GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Sphingomonas histidinilytica UM2

Found 98 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK B5X82_RS00855 B5X82_RS19690
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
acetate acs: acetyl-CoA synthetase, AMP-forming B5X82_RS24705 B5X82_RS19755
alanine cycA: L-alanine symporter CycA B5X82_RS24315
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)
arginine patA: putrescine aminotransferase (PatA/SpuC) B5X82_RS16580 B5X82_RS09405
arginine patD: gamma-aminobutyraldehyde dehydrogenase B5X82_RS22235 B5X82_RS22960
arginine rocE: L-arginine permease B5X82_RS24315
asparagine ans: asparaginase B5X82_RS13450 B5X82_RS20870
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase B5X82_RS25805 B5X82_RS16545
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component B5X82_RS14905 B5X82_RS01540
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 B5X82_RS14910
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 B5X82_RS08130
citrulline rocD: ornithine aminotransferase B5X82_RS11660 B5X82_RS16580
D-alanine cycA: D-alanine:H+ symporter CycA B5X82_RS24315
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA B5X82_RS24315
D-serine dsdA: D-serine ammonia-lyase B5X82_RS18680 B5X82_RS17445
deoxyinosine deoB: phosphopentomutase B5X82_RS01890
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase B5X82_RS09320
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase B5X82_RS11260 B5X82_RS14100
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter B5X82_RS15820
deoxyribonate garK: glycerate 2-kinase
deoxyribose deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase B5X82_RS11260 B5X82_RS14100
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter B5X82_RS15820
deoxyribose drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit B5X82_RS05920 B5X82_RS07160
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit B5X82_RS05915 B5X82_RS20220
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component
deoxyribose garK: glycerate 2-kinase
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase B5X82_RS22235 B5X82_RS22960
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 eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase B5X82_RS16980
gluconate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) B5X82_RS09975
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase B5X82_RS16980
glucuronate uxuB: D-mannonate dehydrogenase B5X82_RS16985
glutamate gltP: L-glutamate:cation symporter GltP/GltT B5X82_RS13905 B5X82_RS14940
isoleucine Bap2: L-isoleucine permease Bap2 B5X82_RS24315
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) B5X82_RS18765
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit B5X82_RS16940
lactose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuC: 3-methylglutaconyl-CoA hydratase B5X82_RS19780 B5X82_RS20125
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit B5X82_RS20680 B5X82_RS15580
leucine liuE: hydroxymethylglutaryl-CoA lyase B5X82_RS19775 B5X82_RS24465
lysine cadA: lysine decarboxylase B5X82_RS12155
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase B5X82_RS19780 B5X82_RS16280
lysine gcdH: glutaryl-CoA dehydrogenase B5X82_RS04280 B5X82_RS20685
lysine lysP: L-lysine:H+ symporter LysP B5X82_RS24315
lysine patA: cadaverine aminotransferase B5X82_RS16580 B5X82_RS09405
lysine patD: 5-aminopentanal dehydrogenase B5X82_RS22090 B5X82_RS22235
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mt2d: mannitol 2-dehydrogenase B5X82_RS16985 B5X82_RS19760
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase B5X82_RS19585 B5X82_RS10250
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 B5X82_RS12720 B5X82_RS14215
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) B5X82_RS09975
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate ppa: phenylacetate permease ppa B5X82_RS16925
phenylalanine ARO10: phenylpyruvate decarboxylase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP B5X82_RS24315
proline CCNA_00435: proline transporter B5X82_RS10835 B5X82_RS14620
propionate putP: propionate transporter; proline:Na+ symporter
putrescine patA: putrescine aminotransferase (PatA/SpuC) B5X82_RS16580 B5X82_RS09405
putrescine patD: gamma-aminobutyraldehyde dehydrogenase B5X82_RS22235 B5X82_RS22960
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase B5X82_RS22235 B5X82_RS22960
rhamnose LRA1: L-rhamnofuranose dehydrogenase B5X82_RS21680 B5X82_RS16245
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase B5X82_RS15785 B5X82_RS11335
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase B5X82_RS14625
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter B5X82_RS13850
sorbitol sdh: sorbitol dehydrogenase B5X82_RS19930 B5X82_RS19760
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) B5X82_RS12945 B5X82_RS12940
threonine snatA: L-threonine transporter snatA B5X82_RS13850
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase B5X82_RS01890
thymidine deoC: deoxyribose-5-phosphate aldolase
trehalose glk: glucokinase B5X82_RS25805 B5X82_RS16545
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan hpaH: anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase B5X82_RS04845 B5X82_RS15940
tyrosine aroP: L-tyrosine transporter (AroP/FywP) B5X82_RS24315
tyrosine maiA: maleylacetoacetate isomerase B5X82_RS14450 B5X82_RS19730
valine Bap2: L-valine permease Bap2 B5X82_RS24315
valine bch: 3-hydroxyisobutyryl-CoA hydrolase B5X82_RS24125 B5X82_RS04265
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase B5X82_RS19780 B5X82_RS16280
valine mmsB: 3-hydroxyisobutyrate dehydrogenase B5X82_RS18185 B5X82_RS24845
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose DKDP-dehydrog: D-2-keto-3-deoxypentoate dehydrogenase B5X82_RS19900 B5X82_RS02810
xylose xad: D-xylonate dehydratase B5X82_RS24850 B5X82_RS25810
xylose xdh: D-xylose dehydrogenase B5X82_RS02960 B5X82_RS19760
xylose xylC: xylonolactonase B5X82_RS19865 B5X82_RS02675
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.

Links

Downloads

Related tools

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