GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Sinorhizobium meliloti 1021

Found 25 low-confidence and 24 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP SMc01869 SMc04407
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC SM_b20724
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component SMc02260 SM_b21138
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 SMa0492 SMc02257
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 SMc02258 SMc00139
D-alanine AZOBR_RS08240: D-alanine ABC transporter, permease component 2 SMc01950
D-alanine dadA: D-alanine dehydrogenase SM_b20267
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase SMa1872 SM_b20432
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase SMc02041 SMc00372
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme SMc01637
deoxyribose deoP: deoxyribose transporter
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate garD: meso-galactarate dehydratase (L-threo-forming) GarD SM_b21107 SMa1351
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) SMa0717 SMc04142
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glucuronate gudD: D-glucarate dehydratase SMa0056
glucuronate uxuL: D-glucaro-1,5-lactonase UxuL or UxuF SMc04142 SMa0717
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase SM_b20753 SMa1400
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lysine hisP: L-lysine ABC transporter, ATPase component HisP SMc02260 SMa0083
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) SMc01498 SMc01626
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase SMc02227 SMc00727
phenylacetate paaK: phenylacetate-CoA ligase SMc00261
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) SMc01951 SMc02359
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK SMc01946 SMc00078
phenylalanine paaH: 3-hydroxyadipyl-CoA dehydrogenase SMc02227 SMc00727
propionate putP: propionate transporter; proline:Na+ symporter
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) SMc01946 SMc00078
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) SMc01951 SMc02359
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) SMc01946 SMc00078
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) SMc01951 SMc02359
thymidine nupG: thymidine permease NupG/XapB
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine acdH: isobutyryl-CoA dehydrogenase SM_b20753 SMa1400
valine bch: 3-hydroxyisobutyryl-CoA hydrolase SM_b20752 SMc01669
valine mmsA: methylmalonate-semialdehyde dehydrogenase SMc00781 SMc00094
valine mmsB: 3-hydroxyisobutyrate dehydrogenase SM_b20751 SMc00274
xylitol PS417_12055: xylitol ABC transporter, substrate-binding component SM_b20072 SM_b20712
xylitol PS417_12065: xylitol ABC transporter, ATPase component SM_b20713 SM_b20503

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