Finding step glpF for glycerol catabolism in Streptacidiphilus oryzae TH49
3 candidates for glpF: glycerol facilitator glpF
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 glpF
- Curated sequence CH_024677: aquaglyceroporin. Glycerol uptake facilitator protein; Aquaglyceroporin. Glycerol facilitator, GlpF. Transports various polyols with decreasing rates as size increases (Heller et al. 1980); also transports arsenite (As(III) and antimonite (Sb(III)) (Meng et al., 2004). Oligomerization may play a role in determining the rate of transport. glycerol facilitator. glycerol facilitator
- Curated sequence CH_091207: aquaporin-9. Aquaporin-9; AQP-9; Aquaglyceroporin-9. Aquaporin-9 (Aqp9) (permeable to glycerol, urea, polyols, carbamides, purines, pyrmidines, nucleosides, monocarboxylates, pentavalent methylated arsenicals and the arsenic chemotherapeutic drug, trisenox
- Curated sequence CH_091783: aquaglyceroporin 1. Aquaporin 1 (permeable to water, glycerol, dihydroxyacetone and urea)
- Curated sequence F9UMX3: Glycerol uptake facilitator protein 4; D/L-lactic acid transporter; Lactic acid channel
- Curated sequence F9UST3: D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel. GlpF1; transports water, dihydroxyacetone and glycerol as well as D,L-lactic acid
- Curated sequence F9USY3: Glycerol uptake facilitator protein 2. GlpF2
- Curated sequence F9UTW9: Glycerol uptake facilitator protein 3. GlpF3
- Curated sequence F9UUB3: Glycerol uptake facilitator protein-like 5. GlpF4. Transports water, dihydroxyacetone and glycerol as well as D,L-lactic acid
- Curated sequence P47862: Aquaporin-3; AQP-3; 31.4 kDa water channel protein; Aquaglyceroporin-3. Aquaporin 3. 95% identical to the human orthologue. Poorly permeable to water, but more permeable to glycerol and arsenic trioxide
- Curated sequence F6QEC2: Aquaporin/glycerol facilitator of 294 aas and 6 TMSs
- Curated sequence P08995: Nodulin-26 aquaporin and glycerol facilitator, NIP (de Paula Santos Martins et al. 2015). Transports NH3 5-fold better than water in Hg2+-sensitive fashion
- Curated sequence P18156: Glycerol facilitator
- Curated sequence P52280: Probable glycerol uptake facilitator protein
- Curated sequence Q6Q1Q6: Major aquaglyceroporin, LmAQP1: transports water, glycerol, methylglyoxal, trivalent metalloids such as arsenite and antimonite, dihydroxyacetone and sugar alcohols. Also takes up the activated form or the drug, pentostam
- Curated sequence Q8WPZ6: Aquaglycerolporin, Aqp (high permeability to ammonium, methylamine, glycerol and water) (Beitz et al., 2004) NH4+/NH3+CH3 transporter
- Curated sequence Q9C4Z5: Hg2+-inhibitable aquaporin, AqpM (transports both water and glycerol as well as CO2) (Kozono et al., 2003; Araya-Secchi et al., 2011). Its 3-d structure has been determined to 1.7 Å. In AqpM, isoleucine replaces a key histidine residue found in the lumen of water channels, which becomes a glycine residue in aquaglyceroporins. As a result of this and other side-chain substituents in the walls of the channel, the channel is intermediate in size and exhibits differentially tuned electrostatics when compared with the other subfamilies
- Ignore hits to O28846 when looking for 'other' hits (MIP family homologue)
- Comment: Ignore an uncharacterized homolog from Archaeoglobus
Or cluster all characterized glpF 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