GapMind for catabolism of small carbon sources

 

Protein WP_014264590.1 in Granulicella mallensis MP5ACTX8

Annotation: NCBI__GCF_000178955.2:WP_014264590.1

Length: 518 amino acids

Source: GCF_000178955.2 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-isoleucine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 99% 644
myo-inositol catabolism mmsA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 99% 644
propionate catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 99% 644
L-threonine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 99% 644
L-valine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 63% 99% 644
L-valine catabolism mmsA med malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 61% 96% 615.9 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-valine catabolism mmsA med mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27) (TIGR01722) 100% 682.1 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 97% 276.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 97% 276.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 97% 276.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 97% 276.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 98% 270 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 98% 270 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 98% 270 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 33% 96% 256.5 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
4-hydroxybenzoate catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 98% 254.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
2'-deoxyinosine catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 98% 254.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
2-deoxy-D-ribose catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 98% 254.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
ethanol catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 98% 254.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-threonine catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 98% 254.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
thymidine catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 98% 254.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-tryptophan catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 98% 254.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-arginine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-citrulline catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
putrescine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 232.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 31% 100% 232.3 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 31% 100% 232.3 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 30% 95% 224.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 33% 99% 223.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 95% 218.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 31% 92% 217.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 31% 92% 217.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 31% 92% 217.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 31% 92% 217.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 31% 92% 217.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 32% 85% 193 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 63% 644.0

Sequence Analysis Tools

View WP_014264590.1 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

MSAAIASPLPTRSSTIDIREITHWISGTAVRGTSGRFADVYHPASGKVQAHVPLASNAEV
DKAVQAAAAAFPEWSSSPPLRRARVLFRFREIYERRLDEVAALLNREHGKVFSDAKGEAT
RGLEVVEFATGIPQLLKGEFTEQVGTGIDSWSMRQPLGVVAGITPFNFPAMVPMWMFPIA
LACGNTFVLKPSERDPSASILLAEMLKEAGLPDGVFNVVHGDKSAVDAILAHPTIQAVSF
VGSTPIAEYVYREGTKHGKRVQALGGAKNHMIVMPDADLDQAADALAGAAYGSAGERCMA
ISIAVTVGHQTADTLIEKLKTRISNLRVGDGAQDASTGEADLGPLVTKNHLDKVTTYVEL
GTTEGAELVVDGRQGALPQGDGFFLGACLFDHVKPEMRIYKEEIFGPVLGVVRVNNFETA
LQLINDHEFGNGTALFTRDGDTARDFARRVQAGMVGINVPIPVPMAFHSFGGWKRSLFGD
HAVHGPEGVRFYTRIKTVTARWPTGIRTGVDTTMPTLG

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