GapMind for catabolism of small carbon sources

 

Protein WP_011385953.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS18195 DUF1487 domain-containing protein

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

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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