Finding step lacZ for lactose catabolism in Rhodococcus qingshengii djl-6-2
2 candidates for lacZ: lactase (homomeric)
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 lacZ
- Curated proteins or TIGRFams with EC 3.2.1.108 (search)
- Curated proteins or TIGRFams with EC 3.2.1.23 (search)
- Ignore hits to A0SWS3 when looking for 'other' hits (beta-galactosidase (EC 3.2.1.23))
- Ignore hits to AAA25267.1 when looking for 'other' hits (β-galactosidase L+M (LacL+LacM) (EC 3.2.1.23))
- Ignore hits to AAL09167.1 when looking for 'other' hits (β-galactosidase (LacL+LacM) (EC 3.2.1.23))
- Ignore hits to ABF72116.1 when looking for 'other' hits (β-galactosidase (Lreu?gal) (LacL + LacM) (EC 3.2.1.23). beta-galactosidase (EC 3.2.1.23))
- Ignore hits to ABJ65308.1 when looking for 'other' hits (LVIS_2259 + LVIS_2258 (EC 3.2.1.23))
- Ignore hits to ACC38286.1 when looking for 'other' hits (β-galactosidase large subunit (LacL) (EC 3.2.1.23))
- Ignore hits to AEG39988.1 when looking for 'other' hits (β-galactosidase large subunit (LacL;WANG_0293) (EC 3.2.1.23))
- Ignore hits to AEJ32720.1 when looking for 'other' hits (β-galactosidase (LacLM;LacL+LacM) (EC 3.2.1.23))
- Ignore hits to BAA20536.1 when looking for 'other' hits (β-galactosidase (LacL) (EC 3.2.1.23))
- Ignore hits to CAA57730.1 when looking for 'other' hits (β-galactosidase L+S (LacL+LacS) (heterodimer) (EC 3.2.1.23))
- Ignore hits to CAD65569.1 when looking for 'other' hits (β-galactosidase (LacL+LacM,lp_3483+lp_3484) (EC 3.2.1.23))
- Ignore hits to CAZ66936.1 when looking for 'other' hits (β-galactosidase (LacL+LacM) (EC 3.2.1.23))
- Ignore hits to Q7WTB4 when looking for 'other' hits (Beta-galactosidase large subunit; Beta-gal large subunit; Lactase large subunit; EC 3.2.1.23)
- Ignore hits to A0SWS4 when looking for 'other' hits (beta-galactosidase (EC 3.2.1.23))
- Ignore hits to Q19R71 when looking for 'other' hits (beta-galactosidase (EC 3.2.1.23))
- Ignore hits to Q7WTB3 when looking for 'other' hits (Beta-galactosidase small subunit; Beta-gal small subunit; Lactase small subunit; EC 3.2.1.23)
- Ignore hits to P83252 when looking for 'other' hits (Beta-galactosidase; Acid beta-galactosidase; Lactase; Exo-(1-->4)-beta-D-galactanase; EC 3.2.1.23. beta-galactosidase (EC 3.2.1.23))
- Ignore hits to AAA79030.1 when looking for 'other' hits (β-glycosidase (Bgly;SSG) (EC 3.2.1.-))
- Ignore hits to AAN05439.1 when looking for 'other' hits (β-glycosidase / β-glucosidase (TTHB087) (EC 3.2.1.21))
- Ignore hits to AAF36392.1 when looking for 'other' hits (β-glycosidase (Gly) (EC 3.2.1.21))
- Ignore hits to AAN05441.1 when looking for 'other' hits (β-glycosidase (BglA) (EC 3.2.1.-))
- Ignore hits to ABW87307.1 when looking for 'other' hits (β-glycosidase (β-gly) (EC 3.2.1.-))
- Ignore hits to AAO15361.1 when looking for 'other' hits (β-glycosidase / β-glucosidase (BglT;BglA) (EC 3.2.1.21|3.2.1.-))
- Ignore hits to AAN05440.1 when looking for 'other' hits (β-glycosidase (tfi β-gly) (EC 3.2.1.-))
- Ignore hits to ABW01253.1 when looking for 'other' hits (Cmaq_0408 (EC 3.2.1.21))
- Ignore hits to AAY81155.1 when looking for 'other' hits (β-glycosidase (BgaS;Saci_1849) (EC 3.2.1.-))
- Ignore hits to CAA34074.1 when looking for 'other' hits (β-glycosidase / β-galactosidase (EC 3.2.1.-))
- Ignore hits to ADL19795.1 when looking for 'other' hits (β-glycosidase (β-Gly;As?-Gly;ASAC_1390) (EC 3.2.1.-))
- Ignore hits to AEE47485.1 when looking for 'other' hits (β-glycosidase (CfBgl3C;Celf_3372) (Bgl3C) (EC 3.2.1.-))
- Ignore hits to ACK41548.1 when looking for 'other' hits (β-glucosidase / β-glycosidase (Dtur_0219) (EC 3.2.1.21))
- Ignore hits to ABX04075.1 when looking for 'other' hits (β-glycosidase (HaGH03;Haur_1431) (EC 3.2.1.-))
- Ignore hits to BAA78713.1 when looking for 'other' hits (β-glycosidase (Tk?gly;TK1761) (EC 3.2.1.-))
- Ignore hits to Q8DR24 when looking for 'other' hits (beta-galactosidase (EC 3.2.1.23))
- Comment: Mark the sequences for lacL or lacM as ignore, and also BGAL_HORVU. Also mark some similar enzymes annotated as beta-glycosidases as ignore.
Or cluster all characterized lacZ 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