chiZ Resolved · high auto-curated
H37Rv Rv2719c · MTBC0 mtbc0_002893 ·
165 aa · 3053455–3053952 (-) ·
RefSeq NP_217235.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | cell wall hydrolase ChiZ |
| Revised (this work) | Cell wall hydrolase ChiZ. Pfam: LysM (PF01476.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YA32
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cell wall hydrolase ChiZ |
| EC (curated) |
EC 3.4.-.-
|
| Curated function | Cell wall hydrolase that modulates cell division process. Probably acts by modulating FtsZ ring assembly. Murein hydrolase activity is targeted to sites of nascent peptidoglycan (PG) synthesis. Overproduction compromises midcell localization of FtsZ rings, but has no effect on the intracellular levels of FtsZ. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | LysM domain |
| Orthologous group | COG1388 |
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains) pseudogene candidate
| pN/pS | 0.806 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.88% of strains (4178) · clonal |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
LysM | PF01476.27 | 8.4e-05 | 116–163 | LysM domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lexA (repressor LexA), high confidence from genomic context alone (score 773 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2720 lexA |
repressor LexA | 859 | 773 ctx | neighborhood:723 textmining:408 |
Rv2743c hyp |
hypothetical protein | 761 | 761 ctx | cooccurence:760 |
Rv2718c nrdR |
transcriptional regulator NrdR | 760 | 761 ctx | neighborhood:747 |
Rv3810 pirG |
cell surface protein | 764 | 756 ctx | cooccurence:751 |
Rv1836c hyp |
hypothetical protein | 748 | 749 ctx | cooccurence:747 |
Rv0479c |
membrane protein | 719 | 719 ctx | cooccurence:718 |
Rv3906c hyp |
hypothetical protein | 715 | 715 ctx | cooccurence:712 |
Rv2042c hyp |
hypothetical protein | 704 | 704 ctx | cooccurence:704 |
Rv0256c PPE2 |
PPE family protein PPE2 | 691 | 692 ctx | cooccurence:691 |
Rv0996 |
transmembrane protein | 683 | 683 ctx | cooccurence:681 |
Rv2876 |
transmembrane protein | 664 | 664 ctx | cooccurence:664 |
Rv0497 |
transmembrane protein | 645 | 646 ctx | cooccurence:644 |
Rv3415c hyp |
hypothetical protein | 640 | 641 ctx | cooccurence:639 |
Rv3707c hyp |
hypothetical protein | 619 | 619 ctx | cooccurence:618 |
Rv0383c ttfA hyp |
hypothetical protein | 619 | 605 ctx | cooccurence:597 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: membrane protein
- MTBC0 PGAP product: cell wall hydrolase ChiZ
- Pfam (hmmscan --cut_ga): LysM PF01476.27 (E=8e-05)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217235.1)
- Domains: Pfam-A via hmmscan --cut_ga — LysM (PF01476.27)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1388 - Curated reference: UniProt I6YA32 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
99 functional partner(s); context anchor
lexA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002893|Rv2719c|chiZ MTPVRPPHTPDPLNLRGPLDGPRWRRAEPAQSRRPGRSRPGGAPLRYHRTGVGMSRTGHGSRPVPPATTVGLALLAAAITLWLGLVAQFGQMITGGSADGSADSTGRVPDRLAVVRVETGESLHDVAVRVAPNAPTRQVADRIRELNGLQTPALAVGQTLIAPVG