GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Pseudomonas fluorescens FW300-N2E3

Found 41 low-confidence and 18 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
deoxyinosine deoB: phosphopentomutase AO353_05595
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AO353_24520 AO353_21770
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter AO353_29035 AO353_24515
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme AO353_07745
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase AO353_19510 AO353_06560
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 AO353_20825 AO353_21390
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
galactose dgoD: D-galactonate dehydratase AO353_03420
galactose galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) AO353_01660 AO353_23170
galacturonate udh: D-galacturonate dehydrogenase AO353_03260 AO353_06770
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter AO353_08820
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate udh: D-glucuronate dehydrogenase AO353_03260 AO353_06770
glucuronate uxuL: D-glucaro-1,5-lactonase UxuL or UxuF
lactose klh: periplasmic 3'-ketolactose hydrolase
lactose lacA': periplasmic lactose 3-dehydrogenase, LacA subunit
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) AO353_23370 AO353_18090
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit
maltose susB: alpha-glucosidase (maltase) AO353_15985 AO353_22940
mannose gluP: mannose:Na+ symporter AO353_25100
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase AO353_25675 AO353_24830
phenylacetate paaK: phenylacetate-CoA ligase AO353_03315 AO353_03310
phenylacetate paaZ1: oxepin-CoA hydrolase AO353_25675 AO353_03780
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa AO353_01865
propionate putP: propionate transporter; proline:Na+ symporter AO353_12815
rhamnose LRA1: L-rhamnofuranose dehydrogenase AO353_24520 AO353_21495
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase AO353_05290
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase AO353_01060 AO353_20700
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
sorbitol sdh: sorbitol dehydrogenase AO353_25900 AO353_01660
thymidine deoB: phosphopentomutase AO353_05595
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase AO353_25145 AO353_01660
xylose gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA AO353_03395
xylose gtsB: xylose ABC transporter, permease component 1 GtsB AO353_03390
xylose gtsC: xylose ABC transporter, permease component 2 GtsC AO353_03385
xylose gtsD: xylose ABC transporter, ATPase component GtsD AO353_03380 AO353_25130
xylose xylA: xylose isomerase

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