Finding step iolT for myo-inositol catabolism in Rhizobium freirei PRF 81
No candidates for iolT: myo-inositol:H+ symporter
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 iolT
- Curated sequence Q8VZR6: Inositol transporter 1. The tonoplast H+:Inositol symporter 1, Int1 (mediates efflux from the tonoplast to the cytoplasm (Schneider et al., 2008) (most similar to 2.A.1.1.63 and 2.A.1.1.62)
- Curated sequence CH_091483: polyol transporter 5. Polyol transporter 5; Protein POLYOL TRANSPORTER 5; AtPLT5; Sugar-proton symporter PLT5. The broad specificity sugar/sugar alcohol (myo-inositol, glycerol, ribose, sorbitol, mannitol, xylitol, erythritol, etc) H+ symporter, AtPLT5 (transports a wide range of hexoses, pentoses, tetroses, sugar alcohols and a sugar acid, but not disaccharides) (Reinders et al., 2005) (expressed in roots, leaves and floral organs)
- Curated sequence CH_091623: Myo-inositol transporter 1. Myo-inositol transporter 1. Myoinositol:H+ symporter
- Curated sequence CH_123508: myo-inositol transporter 2
- Curated sequence O34718: Major myo-inositol transporter IolT. Major myoinositol:H+ symporter, IolT
- Curated sequence P30606: Myo-inositol transporter 2. Myo-inositol transporter 2
- Curated sequence P87110: Myo-inositol transporter 2. MFS myo-inositol transporter
- Curated sequence Q10286: Myo-inositol transporter 1. myo-inositol transporter Itr1
- Curated sequence A8DCT2: Myo inositol uptake porter of 574 aas and 12 TMSs, Fst1
- Curated sequence AIU34725.1: Myo-inositol-specific uptake transporter, ITR1 of 509 aas and 12 TMSs
- Curated sequence Q01440: Myoinositol:H+ symporter, MIT
- Curated sequence Q8NTX0: Myo-Inositol uptake porter, IolT1 (Km=0.2mM)
- Curated sequence E1WAV3: Major myo-inositol transporter, IolT1, of 456 aas
- Curated sequence E1WAV4: Minor myo-inositol transporter, IolT2, of 478 aas
- Curated sequence Q8NL90: Myo-Inositol (Km=0.45mM) uptake porter, IolT2 (Krings et al., 2006). Can not transport D-glucose
- Curated sequence CH_123411: potential myo-inositol transporter
- Curated sequence CH_124311: major myo-inositol transporter iolT
- Comment: Distantly related transporters with the same domain content were grouped together into iolT
Or cluster all characterized iolT 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