GapMind for catabolism of small carbon sources

 

Protein 3607933 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_1341 ABC transporter related (RefSeq)

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

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

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 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