Finding step celEIIC for D-cellobiose catabolism in Klebsiella michiganensis M5al
4 candidates for celEIIC: cellobiose PTS system, EII-C component
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | BWI76_RS11730 | PTS N,N'-diacetylchitobiose transporter subunit IIC | PTS system N,N'-diacetylchitobiose-specific EIIC component; EIIC-Chb; IIcel; N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIC component (characterized) | 88% | 100% | 803.5 | PTCC aka LicC aka CELB, component of Lichenan oligosaccharide (Lic) porter | 33% | 233.8 |
| lo | BWI76_RS14945 | PTS system, cellobiose-specific IIC component | PTS system N,N'-diacetylchitobiose-specific EIIC component; EIIC-Chb; IIcel; N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIC component (characterized) | 32% | 99% | 237.3 | PTS system, cellobiose-specific IIC component, component of N-, N'-diacetylchitobiose PTS permease, IIABCChb | 45% | 379.8 |
| lo | BWI76_RS22405 | PTS cellobiose transporter subunit IIC | PTS system N,N'-diacetylchitobiose-specific EIIC component; EIIC-Chb; IIcel; N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIC component (characterized) | 32% | 99% | 225.7 | VC_1282 aka IIC, component of Glucosamine β(1→4) glucosamine (GlcN)2 (glucosamine dimer) transporter, VC1281-1283 (IIB; IIC; IIA, respectively) | 54% | 516.5 |
| lo | BWI76_RS27750 | PTS lactose/cellobiose family transporter subunit IIC | Permease IIC component (characterized, see rationale) | 30% | 98% | 208.4 | VC_1282 aka IIC, component of Glucosamine β(1→4) glucosamine (GlcN)2 (glucosamine dimer) transporter, VC1281-1283 (IIB; IIC; IIA, respectively) | 48% | 479.6 |
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.
Also see fitness data for the candidates
Definition of step celEIIC
- Curated sequence P17334: PTS system N,N'-diacetylchitobiose-specific EIIC component; EIIC-Chb; IIcel; N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIC component. PTCC aka ChbC aka CELB aka B1737, component of N,N'-diacetylchitobiose (Chb) porter. N,N'-diacetylchitobiose-specific PTS enzyme IIC component (EC 2.7.1.196). N,N'-diacetylchitobiose-specific PTS enzyme IIC component (EC 2.7.1.196)
- Curated sequence Q9CJ32: PTS system cellobiose-specific EIIC component. CelB, component of The cellobiose-specific (PtcA-PtcB-CelB) porter (Kowalczyk et al., 2008 )
- UniProt sequence A0A0H2UNC6: RecName: Full=Permease IIC component {ECO:0000256|PIRNR:PIRNR006351};
- Ignore hits to C4X745 when looking for 'other' hits (PEP-dependent phosphotransferase enzyme II, component of N,N'-diacetylchitobiose (cellobiose) PTS permease, CelABC (IIABC))
- Ignore hits to Q8L3C2 when looking for 'other' hits (protein-Npi-phosphohistidine-N,N'-diacetylchitobiose phosphotransferase (EC 2.7.1.196). ChbC, component of The N,N' -diacetylchitobiose Enzyme II (Toratani et al., 2008) (>80% identical to the E. coli enzyme (4.A.3.2.1)))
Or cluster all characterized celEIIC proteins
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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