Rv3729 Resolved · high auto-curated
H37Rv Rv3729 · MTBC0 - ·
776 aa · 4178285–4180615 (+) ·
RefSeq NP_218246.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transferase. Pfam: Zn_ribbon_HMPTM (PF23545.2), Radical_SAM (PF04055.28), Fer4_12 (PF13353.12), Methyltransf_23 (PF13489.13), Ubie_methyltran (PF01209.25), Methyltransf_31 (PF13847.13), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O69696
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible transferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | 4Fe-4S single cluster domain |
| Orthologous group | COG0500 |
| KEGG orthology |
K06937
|
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 | 1.794 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 15 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.79% of strains (1152) · 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 |
|---|---|---|---|---|
Zn_ribbon_HMPTM | PF23545.2 | 4.2e-17 | 2–45 | HMPTM N-terminal zinc ribbon domain |
Radical_SAM | PF04055.28 | 6.8e-21 | 95–259 | Radical SAM superfamily |
Fer4_12 | PF13353.12 | 4.0e-05 | 99–183 | 4Fe-4S single cluster domain |
Methyltransf_23 | PF13489.13 | 4.2e-10 | 554–707 | Methyltransferase domain |
Ubie_methyltran | PF01209.25 | 6.2e-09 | 561–661 | ubiE/COQ5 methyltransferase family |
Methyltransf_31 | PF13847.13 | 7.9e-15 | 564–679 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 2.8e-19 | 565–660 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 7.1e-19 | 567–661 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 1.9e-10 | 567–661 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3728 (membrane protein), medium confidence from genomic context alone (score 458 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3728 |
membrane protein | 469 | 458 ctx | neighborhood:455 |
Rv3727 |
oxidoreductase | 441 | 441 | |
Rv0213c |
methyltransferase | 442 | 421 | |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 415 | 415 ctx | neighborhood:402 |
Rv3224 |
iron-regulated short-chain dehydrogenase/reductase | 492 | 144 | textmining:432 |
Rv2541 hyp |
hypothetical protein | 870 | 42 | textmining:870 |
Rv2012 hyp |
hypothetical protein | 803 | 42 | textmining:803 |
Rv0991c hyp |
hypothetical protein | 641 | 42 | textmining:641 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transferase
- Pfam (hmmscan --cut_ga): Zn_ribbon_HMPTM PF23545.2 (E=4e-17), Radical_SAM PF04055.28 (E=7e-21), Fer4_12 PF13353.12 (E=4e-05), Methyltransf_23 PF13489.13 (E=4e-10), Ubie_methyltran PF01209.25 (E=6e-09), Methyltransf_31 PF13847.13 (E=8e-15), Methyltransf_25 PF13649.13 (E=3e-19), Methyltransf_11 PF08241.19 (E=7e-19), Methyltransf_12 PF08242.19 (E=2e-10)
- (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_218246.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zn_ribbon_HMPTM (PF23545.2), Radical_SAM (PF04055.28), Fer4_12 (PF13353.12), Methyltransf_23 (PF13489.13), Ubie_methyltran (PF01209.25), Methyltransf_31 (PF13847.13), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19)
- 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
COG0500 - Curated reference: UniProt O69696 (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 —
8 functional partner(s); context anchor
Rv3728 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3729| MFVEYTKSICPVCKVVVDAQVNIRHDKVYLRKRCREHGSFEALVYGDAQMYLESARFNKPGTFPLRFQTEVRDGCPSDCGLCPDHKQHACLGLIEVNTHCNLDCPICFADSGHQPDGYAITAAQCERMLDTLVAAEGEPEVVMFSGGEPTIHKQLLEFVDAAQARPVKTVIINTNGIRLASDRRFVDQLATRNRPGHPVHIYLQFDGLDEATHRRIRGHDLRDVKQRALDNCAAAGLTVSLVAAVERGLNEHELGAVIRHGMAQPGVQPVVFQPVTHAGRHVQFDPLTRLTNSDIIACITAQLPEWFRPGDFFPVPCCFPSCRSITYLLTDGEHVVPIPRLLNVEDYLDYVSNRVIPDLAIREALENLWSASAVPGTDTMTAQLQRATAALNCAEGCGINLPEALTHLTDRVFAIVIQDFQDPYTLNVKQLMKCCVQQITPDGRLIPFCAYNSVGYREQVREQLTGVPVPDIVPNAIPLAGLLADAPHGSKQANTGGSIARLAGPTRGAPMALPPQQIKACCADAYSRDIVALLLGDSFHPGGATLTRRLADQLGLRSTGDPRRVADIAAGPGASARLLASDYGVAVDGVDISEINVKRAQAAVAQTGLTERVRFHLGDAESVPLPDDTFDALVCECAFCTFPDKNAAAQQFARILRPGGLAGITDVTVGDGGLPAELTPLAAWVACIADARTVTDYTDILEGAGLRTRHIESHDESLLDMIDRIDARITALHVAAPEILADNGIRHDSVRDFTALARAAVQTGRIGYTLMIAEKP