Rv2979c Family assigned · medium auto-curated
H37Rv Rv2979c · MTBC0 mtbc0_003164 ·
194 aa · 3356337–3356921 (-) ·
RefSeq NP_217495.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | resolvase |
|---|---|
| MTBC0 PGAP re-annotation | IS607 family transposase |
| Revised (this work) | IS607 family transposase. Pfam: Resolvase (PF00239.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XFU1
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable 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 | 0.888 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
Resolvase | PF00239.27 | 1.8e-18 | 53–189 | Resolvase, N terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tnpB (transposase), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2978c tnpB |
transposase | 995 | 996 ctx | neighborhood:882 cooccurence:759 coexpression:859 |
Rv2977c thiL |
thiamine-monophosphate kinase | 967 | 967 ctx | neighborhood:882 coexpression:732 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 964 | 963 ctx | cooccurence:756 coexpression:850 |
Rv2885c |
transposase | 960 | 959 ctx | cooccurence:760 coexpression:831 |
Rv3827c |
transposase | 937 | 936 ctx | cooccurence:762 coexpression:732 |
Rv2791c tnpB |
transposase | 937 | 935 ctx | cooccurence:761 coexpression:732 |
Rv0605 |
IS1536 family serine type transposase | 861 | 862 | coexpression:860 |
Rv0922 tnpB |
transposase | 791 | 786 ctx | cooccurence:772 |
Rv3828c |
resolvase | 763 | 763 | coexpression:759 |
Rv1765c hyp |
hypothetical protein | 757 | 757 | coexpression:757 |
Rv2976c ung |
uracil-DNA glycosylase | 737 | 737 ctx | neighborhood:721 |
Rv0185 hyp |
hypothetical protein | 734 | 734 | coexpression:734 |
Rv2792c |
resolvase | 733 | 733 | coexpression:730 |
Rv3585 radA |
DNA repair protein RadA | 553 | 553 | coexpression:553 |
Rv2980 hyp |
hypothetical protein | 503 | 502 ctx | neighborhood:502 |
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: resolvase
- MTBC0 PGAP product: IS607 family transposase
- Pfam (hmmscan --cut_ga): Resolvase PF00239.27 (E=2e-18)
- (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_217495.1)
- 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 I6XFU1 (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 —
27 functional partner(s); context anchor
tnpB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003164|Rv2979c| MNLATWAERNGVARGTAYRWFRAGLLSVMARRVGRLILVDEPAGDAGMRSPTAVYARVSSADQKADLDRQVARVTAWATAQQMPVDKVVTEVGSAFNEHRRKFLSLLRDPSVHRIVVEHRDRFCRLGSKYVQAAFAAQGRELVVVDSAEVDDDLVRDMTEILTSMCARLYGKRAAENRTKRALAAAAGEDHEAA