GapMind for catabolism of small carbon sources

 

Protein WP_090272859.1 in Pseudomonas litoralis 2SM5

Annotation: NCBI__GCF_900105005.1:WP_090272859.1

Length: 486 amino acids

Source: GCF_900105005.1 in NCBI

Candidate for 31 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% 100% 610.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 58% 582.0
L-citrulline catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 62% 100% 610.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 58% 582.0
putrescine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 62% 100% 610.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 58% 582.0
L-arginine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 100% 607.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 58% 582.0
L-citrulline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 100% 607.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 58% 582.0
L-lysine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 100% 607.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 58% 582.0
L-proline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 100% 607.1 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 58% 582.0
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 517.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 517.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 517.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 517.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 517.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 517.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 517.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-arabinose catabolism xacF med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 41% 98% 360.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
D-galacturonate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 41% 98% 360.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
D-glucuronate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 41% 98% 360.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
D-xylose catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 41% 98% 360.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 37% 97% 308.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 95% 306.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 95% 306.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 95% 306.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 95% 306.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-arginine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 38% 93% 303.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-citrulline catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 38% 93% 303.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
putrescine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 38% 93% 303.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 38% 98% 285.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-tryptophan catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 38% 98% 285.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 32% 91% 212.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 94% 198.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 94% 198.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 62% 610.1

Sequence Analysis Tools

View WP_090272859.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTLSRLKSPRLFRQQCYVNGQWQNASSGETLAVDNPANGDVLGHVPVLSAAEVGAAVDAA
SSALRQWRKRTAQERADCLLAWHDLMLEHKEDLATLMTLEQGKPLVESQGEIDYAASFIR
WFAEEARRMYGETIPGARIGQHIVVTRQPVGVCAAITPWNFPAAMITRKAGAALAAGCTI
IVKPASATPFSALALAVLAEEAGIPHGVFNVVTGKAGEISEVLTRSPVVRKLSFTGSTDV
GRRLMAQCSEHIQKVSLELGGNAPFIVFDDADISRAVEGAMVCKFRNTGQTCVCANRFLV
QSGVHDKFVAALAEAMGKLRIGDGFEPGVTQSALINGDAVEKVIEHFDDAMAKGAKRVCG
PAPDADRGNYVQPVLLTDINTNMTLCHEETFGPLAAVLRFDTEEEAIELANATPFGLAAY
FYSRDIHRVWRVADALEAGIIGINEGLISNPMAPFGGVKESGLGREGSRHGLDEYTELKY
LCMGAE

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