GapMind for catabolism of small carbon sources

 

Protein WP_033102432.1 in Thermoactinomyces daqus H-18

Annotation: NCBI__GCF_000763315.1:WP_033102432.1

Length: 485 amino acids

Source: GCF_000763315.1 in NCBI

Candidate for 21 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) 49% 100% 482.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 49% 100% 482.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 49% 100% 482.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
ethanol catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 49% 100% 482.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-threonine catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 49% 100% 482.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
thymidine catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 49% 100% 482.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 49% 100% 482.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 38% 97% 297.7 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 38% 97% 297.7 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 38% 97% 297.7 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
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% 100% 279.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
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% 100% 279.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
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% 100% 279.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
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% 100% 279.6 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 93% 215.7 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 93% 215.7 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 93% 215.7 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 93% 215.7 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 93% 215.7 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 31% 98% 201.1 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 31% 98% 201.1 Benzaldehyde dehydrogenase YfmT; Vanillin dehydrogenase; EC 1.2.1.28; EC 1.2.1.67 52% 523.5

Sequence Analysis Tools

View WP_033102432.1 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

MYDFTYWNKQYIGGEWIDGSSPTRYENVNPYNGETLSTLQLANRDDIARAYEKAKQSQKA
WEQLNPYNRAMVMEKAAALMVERADELIEILIAESGSTRIKASIEAKSAFSMLKEAAKYP
FQMNTTVHPSFVVGKENRVYCKPHGVVGIISPSNFPFILSLRAVAPALATGNGVVLKPDS
QTYISGGLFLAKLFEDAGLPKGVFNVVVGEIEEIGDTFIEHPVPRLISFTGSTETGRHIA
QICGKHLKRLHLELGGNNPFIVLEDANIEKAVQAAVFGAFLHQGQICMSINRIIVHKSRY
EEFIRLFAEKVKKLKVGNPAEPDTFIGPLINKNAIPRVLSLIEDAVQQGCRLILEGKAYD
QFLEPYILADVRNDMKIAQTELFAPVACILPVESEEEAIEIANDNSYGLSSAVFSGSIEH
GVRVAQRIQAGMVHVNDQTVNDEPNIPFGGEKASGYGRFGGNWGLGEFTTTKWVSVQNEP
RTFPF

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