Finding step sut for sucrose catabolism in Rhodococcus qingshengii djl-6-2
No candidates for sut: sucrose:proton symporter SUT/SUC
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 sut
- Curated sequence CH_091525: sucrose transport protein SUC3. Sucrose transport protein SUC3; Sucrose permease 3; Sucrose transporter 2; Sucrose-proton symporter 3. Sucrose:H+ symporter, Suc3 or Sut3 of 464 aas. Expressed in cells adjacent to the vascular tissue and in a carpel cell layer). Km (sucrose)= 1.9 mM; maltose is a competitor
- Curated sequence CH_091608: sucrose transport protein SUC1. Sucrose transport protein SUC1; Sucrose permease 1; Sucrose-proton symporter 1. Sucrose:H+ symporter, Suc1 (provides osmotic driving force for anther dehiscence, pollen germination and pollen tube growth; also transports other glucosides such as maltose and phenylglucosides. Km (sucrose)= 0.5 mM. (Stadler et al., 1999)). In wheat (Triticum aesticum), there are at least three isoforms designated Sut2A, Sut2B and Sut2D. sucrose transporter
- Curated sequence A2ZN77: Sucrose transport protein SUT2; SUC4-like protein; Sucrose permease 2; Sucrose transporter 2; OsSUT2; Sucrose-proton symporter 2
- Curated sequence Q0ILJ3: Sucrose transport protein SUT2; SUC4-like protein; Sucrose permease 2; Sucrose transporter 2; OsSUT2; Sucrose-proton symporter 2
- Curated sequence Q10R54: Sucrose transport protein SUT1; Sucrose permease 1; Sucrose transporter 1; OsSUT1; Sucrose-proton symporter 1
- Curated sequence Q39231: Sucrose transport protein SUC2; Sucrose permease 2; Sucrose transporter 1; Sucrose-proton symporter 2. sucrose transporter
- Curated sequence Q67YF8: Sucrose transport protein SUC7; Sucrose permease 7; Sucrose-proton symporter 7
- Curated sequence Q69JW3: Sucrose transport protein SUT5; Sucrose permease 5; Sucrose transporter 5; OsSUT5; Sucrose-proton symporter 5. Sucrose transport protein SUT5 (Sucrose permease 5) (Sucrose transporter 5) (OsSUT5) (Sucrose-proton symporter 5)
- Curated sequence Q6YK44: Sucrose transport protein SUT4; Sucrose permease 4; Sucrose transporter 4; OsSUT4; Sucrose-proton symporter 4
- Curated sequence Q948L0: Sucrose transport protein SUT3; Sucrose permease 3; Sucrose transporter 3; OsSUT3; Sucrose-proton symporter 3
- Curated sequence Q9C8X2: Sucrose transport protein SUC5; Sucrose permease 5; Sucrose-proton symporter 5
- Curated sequence Q9FE59: Sucrose transport protein SUC4; Sucrose permease 4; Sucrose transporter 4; Sucrose-proton symporter 4. Vacuolar sucrose;H+
- Curated sequence Q9FG00: Sucrose transport protein SUC9; Sucrose permease 9; Sucrose-proton symporter 9
- Curated sequence Q9ZVK6: Sucrose transport protein SUC8; Sucrose permease 8; Sucrose-proton symporter 8
- Curated sequence D1GC38: The proton:sucrose uptake symporter, Sut1
- Curated sequence Q9SXM0: Phloem-localized sucrose:H+ symporter, Sut1 (mediates sucrose uptake or efflux dependent on the sucrose gradient and the pmf; Carpaneto et al., 2005). Sut1 is a sucrose protein symporter. Protons can move in the absence of sucrose (Carpaneto et al., 2010), but upon addition of sucrose, it becomes a symporter
- Curated sequence MONOMER-18237: sucrose transporter
- Curated sequence MONOMER-18241: sucrose transporter
Or cluster all characterized sut 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