Finding step manZ for D-glucose catabolism in Nocardiopsis gilva YIM 90087
No candidates for manZ: glucose PTS, enzyme EIID
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 manZ
- Curated sequence P69805: PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component. mannose-specific PTS enzyme IID component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193). mannose-specific PTS enzyme IID component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193)
- Curated sequence E1UCI2: PTS system, mannose/fructose/sorbose family, IID component, component of The primary glucose /mannose uptake transporter, ManLMN
- Curated sequence P69805: PTND aka MANZ aka PTSM aka GPTB aka B1819, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose
- Curated sequence Q04GJ9: PTS system IID component, Man family, component of The hexose (glucose and fructose demonstrated) PTS uptake system
- Curated sequence Q2QKM2: ManN aka EIID, component of Glucose porter, ManLMN
- Curated sequence Q5M5W8: ManN, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN
- Ignore hits to Q5IRC0 when looking for 'other' hits (protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191))
- Ignore hits to D2BKY9 when looking for 'other' hits (Mannose-specific PTS system, IID component, component of Mannose enzyme II complex, IIAB, IIC, IID. IIC/IID serve allows entry of some bacteriocins including pediocin (class IIa) and lactococcin A (class IIc) (Kjos et al., 2011). Transports and phosphorylates Glucose, Mannose and Glucosamine)
- Comment: (The E. coli entry, P69805, is listed twice, because the sequence in TCDB has 3 extra N-terminal residues.) Also similar is Lmo0781 (TC 4.A.6.1.16 / Q8Y8W1) from MpoABCD; should perhaps be ignored.
Or cluster all characterized manZ 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