GapMind for catabolism of small carbon sources

 

Protein 206413 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU0981 multiphosphoryl transfer protein, putative

Length: 854 amino acids

Source: 882 in MicrobesOnline

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism fruI med Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized) 39% 84% 462.6 D-trehalose PTS system, I, HPr, and IIA components 36% 426.0
sucrose catabolism fruI med Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized) 39% 84% 462.6 D-trehalose PTS system, I, HPr, and IIA components 36% 426.0
trehalose catabolism treEIIA lo D-trehalose PTS system, I, HPr, and IIA components (characterized) 36% 95% 426 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 39% 462.6
N-acetyl-D-glucosamine catabolism nagF lo N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 37% 93% 423.3 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 39% 462.6
D-glucosamine (chitosamine) catabolism nagF lo N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 37% 93% 423.3 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 39% 462.6
glycerol catabolism dhaM lo PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized) 50% 54% 226.5 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 39% 462.6
D-gluconate catabolism gntEIIA lo PTS system, IIA component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized) 33% 88% 51.6 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 39% 462.6

Sequence Analysis Tools

View 206413 at MicrobesOnline

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MVGIVVVTHSAVLGQGLRELAEQMTQGRVPLAVAGGIDDPDHPIGTDPVRVMTAIEEVQQ
GDGVLVLMDLGSALMSAETALDLLPPEVASQVRLSAAPLVEGLMAAAVLASTGADLGAVA
EEAQSALAAKRELLGAAAPAAPAMPSAHPEGARDSTVPSSAMPAGEELTLVVPNRLGLHA
RPAARIVTALGPFAADVQLVRGDRVVSARSVNRIATLAVRGGETVTFRAVGGDAALALRA
IEALAAAHFGDAPEAPSKGEAPSPAEAPKDGDMAEAAVSADVQGGGVLRGAAASPGLTVG
NAVWYRPAFDAPDVAPLADDPATEVTRLDAALGAARTELVELERRTVAAAGRKEAEIFAM
HRLLLDDVTIAGAARQRIMDRREAAESAWYEVISDAAATFRQLPEGYMREREADMVDVGA
RVLRLLTGVAAVGPRLGGPSVLLATDLGPSDMATLDPSLVIGIVTVQGGATSHAAILARS
LGIPAVAGLGPALQGVGEGDIVALDGGTGDVWVNPAPGVRAAVEARRDAWLAGREAALAG
AAAPAVTADGRAVHILANIGSSADAGAALKNGAEGVGLFRTEFLFLDRTSPPGEEEQLTA
YVTAAAAMQGRPVVVRTLDIGGDKPVSYLEGFATGEDNPFLGLRGIRFCLERKPLFMTQL
RALLRAAAVHPLKVMFPMVAHPGELAAAKALLDEARATLDAEGMPHGQLDVGIMIEVPAA
VALADQLARDAAFFSIGTNDLAQYVMAADRGNASVAALSDALHPAVLRMVRDTVRAGHAA
GIPVAICGELGGNPEAIPLLVGLELDELSMNGPAIPRAKEVVRGCDTGTCAVLADRAMAL
PDAAAVRRLLQGGS

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