GapMind for catabolism of small carbon sources

 

Protein WP_076477023.1 in Williamsia sterculiae CPCC 203464

Annotation: NCBI__GCF_900156495.1:WP_076477023.1

Length: 500 amino acids

Source: GCF_900156495.1 in NCBI

Candidate for 38 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 45% 98% 404.1 cumic aldehyde dehydrogenase (EC 1.2.1.29) 43% 366.7
L-citrulline catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 45% 98% 404.1 cumic aldehyde dehydrogenase (EC 1.2.1.29) 43% 366.7
L-lysine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 45% 98% 404.1 cumic aldehyde dehydrogenase (EC 1.2.1.29) 43% 366.7
putrescine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 45% 98% 404.1 cumic aldehyde dehydrogenase (EC 1.2.1.29) 43% 366.7
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 40% 92% 349.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 92% 322 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 92% 322 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 92% 322 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 92% 322 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
4-hydroxybenzoate catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 36% 93% 309.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 36% 93% 309.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-tryptophan catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 36% 93% 309.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 37% 97% 307.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 37% 97% 307.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 37% 97% 307.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 37% 97% 307.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 91% 305.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 91% 305.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 91% 305.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-arabinose catabolism xacF lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 39% 97% 295 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
D-galacturonate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 39% 97% 295 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
D-glucuronate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 39% 97% 295 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
D-xylose catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 39% 97% 295 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 97% 287 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 97% 287 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 84% 235.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 84% 235.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 84% 235.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 84% 235.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 84% 235.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 34% 91% 230.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 227.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 227.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 227.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 227.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 94% 227.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 94% 208.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 94% 208.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 45% 404.1

Sequence Analysis Tools

View WP_076477023.1 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

MTLADTTQATVATGWVEGAEFRGSGPLHRVIAPATDEVVATMSLATAADVDTAVAAARRA
LPAWSGATPAQRSTVLLDFARVLDREAHALAVQEVSHTGKTIRLASEFDVPGSIDNVTFF
AGVARDLVGKATAEYSPDHTSSIRREAVGVVGSITPWNYPIQMAVWKALPAIAAGCTLVL
KPAEITPLTTITLARLASEAGLPDGVFNVLTGTGAEVGAALAGHPGVDLVTFTGSTGVGR
QVMAQAAVHGTRVQLELGGKAPFVVFDDADLEAAVHGAVAGSLINAGQDCTAATRAIVAP
ALYDDFVSGVAELMAGVRVGDPTDPATDMGSLSSRHHREKVAAMVDRARDTGIRVVTGGH
VPDGPGAFYPPTLLADVGEGAEVYRDEIFGPVLTVSSFTDDDDALRRAGDTVYGLAASAW
TRDVYRAQRASREIRAGCVWINDHIPIVSEMPHGGLRASGFGKDMSTYSMDEYLTVEHVM
SDITGIARKDWHRTVFGDRS

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