GapMind for catabolism of small carbon sources

 

Protein AZOBR_RS28110 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS28110 C4-dicarboxylate ABC transporter

Length: 457 amino acids

Source: azobra in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-malate catabolism dctA hi Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 53% 98% 464.2 proton/sodium-glutamate symport protein GltT 37% 299.7
fumarate catabolism dctA hi Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 53% 98% 464.2 proton/sodium-glutamate symport protein GltT 37% 299.7
succinate catabolism dctA hi Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 53% 98% 464.2 proton/sodium-glutamate symport protein GltT 37% 299.7
acetate catabolism dctA med Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 53% 98% 464.2 Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate 53% 458.0
L-asparagine catabolism glt med aerobic C4-dicarboxylate transport protein (characterized) 54% 96% 451.8 Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs 53% 464.2
L-aspartate catabolism glt med aerobic C4-dicarboxylate transport protein (characterized) 54% 96% 451.8 Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs 53% 464.2
L-glutamate catabolism gltP lo proton/sodium-glutamate symport protein GltT (characterized) 37% 99% 299.7 Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs 53% 464.2

Sequence Analysis Tools

View AZOBR_RS28110 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MRLQTGEQTPAPTKPKAFYKALYFQVVVGLTLGILAGHFWPDLGASLKPLGDGFVKLVKM
MIAPVVFCTIVSGITSLNDTREIGKTLVKSMALFYALTVAALLIGLAAVMIIEPGVGMHV
SAASLDPTVAARYAKQAAPVGFTDFVLHIIPHSFFGAFAEGEVLPVLLISVLVGFGLTRV
GKAGEPVVQGIESFSHVLFAAFGFIMKLAPIGAFGAMAFTVGKYGIDSIGSLGLLILTFY
VACGVFLMVVIGTLARLHGFSLWKVLRYFREELLIVLGTSSSEPVLPRVLQKLEALGCKK
GVSGLVLPMGYSFNLDGTAIYLTLASLFIAQACDIHLSGGQIFAMLGVMLLTSKGAAGVT
GSGFVALVATLTVMPDLPVAGVALLVGIDRFMSEARALTSIISNCVASIVVSIWENACDR
EVLQRELNQSYASTERCLEEKGDIAVLPLNAPAQPSH

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