GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Klebsiella michiganensis M5al

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

Pathway Step Best candidate 2nd candidate
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BWI76_RS20320 BWI76_RS07590
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BWI76_RS20325 BWI76_RS19230
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BWI76_RS20330 BWI76_RS19235
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component BWI76_RS20340 BWI76_RS19240
deoxyribonate atoA: acetoacetyl-CoA transferase, A subunit BWI76_RS16145
deoxyribonate atoD: acetoacetyl-CoA transferase, B subunit BWI76_RS16140
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BWI76_RS16755 BWI76_RS23630
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
galactose galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BWI76_RS07640 BWI76_RS13720
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BWI76_RS11940
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BWI76_RS23705 BWI76_RS11090
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpC: 2-methylcitrate synthase BWI76_RS08385 BWI76_RS19140
isoleucine prpF: methylaconitate isomerase BWI76_RS04370 BWI76_RS14180
lactose lacA: galactose-6-phosphate isomerase, lacA subunit BWI76_RS02175
lactose lacB: galactose-6-phosphate isomerase, lacB subunit BWI76_RS02175
leucine atoA: acetoacetyl-CoA transferase, A subunit BWI76_RS16145
leucine atoD: acetoacetyl-CoA transferase, B subunit BWI76_RS16140
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BWI76_RS13985 BWI76_RS25540
leucine liuC: 3-methylglutaconyl-CoA hydratase BWI76_RS13115 BWI76_RS20455
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BWI76_RS13115 BWI76_RS20455
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine gcdH: glutaryl-CoA dehydrogenase
phenylacetate ppa: phenylacetate permease ppa BWI76_RS02085
phenylalanine ARO10: phenylpyruvate decarboxylase BWI76_RS20520
propionate acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BWI76_RS11940
propionate prpC: 2-methylcitrate synthase BWI76_RS08385 BWI76_RS19140
propionate prpF: methylaconitate isomerase BWI76_RS04370 BWI76_RS14180
tyrosine atoA: acetoacetyl-CoA transferase, A subunit BWI76_RS16145
tyrosine atoD: acetoacetyl-CoA transferase, B subunit BWI76_RS16140
tyrosine fahA: fumarylacetoacetate hydrolase BWI76_RS03870
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase BWI76_RS16945
tyrosine maiA: maleylacetoacetate isomerase BWI76_RS19575 BWI76_RS25335
valine acdH: isobutyryl-CoA dehydrogenase
valine acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BWI76_RS11940
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BWI76_RS13120 BWI76_RS20065
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BWI76_RS13115 BWI76_RS20455
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BWI76_RS24825 BWI76_RS07000
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpC: 2-methylcitrate synthase BWI76_RS08385 BWI76_RS19140
valine prpF: methylaconitate isomerase BWI76_RS04370 BWI76_RS14180
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) BWI76_RS24865 BWI76_RS19725
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase BWI76_RS11535 BWI76_RS24895

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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