GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Derxia gummosa DSM 723

Found 100 low-confidence and 47 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate dctM: 2-oxoglutarate TRAP transporter, large permease component DctM H566_RS0106500 H566_RS0113345
2-oxoglutarate dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ
4-hydroxybenzoate ligU: 4-oxalomesaconate tautomerase H566_RS0121285
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) H566_RS0117030
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) H566_RS0102680 H566_RS0104990
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H566_RS22525 H566_RS0104985
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) H566_RS0102690 H566_RS0111715
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) H566_RS0102695 H566_RS0113085
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine adiA: arginine decarboxylase (AdiA/SpeA) H566_RS0101800
arginine rocE: L-arginine permease
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component H566_RS0119540 H566_RS0107450
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 H566_RS0119535
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 H566_RS0107440 H566_RS0119535
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline odc: L-ornithine decarboxylase H566_RS0101800
D-alanine AZOBR_RS08240: D-alanine ABC transporter, permease component 2 H566_RS22525 H566_RS0104985
D-alanine AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 H566_RS0111715 H566_RS0102690
D-alanine AZOBR_RS08250: D-alanine ABC transporter, ATPase component 2 H566_RS0102695 H566_RS0104975
D-alanine AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component H566_RS0117030
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase H566_RS0105405
deoxyinosine deoB: phosphopentomutase H566_RS0101360
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase H566_RS23450 H566_RS0112475
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase H566_RS23450 H566_RS0112475
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit H566_RS23550 H566_RS0116000
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component
deoxyribose ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK H566_RS0106830
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose galK: galactokinase (-1-phosphate forming)
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT H566_RS0114650
galacturonate kdgK: 2-keto-3-deoxygluconate kinase H566_RS0119110
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) H566_RS0114125
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase H566_RS0107095 H566_RS0108130
glucuronate exuT: D-glucuronate:H+ symporter ExuT H566_RS0114650
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase H566_RS0110445
glucuronate udh: D-glucuronate dehydrogenase
histidine hutF: N-formiminoglutamate deiminase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component H566_RS23970 H566_RS0119540
histidine PA5505: L-histidine ABC transporter, substrate-binding component H566_RS0108860
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lactose klh: periplasmic 3'-ketolactose hydrolase
lactose lacA': periplasmic lactose 3-dehydrogenase, LacA subunit
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit
leucine liuA: isovaleryl-CoA dehydrogenase H566_RS0120480 H566_RS0116330
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit H566_RS0110680 H566_RS0105270
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine gcdG: succinyl-CoA:glutarate CoA-transferase H566_RS0106900 H566_RS0111790
lysine gcdH: glutaryl-CoA dehydrogenase H566_RS0120480 H566_RS0116330
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase H566_RS0108125 H566_RS0102945
lysine patD: 5-aminopentanal dehydrogenase H566_RS0107095 H566_RS0101815
maltose susB: alpha-glucosidase (maltase) H566_RS0104710
mannitol mt2d: mannitol 2-dehydrogenase H566_RS0106840 H566_RS0105240
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE H566_RS0106865
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) H566_RS0106855
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) H566_RS0106850
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG H566_RS23460 H566_RS0118530
mannose man-isomerase: D-mannose isomerase
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
myoinositol iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase H566_RS23470
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase H566_RS0102425 H566_RS25615
myoinositol PS417_11885: myo-inositol ABC transporter, substrate-binding component H566_RS0119115
myoinositol PS417_11890: myo-inositol ABC transporter, ATPase component H566_RS0119125 H566_RS0119435
myoinositol PS417_11895: myo-inositol ABC transporter, permease component H566_RS0119120
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) H566_RS0114125
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 H566_RS22980
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase H566_RS0116355 H566_RS0118410
phenylacetate paaK: phenylacetate-CoA ligase H566_RS0103055 H566_RS0105380
phenylacetate paaZ1: oxepin-CoA hydrolase H566_RS0112825 H566_RS0111180
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase H566_RS0112825
phenylacetate ppa: phenylacetate permease ppa H566_RS0121750 H566_RS0108955
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase H566_RS0108540
phenylalanine QDPR: 6,7-dihydropteridine reductase H566_RS0114570 H566_RS25695
propionate putP: propionate transporter; proline:Na+ symporter H566_RS0108105
rhamnose LRA1: L-rhamnofuranose dehydrogenase H566_RS0105240 H566_RS0104000
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB
ribose rbsK: ribokinase
sorbitol sdh: sorbitol dehydrogenase H566_RS0106860 H566_RS23450
sucrose ams: sucrose hydrolase (invertase) H566_RS0104710
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) H566_RS0117030
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) H566_RS0102680 H566_RS0104990
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H566_RS22525 H566_RS0104985
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) H566_RS0102690 H566_RS0111715
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) H566_RS0102695 H566_RS0113085
threonine ltaE: L-threonine aldolase H566_RS0104140 H566_RS0104925
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase H566_RS0101360
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase H566_RS0104710 H566_RS0113920
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine hmgA: homogentisate dioxygenase
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) H566_RS0102680 H566_RS0104990
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H566_RS0117030 H566_RS0104995
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) H566_RS22525 H566_RS0104985
valine mmsB: 3-hydroxyisobutyrate dehydrogenase H566_RS24575 H566_RS0109360
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase H566_RS0105240 H566_RS0112475
xylose gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA H566_RS0118555
xylose gtsB: xylose ABC transporter, permease component 1 GtsB H566_RS0118540
xylose gtsC: xylose ABC transporter, permease component 2 GtsC H566_RS0118535
xylose gtsD: xylose ABC transporter, ATPase component GtsD H566_RS0118530 H566_RS23460
xylose xylA: xylose isomerase

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