Rv2897c Family assigned · medium auto-curated
H37Rv Rv2897c · MTBC0 mtbc0_003079 ·
503 aa · 3227260–3228771 (-) ·
RefSeq NP_217413.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YifB family Mg chelatase-like AAA ATPase |
| Revised (this work) | YifB family Mg chelatase-like AAA ATPase. Pfam: Lon_C (PF05362.20), ChlI (PF13541.13), Mg_chelatase (PF01078.28), Mg_chelatase_C (PF13335.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPR1
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized protein Rv2897c |
UniProt still lists this protein as Uncharacterized protein Rv2897c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | comM |
| eggNOG description | chelatase subunit ChlI |
| Orthologous group | COG0606 |
| KEGG orthology |
K07391
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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)
| pN/pS | 0.712 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 13 missense, 0 nonsense, 0 frameshift |
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 |
|---|---|---|---|---|
Lon_C | PF05362.20 | 5.1e-10 | 4–146 | Lon protease (S16) C-terminal proteolytic domain |
ChlI | PF13541.13 | 2.5e-37 | 21–143 | Subunit ChlI of Mg-chelatase |
Mg_chelatase | PF01078.28 | 2.5e-84 | 190–393 | Magnesium chelatase, subunit ChlI |
Mg_chelatase_C | PF13335.13 | 3.6e-24 | 401–497 | Magnesium chelatase, subunit ChlI C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: viuB (mycobactin utilization protein ViuB), high confidence from genomic context alone (score 836 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2896c dprA hyp |
hypothetical protein | 977 | 972 ctx | neighborhood:882 cooccurence:602 |
Rv2898c hyp |
hypothetical protein | 965 | 963 ctx | neighborhood:882 cooccurence:676 |
Rv2895c viuB |
mycobactin utilization protein ViuB | 836 | 836 ctx | neighborhood:836 |
Rv2899c fdhD |
formate dehydrogenase accessory protein FdhD | 728 | 729 ctx | neighborhood:726 |
Rv1364c |
sigma factor regulatory protein | 737 | 726 | coexpression:720 |
Rv2414c hyp |
hypothetical protein | 756 | 724 ctx | cooccurence:661 |
Rv2594c ruvC |
crossover junction endodeoxyribonuclease RuvC | 719 | 689 ctx | cooccurence:683 |
Rv2894c xerC |
tyrosine recombinase XerC | 619 | 602 ctx | neighborhood:601 |
Rv2900c fdhF |
formate dehydrogenase subunit alpha FdhF | 577 | 576 ctx | neighborhood:570 |
Rv0429c def |
polypeptide deformylase | 526 | 526 ctx | cooccurence:485 |
Rv1354c hyp |
hypothetical protein | 689 | 494 | textmining:411 |
Rv2901c hyp |
hypothetical protein | 475 | 475 ctx | neighborhood:473 |
Rv3242c hyp |
hypothetical protein | 568 | 443 | |
Rv2902c rnhB |
ribonuclease HII | 434 | 434 ctx | neighborhood:430 |
Rv2587c secD |
protein translocase subunit SecD | 432 | 433 |
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: hypothetical protein
- MTBC0 PGAP product: YifB family Mg chelatase-like AAA ATPase
- Pfam (hmmscan --cut_ga): Lon_C PF05362.20 (E=5e-10), ChlI PF13541.13 (E=2e-37), Mg_chelatase PF01078.28 (E=3e-84), Mg_chelatase_C PF13335.13 (E=4e-24)
- (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_217413.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lon_C (PF05362.20), ChlI (PF13541.13), Mg_chelatase (PF01078.28), Mg_chelatase_C (PF13335.13)
- 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
COG0606 - Curated reference: UniProt P9WPR1 (SwissProt, reviewed; Inferred from homology)
- 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 —
22 functional partner(s); context anchor
viuB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003079|Rv2897c| MALGRAFSVAVRGLDGEIVEIEADITSGLPGVHLVGLPDAALQESRDRVRAAVTNCGNSWPMARLTLALSPATLPKMGSVYDIALAAAVLSAQQKKPWERLENTLLLGELSLDGRVRPVRGVLPAVLAAKRDGWPAVVVPADNLPEASLVDGIDVRGVRTLGQLQSWLRGSTGLAGRITTADTTPESAADLADVVGQSQARFAVEVAAAGAHHLMLTGPPGVGKTMLAQRLPGLLPSLSGSESLEVTAIHSVAGLLSGDTPLITRPPFVAPHHSSSVAALVGGGSGMARPGAVSRAHRGVLFLDECAEISLSALEALRTPLEDGEIRLARRDGVACYPARFQLVLAANPCPCAPADPQDCICAAATKRRYLGKLSGPLLDRVDLRVQMHRLRAGAFSAADGESTSQVRQRVALAREAAAQRWRPHGFRTNAEVSGPLLRRKFRPSSAAMLPLRTALDRGLLSIRGVDRTLRVAWSLADLAGRTSPGIDEVAAALSFRQTGARR