GapMind for catabolism of small carbon sources

 

Protein WP_076948577.1 in Rhodococcus qingshengii djl-6-2

Annotation: NCBI__GCF_002893965.1:WP_076948577.1

Length: 454 amino acids

Source: GCF_002893965.1 in NCBI

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 med Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized) 39% 82% 286.2 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% 259.6
acetate catabolism deh lo Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized) 33% 95% 252.7 Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A 39% 285.4

Sequence Analysis Tools

View WP_076948577.1 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

MTGTANAPVEHQTETSPGRRSARRRALIAGATGNIVEWFDFTIYGFTAAVLATVFFPPEF
GSGALLATFALYGVAFLARPAGGIFFGRLGDRLGRRRSLSLAITLMGCSTAAIGLLPTYA
SIGVAAPLLLLLCRLVQGFSAGGEYTGAATFVVEHAPSHRRGLYAGIISSSSFVGSILAT
VTVLSFSSVGAEHFADGGWRWPFIIGGVVAMVGLFMRLAVEETPAFKEMQENDSLPTRPL
ADLFRNHWRTLLTSFVYFASLGVVTHMLLGYMPTFLVLSADVPSTVALLMTTGALVLAVP
LFIFFGATVDRIGRRPLVRIGMVMSVFVSVPSYMLIGTGNIFAIAIALAALVLALSLLAA
ALLVILEMMPTHARFTGTAIPYNIAYALFAGTAPLVCAALVNATGSDLSPAFYATAIALI
ALPILWRGIPETKKLVCHAGQPDETFLTTDAPRL

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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