GapMind for catabolism of small carbon sources

 

Protein WP_037458282.1 in Skermanella stibiiresistens SB22

Annotation: NCBI__GCF_000576635.1:WP_037458282.1

Length: 296 amino acids

Source: GCF_000576635.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galacturonate catabolism uxuL med Senescence marker protein-30 family protein (characterized, see rationale) 42% 100% 222.6 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 44% 221.1
D-glucuronate catabolism uxuL med Senescence marker protein-30 family protein (characterized, see rationale) 42% 100% 222.6 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 44% 221.1
D-galactose catabolism galactonolactonase med galactaro-1,5-lactonase (characterized) 42% 98% 221.5 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 44% 221.1
lactose catabolism galactonolactonase med galactaro-1,5-lactonase (characterized) 42% 98% 221.5 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 44% 221.1
L-arabinose catabolism xacC med Gluconolactonase (characterized, see rationale) 41% 92% 203.8 galactaro-1,5-lactonase 42% 221.5
D-xylose catabolism xylC med Xylonolactonase (EC 3.1.1.68) (characterized) 42% 92% 197.6 galactaro-1,5-lactonase 42% 221.5
D-cellobiose catabolism gnl lo Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized) 37% 98% 189.5 galactaro-1,5-lactonase 42% 221.5
D-glucose catabolism gnl lo Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized) 37% 98% 189.5 galactaro-1,5-lactonase 42% 221.5
lactose catabolism gnl lo Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized) 37% 98% 189.5 galactaro-1,5-lactonase 42% 221.5
D-maltose catabolism gnl lo Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized) 37% 98% 189.5 galactaro-1,5-lactonase 42% 221.5
sucrose catabolism gnl lo Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized) 37% 98% 189.5 galactaro-1,5-lactonase 42% 221.5
trehalose catabolism gnl lo Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized) 37% 98% 189.5 galactaro-1,5-lactonase 42% 221.5

Sequence Analysis Tools

View WP_037458282.1 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

MPDSNQPDVGCVLDARATIGECPVWSAEEQALYWVDILAPTLNRLDPVTGATRTWEMPAS
IGSFGLREAGGAVVALRTGFHLFDFDSGALTLLANPEPDQPGNRLNDGKVSPDGSFWAGT
MDEEGMSRPLGSLYRLAPDGSCARMVEGLIVSNGLAWSADGATLFLSDSRGKKIMAFDHD
PATGALSNRRVIAEPTEEIGRPDGAATDREGFYWSAGVSAAVLNRWSPDGRLDRQIPMPC
AAPTMPCFGGPDMRTIYVTSLRHNVLDEKLAAYPLSGGIFAVEVDVPGVPVPKFRG

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