Finding step SSS-glucose for D-glucose catabolism in Sphingobium czechense LL01
No candidates for SSS-glucose: Sodium/glucose cotransporter
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 SSS-glucose
- Curated sequence A0PJK1: Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10. Sodium/glucose cotransporter 5 (Na+/glucose cotransporter 5) (Solute carrier family 5 member 10)
- Curated sequence CH_091086: sodium/glucose cotransporter 1. Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1. Glucose or galactose:Na+ symporter, SGLT1 (galactose > glucose > fucose). Cotransports water against an osmotic gradient (Naftalin, 2008). TMS IV of the high-affinity sodium-glucose cotransporter participates in sugar binding
- Curated sequence P11170: Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1
- Curated sequence P31636: Solute carrier family 5 member 4; Low affinity sodium-glucose cotransporter. Glucose:Na+ symporter 3 (low affinity)
- Curated sequence P31639: Sodium/glucose cotransporter 2; Na(+)/glucose cotransporter 2; Low affinity sodium-glucose cotransporter; Solute carrier family 5 member 2. Sodium/glucose cotransporter 2 (Na+/glucose cotransporter 2) (Low affinity sodium-glucose cotransporter) (Solute carrier family 5 member 2) of 672 aas and 14 TMSs
- Curated sequence P96169: Sodium/glucose cotransporter; Na(+)/glucose symporter. Glucose or galactose:Na+ symporter, SglS or SglT of 543 aas and 14 TMSs (Turk et al. 2006). The 3.0 Å structure is known (Faham et al., 2008). Sodium exit causes a reorientation of transmembrane helix 1 that opens an inner gate required for substrate exit (Watanabe et al., 2010). The involvement of aromatic residue pi interactions, especially with Na+ binding, has been examined
- Curated sequence Q28610: Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; RK-D; Solute carrier family 5 member 10
- Curated sequence Q28728: Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; rKST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11
- Curated sequence Q2M3M2: Sodium/glucose cotransporter 4; Na(+)/glucose cotransporter 4; hSGLT4; Solute carrier family 5 member 9. Sodium/glucose cotransporter 4 (Na+/glucose cotransporter 4) (hSGLT4) (Solute carrier family 5 member 9)
- Curated sequence Q6R4Q5: Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10
- Curated sequence Q8K0E3: Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11
- Curated sequence Q8WWX8: Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11. Myoinositol:Na+ symporter, SMIT2 (also transports D-chiro-inositol, D-glucose and D-xylose)
- Curated sequence Q9NY91: Solute carrier family 5 member 4. Low affinity sodium-glucose cotransporter (Sodium/glucose cotransporter 3) (Na+/glucose cotransporter 3) (Solute carrier family 5 member 4)
- Curated sequence Q9Z1F2: Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; rkST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11
- Curated sequence P26430: Nucleoside or glucose(?):Na+ symporter
- Curated sequence Q2A687: Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs
- Comment: solute_symporter (SSS) family transpoters
Or cluster all characterized SSS-glucose 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