GapMind for catabolism of small carbon sources

 

Protein 3607933 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3607933

Length: 362 amino acids

Source: Dino in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 92% 156 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 155.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 155.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 93% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 93% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 36% 95% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 92% 153.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 93% 152.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 93% 152.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 93% 152.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 93% 152.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 93% 152.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 40% 237.7

Sequence Analysis Tools

View 3607933 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MKHQPIPRLEVSHLVRDFQGQRVVDDVSIRVMPGQVTCLLGPSGCGKSTTLRIIAGVDRQ
DSGTLTVDGEVVSSDDIHLPPEARSVGLMFQDFALFPHLCVADNVGFGLSGSRKEKRARA
HELLDRVGLLGDAGKFPHQLSGGEQQRVALARAIAPRPRVMLMDEPFSGLDNRLRDGIRD
ETLEVLKDEGTAVLLVTHEPEEAMRMADNIALMRGGKIVQQGAPYNVYNSPVDKAAAAFF
SDINVIESTVQGALTETPFGQFLAPGVPNGGRVEIVIRPQHLRIDFDRNGQGPLPTPQDG
TPARGTVQRARFMGAESLVEFRMDFDDVILRAKVPGVFMPKPGTVLWLSMRRDRCFVFPA
RD

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