GapMind for catabolism of small carbon sources

 

Protein WP_086510804.1 in Halomonas desiderata SP1

Annotation: NCBI__GCF_002151265.1:WP_086510804.1

Length: 481 amino acids

Source: GCF_002151265.1 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
L-arginine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 62% 99% 618.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 61% 603.2
L-citrulline catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 62% 99% 618.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 61% 603.2
putrescine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 62% 99% 618.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 61% 603.2
L-arginine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 99% 614.8 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 61% 603.2
L-citrulline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 99% 614.8 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 61% 603.2
L-lysine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 99% 614.8 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 61% 603.2
L-proline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 99% 614.8 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 61% 603.2
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 542 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 542 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 542 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 542 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 542 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 542 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 542 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-fucose catabolism aldA med NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 97% 335.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-rhamnose catabolism aldA med NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 97% 335.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-threonine catabolism aldA med NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 97% 335.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 99% 337.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 99% 337.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 96% 329.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 96% 329.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 96% 329.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 99% 322.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
4-hydroxybenzoate catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 97% 313.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 97% 313.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-tryptophan catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 97% 313.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 260.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 260.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 260.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 260.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 260.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 260.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 35% 87% 227.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 223.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 223.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 618.2

Sequence Analysis Tools

View WP_086510804.1 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

MSLPADIFSDKAFIGGQWRDAERRFDVTNPANGETLASVPDLSADDARDAVAAAEAAWPA
WRRQTAKQRAALLRAWFDAIMAHQESLARMMTLEQGKPLAESRGEVAYGASFVEFYAEQA
KRMAGETLPSHGADKRILVFREPVGVVAAITPWNFPLAMITRKCAPALAAGCPVVIKPAE
ATPLTALALARLAEQVGFPAGVLNVVTASRPAEIGEVLTSDPRVRKVSFTGSTAVGKRLL
AQCAGTVKKASMELGGNAPFIVFDDADLDAAVEGAVASKYRNSGQTCVCTNRLLVQSGVY
EAFVEKLAARVAQLKVGNGLDEGVVQGPLINQAAVDKVQSHIADALAKGARLVCGGEPHA
LGGTFFQPTVVADVTDEMRVAREETFGPLAPVFRFDSDEQAIAMANATEFGLAAYFYARD
YRRIWHVMEGLEYGMVAVNEGILSTELAPFGGVKESGLGREGSHHGLDEFTELKYVCVGG
L

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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