Finding step treEIIA for trehalose catabolism in Gallaecimonas xiamenensis 3-C-1
4 candidates for treEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP)
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Definition of step treEIIA
- Curated sequence P20166: PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69. The glucose IICBA porter (PtsG) 44% identical to 4.A.1.1.1)
- UniProt sequence P50829: RecName: Full=Putative phosphotransferase enzyme IIA component YpqE; AltName: Full=Putative PTS system EIIA component;
- Curated sequence P39816: Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193. The glucosamine IICBA porter (GamP) (40% identical to 4.A.1.1.2) (Plumbridge 2015). The IIA domain in this protein can transfer the phosphoryl moiety to the maltose, N-acetylglucosamine, sucrose and trehalose PTS systems (MalP, NagP, SacP and TreP, respectively)
- Curated sequence CH_088352: glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.-. PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component. Glucose-specific phosphotransferase enzyme IIA component PTGA aka CRR aka GSR aka IEX aka TGS aka TRED aka B2417, component of Glucose porter (PtsG; GlcA; Umg) (transports D-glucose and α-methyl-D-glucopyranoside). Enzyme IIAGlc (EC 2.7.1.199; EC 2.7.1.201; EC 2.7.1.192). Enzyme IIAGlc (EC 2.7.1.199)
- Ignore hits to P0A283 when looking for 'other' hits (PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component)
- Ignore hits to Q8L3C4 when looking for 'other' hits (IIA aka Crr, component of The N,N' -diacetylchitobiose Enzyme II (Toratani et al., 2008) (>80% identical to the E. coli enzyme (4.A.3.2.1)))
- Curated sequence GFF4500: D-trehalose PTS system, I, HPr, and IIA components
- Curated sequence AO353_15995: trehalose-specific PTS system, I, HPr, and IIA components
- Comment: Ignore a close homlog in Serratia (TC 4.A.3.2.5 / Q8L3C4) which is reported to be the II-A component, and the homolog in Salmonella. Include E. coli crr and B. subtilis ptsG, gamP, or ptsA (PMC6148471).
Or cluster all characterized treEIIA 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