GapMind for catabolism of small carbon sources

 

Protein WP_011385953.1 in Magnetospirillum magneticum AMB-1

Annotation: NCBI__GCF_000009985.1:WP_011385953.1

Length: 496 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 35 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 94% 379 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
2'-deoxyinosine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 94% 379 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
2-deoxy-D-ribose catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 94% 379 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
ethanol catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 94% 379 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
L-threonine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 94% 379 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
thymidine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 94% 379 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
L-tryptophan catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 94% 379 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
L-phenylalanine catabolism pad-dh med Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 42% 97% 342.4 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 99% 332 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 99% 332 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-arginine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 36% 95% 305.4 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-citrulline catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 36% 95% 305.4 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
putrescine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 36% 95% 305.4 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 99% 303.9 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 99% 303.9 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 99% 303.9 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 34% 96% 295 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 34% 96% 295 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 34% 96% 295 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 39% 349.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 98% 293.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 35% 93% 288.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 98% 282.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 98% 282.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 98% 282.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 98% 282.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 282.3 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 282.3 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 282.3 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 282.3 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 95% 217.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 95% 217.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 95% 217.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 95% 217.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 95% 217.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 32% 93% 206.8 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 42% 379.0

Sequence Analysis Tools

View WP_011385953.1 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

MTLTPELDPFKLAKALSGKHLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIA
VISAKAAQKDWAKQSARARGKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVL
ADMFTFFGGLGSELKGETIPFNPDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVA
GNSVVVKSAEEAPLTVLRVAEIMNTVLPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGS
VETGRIVYKAAAEKLIPVTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASS
RLFVHESIHDEFVAKVKAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGA
TKHVCSALPTDPKLAKGRFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQAN
DSEYGLAASIWTRDFKLAMDATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLES
MLEHFTHKKTIIFNMK

This GapMind analysis is from Sep 17 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