Finding step sut for sucrose catabolism in Collimonas arenae Ter10
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.
Links
Downloads
Related tools
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