GapMind for catabolism of small carbon sources

 

Protein WP_085770215.1 in Methylocystis bryophila S285

Annotation: NCBI__GCF_002117405.1:WP_085770215.1

Length: 241 amino acids

Source: GCF_002117405.1 in NCBI

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism badH lo BadH (characterized) 36% 98% 146.4 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
phenylacetate catabolism badH lo BadH (characterized) 36% 98% 146.4 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-phenylalanine catabolism badH lo BadH (characterized) 36% 98% 146.4 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
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% 95% 139.8 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 34% 98% 137.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
D-sorbitol (glucitol) catabolism sdh lo L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 37% 92% 134.8 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized) 34% 96% 134 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 34% 97% 129.8 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
4-hydroxybenzoate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
4-hydroxybenzoate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-arginine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-citrulline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-lysine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
phenylacetate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
phenylacetate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-phenylalanine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-phenylalanine catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-proline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 56% 111.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 31% 93% 109.4 Acetoacetyl-CoA reductase; EC 1.1.1.36 73% 363.2

Sequence Analysis Tools

View WP_085770215.1 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

MSRTAVVTGGTRGIGEAISKALKAAGYKVAATYAGNDEAAKKFKEETGIAVFKFDVSNYD
ACVAGIAAIEKELGPVEILVNNAGITKDGLFHKMTLEQWNAVIGTNLNSLFNVTRPVING
MRDRGFGRIIVISSINGQKGQAGQTNYSASKAGDIGFVKALAQESASKGVTVNAIAPGYI
ATEMVKAVPQEILDKNIIPHIAVKRLGEPEEIARAVVFLASDDAGFITGSTLTINGGQYM
T

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