Rv0958 Family assigned · medium auto-curated
H37Rv Rv0958 · MTBC0 mtbc0_001022 ·
459 aa · 1077098–1078477 (+) ·
RefSeq NP_215473.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | magnesium chelatase |
|---|---|
| MTBC0 PGAP re-annotation | ATP-binding protein |
| Revised (this work) | ATP-binding protein. Pfam: Sigma54_activat (PF00158.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71552
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible magnesium chelatase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | chlI |
| eggNOG description | magnesium chelatase |
| Orthologous group | COG1239 |
| EC number |
EC 6.6.1.1
|
| KEGG orthology |
K03405
|
| KEGG pathways |
map00860, map01100, map01110
|
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 | 0.369 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.07% of strains (3007) · 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 |
|---|---|---|---|---|
Sigma54_activat | PF00158.33 | 4.9e-05 | 170–227 | Sigma-54 interaction domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purN (phosphoribosylglycinamide formyltransferase PurN), high confidence from genomic context alone (score 769 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0959 hyp |
hypothetical protein | 984 | 984 ctx | neighborhood:881 cooccurence:774 coexpression:457 |
Rv2850c |
magnesium chelatase | 966 | 964 | experimental:617 database:900 |
Rv1485 hemZ |
ferrochelatase | 926 | 917 | database:900 |
Rv2677c hemY |
protoporphyrinogen oxidase | 909 | 907 | database:900 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 769 | 769 ctx | neighborhood:768 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 769 | 769 ctx | neighborhood:768 |
Rv0955 |
integral membrane protein | 696 | 696 ctx | neighborhood:694 |
Rv1481 |
membrane protein | 713 | 695 | experimental:617 |
Rv0954 |
transmembrane protein | 672 | 673 ctx | neighborhood:671 |
Rv1836c hyp |
hypothetical protein | 673 | 653 | experimental:617 |
Rv0960 vapC9 |
ribonuclease VapC9 | 629 | 629 ctx | neighborhood:627 |
Rv0959A vapB9 |
antitoxin VapB9 | 627 | 627 ctx | neighborhood:627 |
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 542 | 481 | coexpression:451 |
Rv0961 |
integral membrane protein | 453 | 453 ctx | neighborhood:451 |
Rv2133c hyp |
hypothetical protein | 448 | 448 |
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: magnesium chelatase
- MTBC0 PGAP product: ATP-binding protein
- Pfam (hmmscan --cut_ga): Sigma54_activat PF00158.33 (E=5e-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_215473.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma54_activat (PF00158.33)
- 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
COG1239 - Curated reference: UniProt P71552 (TrEMBL, unreviewed; 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 —
24 functional partner(s); context anchor
purN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001022|Rv0958| MSPSNLPRTVGELRAAGHRERGVKQEIRENLLTALADGDNVWPGILGFDDTVIPQVERALIAGHDFVLLGERGQGKTRLLRALAGLLDEWTPVIAGAELGEHPYTPITPESIRRAAQLGDDLPVAWKHRSERYTEKLATPDTSVADLVGDVDPIKVAEGRSLGDPETIAYGLIPRAHRGIVAVNELPDLAERIQVSMLNVMEERDIQVRGYTLRLPLDVLVVASANPEDYTNRGRIITPIKDRFGAEIRTHYPLELEAEMGVIVQEAHLSAQVPDYLMQVLARFARYLRESRSIDQRSGVSARFAIAAAETVAAAARHRGAVLGETDPVARVVDLGTVIDVLRGKLEFESGEEGREQAVLEHLLRRATADTASRVLGGIDVGSLVTAVEGGSAVTTGERVSAKDVLAAVPGLPVVDRIARKLGAESEGERAAALELALEALYLAKRVDKVCGEGQTVYG