Finding step lacZ for lactose catabolism in Snodgrassella alvi wkB2
No candidates for lacZ: lactase (homomeric)
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 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