GapMind for catabolism of small carbon sources


Protein N515DRAFT_0011 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_0011 MFS transporter, MHS family, alpha-ketoglutarate permease

Length: 435 amino acids

Source: Dyella79 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
2-oxoglutarate (alpha-ketoglutarate) catabolism kgtP hi Alpha-ketoglutarate permease, MFS superfamily (characterized) 70% 100% 622.9 TphA aka ProP, component of The Icm/Dot or Dot/Icm multicomponent protein secretion system. IcmS and IcmW form a complex that interacts with and may translocate substrate proteins (Ninio et al., 2005; De Buck et al., 2007; Cambronne and Roy, 2007). The crystal structure of the IcmR-IcmQ complex has been solved (Raychaudhury et al., 2009). Legionella pneumophila survives and replicates inside host cells by secreting ~300 effectors through the defective in organelle trafficking (Dot)/intracellular multiplication (Icm) type IVB secretion system (T4BSS). Ghosal et al. 2019, using electron cryotomography mapped the location of the core and accessory components of the Legionella core transmembrane subcomplex, revealing a well-ordered central channel that opens into a large, windowed secretion chamber with an unusual 13-fold symmetry. Immunofluorescence microscopy deciphered an early-stage assembly process that begins with the targeting of Dot/Icm components to the bacterial poles. Polar targeting of this T4BSS is mediated by two Dot/Icm proteins, DotU and IcmF, that are homologues of the T6SS membrane complex components TssL and TssM, suggesting that the Dot/Icm T4BSS is a hybrid system. Thus, the Dot/Icm complex assembles in an 'axial-to-peripheral' pattern 33% 230.3
citrate catabolism citA lo Citrate:H+ symporter (characterized) 33% 94% 228 Alpha-ketoglutarate permease, MFS superfamily 70% 622.9
L-proline catabolism proP lo Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized) 31% 84% 219.2 Alpha-ketoglutarate permease, MFS superfamily 70% 622.9
acetate catabolism deh lo Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized) 31% 92% 213 Alpha-ketoglutarate permease, MFS superfamily 70% 622.9

Sequence Analysis Tools

View N515DRAFT_0011 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...



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