GapMind for catabolism of small carbon sources

 

Protein WP_028950880.1 in Sulfurihydrogenibium subterraneum DSM 15120

Annotation: NCBI__GCF_000619805.1:WP_028950880.1

Length: 474 amino acids

Source: GCF_000619805.1 in NCBI

Candidate for 46 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 41% 99% 353.6 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 40% 343.6
L-rhamnose catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 41% 99% 353.6 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 40% 343.6
L-threonine catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 41% 99% 353.6 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 40% 343.6
L-arginine catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 37% 90% 314.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-citrulline catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 37% 90% 314.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
putrescine catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 37% 90% 314.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
4-hydroxybenzoate catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 301.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
2'-deoxyinosine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 301.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
2-deoxy-D-ribose catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 301.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
ethanol catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 301.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-threonine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 301.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
thymidine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 301.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-tryptophan catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 301.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-arabinose catabolism xacF lo 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) 36% 97% 297.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
D-galacturonate catabolism dopDH lo 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) 36% 97% 297.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
D-glucuronate catabolism dopDH lo 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) 36% 97% 297.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
D-xylose catabolism dopDH lo 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) 36% 97% 297.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 99% 286.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 99% 286.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 99% 286.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 99% 286.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-arginine catabolism patD lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Gamma-aminobutyraldehyde dehydrogenase; EC 1.2.1.47; EC 1.2.1.3; EC 1.2.1.19 (characterized) 35% 89% 276.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-citrulline catabolism patD lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Gamma-aminobutyraldehyde dehydrogenase; EC 1.2.1.47; EC 1.2.1.3; EC 1.2.1.19 (characterized) 35% 89% 276.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
putrescine catabolism patD lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Gamma-aminobutyraldehyde dehydrogenase; EC 1.2.1.47; EC 1.2.1.3; EC 1.2.1.19 (characterized) 35% 89% 276.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 97% 275.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 97% 275.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 94% 268.5 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 94% 268.5 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 35% 94% 268.5 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 33% 93% 259.2 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-phenylalanine catabolism pad-dh lo Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 34% 97% 252.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 96% 250.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 98% 248.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 98% 248.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 34% 90% 236.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 228.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 228.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 228.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 228.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 228.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 225.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 225.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 225.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 225.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 225.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 99% 218 lactaldehyde dehydrogenase (EC 1.2.1.22) 41% 348.2

Sequence Analysis Tools

View WP_028950880.1 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

MIRLSMLIGGKEVFKDEVIDVIYPYNQQKIGEAVKGSVEDVEKAVEKAKIGLKKLKQLTA
YEKYKMLLKVAQLLEERKEEFAKVITLETGKTIKESRIEVDRAINTITFSAEEAKRIAGE
VVHFDASPNGRGKRGYYFRVPAGIVAAITPFNFPVNLTAHKIAPAIAAGCPFILKPSEKT
PLSPTMLCQLFLEAGVPEEAVSIIPGFADVGQAMTTHSDVRVVSFTGSLKVGEIIAKQAG
LKKIVMELGSNSAVIVDKDANLELAAKKSVLGGFALAGQVCISVQRVLVHKDVADEFENL
LKKEASKLKYGDPMEEDTDVGPVISINEVDRIQTWISEAVMKGAKVSLGGEAEKTLLKPT
IVSEIPEDSKLFYEEAFAPVVAVKRFETIEEAVEMVNKTNYGLQVGIFTNNLKNAWKVIE
EVEVGGVMVNDIPTFRADNMPYGGVKGSGIGREGPKFAIEDYTEIKVVAFDLNA

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