GapMind for catabolism of small carbon sources

 

Protein WP_044621469.1 in Photobacterium gaetbulicola Gung47

Annotation: NCBI__GCF_000940995.1:WP_044621469.1

Length: 365 amino acids

Source: GCF_000940995.1 in NCBI

Candidate for 23 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) 59% 100% 434.5 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) 52% 369.8
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) 52% 96% 369.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
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) 52% 96% 369.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
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) 52% 96% 369.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
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) 52% 96% 369.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
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) 52% 96% 369.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
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) 52% 96% 369.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 40% 95% 253.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 40% 95% 253.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-asparagine catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 64% 250 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-aspartate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 64% 250 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-glutamate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 64% 250 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-asparagine catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 38% 89% 137.1 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-aspartate catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 38% 89% 137.1 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-glutamate catabolism gltK lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 37% 88% 133.7 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 88% 108.2 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 88% 108.2 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 88% 108.2 ABC transporter for D-Alanine, permease component 1 59% 434.5
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) 31% 91% 107.5 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 31% 77% 105.9 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-lysine catabolism hisQ lo Amino acid ABC transporter, membrane protein (characterized, see rationale) 32% 93% 105.9 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-lysine catabolism hisM lo ABC transporter for L-Lysine, permease component 2 (characterized) 32% 84% 99.8 ABC transporter for D-Alanine, permease component 1 59% 434.5
L-citrulline catabolism AO353_03045 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 31% 85% 94.7 ABC transporter for D-Alanine, permease component 1 59% 434.5

Sequence Analysis Tools

View WP_044621469.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MKVFHFSPPEAPPSKMIGISAWLRENLFSSALNTLITGAIAGVIFAAVTSLFQWAFLDAD
WVGLSREDCGRDGACWVFVQARFDQFMFGFYPSDESWRPMTFMLGLAATIAVLLLGKGSV
KKAGLVFALTVFPVLSVVLLYGGLAGLPVVETHLWGGLLITLVIALTGIVVSLPLGVVLA
LGRRSSMPIVRSMSTVYIEFWRGVPLITVLFMASVMLPLFLSGGTEIDKLIRALIGVVLF
NAAYMAEAIRGGLQSIPKGQFEAAEALGLSYWKSTRLIILPQALKISIPSIVNTFIALLK
DTSLVLIIGMFDVLGIAQSANSDPAWLGFSTESFVFAALVFWIMCFGMSRYSIYLEGKLN
TGHSN

This GapMind analysis is from Sep 24 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 (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:

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