Updated Annotations for Echinicola vietnamensis KMM 6221, DSM 17526

Updated annotations for Echinicola vietnamensis KMM 6221, DSM 17526

60 genes with updated (or confirmed) annotations:

Echvi_0119 : Proline dehydrogenase (EC 1.5.5.2)
Original description: Proline dehydrogenase
SEED: Carbapenem antibiotics biosynthesis protein carD
KEGG: proline dehydrogenase
Rationale: Specifically important for utilizing L-Proline. Automated validation from mutant phenotype: the predicted function (1.5.5.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_0120 : 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphate synthase / chorismate mutase (EC 2.5.1.54; EC 5.4.99.5)
Original description: 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
SEED: 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphate synthase I beta (EC 2.5.1.54) / Chorismate mutase I (EC 5.4.99.5)
KEGG: no annotation
Rationale: Important for fitness in most defined media. The N-terminal DHAP region is only 33% identical to the Pyrococcus enzyme (Q8U0A9) but the active site and substrate-binding residues are conserved. The C-terminal chorismate mutase region is diverged but hits PF01817 and no other chorismate mutase was found in the genome.

Echvi_0123 : prephenate and/or arogenate dehydratase (EC 4.2.1.51)
Original description: Prephenate dehydratase
SEED: Prephenate dehydratase (EC 4.2.1.51)
KEGG: prephenate dehydratase
Rationale: Important for fitness in defined media unless phenylalanine is provided. 34% identical to prephenate/arogenate dehydratase from Oryza sativa (Q6Z3Y3). It is uncertain whether dehydration occurs first or transamination (to arogenate) occurs first.

Echvi_0503 : L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
Original description: Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases
SEED: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
KEGG: L-ribulose-5-phosphate 4-epimerase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (RIBULPEPIM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Echvi_0515 : Ribulokinase (EC 2.7.1.16)
Original description: L-ribulokinase
SEED: Ribulokinase (EC 2.7.1.16)
KEGG: L-ribulokinase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (RXN0-5116) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Echvi_0566 : TonB-dependent receptor for glucose (SusC-like)
Original description: TonB-linked outer membrane protein, SusC/RagA family
SEED: SusC, outer membrane protein involved in starch binding
KEGG: no annotation
Rationale: Specifically important for utilization of D-glucose.

Echvi_0567 : outer membrane binding protein for glucose (SusD-like)
Original description: SusD family.
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important for utilization of D-glucose.

Echvi_0577 : Ornithine aminotransferase (EC 2.6.1.13)
Original description: ornithine aminotransferase
SEED: Ornithine aminotransferase (EC 2.6.1.13)
KEGG: ornithine--oxo-acid transaminase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (ORNITHINE-GLU-AMINOTRANSFERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Echvi_0695 : UDP-glucose--hexose-1-phosphate uridylyltransferase (EC 2.7.7.12)
Original description: galactose-1-phosphate uridylyltransferase, family 1
SEED: Galactose-1-phosphate uridylyltransferase (EC 2.7.7.10)
KEGG: UDPglucose--hexose-1-phosphate uridylyltransferase
Rationale: Specifically important for utilizing D-Galactose; this is part of the Leloir pathway

Echvi_0697 : Aldose 1-epimerase (EC 5.1.3.3)
Original description: Galactose mutarotase and related enzymes
SEED: Aldose 1-epimerase (EC 5.1.3.3)
KEGG: aldose 1-epimerase
Rationale: Specifically important for utilizing D-Galactose. Automated validation from mutant phenotype: the predicted function (5.1.3.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_0867 : uvrA paralog in Bacteroidetes
Original description: excinuclease ABC, A subunit
SEED: Excinuclease ABC subunit A paralog in greater Bacteroides group
KEGG: excinuclease ABC subunit A
Rationale: # Specifically important in stress Cisplatin; stress D-Cycloserine. Both the "standard" uvrA and this gene were important for cisplatin resistance. (SEED_correct)

Echvi_1106 : transmembrane glucosamine N-acetyltransferase NagX
Original description: Uncharacterized conserved protein
SEED: N-acetylglucosamine related transporter, NagX
KEGG: no annotation
Rationale: Specifically important for glucosamine utilization. NagX proteins are distantly related to human HGSNAT (uniprot:Q68CP4), which is a transmembrane acetyl-CoA:alpha-glucosaminide N-acetyltransferase.

Echvi_1295 : diaminopimelate decarboxylase (EC 4.1.1.20)
Original description: diaminopimelate decarboxylase
SEED: Diaminopimelate decarboxylase (EC 4.1.1.20)
KEGG: diaminopimelate decarboxylase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01048.

Echvi_1427 : putative N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18)
Original description: amidohydrolase
SEED: N-acetyl-L,L-diaminopimelate deacetylase (EC 3.5.1.47)
KEGG: amidohydrolase
Rationale: # This putative amidohydrolase, and several homologs, are essential, and probably replace the missing DapE

Echvi_1472 : UDP-glucose 4-epimerase (EC 5.1.3.2)
Original description: UDP-glucose-4-epimerase
SEED: UDP-glucose 4-epimerase (EC 5.1.3.2)
KEGG: UDP-glucose 4-epimerase
Rationale: Important for utilizing D-Galactose; this is part of the Leloir pathway

Echvi_1572 : Lactaldehyde dehydrogenase (EC 1.2.1.22); Rhamnulose-1-phosphate aldolase (EC 4.1.2.19)
Original description: rhamnulose-1-phosphate aldolase/alcohol dehydrogenase
SEED: Predicted rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / Predicted lactaldehyde dehydrogenase (EC 1.2.1.22)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Rhamnose monohydrate. Automated validation from mutant phenotype: the predicted function (1.2.1.22, 4.1.2.19) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_1573 : L-rhamnose isomerase (EC 5.3.1.14)
Original description: Predicted sugar isomerase
SEED: L-rhamnose isomerase (EC 5.3.1.14)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Rhamnose monohydrate. Automated validation from mutant phenotype: the predicted function (5.3.1.14) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_1574 : Rhamnulokinase (EC 2.7.1.5)
Original description: Sugar (pentulose and hexulose) kinases
SEED: Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Rhamnose monohydrate. Automated validation from mutant phenotype: the predicted function (2.7.1.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_1587 : Saccharopine dehydrogenase (NADP(+), L-lysine-forming) (EC 1.5.1.8); Saccharopine dehydrogenase (NAD(+), L-glutamate-forming) (EC 1.5.1.9)
Original description: Alanine dehydrogenase
SEED: Lysine ketoglutarate reductase (EC 1.5.1.8) (LOR) (LKR) / Saccharopine dehydrogenase (EC 1.5.1.9)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (1.5.1.8, 1.5.1.9) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_1617 : L-rhamnose transporter
Original description: hypothetical protein
SEED: Pedicted L-rhamnose permease, NCS1 Family
KEGG: no annotation
Rationale: Specifically important for utilizing L-rhamnose. Predicted to have 11 transmembrane helices and belongs to the Solute carrier families 5 and 6-like superfamily (CDD cl00456).

Echvi_1841 : predicted cytochrome c component of periplasmic glycoside 3-dehydrogenase (EC 1.1.99.13)
Original description: Cytochrome c551/c552
SEED: Cytochrome c551/c552
KEGG: no annotation
Rationale: Important for utilizing various glucosides (salicin, trehalose, cellobiose, and perhaps lactose). In a conserved cluster with the 3-ketoglycoside pathway starting with lacAC.

Echvi_1842 : 3-ketohexose dehydratase
Original description: Sugar phosphate isomerases/epimerases
SEED: Inosose isomerase (EC 5.3.99.-)
KEGG: no annotation
Rationale: Important for utilizing various glycosides (salicin, trehalose, cellobiose, and lactose). In a conserved cluster with the 3-ketoglycoside pathway starting with lacAC. 67% identical to the Agrobacterium enzyme (AtHyd, PMC10628242). The role in beta-lactose utilization suggests that it is a 3-ketogalactose dehydratase as well as a 3-ketoglucose dehydratase..

Echvi_1844 : 3-ketohexose reductase (NADH)
Original description: Predicted dehydrogenases and related proteins
SEED: Nucleoside-diphosphate-sugar epimerases
KEGG: no annotation
Rationale: Specifically important for utilization of salicin and cellobiose. In a conserved cluster with the 3-ketoglycoside pathway starting with lacAC. 29% identical to 3-ketoglucose reductase lgdC (BCB28826.1, see PMC7676230), which uses NADH as the electron donor.

Echvi_1845 : 2-hydroxy-3-keto-glucal transporter
Original description: Nucleoside H+ symporter.
SEED: Putative nucleoside transporter yegT
KEGG: no annotation
Rationale: Specifically important in carbon source D-Salicin; carbon source D-Trehalose dihydrate. In a conserved cluster with the 3-ketoglycoside pathway starting with lacAC. The 3-ketoglycoside is probably cleaved in the periplasm by Echvi_2921 or Echvi_1840, yielding 2-hydroxy-3-keto-glucal. Hydration of the product to 3-ketoglucose appears to occur in the cytoplasm (Echvi_1842), so this is probably a 2-hydroxy-3-keto-glucal transporter.

Echvi_1846 : 3-keto-beta-glycoside 1,2-lyase
Original description: Hydroxypyruvate isomerase
SEED: Hydroxypyruvate isomerase (EC 5.3.1.22)
KEGG: hydroxypyruvate isomerase
Rationale: Specifically important in carbon source D-Salicin. In a conserved cluster with the 3-ketoglycoside pathway starting with lacAC. Distantly related to BT2156, which is a 3-keto-beta-glucoside lyase (PMID:38898276).

Echvi_1847 : periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13)
Original description: Choline dehydrogenase and related flavoproteins
SEED: Glucose-methanol-choline (GMC) oxidoreductase:NAD binding site
KEGG: no annotation
Rationale: Important for utilization of various glucosides (trehalose, salicin, cellobiose, and perhaps lactose). Related to lacA of Caulobacter crescentus which is a component of lactose 3-dehydrogenase.

Echvi_1848 : periplasmic glucoside 3-dehydrogenase (lacC subunit) (EC 1.1.99.13)
Original description: hypothetical protein
SEED: FIG01111510: hypothetical protein
KEGG: no annotation
Rationale: Important for utilization of various glucosides (trehalose, salicin, cellobiose, and perhaps lactose). Related to lacC of Caulobacter crescentus which is a component of lactose 3-dehydrogenase.

Echvi_1871 : transporter for D-glucose/D-galactose/D-xylose/methyl-beta-D-galactopyranoside
Original description: transporter, SSS family
SEED: Predicted sodium-dependent galactose transporter
KEGG: solute:Na+ symporter, SSS family
Rationale: Important for utilizing glucose, galactose, xylose, and methyl-b-D-galactopyranoside, but not in most other carbon source experiments

Echvi_1875 : xylulokinase (EC 2.7.1.17)
Original description: Sugar (pentulose and hexulose) kinases
SEED: Xylulose kinase (EC 2.7.1.17)
KEGG: xylulokinase
Rationale: Specifically important for xylose utilization. Also important during utilization of some nitrogen sources (with glucose as the carbon source), which is not explained.

Echvi_1876 : Xylose isomerase (EC 5.3.1.5)
Original description: xylose isomerase
SEED: Xylose isomerase (EC 5.3.1.5)
KEGG: xylose isomerase
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLISOM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Echvi_1879 : L-arabinose isomerase (EC 5.3.1.4)
Original description: L-arabinose isomerase
SEED: L-arabinose isomerase (EC 5.3.1.4)
KEGG: L-arabinose isomerase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (ARABISOM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Echvi_1880 : L-arabinose symporter
Original description: transporter, SSS family
SEED: Predicted sodium-dependent galactose transporter
KEGG: solute:Na+ symporter, SSS family
Rationale: Specifically important for L-arabinose utilization.

Echvi_1890 : molybdopterin molybdotransferase MoeA (EC 2.10.1.1)
Original description: molybdenum cofactor synthesis domain
SEED: Molybdopterin biosynthesis protein MoeA
KEGG: molybdopterin biosynthesis protein MoeA
Rationale: Specific phenotype: utilization of nitrate. There’s another protein with this domain but it has no relevant phenotypes, showing that this is MoeA. (molybdenum cofactor is required for nitrate reduction)

Echvi_1901 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase [NAD(P)H], large subunit
SEED: Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
KEGG: nitrite reductase (NAD(P)H) large subunit
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_1912 : Nitrate reductase (EC 1.7.99.4)
Original description: Uncharacterized anaerobic dehydrogenase
SEED: Assimilatory nitrate reductase large subunit (EC:1.7.99.4)
KEGG: no annotation
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.99.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_2000 : aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3)
Original description: aspartate kinase
SEED: Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)
KEGG: bifunctional aspartokinase / homoserine dehydrogenase 1
Rationale: Important for fitness in most defined media. 40% identical to a bifunctional aspartokinase/homoserine dehydrogenase from Arabidopsis (O81852).

Echvi_2001 : homoserine kinase (EC 2.7.1.39)
Original description: homoserine kinase
SEED: Homoserine kinase (EC 2.7.1.39)
KEGG: homoserine kinase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00191.

Echvi_2057 : acetohydroxybutanoate synthase regulatory subunit (EC 2.2.1.6)
Original description: acetolactate synthase, small subunit
SEED: Acetolactate synthase small subunit (EC 2.2.1.6)
KEGG: acetolactate synthase I/III small subunit
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00119.

Echvi_2220 : pif1-like DNA repair helicase
Original description: PIF1 helicase.
SEED: RecD-like DNA helicase Atu2026
KEGG: exodeoxyribonuclease V
Rationale: # Specifically important in stress Cisplatin; stress Nalidixic acid sodium salt; stress Lomefloxacin hydrochloride. Contains a pif1-like helicase domain and probably part of the RecD superfamily (see CDD). (SEED_correct)

Echvi_2275 : translesion DNA polymerase (imuC-like)
Original description: DNA polymerase III, alpha subunit
SEED: DNA polymerase III alpha subunit (EC 2.7.7.7)
KEGG: DNA polymerase III subunit alpha
Rationale: # Specifically important in stress Cisplatin. Distantly related (less than 30% identity) to imuC (also known as dnaE2), which is a translesion DNA polymerase that is involved in DNA repair in Pseudomonas and Mycobacteria (see PMC3090020).

Echvi_2395 : 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
Original description: dihydrodipicolinate reductase
SEED: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
KEGG: dihydrodipicolinate reductase
Rationale: A conserved essential gene. This activity is necessary to explain lysine biosynthesis. 34% identical to dapB from Thermotoga maritima (Q9X1K8).

Echvi_2515 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
SEED: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
KEGG: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00007.

Echvi_2564 : DNA repair nuclease with dnaQ and GIY-YIG domains
Original description: exonuclease, DNA polymerase III, epsilon subunit family
SEED: DNA polymerase III epsilon subunit (EC 2.7.7.7)
KEGG: DNA polymerase III subunit epsilon
Rationale: # Specifically important in stress Cisplatin. Contains a domain that is similar to DnaQ (the epsilon subunit of replicative DNA polymerase which is the exonuclease for proofreading) as well as a GIY-YIG nuclease domain.This protein is often misannotated as DnaQ, but the proofreading activity of the replicative DNA polymerase seems to reside in the same polypeptide as the catalytic subunit (see Echvi_2020 or discussion in PMC3919608).

Echvi_2633 : gamma-glutamylphosphate reductase (EC 1.2.1.41)
Original description: gamma-glutamyl phosphate reductase
SEED: Gamma-glutamyl phosphate reductase (EC 1.2.1.41)
KEGG: glutamate-5-semialdehyde dehydrogenase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00407.

Echvi_2777 : fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3)
Original description: Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like
SEED: D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
KEGG: D-3-phosphoglycerate dehydrogenase
Rationale: # Important for fitness in defined media, unless serine is added as a nitrogen source. The N-terminal part is distantly related to the phosphoserine phosphatase from Arabidopsis, and no other candidate was found for this step. The C-terminal part is 52% identical to E. coli phosphoglycerate dehydrogenase.

Echvi_2804 : Fructokinase (EC 2.7.1.4)
Original description: Sugar kinases, ribokinase family
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing D-Fructose. Automated validation from mutant phenotype: the predicted function (2.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_2850 : Alpha-amylase (EC 3.2.1.1)
Original description: Glycosidases
SEED: Alpha-amylase (EC 3.2.1.1)
KEGG: no annotation
Rationale: Specifically important for utilizing a-Cyclodextrin. Automated validation from mutant phenotype: the predicted function (3.2.1.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Echvi_2921 : 3-keto-alpha-glucoside 1,2-lyase
Original description: Domain of Unknown Function (DUF1080).
SEED: putative multi-domain protein
KEGG: no annotation
Rationale: Specifically important in carbon source D-Trehalose dihydrate, which appears to be catabolized via the 3-ketoglycoside pathway. Distantly related to the 3-ketoglycoside lyase BT2157. This protein may be partially redundant with homologs (i.e. Echvi_1840, which is in a conserved cluster with the 3-ketoglycoside pathway starting with lacABC). Echvi_2921 is probably periplasmic.

Echvi_3375 : 3-ketohexose reductase (NADH)
Original description: Predicted dehydrogenases and related proteins
SEED: Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
KEGG: no annotation
Rationale: Specifically important in carbon source D-Salicin, which appears to be catabolized via the 3-ketoglycoside pathway. 51% identical to 3-ketoglucose reductase lgdC (BCB28826.1, see PMC7676230), which uses NADH as the electron donor.

Echvi_3774 : nitrite transporter, HPP family
Original description: CBS-domain-containing membrane protein
SEED: no annotation
KEGG: no annotation
Rationale: # Specifically detrimental during growth at high nitrite concentrations. Related to Synpcc7942_1745, which is a nitrite transporter (PMID:24904028)

Echvi_3833 : 2-isopropylmalate synthase (EC 2.3.3.13)
Original description: Isopropylmalate/homocitrate/citramalate synthases
SEED: 2-isopropylmalate synthase (EC 2.3.3.13)
KEGG: 2-isopropylmalate synthase
Rationale: Important for fitness in defined media unless leucine is provided. 55% identical to 2-isopropylmalate synthase from Leptospira interrogans (Q8F445).

Echvi_3845 : N-succinylglutamate synthase
Original description: N-acetylglutamate synthase and related acetyltransferases
SEED: FIG00651573: hypothetical protein
KEGG: no annotation
Rationale: This gene is in an operon with and conserved cofit with other arginine synthesis genes. The traditional synthase (argA) is not present. This protein is 63% identical to Cabys_1732 which is reported to be a N-acetylglutamate synthase (PMID:28265262). However, Bacteroidetes are thought to use succinylated intermediates for arginine synthesis (see PMID:32576650)

Echvi_3847 : N-succinylglutamylphosphate reductase (EC 1.2.1.-)
Original description: N-acetyl-gamma-glutamyl-phosphate reductase, common form
SEED: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
KEGG: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
Rationale: Important for fitness in most defined media, except when arginine or citrulline is provided. Hits TIGR01850, which is described as N-acetyl-gamma-glutamyl-phosphate reductase, but Bacteroidetes use succinylated intermediates for arginine synthesis (see PMC7311316).

Echvi_3848 : N-succinylornithine aminotransferase (EC 2.6.1.81)
Original description: Ornithine/acetylornithine aminotransferase
SEED: Acetylornithine aminotransferase (EC 2.6.1.11)
KEGG: acetylornithine aminotransferase
Rationale: Important for fitness in most defined media, except when arginine or citrulline is provided. Similar to acetylornithine aminotransferases (such as argD from B. subtilis), but Bacteroidetes use succinylated intermediates for arginine synthesis (see PMC7311316).

Echvi_3849 : N-succinylornithine carbamoyltransferase (EC 2.1.3.11)
Original description: Ornithine carbamoyltransferase
SEED: Ornithine carbamoyltransferase (EC 2.1.3.3)
KEGG: N-succinyl-L-ornithine transcarbamylase
Rationale: Important for fitness in most defined media, except when arginine is provided. 45% identical to the N-succinylornithine carbamoyltransferase of B. fragilis (E1WKT5)

Echvi_3851 : N-succinylcitrulline desuccinylase (EC 3.5.1.-)
Original description: Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases
SEED: Acetylornithine deacetylase (EC 3.5.1.16)
KEGG: acetylornithine deacetylase
Rationale: Important for fitness in most defined media, except when arginine is provided. Distantly related to succinyl-diaminopimelate desuccinylases, so this probably provides the missing N-succinylcitrulline desuccinylase activity. See PMC7311316.

Echvi_3852 : arginosuccinate lyase (EC 4.3.2.1)
Original description: argininosuccinate lyase
SEED: Argininosuccinate lyase (EC 4.3.2.1)
KEGG: argininosuccinate lyase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00838.

Echvi_4033 : glutamate 5-kinase (EC 2.7.2.11)
Original description: glutamate 5-kinase
SEED: no annotation
KEGG: glutamate 5-kinase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01027.

Echvi_4214 : lysine/tyrosine outer membrane transporter, TonB-dependent receptor component
Original description: Outer membrane receptor proteins, mostly Fe transport
SEED: no annotation
KEGG: no annotation
Rationale: # Specifically important in nitrogen source L-Lysine; nitrogen source L-tyrosine disodium salt. Echvi_4214 is a TonB-dependent outer membrane transporter that is required for utilization of lysine. Mutants also have a defect in tyrosine utilization. It probably functions with Echvi_4215, which is cofit and part of a conserved gene cluster. Inner membrane protein Echvi_4216 (PFam PepSY_TM) is also conserved nearby but does not have a phenotype; it may have a regulatory role.

Echvi_4215 : lysine/tyrosine outer membrane transporter, accessory component
Original description: hypothetical protein
SEED: no annotation
KEGG: no annotation
Rationale: # Specifically important in nitrogen source L-Lysine; nitrogen source L-tyrosine disodium salt. Echvi_4215 is an outer membrane lipoprotein that has very similar phenotypes as an adjacent TonB-dependent receptor (Echvi_4214). Jackhmmer searches found that Echvi_4215 is distantly related to DUF4374; both Echvi_4215 and DUF4374 have conserved proximity to TonB-dependent receptors. Echvi_4215 and relatd proteins are probably accessory proteins for uptake, analagous to the SusD family, but not homolgous. (SusD-like proteins are not found in proximity to Echvi_4214 or its homologs.)

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