Finding step uxuA for D-glucuronate catabolism in Rhizobium freirei PRF 81
3 candidates for uxuA: D-mannonate dehydratase
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 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