GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Pseudomonas putida KT2440

Found 57 low-confidence and 13 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
D-serine dsdA: D-serine ammonia-lyase PP_5149 PP_3446
deoxyinosine deoB: phosphopentomutase PP_4716
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 PP_2784 PP_1946
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme PP_0303
deoxyribose deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase PP_2784 PP_1946
deoxyribose ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme PP_0303
fucose aldA: lactaldehyde dehydrogenase PP_3463 PP_2487
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucU: L-fucose mutarotase FucU
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component PP_2456 PP_2761
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
galactose galE: UDP-glucose 4-epimerase PP_0501 PP_3129
galactose galK: galactokinase (-1-phosphate forming)
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) PP_5409
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
lactose klh: periplasmic 3'-ketolactose hydrolase
lactose lacA': periplasmic lactose 3-dehydrogenase, LacA subunit
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit
maltose susB: alpha-glucosidase (maltase) PP_4059
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannose manP: mannose PTS system, EII-CBA components PP_0795
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 PP_2602
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase PP_4960
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) PP_5409
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
propionate putP: propionate transporter; proline:Na+ symporter PP_4946
rhamnose aldA: lactaldehyde dehydrogenase PP_3463 PP_2487
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
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase PP_1817 PP_2723
sucrose ams: sucrose hydrolase (invertase) PP_4059
thymidine deoA: thymidine phosphorylase DeoA PP_4248
thymidine deoB: phosphopentomutase PP_4716
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase PP_4041 PP_4059
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA PP_3161
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB PP_3162
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC PP_3163 PP_1163
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) PP_0795
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase PP_0552 PP_3839
xylose gtsD: xylose ABC transporter, ATPase component GtsD PP_1018 PP_0411
xylose xad: D-xylonate dehydratase PP_5128
xylose xdh: D-xylose dehydrogenase PP_1946 PP_1817
xylose xylC: xylonolactonase PP_3180 PP_1170

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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