GapMind for catabolism of small carbon sources


Protein N515DRAFT_2216 in Dyella japonica UNC79MFTsu3.2

Annotation: FitnessBrowser__Dyella79:N515DRAFT_2216

Length: 225 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 6 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 40% 68% 164.1 cell division ATP-binding protein ftsE 56% 240.0
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 36% 81% 140.2 cell division ATP-binding protein ftsE 56% 240.0
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 36% 85% 139.8 cell division ATP-binding protein ftsE 56% 240.0
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 35% 92% 139 cell division ATP-binding protein ftsE 56% 240.0
L-arginine catabolism artP lo Histidine transport ATP-binding protein HisP (characterized) 34% 90% 135.6 cell division ATP-binding protein ftsE 56% 240.0
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 34% 90% 135.6 cell division ATP-binding protein ftsE 56% 240.0

Sequence Analysis Tools

View N515DRAFT_2216 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.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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