GapMind for catabolism of small carbon sources

 

Protein WP_035135345.1 in Flavobacterium beibuense F44-8

Annotation: NCBI__GCF_000769915.1:WP_035135345.1

Length: 250 amino acids

Source: GCF_000769915.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
ethanol catabolism etoh-dh-nad med alcohol dehydrogenase (EC 1.1.1.1) (characterized) 41% 98% 181.4 cyclohexanol dehydrogenase 51% 245.0
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 38% 91% 167.5 cyclohexanol dehydrogenase 51% 245.0
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 38% 91% 167.5 cyclohexanol dehydrogenase 51% 245.0
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 38% 91% 167.5 cyclohexanol dehydrogenase 51% 245.0
L-fucose catabolism fucDH lo SDR family oxidoreductase (characterized, see rationale) 39% 97% 158.3 cyclohexanol dehydrogenase 51% 245.0
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 39% 97% 158.3 cyclohexanol dehydrogenase 51% 245.0
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 37% 96% 154.1 cyclohexanol dehydrogenase 51% 245.0
L-rhamnose catabolism LRA1 lo L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized) 37% 97% 143.7 cyclohexanol dehydrogenase 51% 245.0
D-sorbitol (glucitol) catabolism sdh lo L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 36% 93% 143.3 cyclohexanol dehydrogenase 51% 245.0
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 35% 95% 140.2 cyclohexanol dehydrogenase 51% 245.0
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 34% 97% 134.4 cyclohexanol dehydrogenase 51% 245.0
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 34% 97% 134.4 cyclohexanol dehydrogenase 51% 245.0
D-mannitol catabolism mt2d lo Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized) 32% 88% 131.7 cyclohexanol dehydrogenase 51% 245.0
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 31% 97% 124 cyclohexanol dehydrogenase 51% 245.0
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 31% 97% 124 cyclohexanol dehydrogenase 51% 245.0
4-hydroxybenzoate catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
4-hydroxybenzoate catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
L-arginine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
L-citrulline catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
L-isoleucine catabolism ivdG lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
L-lysine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
phenylacetate catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
phenylacetate catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
L-phenylalanine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
L-phenylalanine catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
L-proline catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 34% 95% 120.9 cyclohexanol dehydrogenase 51% 245.0
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 31% 94% 120.2 cyclohexanol dehydrogenase 51% 245.0
L-fucose catabolism fdh lo Short-chain dehydrogenase (characterized, see rationale) 33% 97% 107.8 cyclohexanol dehydrogenase 51% 245.0

Sequence Analysis Tools

View WP_035135345.1 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

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Sequence

MSLLKDKVAVVSGAGSGIGRAIAETYAREGAKVVITDINEAHGEETVAAIKKAGGEAFFI
KADSSKAEDNKKLVEAVVAKYGRLDVACNNAGMGGPAAPTGEYDIDGWDRVIALNLSGVF
YACRYQIEQMMKNGGGSIVNIASIHGTVAAPNSPAYTASKHGVVGLTKNIAAEYGQKNIR
CNAVGPGYIETPLLTDHLNKEMMDAVASKSTMNRLGTPQEIAELVTFLSSEKSSFTTGSY
VIADGGYTSI

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