GapMind for catabolism of small carbon sources

 

Protein GFF2619 in Phaeobacter inhibens BS107

Annotation: PGA1_c26600 amino acid ABC transporter, permease protein

Length: 273 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 34% 62% 133.3 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 34% 62% 133.3 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 35% 87% 132.9 Basic amino acid uptake transporter, BgtAB 40% 164.5
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-Glucosamine Hydrochloride, permease component 2 (characterized) 32% 94% 125.2 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-histidine catabolism Ac3H11_2554 lo ABC transporter for L-Histidine, permease component 1 (characterized) 33% 91% 122.5 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-citrulline catabolism PS417_17595 lo ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale) 34% 90% 117.1 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-asparagine catabolism aapM lo AapM, 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) 32% 58% 116.7 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-aspartate catabolism aapM lo AapM, 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) 32% 58% 116.7 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-glutamate catabolism aapM lo AapM, 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) 32% 58% 116.7 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-histidine catabolism aapM lo AapM, 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) 32% 58% 116.7 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-leucine catabolism aapM lo AapM, 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) 32% 58% 116.7 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-proline catabolism aapM lo AapM, 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) 32% 58% 116.7 Basic amino acid uptake transporter, BgtAB 40% 164.5
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 32% 58% 113.2 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 32% 80% 113.2 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 32% 80% 113.2 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-arginine catabolism artQ lo Histidine transport system permease protein HisQ (characterized) 33% 97% 108.6 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-histidine catabolism hisQ lo Histidine transport system permease protein HisQ (characterized) 33% 97% 108.6 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 88% 107.5 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 88% 107.5 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 88% 107.5 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 34% 93% 101.3 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 31% 97% 101.3 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-asparagine catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 31% 93% 92 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-aspartate catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 31% 93% 92 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-glutamate catabolism gltK lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 31% 93% 92 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-asparagine catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 30% 50% 80.5 Basic amino acid uptake transporter, BgtAB 40% 164.5
L-aspartate catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 30% 50% 80.5 Basic amino acid uptake transporter, BgtAB 40% 164.5

Sequence Analysis Tools

View GFF2619 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSAQEPKPRRPDGKKDDFPWWLAAVLLIGGTLIWRVASDDLYLSILSTLMRGVQLTIFVT
LISFFLASLLGLGLALAAGSRWLVIRQGARFYIEVVRGIPIIVLLLYVAFVLAPALVELR
NWLGDHIGLDPIRTRNFPLLWRAIIALMIAYSAFISEVFRAGLQSVDEGQIEAAKSLGLS
RWHRFRFIVFPQAIRTILPPLGNDFVALVKDSSLVSVLGVADVTQLGKLTAVGNFRYFET
YNVVALIYLTLTIGLSLLLRRFEKHLRRREERR

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