Updated Annotations for Bacteroides thetaiotaomicron VPI-5482

Updated annotations for Bacteroides thetaiotaomicron VPI-5482

83 genes with updated (or confirmed) annotations:

BT0202 : histidinol-phosphate aminotransferase (EC 2.6.1.9)
Original description: histidinol-phosphate aminotransferase (NCBI ptt file)
SEED: Histidinol-phosphate aminotransferase (EC 2.6.1.9)
KEGG: histidinol-phosphate aminotransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01141.

BT0272 : TonB-dependent receptor for (+)-arabinogalactan (SusC-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: # Specifically important in carbon source (+)-Arabinogalactan

BT0273 : Outer membrane binding protein for (+)-arabinogalactan (SusD-like)
Original description: hypothetical protein (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: # Important on (+)-Arabinogalactan along with SusC-like BT0272

BT0350 : ribulokinase (EC 2.7.1.16)
Original description: xylulose kinase (xylulokinase) (NCBI ptt file)
SEED: Ribulokinase (EC 2.7.1.16)
KEGG: no annotation
Rationale: Specifically important for L-arabinose utilization, along with the arabinose isomerase BT0351, which forms ribulose, and the ribulose-5-phosphate epimerase BT0353. Also important for D-arabinose utilization, which is not explained.

BT0355 : L-arabinose/L-arabinobiose symporter
Original description: Na+/glucose cotransporter (NCBI ptt file)
SEED: Predicted sodium-dependent galactose transporter
KEGG: solute:Na+ symporter, SSS family
Rationale: Specifically important for L-arabinose utilization and also required for arabinobiose utilization (see PMC5061871). PMC5061871 proposed that it takes up arabinobiose, but because the arabinobiose hydrolase was not identified, it is not certain if arabinobiose is transported. Also important for D-arabinose utilization, but this seems to be a polar effect.

BT0528 : phosphoribosylanthranilate isomerase (EC 5.3.1.24)
Original description: putative N-(5'-phosphoribosyl)anthranilate isomerase (NCBI ptt file)
SEED: Phosphoribosylanthranilate isomerase (EC 5.3.1.24)
KEGG: phosphoribosylanthranilate isomerase
Rationale: Important for fitness in most defined media and strongly cofit with anthranilate phosphoribosyltransferase (BT0530). 37% identical to phosphoribosylanthranilate isomerase from Thermotoga maritima (Q56320)

BT0530 : anthranilate phosphoribosyltransferase (EC 2.4.2.18)
Original description: anthranilate phosphoribosyltransferase (NCBI ptt file)
SEED: Anthranilate phosphoribosyltransferase (EC 2.4.2.18)
KEGG: anthranilate phosphoribosyltransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01245.

BT0588 : BexA: efflux pump for ciprofloxacin, lomefloxacin, and paraquat
Original description: BexA, multidrug efflux pump (NCBI ptt file)
SEED: BexA, multidrug efflux pump
KEGG: no annotation
Rationale: Specifically important in stress Paraquat dichloride; stress Lomefloxacin hydrochloride; and potentially important during growth in ciprofloxacin, which is reported to be a substrate of this efflux pump (PMCID:PMC90835), along with norfloxacin and ethidium bromide.

BT0792 : xylulokinase (EC 2.7.1.17)
Original description: xylulose kinase (xylulokinase) (NCBI ptt file)
SEED: Xylulose kinase (EC 2.7.1.17)
KEGG: xylulokinase
Rationale: Specifically important for D-xylose utilization.

BT1118 : outer membrane binding protein for D-galacturonate and 1,4-beta-D-galactobiose (SusD-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: SusD, outer membrane protein
KEGG: no annotation
Rationale: Specifically important in carbon source D-Galacturonic Acid monohydrate and carbon source 1,4-B-D-Galactobiose along with the adjacent SusC-like protein (BT1119). This is a SusD-like protein that is probably on the outer membrane and binds the substrates.

BT1119 : TonB-dependent receptor for D-galacturonate and 1,4-beta-D-galactobiose (SusC-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: SusC, outer membrane protein involved in starch binding
KEGG: no annotation
Rationale: Specifically important in carbon source D-Galacturonic Acid monohydrate and perhaps 1,4-beta-D-galactobiose, along with the adjacent SusD-like protein (BT1118). This is a SusC-like protein that is probably a TonB-dependent receptor for uptake through the outer membrane.

BT1274 : L-fuculose-1-phosphate aldolase FucA (4.1.2.17); D-ribulose-1-phosphate aldolase
Original description: L-fuculose-1-phosphate aldolase (NCBI ptt file)
SEED: L-fuculose phosphate aldolase (EC 4.1.2.17)
KEGG: no annotation
Rationale: Specifically important for utilizing L-fucose and D-arabinose, which are catabolized via L-fucolose-1-phosphate or D-ribulose-1-phosphate.

BT1275 : L-fuculose kinase fucK (EC 2.7.1.51); D-ribulose kinase (EC 2.7.1.47)
Original description: L-fuculose kinase (NCBI ptt file)
SEED: L-fuculokinase (EC 2.7.1.51)
KEGG: L-fuculokinase
Rationale: Specifically important for L-fucose utilization, along with fucose isomerase BT1273 and fuculose-phosphate aldolase BT1274. Also important for D-arabinose utilization, so it is probably a D-ribulokinase as well.

BT1276 : L-fucose mutarotase FucU (EC 5.1.3.29)
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: L-fucose mutarotase, type 2
KEGG: no annotation
Rationale: Specifically important for utilization of L-fucose and D-arabinose. The phenotype on D-arabinose is strand-dependent and may be a polar effect on the downstream permease.

BT1277 : L-fucose/D-arabinose symporter FucP
Original description: L-fucose permease (NCBI ptt file)
SEED: Fucose permease
KEGG: MFS transporter, FHS family, L-fucose permease
Rationale: Specifically important for utilizing L-fucose and D-arabinose. The transporter BT0355 also has negative fitness during D-arabinose utilization, but the effect is strand-dependent, which suggests that it is a polar effect. BT1277 is probably the main D-arabinose transporter.

BT1374 : diaminopimelate decarboxylase (EC 4.1.1.20)
Original description: diaminopimelate decarboxylase (NCBI ptt file)
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.

BT1379 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (NCBI ptt file)
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.

BT1439 : Outer membrane binding protein for vancomycin (SusD-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: Specifically detrimental during vancomycin stress in BHIS media, along with the adjacent SusC-like protein BT1440

BT1440 : TonB-dependent receptor for vancomycin (SusC-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: SusC, outer membrane protein involved in starch binding
KEGG: no annotation
Rationale: Specifically detrimental during vancomycin stress in BHIS media, along with the adjacent SusD-like protein BT1439

BT1758 : fructose transporter
Original description: glucose/galactose transporter (NCBI ptt file)
SEED: Predicted glucose transporter in maltodextrin utilization gene cluster
KEGG: no annotation
Rationale: Specifically important for utilizing fructose. Also important for utilizing fructooligosaccharides. Part of a PUL for utilizing levan (PMC3225772).

BT1762 : Fructo-oligosaccharide transporter (SusD component)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: Specific phenotype: utilization of Fructooligosaccharides (FOS); also see PMC7782687 with biochemical data

BT1858 : (R)-citramalate synthase (EC 2.3.1.182)
Original description: 2-isopropylmalate synthase (NCBI ptt file)
SEED: (R)-citramalate synthase (EC 2.3.1.182)
KEGG: D-citramalate synthase
Rationale: Important for fitness in most defined media. Sometimes annotated as 2-isopropylmalate synthase, but that is probably BT1861.

BT1861 : 2-isopropylmalate synthase (EC 2.3.3.13)
Original description: 2-isopropylmalate synthase (NCBI ptt file)
SEED: 2-isopropylmalate synthase (EC 2.3.3.13)
KEGG: 2-isopropylmalate synthase
Rationale: Important for fitness in most defined media. Hits TIGR00973 and 47% identical to the 2-isopropylmalate synthase from Leptospira interrogans (Q8F445).

BT2076 : acetohydroxybutanoate synthase regulatory subunit (EC 2.2.1.6)
Original description: acetohydroxyacid synthase small subunit (NCBI ptt file)
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.

BT2080 : L-cysteine desulfidase cdsB
Original description: conserved hypothetical protein, putative inner membrane protein (NCBI ptt file)
SEED: Putative inner membrane protein
KEGG: no annotation
Rationale: # 44% identical to cdsB ADO66727.1 from Yersinia ruckeri (PMC3028680); important for fitness in minimal media with cysteine as a reductant, for cysteine detoxification

BT2157 : 3-keto-alpha-glucoside 1,2-lyase; 3-ketoglucose dehydratase
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: Probable secreted glycosyl hydrolase
KEGG: no annotation
Rationale: Important for the utilization of palatinose, D-trehalose, D-leucrose, and possibly raffinose. This gene is in a conserved cluster for disaccharide catabolism via the 3-ketoglycoside pathway. Originally proposed to be a hydrolase (PMC8121099), it is a lyase, forming 2-hydroxy-3-keto-D-glucal (PMID:38898276, PMID:37932298). It prefers 3-keto-alpha-glycoside substrates over beta substrates (PMID:38898276, PMID:37932298). At a lower rate than the lyase reaction, it hydrates 2-hydroxy-3-keto-D-glucal to 3-ketoglucose (PMID:38898276, PMID:37932298); this activity is also thought to be required for the 3-ketoglycoside pathway, as the 3-ketoglucose is converted to glucose for catabolism (see BT2159). This enzyme is probably in the periplasm.

BT2158 : glycoside 3-dehydrogenase (EC 1.1.99.13)
Original description: putative dehydrogenases and related proteins (NCBI ptt file)
SEED: Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
KEGG: no annotation
Rationale: This is a glycoside 3-dehydrogenase (PMID:38898276). It was difficult to map insertions in this gene because of a paralog, but reexamination of the data suggests that this gene has a similar fitness pattern as the surrounding genes and is important for growth on trehalose, leucrose, palatinose, and raffinose. And a clean deletion mutant failed to grow on trehalose. It has a TAT (twin arginine transport) signal and is probably exported together with its NAD(P) cofactor, as with the glucose:fructose oxidoreductase Gfo. It's unclear what the electron acceptor could be, given that this enzyme is in the periplasm and B.theta has a very limited electron transport chain. After cleavage by BT2157 (or BT2156, see PMID:38898276) and hydration by BT2157, the resulting 3-ketoglucose is reduced by BT2159, which appears to be cytoplasmic.

BT2159 : 3-ketoglucose reductase (NAD(P)H)
Original description: putative oxidoreductase (NCBI ptt file)
SEED: Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
KEGG: no annotation
Rationale: Specifically important in carbon source D-Trehalose dihydrate; carbon source palatinose hydrate; carbon source D-Raffinose pentahydrate; carbon source D-Leucrose. Reduces 3-ketoglucose (PMID:38898276). This enzyme appears to be cytoplasmic and the electron donor is probably NAD(P)H.

BT2160 : SusR4: regulator of disaccharide catabolism (SusR4)
Original description: putative regulatory protein (NCBI ptt file)
SEED: Regulatory protein SusR
KEGG: no annotation
Rationale: Specifically important in carbon source D-Trehalose dihydrate; carbon source palatinose hydrate; carbon source D-Raffinose pentahydrate; carbon source D-Leucrose. Predicted to regulate the operon BT2160:BT2156 (PMCID:PMC3878776)

BT2175 : L-fuculose kinase FucK (EC 2.7.1.51); D-ribulose 1-kinase
Original description: hypothetical protein (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important for utilizing L-fucose and D-arabinose, which are catabolized via L-fucolose-1-phosphate or D-ribulose-1-phosphate.

BT2186 : 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19)
Original description: 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file)
SEED: 5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19)
KEGG: 3-phosphoshikimate 1-carboxyvinyltransferase
Rationale: # This protein is essential, but a close homolog (HMPREF1058_RS13970) is cofit with other chorismate synthesis genes. Furthermore, this gene (also known as BT_RS11065) complemented an aroA- mutant of E. coli (data of PMID:39375541)

BT2403 : aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3)
Original description: aspartokinase/homoserine dehydrogenase (NCBI ptt file)
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. 37% identical to a bifunctional aspartokinase/homoserine dehydrogenase from Arabidopsis (O81852).

BT2792 : regulator of the bile salt efflux system
Original description: AraC/XylS family transcriptional regulator (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important in stress Bile salts; stress Deoxycholic acid; stress Chenodeoxycholic acid. In a putative operon with the bile salt efflux system. This is a two-component response regulator of the yesN superfamily (CDD) and is probably the regulator of the operon.

BT2793 : bile salt tripartite efflux system, inner membrane component
Original description: putative MFS transporter (NCBI ptt file)
SEED: Inner membrane component of tripartite multidrug resistance system
KEGG: no annotation
Rationale: Specifically important in stress Bile salts; stress Deoxycholic acid; stress Chenodeoxycholic acid. This protein is distantly related to emrB-type efflux pumps (see CDD).

BT2794 : bile salt tripartite efflux system, membrane fusion component
Original description: putative multidrug resistance protein (NCBI ptt file)
SEED: Membrane fusion component of tripartite multidrug resistance system
KEGG: no annotation
Rationale: Specifically important in stress Bile salts; stress Deoxycholic acid; and perhaps stress chenodeoxycholate. This protein belongs to the EmrA/HlyD family of membrane fusion proteins.

BT2795 : bile salt tripartite efflux system, outer membrane component
Original description: outer membrane efflux protein precursor (NCBI ptt file)
SEED: Outer membrane component of tripartite multidrug resistance system
KEGG: outer membrane factor, OMF family
Rationale: Specifically important in stress Bile salts; stress Deoxycholic acid; and perhaps chenodeoxycholate. This protein belongs to the TolC family of outer membrane export proteins.

BT2802 : conserved protein required for D-ribose utilization
Original description: hypothetical protein (NCBI ptt file)
SEED: FIG00413071: hypothetical protein
KEGG: no annotation
Rationale: Specifically important in carbon source D-Ribose. This protein is in conserved proximity to ribose kinase. It has no apparent homology to characterized proteins. It is often divergent from the ribose kinase, which hints that it has a regulatory role.

BT2803 : ribokinase (EC 2.7.1.15)
Original description: ribokinase (NCBI ptt file)
SEED: Ribokinase (EC 2.7.1.15)
KEGG: ribokinase
Rationale: Specifically important in carbon source D-Ribose. An adjacent protein (BT2804) is also expected to be a ribokinase and is also required. It is not clear why both proteins are required.

BT2804 : ribokinase (EC 2.7.1.15)
Original description: ribokinase (NCBI ptt file)
SEED: Ribokinase (EC 2.7.1.15)
KEGG: ribokinase
Rationale: Specifically important in carbon source D-Ribose. An adjacent protein (BT2803) is also expected to be a ribokinase and is also required. It is not clear why both proteins are required.

BT2809 : D-ribose transporter
Original description: putative integral membrane protein (NCBI ptt file)
SEED: FIG00761799: membrane protein
KEGG: no annotation
Rationale: Specifically important in carbon source D-Ribose. It belongs to a family of sugar transporters. It probably moves D-ribose through the inner membrane.

BT3089 : Outer membrane binding protein for dextran (SusD-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: # Specifically important in carbon source dextran; may also be important for utilization of red arabinan from sugar-beet; part of the BT3087-BT3090 complex for uptake and hydrolysis (PMID:37286596)

BT3090 : TonB-dependent receptor for dextran (SusC-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: SusC, outer membrane protein involved in starch binding
KEGG: no annotation
Rationale: # Specifically important in carbon source dextran; may also be important for utilization of red arabinan from sugar-beet; previously proposed to be involved in dextran utilization, see PMC3878776; part of the BT3087-BT3090 complex for uptake and hydrolysis (PMID:37286596)

BT3233 : predicted glycosaminoglycan binding protein (DUF4861)
Original description: hypothetical protein (NCBI ptt file)
SEED: FIG00405395: hypothetical protein
KEGG: no annotation
Rationale: Specifically important in carbon source Heparin sodium salt from porcine intestinal mucosa; carbon source Chondroitin sulfate A sodium salt from bovine trachea; and perhaps carbon source hyaluronic acid. Belongs to the galactose mutarotase-like domain superfamily, which are thought to be carbohydrate-binding proteins (see InterPro IPR011013). Also, this family (PF16153) is predicted by the PFam curators to bind carbohydrates because of its conserved proximity to glycosyl hydrolyase family 88.

BT3328 : hyaluronic acid endo-lyase (PL29)
Original description: hypothetical protein (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important in carbon source Hyaluronic acid sodium salt from Streptococcus equi. In vitro, it also degrades other glycosaminoglycans such as chondroitin sulfate and dermatan sulfate (PMCID:PMC6240882), but it is not important for utilizing chondroitin sulfate. We do not have fitness data for dermatan sulfate.

BT3331 : Outer membrane binding protein for chondroitin sulfate and hyaluronic acid (susD-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: Putative outer membrane protein, probably involved in nutrient binding
KEGG: no annotation
Rationale: Specifically important in carbon source Hyaluronic acid sodium salt from Streptococcus equi; carbon source Chondroitin sulfate A sodium salt from bovine trachea. The adjacent susC-like protein BT3332 has similar phenotypes.

BT3332 : TonB-dependent receptor for chondroitin sulfate and hyaluronic acid (susC-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: TonB family protein / TonB-dependent receptor
KEGG: no annotation
Rationale: Specifically important in carbon source Hyaluronic acid sodium salt from Streptococcus equi; carbon source Chondroitin sulfate A sodium salt from bovine trachea. The adjacent susD-like protein BT3331 has similar phenotypes.

BT3337 : RND efflux system for fusidic acid, chlorpromazine, and thioridazine, outer membrane component
Original description: outer membrane protein oprM precursor, multidrug resistance protein (NCBI ptt file)
SEED: RND efflux system, outer membrane lipoprotein CmeC
KEGG: no annotation
Rationale: Specifically important in stress Fusidic acid sodium salt; stress Chlorpromazine hydrochloride; stress Bile salts; stress Thioridazine hydrochloride; stress Rifampicin; stress Cefoxitin sodium salt. This protein belongs to the NodT family of outer membrane exporters.

BT3338 : RND efflux system for fusidic acid, chlorpromazine, and thioridazine, inner membrane component
Original description: AcrB/AcrD family multidrug resistance protein (NCBI ptt file)
SEED: RND efflux system, inner membrane transporter CmeB
KEGG: hydrophobic/amphiphilic exporter-1 (mainly G- bacteria), HAE1 family
Rationale: Specifically important in stress Fusidic acid sodium salt; stress Chlorpromazine hydrochloride; stress Thioridazine hydrochloride; stress Cefoxitin sodium salt. This protein belongs to the RND family of inner membrane transporters.

BT3339 : RND efflux system for fusidic acid, chlorpromazine, and thioridazine, membrane fusion component
Original description: AcrA/AcrE family multidrug resistance protein (NCBI ptt file)
SEED: Membrane fusion protein of RND family multidrug efflux pump
KEGG: membrane fusion protein
Rationale: Specifically important in stress Fusidic acid sodium salt; stress Chlorpromazine hydrochloride; and perhaps thioridazine. This protein belongs to the hlyD/MFP family of membrane fusion proteins.

BT3340 : Beta-galactosidase (EC 3.2.1.23)
Original description: beta-galactosidase (NCBI ptt file)
SEED: Beta-galactosidase (EC 3.2.1.23)
KEGG: beta-galactosidase
Rationale: Specific phenotype: utilization of Beta-Lactose, Lactulose

BT3348 : unsaturated glucuronide lyase acting on chondroitin/heparin disaccharides (EC 3.2.1.180)
Original description: putative unsaturated glucuronyl hydrolase (NCBI ptt file)
SEED: Glucuronyl hydrolase
KEGG: no annotation
Rationale: Specifically important in carbon source Hyaluronic acid sodium salt from Streptococcus equi; carbon source Chondroitin sulfate A sodium salt from bovine trachea; carbon source Heparin sodium salt from porcine intestinal mucosa. It is 51% identical to C6Y0D8 which preferentially cleaves 1,4-type unsaturated glucuronides that arise during heparin degradation (PMC3931040). B. thetaiotaomicron is believed to degrade chondroitin sulfate via unsaturated 1,3-glucoronides (PMID:25041429). This in combination with the mutant phenotypes suggest that BT3348 has a broader specificity.

BT3349 : chondroitin disaccharide sulfatase
Original description: putative sulfatase yidJ (NCBI ptt file)
SEED: Choline-sulfatase (EC 3.1.6.6)
KEGG: no annotation
Rationale: Specifically important in carbon source Chondroitin sulfate A sodium salt from bovine trachea. It probably acts on unsaturated chondroitin disaccharides (see PMID:25041429)

BT3395 : N-succinylglutamate kinase (EC 2.7.2.-)
Original description: putative acetylglutamate kinase (NCBI ptt file)
SEED: Acetylglutamate kinase (EC 2.7.2.8)
KEGG: acetylglutamate/acetylaminoadipate kinase
Rationale: Important for fitness in most defined media, except when arginine is provided. Bacteroidetes use succinylated intermediates, and a close homolog from B. fragilis prefers N-succinylglutamate as a substrate (see PMC7311316 and references therein), so this is N-succinylglutamate kinase, not N-acetylglutamate kinase.

BT3549 : N-succinylcitrulline desuccinylase (EC 3.5.1.-)
Original description: acetylornithine deacetylase (NCBI ptt file)
SEED: Acetylornithine deacetylase (EC 3.5.1.16)
KEGG: no annotation
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.

BT3567 : periplasmic beta-1,2-glucosidase / beta-1,3-glucosidase
Original description: periplasmic beta-glucosidase precursor (NCBI ptt file)
SEED: Periplasmic beta-glucosidase (EC 3.2.1.21)
KEGG: beta-glucosidase
Rationale: Specifically important in carbon source Laminaribiose (beta-D-glucose-(1->3)-D-glucose). Cleaves beta,1-2 and beta,1-3 linkages and has little activity on cellobiose (PMID:28343388).

BT3568 : outer membrane binding protein for laminaribiose (SusD-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important in carbon source Laminaribiose. An adjacent SusC-like protein (BT3569) has similar phenotypes. BT3568 probably binds laminaribiose and promotes transport by BT3569 through the outer membrane.

BT3569 : TonB-dependent receptor for laminaribiose (SusC-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: TonB family protein / TonB-dependent receptor
KEGG: no annotation
Rationale: Specifically important in carbon source Laminaribiose. An adjacent SusD-like protein (BT3568) has similar phenotypes. BT3569 probably moves laminaribiose through the outer membrane.

BT3698 SusG : Alpha-amylase susG (EC 3.2.1.1)
Original description: alpha-amylase, susG (NCBI ptt file)
SEED: Alpha-amylase (EC 3.2.1.1)
KEGG: no annotation
Rationale: Specific phenotype: utilization of amylopectin from maize, polygalacturonic acid, Starch; also see structure in PMID:20159465 and older genetic studies

BT3699 SusF : SusF: Outer membrane amylopectin-binding protein
Original description: outer membrane protein SusF (NCBI ptt file)
SEED: Outer membrane protein SusF
KEGG: no annotation
Rationale: Specifically important in carbon source amylopectin from maize. It is part of the starch utilization system (Sus) and binds starch (PMCID:PMC3464567). Given the phenotypic information, it probably binds specifically to the amylopectin part of starch.

BT3700 SusE : SusE: Outer membrane amylopectin-binding protein
Original description: outer membrane protein SusE (NCBI ptt file)
SEED: Outer membrane protein SusE
KEGG: no annotation
Rationale: Specifically important in carbon source amylopectin from maize. It is part of the starch utilization system (Sus) and binds starch (PMCID:PMC3464567). Given the phenotypic information, it probably binds specifically to the amylopectin part of starch.

BT3704 SusA : SusA: alpha-amylase / neopullulanase / cyclomaltodextrinase (EC 3.2.1.135; EC 3.2.1.54)
Original description: alpha-amylase (neopullulanase) SusA (NCBI ptt file)
SEED: Alpha-amylase (Neopullulanase) SusA (EC 3.2.1.135)
KEGG: no annotation
Rationale: Specifically important in carbon source a-Cyclodextrin SusA. Some homlogs are also specifically required for utilizing cyclodextrin. SusA was previously shown to account for most of the neopullulanase activity of cell extracts (PMCID:PMC178630)

BT3717 : N-succinylornithine carbamoyltransferase (EC 2.1.3.11)
Original description: ornithine carbamoyltransferase (NCBI ptt file)
SEED: N-acetylornithine carbamoyltransferase (EC 2.1.3.9)
KEGG: N-succinyl-L-ornithine transcarbamylase
Rationale: Important for fitness in most defined media, except when arginine is provided. Over 90% identical to the N-succinylornithine carbamoyltransferase of B. fragilis (E1WKT5)

BT3719 : glutamate 5-kinase (EC 2.7.2.11)
Original description: glutamate 5-kinase (NCBI ptt file)
SEED: Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA
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.

BT3733 : arginosuccinate lyase (EC 4.3.2.1)
Original description: argininosuccinate lyase (NCBI ptt file)
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.

BT3757 : pyrroline-5-carboxylate reductase (EC 1.5.1.2)
Original description: pyrroline-5-carboxylate reductase (NCBI ptt file)
SEED: Pyrroline-5-carboxylate reductase (EC 1.5.1.2)
KEGG: pyrroline-5-carboxylate reductase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00112.

BT3758 : N-succinylornithine aminotransferase (EC 2.6.1.81)
Original description: acetylornithine aminotransferase (NCBI ptt file)
SEED: Acetylornithine aminotransferase (EC 2.6.1.11)
KEGG: acetylornithine aminotransferase
Rationale: Important for fitness in most defined media, except when arginine is provided. Similar to acetylornithine aminotransferases (such as argD from B. subtilis), but Bacteroidetes use succinylated intermediates for arginine synthesis (see PMC7311316).

BT3759 : N-succinylglutamylphosphate reductase (EC 1.2.1.-)
Original description: N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file)
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 is provided. Hits TIGR01850, which is described as N-acetyl-gamma-glutamyl-phosphate reductase, but Bacteroidetes use succinylated intermediates for arginine synthesis (see PMC7311316).

BT3760 : arginosuccinate synthetase (EC 6.3.4.5)
Original description: argininosuccinate synthase (NCBI ptt file)
SEED: Argininosuccinate synthase (EC 6.3.4.5)
KEGG: argininosuccinate synthase
Rationale: Important for fitness in most defined media, except when arginine is provided. 32% identical to argininosuccinate synthase from Leishmania (H9BG20).

BT3761 : N-succinylglutamate synthase
Original description: hypothetical protein (NCBI ptt file)
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) was not found in the genome. This protein is 59% identical to Cabys_1732 which is reported to form N-acetylglutamate (PMID:28265262). However, Bacteroides are believed to use succinylated intermediates for arginine synthesis, as they have N-succinylornithine carbamoyltransferase (PMID:16704984) and N-succinylglutamate kinase (PhD thesis of Juan Manuel Cabrera Luque, 2010). The prior studies were of Bacteroides fragilis, but Bacteroides thetaiotaomicron has close homologs (the carbamoyltransferase is BT3717; the kinase is BT3395; mutants of all of these genes from B. thetaiotaomicron appear to be arginine auxotrophs)

BT3765 : L-rhamnose:H+ symporter
Original description: L-rhamnose/H+ symporter (NCBI ptt file)
SEED: L-rhamnose-proton symporter
KEGG: L-rhamnose-H+ transport protein
Rationale: Specifically important for utilizing L-rhamnose.

BT3766 : rhamnulose 1-phosphate aldolase RhaD (EC 4.1.2.19)
Original description: rhamnulose-1-phosphate aldolase (NCBI ptt file)
SEED: Rhamnulose-1-phosphate aldolase (EC 4.1.2.19)
KEGG: rhamnulose-1-phosphate aldolase
Rationale: Specifically important for utilizing L-rhamnose and rhamnogalacturonan from potato.

BT3767 : L-lactaldehyde reductase FucO (EC 1.1.1.77)
Original description: lactaldehyde reductase (NCBI ptt file)
SEED: Lactaldehyde reductase (EC 1.1.1.77)
KEGG: lactaldehyde reductase
Rationale: Specifically important for utilizing L-rhamnose.

BT3788 : TonB-dependent receptor for alpha-mannan (SusC-like)
Original description: putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)
SEED: TonB family protein / TonB-dependent receptor
KEGG: no annotation
Rationale: Specifically important in carbon source Mannan from Saccharomyces cerevisiae. Part of a polysaccharide utilization locus that is induced by mannan and is required for mannan utilization (see PMCID:PMC4978465).

BT3789 : Outer membrane binding protein for alpha-mannan (SusD-like)
Original description: hypothetical protein (NCBI ptt file)
SEED: Putative outer membrane protein, probably involved in nutrient binding
KEGG: no annotation
Rationale: Specifically important in carbon source Mannan from Saccharomyces cerevisiae. Part of a polysaccharide utilization locus that is induced by mannan and is required for mannan utilization (see PMCID:PMC4978465).

BT3866 : ammonium-dependent carbamoyl phosphate synthetase CarB2 (EC 6.3.4.16)
Original description: glutamine-dependent carbamyl phosphate synthetase (NCBI ptt file)
SEED: Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)
KEGG: carbamoyl-phosphate synthase large subunit
Rationale: Important for fitness when ammonia is added, and it seems to function without any glutaminase partner. BT0557 is a glutaminase component, but the fitness data suggests that BT0557 functions solely with BT0556

BT3933 : prephenate dehydrogenase (EC 1.3.1.13)
Original description: chorismate mutase/prephenate dehydratase (tyrA) (NCBI ptt file)
SEED: Prephenate and/or arogenate dehydrogenase (unknown specificity) (EC 1.3.1.12)(EC 1.3.1.43)
KEGG: prephenate dehydrogenase ; chorismate mutase
Rationale: Important for fitness in defined media. Distantly related (under 25% identity) to the prephenate dehydrogenase portion of E. coli tyrA. This is sometimes annotated as chorismate mutase as well, but it lacks that domain.

BT3936 : prephenate and/or arogenate dehydratase (EC 4.2.1.51)
Original description: prephenate dehydratase (NCBI ptt file)
SEED: Prephenate dehydratase (EC 4.2.1.51)
KEGG: prephenate dehydratase
Rationale: Important for fitness in defined media. 35% identical to the prephenate dehydratase and ACT (regulatory) domains of D3U717 from Petunia. It is uncertain whether dehydration occurs first or transamination (to arogenate) occurs first.

BT4105 : D-galacturonate transporter ExuT
Original description: hexuronate transporter (NCBI ptt file)
SEED: Hexuronate transporter
KEGG: MFS transporter, ACS family, hexuronate transporter
Rationale: Specifically important for D-galacturonate utilization. Also important for utilization of galacturonate-containing polysaccharides polygalacturonate and rhamnogalacturonan from potato, and probably important for pectin utilization as well

BT4187 : exo-alpha-D-galacturonosidase for catabolism of rhamnogalacturonan I and polygalacturonate
Original description: exo-poly-alpha-D-galacturonosidase precursor (NCBI ptt file)
SEED: Polygalacturonase (EC 3.2.1.15)
KEGG: no annotation
Rationale: Specifically important in carbon source Rhamnogalacturonan - from potato; carbon source polygalacturonic acid. Rhamnogalacturonan I is a polymer of D-galacturonate and L-rhamnose. This protein is 64% identical to BT4123, which is an exo-alpha-D-galacturonidase (PMC:PMC5784806). BT4187 is expected to be secreted, but no specific signal for protein export was identified by PSORT-b.

BT4215 : shikimate dehydrogenase (EC 1.1.1.25)
Original description: shikimate 5-dehydrogenase (NCBI ptt file)
SEED: Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
KEGG: shikimate dehydrogenase
Rationale: A conserved essential gene. This activity is necessary to explain chorismate biosynthesis. 36% identical to shikimate dehydrogenase from Aquifex aeolicus (O67049).

BT4410 : endo-hyaluronase
Original description: hypothetical protein (NCBI ptt file)
SEED: FIG00896938: hypothetical protein
KEGG: no annotation
Rationale: # Specifically important in carbon source Hyaluronic acid sodium salt from Streptococcus equi. 68% identical to endo-hyaluronanase ALJ61728.1 (PMID:30850540). Probably functions with the BT4411, which has a similar phenotype and is probably a hyaluronic acid binding protein.

BT4411 : predicted hyaluronic acid binding protein (DUF4627)
Original description: hypothetical protein (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important in carbon source Hyaluronic acid sodium salt from Streptococcus equi. The adjacent polysaccharide lyase BT4410 has similar phenotypes. Both proteins are periplasmic and this protein belongs to DUF4627, which is related to a family of carbohydrate binding proteins (PF02018).

BT4652 : heparan sulfate cleaving enzyme
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: oligo alginate lyase
KEGG: no annotation
Rationale: # Specifically important in carbon source Heparin sodium salt from porcine intestinal mucosa. 66% identical to the heparan sulfate cleaving enzyme ALJ58962.1 (PMID:30850540)

Or download reannotations for Bacteroides thetaiotaomicron VPI-5482 or for all organisms as tab-delimited tables