GapMind for catabolism of small carbon sources

 

Protein GFF3102 in Pseudomonas stutzeri RCH2

Annotation: Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Length: 365 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 22 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_5404 hi ABC transporter for D-Alanine, permease component 1 (characterized) 78% 100% 603.6 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) 54% 388.3
L-asparagine catabolism aapM med 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) 54% 96% 388.3 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-aspartate catabolism aapM med 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) 54% 96% 388.3 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-glutamate catabolism aapM med 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) 54% 96% 388.3 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-histidine catabolism aapM med 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) 54% 96% 388.3 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-leucine catabolism aapM med 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) 54% 96% 388.3 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-proline catabolism aapM med 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) 54% 96% 388.3 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-asparagine catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 48% 68% 245.7 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-aspartate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 48% 68% 245.7 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-glutamate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 48% 68% 245.7 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 40% 88% 239.6 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 40% 88% 239.6 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-asparagine catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 37% 97% 141.7 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-aspartate catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 37% 97% 141.7 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-glutamate catabolism gltK lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 37% 97% 141.7 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-glutamate catabolism gltJ lo Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 36% 90% 109.8 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 33% 85% 108.2 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 33% 85% 108.2 ABC transporter for D-Alanine, permease component 1 78% 603.6
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-glucosamine, permease component 1 (characterized) 34% 90% 105.9 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-lysine catabolism hisQ lo Amino acid ABC transporter, membrane protein (characterized, see rationale) 30% 97% 98.2 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 33% 61% 95.5 ABC transporter for D-Alanine, permease component 1 78% 603.6
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 33% 61% 95.5 ABC transporter for D-Alanine, permease component 1 78% 603.6

Sequence Analysis Tools

View GFF3102 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

MTIHTFKPDLPPPTISIGALGWLRANLFSSWINTLLTLVGLYLLWLIVPPVLEWAIFKAD
WTGETRADCSREGACWVFIQTRFGQFMYGFYPTELRWRVDAAAWLAIIGAAPLFLRQMPH
KLRYGIGYLLVYPLLAYWLLHGGFLGLQTVPTSQWGGLMLTVVIAAVGIAGALPLGILLA
LGRRSDMPAIRVLCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNLDKLLRAMLMVVFF
EAAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSTLLVILPQALKLVIPGIVNTFIALFK
DTSLVIIIGLFDFLNSIKRATADPAWLGMSTEGYVFAALVYWMFCFGMSRYSMRLERKLD
TGHKH

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