Finding step xylT for D-xylose catabolism in Snodgrassella alvi wkB2
No candidates for xylT: D-xylose transporter
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 xylT
- Curated sequence O52733: D-xylose transporter; D-xylose-proton symporter. The D-xylose:H+ symporter, XylT (Km=220 μM; inhibited competitively by 6-deoxyglucose (Ki=220 μM), but not by other sugars tested)
- Curated sequence CH_091400: low-affinity glucose transporter HXT4. Low-affinity glucose transporter HXT4; Low-affinity glucose transporter LGT1. Low affinity, constitutive, glucose (hexose; xylose) uniporter, Hxt4 (LGT1; Rag1) (also transports arsenic trioxide [As(OH)3] as do Hxtl, 3, 5, 7 and 9)
- Curated sequence CH_091493: sugar transport protein 6. Sugar transport protein 6; Hexose transporter 6. High affinity monosaccharide (KM ≈ 20 µM):H+ symporter, Stp6 (takes up glucose, 3-O-methylglucose, mannose, fructose, galactose and to a lesser extent, xylose and ribulose.
- Curated sequence CH_109760: D-xylose-proton symporter. D-xylose-proton symporter; D-xylose transporter. Xylose (xylopyranose):H+ symporter of 491 aas and 12 TMSs. D-xylose:H+ symporter. D-xylose:H+ symporter
- Curated sequence P0AE24: Arabinose-proton symporter; Arabinose transporter. Arabinose (xylose; galactose):H+ symporter, AraE (low affinity high capacity). arabinose:H+ symporter. arabinose:H+ symporter
- Curated sequence P96710: Arabinose-proton symporter; Arabinose transporter. L-arabinose:proton symporter, AraE (Sa-Nogueira and Ramos, 1997). Also transports xylose, galactose and α-1,5 arabinobiose
- Curated sequence C4B4V9: Arabinose/xylose transporter, AraE
- Curated sequence Q0WWW9: D-xylose-proton symporter-like 3, chloroplastic
- Curated sequence Q2MDH1: Glucose/xylose facilitator-1, GXF1 (functions by sugar uniport; low affinity
- Curated sequence Q2MEV7: Glucose/xylose: H+ symporter, Gsx1
- Curated sequence Q64L87: The xylose facilitator, Xylhp
- Curated sequence Q9XIH7: The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida
- UniProt sequence A0A0H3C6H3: SubName: Full=Glucose/fructose transport protein {ECO:0000313|EMBL:ACL94322.2};
- Comment: Fitness data identified CCNA_00857 (CC0814; A0A0H3C6H3) as the xylose transporter in Caulobacter crescentus, consistent with a previous report (PMC2168598).
Or cluster all characterized xylT 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