GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Novosphingobium aromaticivorans DSM 12444

Found 82 low-confidence and 35 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP SARO_RS10545 SARO_RS13230
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK SARO_RS07960
alanine snatA: L-alanine symporter SnatA SARO_RS01345
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter SARO_RS16065
arginine adiA: arginine decarboxylase (AdiA/SpeA)
arginine patD: gamma-aminobutyraldehyde dehydrogenase SARO_RS14550 SARO_RS19930
arginine rocE: L-arginine permease
asparagine ans: asparaginase
cellobiose glk: glucokinase SARO_RS09495 SARO_RS09440
citrate citA: citrate:H+ symporter CitA SARO_RS10545 SARO_RS00790
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component SARO_RS05745 SARO_RS11475
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 rocD: ornithine aminotransferase SARO_RS13120 SARO_RS14875
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
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 SARO_RS05490
deoxyinosine deoB: phosphopentomutase SARO_RS02415 SARO_RS16840
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase SARO_RS19160 SARO_RS14535
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter SARO_RS17880
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase SARO_RS00750
deoxyribose deoP: deoxyribose transporter SARO_RS12220
fructose glcP: fructose:H+ symporter GlcP SARO_RS16065
fucose fucU: L-fucose mutarotase FucU SARO_RS12215
galactose galE: UDP-glucose 4-epimerase SARO_RS16630 SARO_RS08110
galactose galP: galactose:H+ symporter GalP SARO_RS16065
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase SARO_RS19260
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) SARO_RS12135
glucose glk: glucokinase SARO_RS09495 SARO_RS09440
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate uxaC: D-glucuronate isomerase SARO_RS19260
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine Bap2: L-isoleucine permease Bap2
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC SARO_RS12910
lactose galE: UDP-glucose 4-epimerase SARO_RS16630 SARO_RS08110
lactose glk: glucokinase SARO_RS09495 SARO_RS09440
lactose lacP: lactose permease LacP
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuC: 3-methylglutaconyl-CoA hydratase SARO_RS04305 SARO_RS07105
leucine liuE: hydroxymethylglutaryl-CoA lyase SARO_RS00880
lysine davA: 5-aminovaleramidase SARO_RS15710
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase SARO_RS17165 SARO_RS14885
lysine lysP: L-lysine:H+ symporter LysP
maltose glk: glucokinase SARO_RS09495 SARO_RS09440
mannitol mt2d: mannitol 2-dehydrogenase SARO_RS19265 SARO_RS09380
mannitol PLT5: polyol transporter PLT5
mannose gluP: mannose:Na+ symporter SARO_RS04365 SARO_RS12220
mannose man-isomerase: D-mannose isomerase
myoinositol iolG: myo-inositol 2-dehydrogenase
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 SARO_RS16065
myoinositol uxaE: D-tagaturonate epimerase
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 SARO_RS04305 SARO_RS18985
phenylacetate paaK: phenylacetate-CoA ligase SARO_RS06055
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase SARO_RS18110 SARO_RS06415
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine QDPR: 6,7-dihydropteridine reductase SARO_RS14020
propionate putP: propionate transporter; proline:Na+ symporter
putrescine patD: gamma-aminobutyraldehyde dehydrogenase SARO_RS14550 SARO_RS19930
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose rhaM: L-rhamnose mutarotase
ribose rbsK: ribokinase SARO_RS00750
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter SARO_RS01345
sorbitol sdh: sorbitol dehydrogenase SARO_RS19125 SARO_RS07815
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc SARO_RS12910
sucrose glk: glucokinase SARO_RS09495 SARO_RS09440
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) SARO_RS09270 SARO_RS09275
threonine ltaE: L-threonine aldolase SARO_RS16590 SARO_RS11270
threonine snatA: L-threonine transporter snatA SARO_RS01345
thymidine deoA: thymidine phosphorylase DeoA SARO_RS18780
thymidine deoB: phosphopentomutase SARO_RS02415 SARO_RS16840
thymidine deoC: deoxyribose-5-phosphate aldolase
trehalose glk: glucokinase SARO_RS09495 SARO_RS09440
trehalose treF: trehalase SARO_RS09470 SARO_RS07540
tryptophan andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa SARO_RS16995 SARO_RS01080
tryptophan andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase SARO_RS13615
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine hmgA: homogentisate dioxygenase
valine acdH: isobutyryl-CoA dehydrogenase SARO_RS04295 SARO_RS08250
valine Bap2: L-valine permease Bap2
xylitol PLT5: xylitol:H+ symporter PLT5 SARO_RS16065
xylitol xdhA: xylitol dehydrogenase SARO_RS19090 SARO_RS12445

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 09 2024. 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