GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_0246 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_0246 extracellular solute-binding protein, family 3

Length: 359 amino acids

Source: SynE 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
L-asparagine catabolism natF hi Extracellular solute-binding protein, family 3 (characterized, see rationale) 100% 100% 716.1 AapJ, 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) 51% 340.5
L-aspartate catabolism natF hi Extracellular solute-binding protein, family 3 (characterized, see rationale) 100% 100% 716.1 AapJ, 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) 51% 340.5
L-asparagine catabolism aapJ med AapJ, 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) 51% 97% 340.5 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
L-aspartate catabolism aapJ med AapJ, 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) 51% 97% 340.5 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
L-glutamate catabolism aapJ med AapJ, 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) 51% 97% 340.5 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
L-histidine catabolism aapJ med AapJ, 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) 51% 97% 340.5 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
L-leucine catabolism aapJ med AapJ, 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) 51% 97% 340.5 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
L-proline catabolism aapJ med AapJ, 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) 51% 97% 340.5 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
L-asparagine catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 47% 94% 306.6 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
L-aspartate catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 47% 94% 306.6 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
L-glutamate catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 47% 94% 306.6 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2
D-alanine catabolism Pf6N2E2_5402 med ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized) 42% 100% 291.6 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 52% 380.2

Sequence Analysis Tools

View Synpcc7942_0246 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

MKAILLSGGPMPAIASRFLLVLLCFLPLAACRSLGGNETESNSRLNQVQARGKLLCGVEG
RLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYRSLDSVERFPALASGEVDLLSR
NTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNSGIQSLQDFQGKSICVETGTTSELNL
ADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDRSQLAARRTTLSDADQHQLLDAV
ISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQANIDQFKTSKNPEIRRFLGLEG
ELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPLKLNRGLNQLYKNGGLLYSPPFR

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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, the preprint 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