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 (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:

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