GapMind for catabolism of small carbon sources

 

Protein WP_091293957.1 in Amycolatopsis xylanica CPCC 202699

Annotation: NCBI__GCF_900107045.1:WP_091293957.1

Length: 477 amino acids

Source: GCF_900107045.1 in NCBI

Candidate for 30 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 hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 47% 95% 430.3 aldehyde dehydrogenase 46% 405.6
2'-deoxyinosine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 47% 95% 430.3 aldehyde dehydrogenase 46% 405.6
2-deoxy-D-ribose catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 47% 95% 430.3 aldehyde dehydrogenase 46% 405.6
ethanol catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 47% 95% 430.3 aldehyde dehydrogenase 46% 405.6
L-threonine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 47% 95% 430.3 aldehyde dehydrogenase 46% 405.6
thymidine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 47% 95% 430.3 aldehyde dehydrogenase 46% 405.6
L-tryptophan catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 47% 95% 430.3 aldehyde dehydrogenase 46% 405.6
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 46% 92% 401.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 94% 387.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 94% 387.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 94% 387.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 44% 95% 377.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 44% 95% 377.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 96% 370.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 96% 370.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 96% 370.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 96% 370.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 256.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 256.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 256.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 256.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 256.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 95% 247.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 245.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 245.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 245.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 245.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 245.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 32% 90% 201.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 32% 90% 201.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 496.9

Sequence Analysis Tools

View WP_091293957.1 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

MGIFEYAPAPESRDIANLKPNYRPFINGEFVDGNGEPLKTINPATEEVLAEVGTASVSDV
DTAVKAARKAYTNVWSKMPGSERAKYLFRIARLIQERSRELAVLESLDNGKPIKESRDSD
VPTAAAHFFYHAGWADKLDYAGLGPNPQPLGVAGQIIPWNFPLLMLAWKIAPALATGNTV
VLKPAETTPLTALVFAEICQQAELPPGVVNILPGAGDIGQSIVEHGDVNKIAFTGSTDVG
KLIQRQVAGTSKKLTLELGGKAANVVFDDAPLDQAVEGIVNGIFFNQGHVCCAGSRLLVQ
ESVAEEVMEKLKYRVSTLRLGDPLDKNTDIGAINSAEQLSKIKGLVESGDTEGAHRWTSP
CPVPERGFFFAPTVFSDVQQSMRIAREEIFGPVLSVLTFRTPDEAVTKANNTPYGLSAGI
WTEKGSRILWMANQLRAGVVWANTFNRFDPAAPFGGYQESGFGREGGRTGLEAYLNV

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