GapMind for catabolism of small carbon sources

 

Protein WP_043917993.1 in Jannaschia aquimarina GSW-M26

Annotation: NCBI__GCF_000877395.1:WP_043917993.1

Length: 495 amino acids

Source: GCF_000877395.1 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD med succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 39% 98% 316.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 36% 307.8
L-citrulline catabolism gabD med succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 39% 98% 316.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 36% 307.8
putrescine catabolism gabD med succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 39% 98% 316.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 36% 307.8
L-arginine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 38% 98% 315.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 36% 307.8
L-citrulline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 38% 98% 315.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 36% 307.8
L-lysine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 38% 98% 315.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 36% 307.8
L-proline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 38% 98% 315.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 36% 307.8
4-hydroxybenzoate catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 90% 285.8 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
2'-deoxyinosine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 90% 285.8 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
2-deoxy-D-ribose catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 90% 285.8 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
ethanol catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 90% 285.8 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-threonine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 90% 285.8 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
thymidine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 90% 285.8 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-tryptophan catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 90% 285.8 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 100% 256.5 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 100% 256.5 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 100% 256.5 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 36% 92% 246.5 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 36% 92% 246.5 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 87% 214.2 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 87% 214.2 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 87% 214.2 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 87% 214.2 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 87% 214.2 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 32% 79% 181 succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 39% 316.2

Sequence Analysis Tools

View WP_043917993.1 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

MNVQSEIRVAPTQAALIDGKWCDTAESFEVRNPHDGSLVAEVGLGGQSEVDAAVAAARAA
QPAWAALSVIERAQIMRRIHQIFLERAEPIAQKITQEIGKTITDAREEVFEYSAPSWAKS
AEEILRHRGLSFPSTQERTTNKRLVMNHRPLGVVAAITPYNFPTDISSIALAHIVAAGNC
VIWKPSEYAAVSCAMLADVFKEAGVPDGVINVVQGKGEAGAALVNHKGVDGVFFTGSTAT
GRKIAEACALRPHLLELGGDGPFIILPDADIDAAVDGAMNGCFYYSGQVCTSAERLLVHE
AVYDEFLEKFRAKAAALKIGDPMAEDTEMGPLCNADTLARVKRHVDDARAKGATIEQFGK
EEGLYFPATILTDVTLDMEIMQEETFGPVAPIYKIRSAEEAIDIAHMSGLGLIASLWTQD
LATAWRVGEALPHGSVNINETSNYWDQLAPFGGAGQSGVGRELSQWFLETFTEKKLLVFD
LGGAQRYDRRAEGGW

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