Rv2850c Family assigned · medium auto-curated
H37Rv Rv2850c · MTBC0 mtbc0_003029 ·
629 aa · 3178831–3180720 (-) ·
RefSeq NP_217366.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | magnesium chelatase |
|---|---|
| MTBC0 PGAP re-annotation | magnesium chelatase subunit D family protein |
| Revised (this work) | Magnesium chelatase subunit D family protein. Pfam: AAA_5 (PF07728.21), MCM (PF00493.30), Mg_chelatase (PF01078.28), AAA_lid_2 (PF17863.8), VWA_2 (PF13519.13), VWA (PF00092.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPR3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2850c |
UniProt still lists this protein as Uncharacterized protein Rv2850c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | chlI |
| eggNOG description | von Willebrand factor, type A |
| Orthologous group | COG1239 |
| EC number |
EC 6.6.1.1
|
| KEGG orthology |
K03404, 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 | 1.085 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 13 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 9.65% of strains (14015) · 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 |
|---|---|---|---|---|
AAA_5 | PF07728.21 | 1.4e-13 | 32–166 | AAA domain (dynein-related subfamily) |
MCM | PF00493.30 | 4.3e-06 | 32–158 | MCM P-loop domain |
Mg_chelatase | PF01078.28 | 6.5e-08 | 88–153 | Magnesium chelatase, subunit ChlI |
AAA_lid_2 | PF17863.8 | 1.9e-15 | 232–301 | AAA lid domain |
VWA_2 | PF13519.13 | 1.6e-13 | 452–558 | von Willebrand factor type A domain |
VWA | PF00092.35 | 4.5e-08 | 452–574 | von Willebrand factor type A domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cobO (cob(I)alamin adenosyltransferase), high confidence from genomic context alone (score 922 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0958 |
magnesium chelatase | 966 | 964 | experimental:617 database:900 |
Rv2677c hemY |
protoporphyrinogen oxidase | 992 | 943 | coexpression:436 database:900 textmining:875 |
Rv2849c cobO |
cob(I)alamin adenosyltransferase | 985 | 922 ctx | neighborhood:857 cooccurence:458 textmining:818 |
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 965 | 915 ctx | cooccurence:774 coexpression:480 textmining:610 |
Rv1485 hemZ |
ferrochelatase | 942 | 911 | database:900 |
Rv2848c cobB |
cobyrinic acid A,C-diamide synthase | 988 | 903 ctx | neighborhood:857 textmining:889 |
Rv2851c |
GCN5-like N-acetyltransferase | 984 | 889 ctx | neighborhood:881 textmining:870 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 858 | 838 ctx | neighborhood:544 cooccurence:648 |
Rv2852c mqo |
malate:quinone oxidoreductase | 809 | 809 ctx | neighborhood:804 |
Rv2072c cobL |
precorrin-6Y C(5,15)-methyltransferase | 834 | 733 ctx | neighborhood:544 cooccurence:432 textmining:407 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 782 | 713 ctx | neighborhood:709 |
Rv2846c efpA |
MFS-type transporter EfpA | 699 | 700 ctx | neighborhood:698 |
Rv2854 hyp |
hypothetical protein | 689 | 690 ctx | neighborhood:688 |
Rv2855 mtr |
mycothione reductase | 685 | 685 ctx | neighborhood:683 |
Rv1481 |
membrane protein | 690 | 670 | experimental:617 |
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: magnesium chelatase subunit D family protein
- Pfam (hmmscan --cut_ga): AAA_5 PF07728.21 (E=1e-13), MCM PF00493.30 (E=4e-06), Mg_chelatase PF01078.28 (E=6e-08), AAA_lid_2 PF17863.8 (E=2e-15), VWA_2 PF13519.13 (E=2e-13), VWA PF00092.35 (E=4e-08)
- (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_217366.1)
- Domains: Pfam-A via hmmscan --cut_ga — AAA_5 (PF07728.21), MCM (PF00493.30), Mg_chelatase (PF01078.28), AAA_lid_2 (PF17863.8), VWA_2 (PF13519.13), VWA (PF00092.35)
- 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 P9WPR3 (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 —
42 functional partner(s); context anchor
cobO - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003029|Rv2850c| MKPYPFSAIVGHDRLRLALLLCAVRPEIGGALIRGEKGTAKSTAVRGLAALLSVATGSTETGLVELPLGATEDRVVGSLDLQRVMRDGEHAFSPGLLARAHGGVLYVDEVNLLHDHLVDILLDAAAMGRVHVERDGISHSHEARFVLIGTMNPEEGELRPQLLDRFGLTVDVQASRDIDVRVQVIRRRMAYEADPDAFVARYADADAELAHRIAAARATVDDVVLGDNELRRIAALCAAFDVDGMRADLVVARTAAAHAAWRGVRTVEEQDIRAAAELALPHRRRRDPFDDHGIDRDQLDEALALASVDPEPEPDPPGGGQSANEPASQPNSRSKSTEPGAPSSMGDDPPRPASPRLRSSPRPSAPPSKIFRTRALRVPGVGTGAPGRRSRARNASGSVVAAAEVSDPDAHGLHLFATLLAAGERAFGAGPLRPWPDDVRRAIREGREGNLVIFVVDASGSMAARDRMAAVSGATLSLLRDAYQRRDKVAVITFRQHEATLLLSPTSSAHIAGRRLARFSTGGKTPLAEGLLAARALIIREKVRDRARRPLVVVLTDGRATAGPDPLGRSRTAAAGLVAEGAAAVVVDCETSYVRLGLAAQLARQLGAPVVRLEQLHADYLVHAVRGVA