GapMind for catabolism of small carbon sources

 

Protein WP_017177453.1 in Actinomyces timonensis 7400942

Annotation: NCBI__GCF_000295095.1:WP_017177453.1

Length: 300 amino acids

Source: GCF_000295095.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 90% 186.8 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 68% 153.3 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 68% 151 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 68% 151 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 63% 150.2 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 63% 150.2 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 39% 60% 148.7 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 59% 147.9 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 59% 147.9 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 59% 147.9 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 40% 52% 147.5 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 52% 140.2 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 39% 65% 140.2 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 46% 206.8

Sequence Analysis Tools

View WP_017177453.1 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

MTKNATSAPAAPDPGSTTSTAERPRGAEVALTGVTHRYPLHHELDHGWVPWAIRQVSPAA
RARYEAEAAKGSSLHVLDDVTLTIPPGQFVAVVGQSGCGKSTILRLLAGLETPSQGSVVV
DGERITRPAPERAMAFQDATLLPWRTVRDNVALGPQARGRLAIDQRRIDAALEIVGLRDF
AGAYPSTLSGGMAQRAALARALVNRPRLFLLDEPFGKLDALTRLGLQDEFARLWSSQAFT
AILVTHDVDEALRLAERVVVLSERPAHVVADLEVPAALADAPASTEYQDLKARILALLGR

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