Rv3828c Resolved · high auto-curated
H37Rv Rv3828c · MTBC0 - ·
203 aa · 4302786–4303397 (-) ·
RefSeq NP_218345.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | resolvase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Resolvase. Pfam: Resolvase (PF00239.27). |
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 |
O07795
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible resolvase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | resolvase |
| Orthologous group | COG2452 |
| KEGG orthology |
K07450
|
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 | 2.45 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.16% of strains (231) · 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 |
|---|---|---|---|---|
Resolvase | PF00239.27 | 2.4e-10 | 63–188 | Resolvase, N terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3827c (transposase), high confidence from genomic context alone (score 978 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3827c |
transposase | 978 | 978 ctx | neighborhood:882 cooccurence:761 |
Rv2885c |
transposase | 894 | 891 ctx | cooccurence:759 coexpression:553 |
Rv2978c tnpB |
transposase | 843 | 839 ctx | cooccurence:758 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 831 | 826 ctx | cooccurence:757 |
Rv2791c tnpB |
transposase | 820 | 815 ctx | cooccurence:759 |
Rv0605 |
IS1536 family serine type transposase | 799 | 799 | coexpression:796 |
Rv0922 tnpB |
transposase | 791 | 786 ctx | cooccurence:772 |
Rv3829c |
dehydrogenase | 775 | 774 ctx | neighborhood:773 |
Rv2979c |
resolvase | 763 | 763 | coexpression:759 |
Rv3830c |
TetR family transcriptional regulator | 629 | 629 ctx | neighborhood:625 |
Rv3831 hyp |
hypothetical protein | 460 | 460 ctx | neighborhood:457 |
Rv2736c recX |
regulatory protein RecX | 446 | 296 | |
Rv0071 |
maturase | 412 | 181 | |
Rv3334 |
MerR family transcriptional regulator | 645 | 47 | textmining:643 |
Rv2956 hyp |
hypothetical protein | 514 | 47 | textmining:511 |
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): resolvase
- Pfam (hmmscan --cut_ga): Resolvase PF00239.27 (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_218345.1)
- Domains: Pfam-A via hmmscan --cut_ga — Resolvase (PF00239.27)
- 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
COG2452 - Curated reference: UniProt O07795 (TrEMBL, unreviewed; Predicted)
- 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 —
21 functional partner(s); context anchor
Rv3827c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3828c| MSVVCCRNRWMNLAVWAERNGVAWVIAYRWFRAGLLPVPAQRVGRLILVNDPAVEESGRGRTLVYARVSSADQRSDLDRRVARVTAWATSQHLSVDKVVAEGGWALNGHRRKFFALLGDPVVTRIVVEHRDRFCWFGSEYVEAALVAQGRELVVVDLAEVDDDLVGDMTEILTSMCARLYGERAAQNGAKRALAAAVGDAEAA