Finding step ptsG for D-cellobiose catabolism in Roseivirga spongicola UST030701-084
No candidates for ptsG: glucose PTS, enzyme IICB
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step ptsG
- Ignore hits to Q9AGA7 when looking for 'other' hits (PTS system alpha-glucoside-specific EIICB component; EC 2.7.1.-. The α-glucoside-specific IICB, AglB (transports glucose, methyl-α-glucoside, maltitol, isomaltose, trehalulose α(1→1), turanose α(1→3), maltulose α(1→4), leucrose α(1→5), and palatinose α(1→6), but not sucrose (most resembles 4.A.1.1.4 and 4.A.1.1.8))
- Curated sequence P69786: protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199). PTS system glucose-specific EIICB component; EC 2.7.1.69. PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199. PTS system glucose-specific EIICB component PTGB aka PTSG aka GLCA aka UMG aka B1101, component of Glucose porter (PtsG; GlcA; Umg) (transports D-glucose and α-methyl-D-glucopyranoside). glucose-specific PTS enzyme IIBC component (EC 2.7.1.199). glucose-specific PTS enzyme IIBC component (EC 2.7.1.199)
- Curated sequence P37439: PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199
- Ignore hits to O51590 when looking for 'other' hits (Glucose-specific Enzyme IIBC of the PTS, PtsG)
- Ignore hits to P19642 when looking for 'other' hits (PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69. PTS system maltose-specific EIICB component; EC 2.7.1.208. Maltose porter (MalX). PTS enzyme IIBC component MalX. PTS enzyme IIBC component MalX)
- Comment: EII-CB proteins. Ignore O51590 (4.A.1.1.18) from Borrelia burgdorferi, which is not characterized and the EIIA component is uncertain. Ignore E. coli malX (P19642), which facilitates diffusion of glucose (no phosphorylation); its physiological function is unclear so it is not listed as a sole glucose transporter. Ignore PTUCB_KLEPN / Q9AGA7 from Klebsiella, as the EII-A component was not described
Or cluster all characterized ptsG proteins
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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