GapMind for catabolism of small carbon sources

 

Protein WP_029134950.1 in Sedimenticola selenatireducens DSM 17993

Annotation: NCBI__GCF_000428045.1:WP_029134950.1

Length: 480 amino acids

Source: GCF_000428045.1 in NCBI

Candidate for 45 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 Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 41% 99% 347.4 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 41% 99% 347.4 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 41% 99% 347.4 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
ethanol catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 41% 99% 347.4 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-threonine catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 41% 99% 347.4 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
thymidine catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 41% 99% 347.4 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 41% 99% 347.4 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
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) 39% 90% 354.8 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
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) 39% 90% 354.8 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
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) 39% 90% 354.8 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 350.9 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 350.9 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 350.9 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 350.9 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 93% 332.4 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 98% 319.7 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 98% 319.7 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 98% 319.7 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 98% 319.7 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 100% 314.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 100% 314.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 100% 314.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 38% 100% 313.2 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-tryptophan catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 38% 100% 313.2 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-arginine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 304.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 304.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-citrulline catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 304.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 304.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
putrescine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 304.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 304.3 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 36% 99% 296.6 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 37% 90% 280 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 37% 90% 280 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 37% 90% 280 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 37% 90% 280 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 37% 90% 280 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 266.5 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 266.5 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 266.5 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 266.5 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 266.5 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 266.5 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-lysine catabolism amaB lo Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) 30% 87% 218 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 93% 199.5 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 93% 199.5 p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64) 43% 403.3

Sequence Analysis Tools

View WP_029134950.1 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

MQEYRLFINGEWVETQDGEVLDDINPSTGEVFARVHQAGPKDVEHAITAASAASVAWGKT
QPAVREEILIKAADCLQARIHEIADVLIDEAGSTFGKAMFEASFVVNLLRSAAGEARRIF
GETMPSDGPDIFSMSVRRPLGVIAGIAPFNFPFLLACKKVALAIAAGNAFVLKPSEETAV
TGLKIAEIFEQAGLPKGVLNVIPGSGPEVGGRLVDDPRVKMITFTGSTVVGKKLAVQAAQ
QLKKITLELGGKSPLIVLADADLDYAVDAACFGIFLHQGQVCMANSKLIVEAAVYDAFCD
KFAAKVKSLKVGDPRQPNTVIGPLIRGAQCQVIDRHVQDALDKGARLLTGGSSESNFYQP
TVMADVGPDMQIYREESFGPVVSIIKADDHEAALYIANDSEYGLSSAVITNDLQKAMELS
LRLEAGMVHINDCTVFDEPHVPFGGVKKSGFGREGGRYSMEEMTEVKWITIQMGKRHFPF

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