GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Methylobacterium nodulans ORS 2060

Found 49 low-confidence and 55 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) MNOD_RS30055 MNOD_RS10965
4-hydroxybenzoate pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) MNOD_RS30060 MNOD_RS10970
arabinose araE: L-arabinose:H+ symporter
arabinose xacB: L-arabinose 1-dehydrogenase MNOD_RS16255 MNOD_RS26775
arabinose xacC: L-arabinono-1,4-lactonase MNOD_RS02055
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase MNOD_RS35860
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrulline arcC: carbamate kinase
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component MNOD_RS31675
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1 MNOD_RS24390 MNOD_RS21095
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2 MNOD_RS24385 MNOD_RS04315
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component MNOD_RS24380 MNOD_RS18765
D-serine cycA: D-serine:H+ symporter CycA MNOD_RS23565 MNOD_RS04385
D-serine dsdA: D-serine ammonia-lyase MNOD_RS00715 MNOD_RS35840
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter MNOD_RS31250 MNOD_RS35665
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter MNOD_RS31250 MNOD_RS35665
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component MNOD_RS39985
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase MNOD_RS32090 MNOD_RS35765
fucose fucA: L-fuculose-phosphate aldolase FucA MNOD_RS22685
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 dgoD: D-galactonate dehydratase MNOD_RS08060 MNOD_RS02225
galactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) MNOD_RS02055
galactose galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) MNOD_RS16255 MNOD_RS26775
galactose galP: galactose:H+ symporter GalP
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase MNOD_RS07140 MNOD_RS18760
galacturonate PS417_04205: D-galacturonate transporter MNOD_RS07060
galacturonate udh: D-galacturonate dehydrogenase
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) MNOD_RS02055
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
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 uxaC: D-glucuronate isomerase
glycerol glpF: glycerol facilitator glpF MNOD_RS21880 MNOD_RS27030
histidine hutF: N-formiminoglutamate deiminase
lactose dgoD: D-galactonate dehydratase MNOD_RS08060 MNOD_RS02225
lactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) MNOD_RS02055
lactose galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) MNOD_RS16255 MNOD_RS26775
lactose glk: glucokinase MNOD_RS01530 MNOD_RS24865
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit MNOD_RS09065 MNOD_RS28580
leucine liuE: hydroxymethylglutaryl-CoA lyase MNOD_RS23140 MNOD_RS13215
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) MNOD_RS24385 MNOD_RS04315
lysine hisP: L-lysine ABC transporter, ATPase component HisP MNOD_RS30125 MNOD_RS17355
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) MNOD_RS24390 MNOD_RS11495
lysine lat: L-lysine 6-aminotransferase MNOD_RS26085 MNOD_RS13870
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
mannitol mt1d: mannitol 1-dehydrogenase MNOD_RS29080
mannitol PLT5: polyol transporter PLT5
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase MNOD_RS00720 MNOD_RS18785
phenylacetate ppa: phenylacetate permease ppa MNOD_RS24620 MNOD_RS14975
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) MNOD_RS08415 MNOD_RS05310
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK MNOD_RS08385 MNOD_RS14755
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase MNOD_RS00720 MNOD_RS18785
phenylalanine pad-dh: phenylacetaldehyde dehydrogenase MNOD_RS35765 MNOD_RS07620
phenylalanine PPDCalpha: phenylpyruvate decarboxylase, alpha subunit MNOD_RS15970 MNOD_RS30740
phenylalanine PPDCbeta: phenylpyruvate decarboxylase, beta subunit MNOD_RS15975 MNOD_RS30745
propionate lctP: propionate permease MNOD_RS33350
putrescine patD: gamma-aminobutyraldehyde dehydrogenase MNOD_RS36935 MNOD_RS32090
rhamnose LRA1: L-rhamnofuranose dehydrogenase MNOD_RS20615 MNOD_RS38835
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase MNOD_RS28645 MNOD_RS06090
ribose rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) MNOD_RS08385 MNOD_RS14755
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) MNOD_RS08415 MNOD_RS18715
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) MNOD_RS08410 MNOD_RS05615
sorbitol sdh: sorbitol dehydrogenase MNOD_RS16255 MNOD_RS12985
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine ltaE: L-threonine aldolase MNOD_RS05645 MNOD_RS25045
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoC: deoxyribose-5-phosphate aldolase
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase MNOD_RS24905 MNOD_RS39365
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA MNOD_RS11385
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB MNOD_RS11390
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC MNOD_RS11395
tryptophan aroP: tryptophan:H+ symporter AroP MNOD_RS23565 MNOD_RS04385
tryptophan catB: muconate cycloisomerase MNOD_RS11410
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase MNOD_RS05790 MNOD_RS15960
tryptophan pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) MNOD_RS30055 MNOD_RS10965
tryptophan pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) MNOD_RS30060 MNOD_RS10970
tyrosine aroP: L-tyrosine transporter (AroP/FywP) MNOD_RS23565 MNOD_RS04385
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase MNOD_RS00570
valine bch: 3-hydroxyisobutyryl-CoA hydrolase MNOD_RS35815 MNOD_RS16435
valine mmsA: methylmalonate-semialdehyde dehydrogenase MNOD_RS12075 MNOD_RS10495
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase MNOD_RS17750 MNOD_RS04730
xylose xdh: D-xylose dehydrogenase MNOD_RS17780 MNOD_RS34420
xylose xylC: xylonolactonase MNOD_RS02055
xylose xylT: D-xylose transporter

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