GapMind for catabolism of small carbon sources

 

Protein WP_022529986.1 in Lactobacillus shenzhenensis LY-73

Annotation: NCBI__GCF_000469325.1:WP_022529986.1

Length: 218 amino acids

Source: GCF_000469325.1 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-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 33% 96% 140.6 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 34% 95% 136.7 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 34% 95% 136.7 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-glutamate catabolism gltK 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) 35% 100% 131 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 54% 130.6 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 80% 130.6 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 54% 130.6 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 80% 130.6 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 80% 130.6 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-asparagine catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 35% 99% 129.8 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-aspartate catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 35% 99% 129.8 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 36% 57% 129.4 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
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) 38% 54% 124.8 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
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) 38% 54% 124.8 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
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) 38% 54% 124.8 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
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) 38% 54% 124.8 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
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) 38% 54% 124.8 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 34% 58% 120.6 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 32% 79% 120.6 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 31% 94% 105.5 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 30% 73% 100.9 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 30% 73% 100.9 Probable glutamine ABC transporter permease protein GlnP 52% 228.0
D-alanine catabolism Pf6N2E2_5403 lo ABC transporter for D-Alanine, permease component 2 (characterized) 31% 57% 91.7 Probable glutamine ABC transporter permease protein GlnP 52% 228.0

Sequence Analysis Tools

View WP_022529986.1 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

MGDFAGAYQWINIRYLLQGLWVTVSLSAVSIVFSVIFGSILGLLRYMKIPVLSLIVGFII
DIIRNLPLLLILFFTYFGLPNIGIRLDALPAAMVAMTVFESMMLAEIIRGGIQAVDPGQM
EAARSNGLSYGQAMLHIILPQAFKKMIPAIVSQLISLVKDTSLATIIVLPELMYHGQVIY
GQNTNYMVPIFIALTVLYFIVCFSLSVISRYLDRRLAA

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