GapMind for catabolism of small carbon sources

 

Protein WP_055435367.1 in Lacinutrix algicola AKS293

Annotation: NCBI__GCF_001418085.1:WP_055435367.1

Length: 246 amino acids

Source: GCF_001418085.1 in NCBI

Candidate for 36 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 98% 152.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 98% 152.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 98% 152.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 37% 98% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 37% 98% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 37% 98% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-alanine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 34% 96% 140.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-isoleucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 34% 96% 140.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-leucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 34% 96% 140.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-proline catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 34% 96% 140.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-serine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 34% 96% 140.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-threonine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 34% 96% 140.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-valine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 34% 96% 140.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 136 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 31% 98% 134 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 95% 132.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 95% 132.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 95% 132.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 127.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 127.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 127.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 127.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-alanine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 125.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 125.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-leucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 125.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-proline catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 125.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-serine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 125.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-threonine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 125.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 125.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 92% 119.8 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 98% 118.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 98% 118.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 98% 118.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 91% 117.5 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 91% 117.5 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 91% 117.5 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 275.4

Sequence Analysis Tools

View WP_055435367.1 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

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Sequence

MKLKAEHLMKSYNGRKVVKDVSLEVNTGEIVGLLGPNGAGKTTSFYMIVGLIKPNGGNIF
LEGTNITKYPMYKRAQNGIGYLAQEASVFRKLSIEDNILSVLQLTKLSKKEQLHKMESLI
DEFSLGHIRKSRGDLLSGGERRRTEIARALATDPNFILLDEPFAGVDPVAVEDIQRIIAR
LAKKDIGILITDHNVQETLAITDRTYLMFEGGILKAGEPEELAADEMVRKVYLGQNFELR
KTKIDF

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