GapMind for catabolism of small carbon sources

 

Protein WP_003471449.1 in Gracilibacillus halophilus YIM-C55.5

Annotation: NCBI__GCF_000359605.1:WP_003471449.1

Length: 473 amino acids

Source: GCF_000359605.1 in NCBI

Candidate for 41 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 100% 380.2 succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 37% 317.0
L-rhamnose catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 100% 380.2 succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 37% 317.0
L-threonine catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 100% 380.2 succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 37% 317.0
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 37% 100% 317 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 37% 100% 317 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 37% 100% 317 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
4-hydroxybenzoate catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 35% 90% 287.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
2'-deoxyinosine catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 35% 90% 287.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
2-deoxy-D-ribose catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 35% 90% 287.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
ethanol catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 35% 90% 287.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-threonine catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 35% 90% 287.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
thymidine catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 35% 90% 287.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-tryptophan catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 35% 90% 287.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-arginine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 96% 285 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 96% 285 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-citrulline catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 96% 285 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 96% 285 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
putrescine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 96% 285 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 96% 285 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 98% 282.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 98% 282.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 98% 282.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 98% 282.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 97% 270.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 97% 270.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 90% 270 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 90% 270 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 90% 270 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 90% 270 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 90% 270 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 32% 97% 266.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 94% 265 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-phenylalanine catabolism pad-dh lo Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 35% 96% 260 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-arabinose catabolism xacF lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 35% 97% 258.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
D-galacturonate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 35% 97% 258.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
D-glucuronate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 35% 97% 258.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
D-xylose catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 35% 97% 258.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 31% 99% 200.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 31% 87% 196.8 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 31% 94% 185.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 31% 94% 185.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 44% 380.2

Sequence Analysis Tools

View WP_003471449.1 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

MERYALYINGGWVETEETIDVLDKYSQTTYATVAKASREHVDEAISSATKAYRKNQLSPY
QRFEILRNVSTLMKNNKEELAYTITKEAGKPLKQARTEIDRSAETFLLAAEEAKRIHGEG
VPVEAAPGSEHRMAFTIKVPVGVVGAISPFNFPLNLVAHKVAPALAAGNAVVLKPASKTP
LASLKLAKLLEEAGLPKGLLQVVVGSGSVVGQQMMDDERIDLYTFTGSAEVGLQLKQNTG
LNRLILELGNNSPVIVDKEADIDHAAKTLAGQSFAFAGQVCISVQRVYVHESIQERFLET
FSEQIKQLLVGDPTDATTDVGPMISVSEAERAETWIHEAVDKGAKVVLGGKREGALLEPT
ILTDVKPEMRVVCEEIFAPVVSVIAYTDLDSCIEEVNQSVYGLQGGIFTQNIDTAYYAAK
RVEVGGFMINDGSQYRVDLMPYGGVKDSGNGKEGPKYSIEEMTEERLIVMNLR

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