GapMind for catabolism of small carbon sources

 

Protein WP_092344789.1 in Desulfuromusa kysingii DSM 7343

Annotation: NCBI__GCF_900107645.1:WP_092344789.1

Length: 452 amino acids

Source: GCF_900107645.1 in NCBI

Candidate for 34 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) 52% 100% 471.9
L-citrulline catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 52% 100% 471.9
putrescine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 52% 100% 471.9
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 97% 414.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 97% 414.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 97% 414.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 97% 414.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 97% 414.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 97% 414.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 97% 414.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 92% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 92% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 92% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 92% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 88% 243 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 32% 94% 242.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 32% 94% 242.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 30% 92% 241.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 30% 92% 241.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 30% 92% 241.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 33% 95% 241.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-arabinose catabolism xacF lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 236.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
D-galacturonate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 236.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
D-glucuronate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 236.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
D-xylose catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 236.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 31% 92% 229.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 31% 92% 229.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 31% 92% 229.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 93% 225.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 30% 91% 220.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 30% 91% 220.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 30% 91% 220.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 30% 91% 169.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 30% 91% 169.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 52% 471.9

Sequence Analysis Tools

View WP_092344789.1 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

MALESLNPATGEVLETFDEWSDEQVATTIEAVHGAYQNWRTTSFAERKSLLLKAAVILRQ
RKDEFATMMALEMGKPVVEGRAEIEKCALVCNYYAENAEQMLAPEPIASDASRSYVAFRP
QGIVLAVMPWNFPFWQVFRFAAPALMAGNVGVLKHASNVPRCALAIEQVFVEAGYPADVF
RTLMIGSGKVAQVIEHPYVVATTLTGSDIAGRKVAEKSGAMLKKSVMELGGSDPFIVLND
ADLDLAASVAVTARCINSGQSCIAAKRFIVEDGIYETFLEKFKANMAALKMGDPCDETTQ
VGPQAREDLMRELHRQVEGSVAKGAKVILGGMPGEAAFYPPTILTQVSKGMPAYNEEFFG
PVAIVIRVKDAEEALFVANDTEFGLGGSVWTRDIIKGEKIAGEIRSGAVFVNSMTKSDPR
LPFGGVGISGFGRELSHYGIKEFVNIQTVWIQ

This GapMind analysis is from Apr 09 2024. 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