GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS12995 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS12995 MFS transporter

Length: 489 amino acids

Source: BFirm in FitnessBrowser

Candidate for 2 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism proP hi Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized) 50% 97% 506.5 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 34% 275.8
acetate catabolism deh lo The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized) 36% 57% 218.8 Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A 50% 506.5

Sequence Analysis Tools

View BPHYT_RS12995 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTASSNGFWRHHKEEQRLSLDDITVVDKSLLKRAVGAMALGNAMEWFDFGVYSYIAVTLG
KVFFPSASPAAQLIATFGTFAAAFLVRPVGGMVFGPLGDRIGRQRVLAMTMIMMALGTFA
IGLIPSYTTIGIFAPMLLLVARLVQGFSTGGEYGGAATFIAEFSTDKRRGFMGSFLEFGT
LIGYVLGAGTVAVLTATLSNDALLSWGWRVPFLIAGPLGLVGLYIRMKLEETPAFKKQAE
QREAEDKAVPKQSFGQLLAQQWKPLLLCVGLVLIFNVTDYMALSYLPSYLSATLHFNETH
GLFLVLLVMVLMMPMTLAAGRLSDTIGRKPVMLFGCVGLFALSIPALLLIRMGTVLPVFG
GLMILGVLLSCFTGVMPSALPALFPTKIRYGALAIGFNISVSLFGGTTPLVTAWLVDRTG
NLMMPAYYLMGASLIGIVSVVALRETARKPLLGSGPCVATRAEAHAVLRGEREAEEMDER
YAATATARA

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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