Finding step uxuA for D-glucuronate catabolism in Shewanella halifaxensis HAW-EB4
No candidates for uxuA: D-mannonate dehydratase
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 uxuA
- Curated proteins or TIGRFams with EC 4.2.1.8 (search)
- Ignore hits to A4WA78 when looking for 'other' hits (D-galactonate dehydratase family member Ent638_1932; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.8)
- Ignore hits to A5KUH4 when looking for 'other' hits (D-galactonate dehydratase family member VSWAT3_13707)
- Ignore hits to A6AMN2 when looking for 'other' hits (D-galactonate dehydratase family member A1Q3065)
- Ignore hits to A6M2W4 when looking for 'other' hits (D-galactonate dehydratase family member Cbei_4837)
- Ignore hits to A6VRA1 when looking for 'other' hits (D-galactonate dehydratase family member Mmwyl1_0037; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.8)
- Ignore hits to A8RQK7 when looking for 'other' hits (D-galactonate dehydratase family member CLOBOL_02770)
- Ignore hits to B1ELW6 when looking for 'other' hits (D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8)
- Ignore hits to B3PDB1 when looking for 'other' hits (D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8)
- Ignore hits to B5GCP6 when looking for 'other' hits (D-galactonate dehydratase family member SSBG_02010)
- Ignore hits to B5QBD4 when looking for 'other' hits (D-galactonate dehydratase family member SeV_A0456; D-gluconate dehydratase; EC 4.2.1.-; EC 4.2.1.39)
- Ignore hits to B5R541 when looking for 'other' hits (D-galactonate dehydratase family member SEN1436; D-gluconate dehydratase; EC 4.2.1.-; EC 4.2.1.39)
- Ignore hits to B5RAG0 when looking for 'other' hits (D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8)
- Ignore hits to B8HCK2 when looking for 'other' hits (D-galactonate dehydratase family member Achl_0790)
- Ignore hits to C6CBG9 when looking for 'other' hits (D-galactonate dehydratase family member Dd703_0947; D-gluconate dehydratase; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.39; EC 4.2.1.8)
- Ignore hits to C6CVY9 when looking for 'other' hits (D-galactonate dehydratase family member Pjdr2_1176)
- Ignore hits to C6D9S0 when looking for 'other' hits (D-galactonate dehydratase family member PC1_0802; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.8)
- Ignore hits to C6DI84 when looking for 'other' hits (D-galactonate dehydratase family member PC1_4063)
- Ignore hits to C7PW26 when looking for 'other' hits (D-galactonate dehydratase family member Caci_4410)
- Ignore hits to C8ZZN2 when looking for 'other' hits (D-galactonate dehydratase family member EGBG_01401)
- Ignore hits to C9A1P5 when looking for 'other' hits (D-galactonate dehydratase family member EGBG_02030)
- Ignore hits to C9CN91 when looking for 'other' hits (D-galactonate dehydratase family member ECAG_02205)
- Ignore hits to C9NUM5 when looking for 'other' hits (D-galactonate dehydratase family member VIC002985)
- Ignore hits to C9Y5D5 when looking for 'other' hits (D-galactonate dehydratase family member Ctu_1p00430)
- Ignore hits to D0KC90 when looking for 'other' hits (D-galactonate dehydratase family member Pecwa_4254)
- Ignore hits to D0X4R4 when looking for 'other' hits (D-galactonate dehydratase family member VME_00770)
- Ignore hits to D4GJ14 when looking for 'other' hits (D-galactonate dehydratase family member RspA; D-gluconate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.39)
- Ignore hits to D7BPX0 when looking for 'other' hits (D-galactonate dehydratase family member SBI_01856; D-gluconate dehydratase; EC 4.2.1.-; EC 4.2.1.39)
- Ignore hits to D8ADB5 when looking for 'other' hits (D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8)
- Ignore hits to D9UNB2 when looking for 'other' hits (D-galactonate dehydratase family member SSLG_02014; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.8)
- Ignore hits to E1V4Y0 when looking for 'other' hits (D-galactonate dehydratase family member RspA; D-gluconate dehydratase; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.39; EC 4.2.1.8)
- Ignore hits to Q1QT89 when looking for 'other' hits (D-galactonate dehydratase family member ManD; D-gluconate dehydratase; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.39; EC 4.2.1.8)
- Ignore hits to Q2CIN0 when looking for 'other' hits (D-galactonate dehydratase family member OG2516_05608)
- Ignore hits to Q6DAR4 when looking for 'other' hits (D-galactonate dehydratase family member ECA0189)
- Ignore hits to Q8FHC7 when looking for 'other' hits (D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8)
- Comment: Many proteins are annotated in SwissProt as "D-galactonate dehydratase family member" but have little activity on D-mannonoate; it is probably not the physiological substrate
Or cluster all characterized uxuA 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