GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Sphingomonas indica Dd16

Found 126 low-confidence and 27 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
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 snatA: L-alanine symporter SnatA B9N75_RS07265
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocD: ornithine aminotransferase B9N75_RS01575
arginine rocE: L-arginine permease
asparagine ans: asparaginase B9N75_RS02880 B9N75_RS07065
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase B9N75_RS08670
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component B9N75_RS12690 B9N75_RS06700
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 B9N75_RS01320
citrulline rocD: ornithine aminotransferase B9N75_RS01575
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase B9N75_RS00300
D-lactate D-LDH: D-lactate dehydrogenase B9N75_RS02270 B9N75_RS08140
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 B9N75_RS00120 B9N75_RS05700
deoxyinosine deoB: phosphopentomutase B9N75_RS02645
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 B9N75_RS08485 B9N75_RS11295
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 deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose 1pfk: 1-phosphofructokinase
fructose fba: fructose 1,6-bisphosphate aldolase B9N75_RS00245
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase B9N75_RS04360 B9N75_RS09590
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
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase B9N75_RS13635
galacturonate udh: D-galacturonate dehydrogenase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase B9N75_RS10445
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) B9N75_RS11195
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 B9N75_RS13635
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltP: L-glutamate:cation symporter GltP/GltT B9N75_RS12045 B9N75_RS12050
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase B9N75_RS03795 B9N75_RS12035
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase B9N75_RS13445 B9N75_RS08665
isoleucine Bap2: L-isoleucine permease Bap2
L-lactate L-LDH: L-lactate dehydrogenase B9N75_RS05000 B9N75_RS04945
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase B9N75_RS08670
lactose lacP: lactose permease LacP
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuC: 3-methylglutaconyl-CoA hydratase B9N75_RS13460 B9N75_RS12955
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine cadA: lysine decarboxylase B9N75_RS00125 B9N75_RS09735
lysine davD: glutarate semialdehyde dehydrogenase B9N75_RS04360 B9N75_RS09590
lysine davT: 5-aminovalerate aminotransferase B9N75_RS01575
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase B9N75_RS01575
lysine patD: 5-aminopentanal dehydrogenase B9N75_RS04360 B9N75_RS09590
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mak: mannose kinase
mannitol mt1d: mannitol 1-dehydrogenase B9N75_RS04565
mannitol PLT5: polyol transporter PLT5
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
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) B9N75_RS11195
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase B9N75_RS13460 B9N75_RS12955
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase B9N75_RS13460 B9N75_RS12955
proline CCNA_00435: proline transporter B9N75_RS00325 B9N75_RS03485
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase B9N75_RS04360 B9N75_RS09590
putrescine gabT: gamma-aminobutyrate transaminase B9N75_RS01575
putrescine patA: putrescine aminotransferase (PatA/SpuC) B9N75_RS01575
putrescine patD: gamma-aminobutyraldehyde dehydrogenase B9N75_RS04360 B9N75_RS00315
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase B9N75_RS04360 B9N75_RS09590
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 B9N75_RS07265
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase B9N75_RS08485 B9N75_RS07690
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) B9N75_RS01355 B9N75_RS01360
threonine ltaE: L-threonine aldolase B9N75_RS05140 B9N75_RS01275
threonine snatA: L-threonine transporter snatA B9N75_RS07265
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase B9N75_RS02645
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase B9N75_RS13340
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine acdH: isobutyryl-CoA dehydrogenase B9N75_RS13445 B9N75_RS08665
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase B9N75_RS13455 B9N75_RS13460
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