GapMind for catabolism of small carbon sources

 

Protein WP_011514164.1 in Psychrobacter cryohalolentis K5

Annotation: NCBI__GCF_000013905.1:WP_011514164.1

Length: 508 amino acids

Source: GCF_000013905.1 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
4-hydroxybenzoate catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 72% 100% 776.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 71% 767.7
2'-deoxyinosine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 72% 100% 776.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 71% 767.7
2-deoxy-D-ribose catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 72% 100% 776.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 71% 767.7
ethanol catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 72% 100% 776.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 71% 767.7
L-threonine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 72% 100% 776.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 71% 767.7
thymidine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 72% 100% 776.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 71% 767.7
L-tryptophan catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 72% 100% 776.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 71% 767.7
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 95% 387.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 94% 375.6 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 94% 375.6 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 94% 375.6 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 94% 375.6 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 97% 357.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 97% 357.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 97% 357.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 99% 342 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 99% 342 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 39% 100% 360.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-arginine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 95% 330.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-citrulline catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 95% 330.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
putrescine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 95% 330.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 99% 318.2 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 99% 285.4 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 99% 285.4 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 99% 285.4 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 99% 285.4 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 215.3 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 215.3 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 215.3 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 215.3 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 215.3 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 72% 776.5

Sequence Analysis Tools

View WP_011514164.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLYAYPNTENSPVQFREKYGNFINGEWVAPIDGEYFDNSSPIDGKIFCQIARSKEADVEA
ALDAAHAAKDAWGKTSVTERSNMLLKLADGIEANLEAIAIAESYENGKPVRETLAADIPI
AIDHLRYFAGVIRAQEGGISQIDEDTVAYHFHEPLGVVGQIIPWNFPILMAIWKIAPALA
AGNCVVLKPAEQTPASVLFMLDLIGAADILPKGVLNVVNGFGVEAGKPIASNPRIDKVSF
TGETTTGRLIMQYASENIIPVTLELGGKSPNIFFADIMDEDDDFLDKAVEGLVMFALNQG
EVCTCPSRALVHESIYDEFMKRCIARVKAIKMGNPLDTDTMIGAQASSDQLEKILSYLDI
GKKEGAKVLVGGELAKHDGDMANGYYVQPTIFEGTNDMRVFQEEIFGPVLAVTTFKDDEE
AMALANDTLYGLGAGVWTRNGTRAYRFGRGIKAGRVWTNCYHLYPAHSAFGGYKQSGIGR
ENHLMMLDHYQQTKNMLVSYSPKAMGFF

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