauca | 6 | Sgl01897, Sgl01898, Sgl07038, Sgl07039, Sgl44504, Sgl49273 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000011743, gene:ENSEOMG00000030441 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.3AG0011030, CQ.Regalona.r1.3BG0011260 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30243490 |
| Apiaceae | Apium graveolens | 1 | Ag5G02859 |
| Arecaceae | Cocos nucifera | 1 | COCNU_12G004560 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103705082 |
| Asparagaceae | Asparagus officinalis | 4 | AsparagusV1_04.1953.V1.1, AsparagusV1_04.1955.V1.1 ... |
| Asteraceae | Flaveria trinervia | 2 | Ftri11G03059, Ftri12G07723 |
| Brassicaceae | Arabidopsis thaliana | 4 | AT1G18500.1, AT1G74040.1, AT5G23010.1, AT5G23020.1 |
| Brassicaceae | Eutrema salsugineum | 5 | Thhalv10003976m.g.v1.0, Thhalv10004072m.g.v1.0 ... |
| Brassicaceae | Schrenkiella parvula | 5 | Sp1g16450.v2.2, Sp2g24100.v2.2, Sp2g24110.v2.2 ... |
| Brassicaceae | Brassica nigra | 8 | BniB02g076300.2N, BniB02g076310.2N, BniB03g028050.2N ... |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq06G2205, Ceq09G0942 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl06G2325, Cgl09G1024 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno05g02310 |
| Dunaliellaceae | Dunaliella salina | 2 | Dusal.0217s00013.v1.0, Dusal.0217s00014.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate08g08470 |
| Nitrariaceae | Nitraria sibirica | 4 | evm.TU.LG02.2457, evm.TU.LG11.123, evm.TU.LG11.124 ... |
| Plantaginaceae | Plantago ovata | 2 | Pov_00023467, Pov_00026884 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb7G33591 |
| Poaceae | Echinochloa crus-galli | 10 | AH02.813, AH04.240, AH05.159, BH02.108, BH02.135, BH04.237 ... |
| Poaceae | Eleusine coracana subsp. coracana | 4 | gene-QOZ80_5AG0380830, gene-QOZ80_5BG0427930 ... |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0460900.1 |
| Poaceae | Lolium multiflorum | 3 | gene-QYE76_003279, gene-QYE76_003349, gene-QYE76_052410 |
| Poaceae | Oryza coarctata | 4 | Oco21G000770, Oco22G001620, Oco23G001530, Oco24G000960 |
| Poaceae | Oryza sativa | 2 | LOC_Os11g04670.1, LOC_Os12g04440.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_05G039500 |
| Poaceae | Puccinellia tenuiflora | 3 | Pt_Chr0500049, Pt_Chr0703001, Pt_Chr0703081 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr16G009170, Chr17G008190 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G238500 |
| Poaceae | Triticum dicoccoides | 3 | gene_TRIDC5AG022230, gene_TRIDC5BG023720 ... |
| Poaceae | Triticum aestivum | 4 | TraesCS5A02G131300.1, TraesCS5B02G133500.1 ... |
| Poaceae | Zea mays | 4 | Zm00001eb093160_P001, Zm00001eb196510_P001 ... |
| Poaceae | Zoysia japonica | 2 | nbis-gene-27033, nbis-gene-51079 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g18398 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG04.828, evm.TU.LG05.2106, evm.TU.LG06.1512 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc01g05010 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_3_RagTag.1457 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-1766 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-1548 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-2684 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000019l.366 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00001810 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-12297 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-12819 |
| Salicaceae | Populus euphratica | 1 | populus_peu13845 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132609321, gene-LOC132643462 |
| Solanaceae | Solanum chilense | 3 | SOLCI004281200, SOLCI006467400, SOLCI006806900 |
| Solanaceae | Solanum pennellii | 5 | gene-LOC107023302, gene-LOC107026725, gene-LOC107026726 ... |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.14313_chr08_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC12G1851 |
| Zosteraceae | Zostera marina | 2 | Zosma02g23460.v3.1, Zosma03g21940.v3.1 |