Finding step xylH for D-xylose catabolism in Tatumella morbirosei LMG 23360
5 candidates for xylH: ABC transporter for xylose, permease component xylH
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| med | HA49_RS18540 | ribose ABC transporter permease | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 42% | 98% | 231.1 | Ribose import permease protein RbsC | 87% | 544.7 |
| lo | HA49_RS17405 | ABC transporter permease | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 36% | 94% | 203.4 | RbsC, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 39% | 242.7 |
| lo | HA49_RS07340 | galactose/methyl galactoside ABC transporter permease MglC | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 34% | 98% | 186.4 | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter | 87% | 583.6 |
| lo | HA49_RS16025 | L-arabinose ABC transporter permease AraH | D-xylose ABC transporter, permease protein (characterized) | 36% | 63% | 141.4 | L-arabinose ABC transporter, permease protein AraH | 83% | 538.5 |
| lo | HA49_RS09740 | ABC transporter permease | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 32% | 64% | 115.5 | Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved | 35% | 171.0 |
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Definition of step xylH
- Curated sequence A6LW12: Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas
- Curated sequence CH_024441: D-xylose ABC transporter, permease protein. Xylose transport system permease protein XylH aka B3568, component of Xylose porter. xylose ABC transporter membrane subunit (EC 7.5.2.13; EC 7.5.2.10). xylose ABC transporter membrane subunit (EC 7.5.2.13)
- Curated sequence G4FGN4: Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR
- Curated sequence O05177: GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
Or cluster all characterized xylH 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