GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Rubrivirga marina SAORIC-28

Found 106 low-confidence and 41 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) BSZ37_RS03660 BSZ37_RS15140
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase BSZ37_RS18480 BSZ37_RS00305
acetate actP: cation/acetate symporter ActP BSZ37_RS00955
arginine rocD: ornithine aminotransferase BSZ37_RS09720 BSZ37_RS12205
arginine rocE: L-arginine permease
arginine rocF: arginase
citrate SLC13A5: citrate:Na+ symporter BSZ37_RS02895
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BSZ37_RS07035 BSZ37_RS11430
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase BSZ37_RS13595 BSZ37_RS16550
citrulline rocD: ornithine aminotransferase BSZ37_RS09720 BSZ37_RS12205
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase BSZ37_RS14680 BSZ37_RS15930
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) BSZ37_RS03660 BSZ37_RS15140
deoxyribonate aacS: acetoacetyl-CoA synthetase BSZ37_RS15895
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BSZ37_RS00205 BSZ37_RS07205
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) BSZ37_RS03660 BSZ37_RS15140
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter BSZ37_RS05870
ethanol adh: acetaldehyde dehydrogenase (not acylating) BSZ37_RS03660 BSZ37_RS15140
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BSZ37_RS13905 BSZ37_RS02760
fucose aldA: lactaldehyde dehydrogenase BSZ37_RS15140 BSZ37_RS03660
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP BSZ37_RS05870
fucose fucU: L-fucose mutarotase FucU
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaC: D-galacturonate isomerase BSZ37_RS02530
gluconate gntT: gluconate:H+ symporter GntT BSZ37_RS04275
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter BSZ37_RS02325
glucuronate dctP: D-glucuronate TRAP transporter, solute receptor component BSZ37_RS02460 BSZ37_RS05240
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glucuronate uxaC: D-glucuronate isomerase BSZ37_RS02530
glucuronate uxuB: D-mannonate dehydrogenase
histidine Ga0059261_1577: L-histidine transporter BSZ37_RS12075
histidine hutG: N-formiminoglutamate formiminohydrolase BSZ37_RS02085
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BSZ37_RS13280 BSZ37_RS13070
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BSZ37_RS09890 BSZ37_RS13325
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BSZ37_RS19830 BSZ37_RS15265
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BSZ37_RS07160 BSZ37_RS15465
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BSZ37_RS01760 BSZ37_RS05225
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BSZ37_RS03450 BSZ37_RS19550
L-lactate L-LDH: L-lactate dehydrogenase BSZ37_RS16750 BSZ37_RS09590
L-lactate Shew_2732: L-lactate:Na+ symporter, small component BSZ37_RS00950
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
leucine aacS: acetoacetyl-CoA synthetase BSZ37_RS15895
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BSZ37_RS09890 BSZ37_RS13325
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BSZ37_RS19830 BSZ37_RS15265
leucine liuA: isovaleryl-CoA dehydrogenase BSZ37_RS13280 BSZ37_RS13070
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BSZ37_RS03450 BSZ37_RS19550
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BSZ37_RS17550 BSZ37_RS18910
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BSZ37_RS15140 BSZ37_RS03660
lysine hglS: D-2-hydroxyglutarate synthase
lysine lysN: 2-aminoadipate transaminase BSZ37_RS19375 BSZ37_RS15130
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase BSZ37_RS08330
mannitol mt2d: mannitol 2-dehydrogenase BSZ37_RS01760 BSZ37_RS00215
mannitol PLT5: polyol transporter PLT5 BSZ37_RS03790
mannose gluP: mannose:Na+ symporter BSZ37_RS05870
mannose manA: mannose-6-phosphate isomerase BSZ37_RS13865 BSZ37_RS19680
myoinositol iolG: myo-inositol 2-dehydrogenase BSZ37_RS14530 BSZ37_RS00375
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter BSZ37_RS03790
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase BSZ37_RS07160 BSZ37_RS10165
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BSZ37_RS07160 BSZ37_RS08645
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BSZ37_RS15460 BSZ37_RS16360
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BSZ37_RS15460 BSZ37_RS16360
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BSZ37_RS16300 BSZ37_RS07160
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase BSZ37_RS15895
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase BSZ37_RS14860
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline CCNA_00435: proline transporter BSZ37_RS12075
propionate pccA: propionyl-CoA carboxylase, alpha subunit BSZ37_RS03450 BSZ37_RS19550
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase BSZ37_RS00105 BSZ37_RS09720
putrescine patA: putrescine aminotransferase (PatA/SpuC) BSZ37_RS00105 BSZ37_RS12205
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BSZ37_RS15140 BSZ37_RS03660
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate actP: large subunit of pyruvate transporter (actP-like) BSZ37_RS00955
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) BSZ37_RS00950
rhamnose aldA: lactaldehyde dehydrogenase BSZ37_RS15140 BSZ37_RS03660
rhamnose LRA1: L-rhamnofuranose dehydrogenase BSZ37_RS02510 BSZ37_RS20795
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase BSZ37_RS02455
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase BSZ37_RS02510 BSZ37_RS05180
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 BSZ37_RS03790
sucrose ams: sucrose hydrolase (invertase) BSZ37_RS02740 BSZ37_RS02390
threonine adh: acetaldehyde dehydrogenase (not acylating) BSZ37_RS03660 BSZ37_RS15140
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) BSZ37_RS03660 BSZ37_RS15140
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase BSZ37_RS15895
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BSZ37_RS13280 BSZ37_RS13070
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BSZ37_RS07160 BSZ37_RS16300
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BSZ37_RS09890 BSZ37_RS13325
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BSZ37_RS19830 BSZ37_RS15265
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BSZ37_RS07160 BSZ37_RS10165
valine mmsA: methylmalonate-semialdehyde dehydrogenase BSZ37_RS15140
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BSZ37_RS07570
valine pccA: propionyl-CoA carboxylase, alpha subunit BSZ37_RS03450 BSZ37_RS19550
xylitol PLT5: xylitol:H+ symporter PLT5 BSZ37_RS03790
xylitol xdhA: xylitol dehydrogenase BSZ37_RS00205 BSZ37_RS20795
xylose xylT: D-xylose transporter BSZ37_RS03790

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory