GapMind for catabolism of small carbon sources

 

Protein WP_053937126.1 in Amantichitinum ursilacus IGB-41

Annotation: NCBI__GCF_001294205.1:WP_053937126.1

Length: 507 amino acids

Source: GCF_001294205.1 in NCBI

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 100% 659.8
myo-inositol catabolism mmsA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 100% 659.8
propionate catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 100% 659.8
L-threonine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 100% 659.8
L-valine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 100% 659.8
L-valine catabolism mmsA med Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 60% 99% 610.9 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-valine catabolism mmsA med mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27) (TIGR01722) 100% 704.9 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 282.3 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 282.3 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 282.3 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 282.3 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-phenylalanine catabolism pad-dh lo Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 32% 95% 227.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
4-hydroxybenzoate catabolism adh lo Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 31% 96% 222.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
2'-deoxyinosine catabolism adh lo Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 31% 96% 222.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
2-deoxy-D-ribose catabolism adh lo Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 31% 96% 222.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
ethanol catabolism adh lo Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 31% 96% 222.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-threonine catabolism adh lo Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 31% 96% 222.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
thymidine catabolism adh lo Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 31% 96% 222.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-tryptophan catabolism adh lo Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 31% 96% 222.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 32% 98% 218.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 32% 98% 218.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 32% 98% 218.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 97% 214.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 97% 214.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 97% 214.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 97% 214.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 97% 211.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-arginine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 94% 211.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 97% 211.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-citrulline catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 94% 211.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 97% 211.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 97% 211.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
putrescine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 94% 211.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 31% 81% 169.1 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 659.8

Sequence Analysis Tools

View WP_053937126.1 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

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Sequence

MTSNQDLQQLKLAGHWINGLAVAGQSDRFGEVFCPAEGKVSGRVSLANVDEVASAVASAK
AAFPAWAATPPLRRARVMFRFRQIVEDNIDTLAHLIATEHGKVLADAVGEIQRGLEVVEF
ATGIPSLLKSEMTENVGTGVDSYSLRQPLGVVAGVTPFNFPAMVPLWMFPVALASGNCFV
LKPSERVPGASLLLAQWLKQAGLPDGVFNVVQGDKVAVDALLDHPDVQALSFVGSTPIAR
YIYQRGTANGKRVQALGGAKNHMVVMPDADLDQAADALMGAAYGAAGERCMAISVVVPVG
AATADALREKLVARLAKLRVSYSLDSQAEMGPLISAPHRDKVRGYIDSGVAEGADLVVDG
RGLHVAGHEAGFFLGGSLFDHVTPSMKIYREEIFGPVLAITRAPDYATALNLVNAHEFGN
GAAIFTRDGATARHFASHVQIGMVGVNVPIPVPMAFHSFGGWKASLFGDHHMHGPEGVRF
YTRLKTITERWPDNVAAGAEFVMPTMK

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