GapMind for catabolism of small carbon sources


Protein HSERO_RS19365 in Herbaspirillum seropedicae SmR1

Annotation: FitnessBrowser__HerbieS:HSERO_RS19365

Length: 254 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 4 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism fucDH hi Short-chain alcohol dehydrogenase protein (characterized, see rationale) 100% 100% 491.1 3-hydroxybutyrate dehydrogenase type 2; Dehydrogenase/reductase SDR family member 6; R-beta-hydroxybutyrate dehydrogenase; EC 1.1.1.-; EC 58% 280.8
D-xylose catabolism DKDP-dehydrog hi SDR family oxidoreductase (characterized, see rationale) 97% 100% 476.5 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- 60% 291.6
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 33% 94% 125.9 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- 60% 291.6
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 33% 94% 125.9 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- 60% 291.6

Sequence Analysis Tools

View HSERO_RS19365 at FitnessBrowser

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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This GapMind analysis is from Sep 17 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