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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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