GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Flavobacterium sp. LM5

Found 127 low-confidence and 40 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP BXU11_RS15540
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
alanine TRIC: TRIC-type L-alanine transporter BXU11_RS06425
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocE: L-arginine permease
arginine rocF: arginase BXU11_RS08770
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BXU11_RS03565 BXU11_RS07070
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
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 BXU11_RS11020 BXU11_RS11050
deoxyinosine deoB: phosphopentomutase BXU11_RS09765
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BXU11_RS13235
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BXU11_RS01015 BXU11_RS13235
fructose 1pfk: 1-phosphofructokinase BXU11_RS00305
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase BXU11_RS01185 BXU11_RS04005
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
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA BXU11_RS13550
galactose galP: galactose:H+ symporter GalP
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase BXU11_RS02855
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase BXU11_RS02860
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase
glucosamine nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX BXU11_RS07795
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent BXU11_RS00950
glutamate gltP: L-glutamate:cation symporter GltP/GltT BXU11_RS13550
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF BXU11_RS05965
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase BXU11_RS13535
histidine LAT2: L-histidine transporter BXU11_RS07315
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BXU11_RS04315 BXU11_RS10875
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BXU11_RS10670 BXU11_RS11535
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BXU11_RS09535 BXU11_RS00525
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BXU11_RS02105 BXU11_RS06935
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BXU11_RS13235 BXU11_RS03085
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BXU11_RS09415 BXU11_RS02955
L-lactate L-LDH: L-lactate dehydrogenase BXU11_RS06540
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate dctA: L-malate:H+ symporter DctA BXU11_RS13550
lactose glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) BXU11_RS00715 BXU11_RS13915
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BXU11_RS10670 BXU11_RS11535
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BXU11_RS09535 BXU11_RS00525
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase BXU11_RS04315 BXU11_RS10875
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BXU11_RS09415 BXU11_RS02955
leucine liuC: 3-methylglutaconyl-CoA hydratase BXU11_RS02105
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BXU11_RS08190 BXU11_RS09410
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase BXU11_RS08775 BXU11_RS14330
lysine lysN: 2-aminoadipate transaminase BXU11_RS03965 BXU11_RS08775
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose glk: glucokinase
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase BXU11_RS05330 BXU11_RS14985
mannose manP: mannose PTS system, EII-CBA components
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
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
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 paaF: 2,3-dehydroadipyl-CoA hydratase BXU11_RS02105
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BXU11_RS02105
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BXU11_RS06925 BXU11_RS13695
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BXU11_RS06925 BXU11_RS13695
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase BXU11_RS11110
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase BXU11_RS07730
propionate pccA: propionyl-CoA carboxylase, alpha subunit BXU11_RS09415 BXU11_RS02955
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase BXU11_RS01185 BXU11_RS12805
putrescine gabT: gamma-aminobutyrate transaminase BXU11_RS08775 BXU11_RS07400
putrescine patA: putrescine aminotransferase (PatA/SpuC) BXU11_RS08775 BXU11_RS07400
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BXU11_RS01185 BXU11_RS12805
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase BXU11_RS01185 BXU11_RS04005
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter BXU11_RS04800
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BXU11_RS13235 BXU11_RS13510
sucrose 1pfk: 1-phosphofructokinase BXU11_RS00305
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
threonine snatA: L-threonine transporter snatA BXU11_RS04800
thymidine deoA: thymidine phosphorylase DeoA BXU11_RS10650
thymidine deoB: phosphopentomutase BXU11_RS09765
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BXU11_RS04315 BXU11_RS10875
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BXU11_RS02105
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BXU11_RS10670 BXU11_RS11535
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BXU11_RS09535 BXU11_RS00525
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BXU11_RS02105 BXU11_RS13795
valine mmsA: methylmalonate-semialdehyde dehydrogenase BXU11_RS01185
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit BXU11_RS09415 BXU11_RS02955
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

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