GapMind for catabolism of small carbon sources

 

Protein WP_109967802.1 in Methanospirillum lacunae Ki8-1

Annotation: NCBI__GCF_003173355.1:WP_109967802.1

Length: 229 amino acids

Source: GCF_003173355.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 82% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 82% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-asparagine catabolism aapP lo AapP, 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) 40% 87% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-aspartate catabolism aapP lo AapP, 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) 40% 87% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-glutamate catabolism aapP lo AapP, 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) 40% 87% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-histidine catabolism aapP lo AapP, 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) 40% 87% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-leucine catabolism aapP lo AapP, 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) 40% 87% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-proline catabolism aapP lo AapP, 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) 40% 87% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 40% 83% 132.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 40% 83% 132.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 38% 83% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 38% 83% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 82% 124.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 204.9

Sequence Analysis Tools

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

MTDTEPVMEFIGVSKIYPLSSENVTALSDISLKVFSGEFIAIMGPSGSGKSTLLNMMGCL
DVPSKGDVYIRGRSIKSLSDDQLTTLRRDELGFIFQQFNLIPLLNALENVRYPLILKNGM
TASRERCQEILSAVGLAPALWNHRPNQLSGGQQQRVAIARSLINNPAILLCDEPTGNLDT
KTGQAIMALLERLCHDEGKTIIMVTHDPKTAEYAHRVIRIEDGHIQEET

This GapMind analysis is from Sep 24 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 (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