GapMind for catabolism of small carbon sources

 

Protein WP_083875613.1 in Gracilibacillus halophilus YIM-C55.5

Annotation: NCBI__GCF_000359605.1:WP_083875613.1

Length: 492 amino acids

Source: GCF_000359605.1 in NCBI

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 36% 98% 293.9 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 96% 288.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 96% 288.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 96% 288.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 96% 288.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-arginine catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 34% 95% 286.2 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-citrulline catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 34% 95% 286.2 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
putrescine catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 34% 95% 286.2 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
4-hydroxybenzoate catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 33% 97% 278.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
2'-deoxyinosine catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 33% 97% 278.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
2-deoxy-D-ribose catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 33% 97% 278.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
ethanol catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 33% 97% 278.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-threonine catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 33% 97% 278.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
thymidine catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 33% 97% 278.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-tryptophan catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 33% 97% 278.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 98% 273.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 98% 273.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 98% 273.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 98% 273.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 33% 97% 271.2 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 33% 97% 271.2 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-fucose catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 100% 265.4 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-rhamnose catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 100% 265.4 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-threonine catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 100% 265.4 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 100% 264.2 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 100% 264.2 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 33% 97% 230.7 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 95% 217.6 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 95% 217.6 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 95% 217.6 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 95% 217.6 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 30% 75% 167.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 55% 132.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 55% 132.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 38% 318.5

Sequence Analysis Tools

View WP_083875613.1 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

MMTEPIEIHAMINGETYKTEENKPRENPTHPDEIVGYAPVNTKEETIQAIDAAHETFKTW
RRSEISERVERMRNAIEKLKEETPNLAELLSREHGKPLYDAEGEVTISIMWMEYACDNVE
DVLKDQVEDHDNGRTLIARDAIGVVSAISPWNYPISLSTIKIAPALLTGNTMVLKPSPMA
PLAVSKCTEMIANEFPAGVLNMVHGEADVGVELTSNPKVAKIAFTGGTETAKSIMKSAAD
TIKQMTLELGGNDAAIILDDFDVHDEEAMRRLVISNFLTAGQICMIAKRIYVAKSIYEEF
VEKYIEAANKWIRVGDPFGDEVTIGPVNNKNQIEHVQSLIDDAKEKGAEVIKLGEILDSD
LFEEGYYMQPSVVLGASQDDPIVQKEQFGPTVPILPFEDDEHALQLANDSIYGLTSSVWG
EETHALEIAKRIQAGTTMINTAAVQGLDVRFPFGGVKQSGIGREYGKEGLLAYTETHVIN
LPDELDLPYIPK

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