GapMind for catabolism of small carbon sources

 

Protein HSERO_RS19370 in Herbaspirillum seropedicae SmR1

Annotation: FitnessBrowser__HerbieS:HSERO_RS19370

Length: 302 amino acids

Source: HerbieS in FitnessBrowser

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 lo Senescence marker protein-30 family protein (characterized, see rationale) 37% 94% 181 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
D-glucuronate catabolism uxuL lo Senescence marker protein-30 family protein (characterized, see rationale) 37% 94% 181 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
D-xylose catabolism xylC lo xylono-1,5-lactonase (EC 3.1.1.110) (characterized) 37% 99% 176.8 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
D-galactose catabolism galactonolactonase lo galactaro-1,5-lactonase (characterized) 38% 95% 173.7 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
lactose catabolism galactonolactonase lo galactaro-1,5-lactonase (characterized) 38% 95% 173.7 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
D-cellobiose catabolism gnl lo gluconolactonase (EC 3.1.1.17) (characterized) 32% 99% 166.8 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
D-glucose catabolism gnl lo gluconolactonase (EC 3.1.1.17) (characterized) 32% 99% 166.8 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
lactose catabolism gnl lo gluconolactonase (EC 3.1.1.17) (characterized) 32% 99% 166.8 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
D-maltose catabolism gnl lo gluconolactonase (EC 3.1.1.17) (characterized) 32% 99% 166.8 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
sucrose catabolism gnl lo gluconolactonase (EC 3.1.1.17) (characterized) 32% 99% 166.8 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
trehalose catabolism gnl lo gluconolactonase (EC 3.1.1.17) (characterized) 32% 99% 166.8 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6
L-arabinose catabolism xacC lo Gluconolactonase (characterized, see rationale) 36% 92% 161.8 6-deoxy-6-sulfogluconolactonase; 6-deoxy-6-sulfogluconolactone lactonase; SGL lactonase; EC 3.1.1.99 51% 264.6

Sequence Analysis Tools

View HSERO_RS19370 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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Sequence

MSVPSPSAAAVTVAFPEPMLLGESPLWHAQEAALYWIDIPGKAVHRLHPESGQHKRWDLP
EEPGSIVRHAQGGLVVAIRTGMFHLNTDTGALTLLLAAPYDSSRIRFNDGRCDASGRFWC
GTIYEPRDRDGGTLYCFERNALRDAHHAVVTSNGLAFSSDQRLMYHANTPAHRINLYDYD
LATGATSNCRLLRQFDSDKSAPDYGGRPDGAAVDSQGAYWCAMFEGGRVLRLSPQGEILQ
EIRLPARCPTMVAFGGDDLRTLYITTGRNGRSPAELAQYPESGCVLAVRVDVPGQLEYSY
RP

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