Rv2885c Resolved · high auto-curated
H37Rv Rv2885c · MTBC0 - ·
460 aa · 3194166–3195548 (-) ·
RefSeq NP_217401.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transposase. Pfam: HTH_OrfB_IS605 (PF12323.15), OrfB_IS605 (PF01385.26), Cas12f1-like_TNB (PF07282.19). |
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 |
P9WL37
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative RNA-guided DNA endonuclease Rv2885c |
| EC (curated) |
EC 3.1.21.-
|
| Curated function | An RNA-guided dsDNA endonuclease. When guided by an RNA derived from the right-end element of its insertion sequence element (IS), cleaves DNA downstream of the transposon-associated motif (TAM). Cleaves supercoiled and linear DNA in a staggered manner 15-21 bases from the TAM yielding 5'-overhangs. Binds reRNA, an approximately 150 nucleotide base sRNA derived from the 3' end of its own gene, the right end (RE) of the insertion sequence (IS) plus sequence downstream of the IS. |
UniProt still lists this protein as Putative RNA-guided DNA endonuclease Rv2885c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Transposase |
| Orthologous group | COG0675 |
| KEGG orthology |
K07496
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.705 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 12 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 49.03% of strains (71203) · 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 |
|---|---|---|---|---|
HTH_OrfB_IS605 | PF12323.15 | 3.7e-08 | 14–49 | Helix-turn-helix domain |
OrfB_IS605 | PF01385.26 | 8.8e-28 | 204–322 | Probable transposase |
Cas12f1-like_TNB | PF07282.19 | 1.3e-15 | 345–406 | Cas12f1-like, TNB domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2979c (resolvase), high confidence from genomic context alone (score 959 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2979c |
resolvase | 960 | 959 ctx | cooccurence:760 coexpression:831 |
Rv0605 |
IS1536 family serine type transposase | 954 | 953 ctx | cooccurence:761 coexpression:806 |
Rv2886c |
resolvase | 948 | 947 ctx | neighborhood:781 cooccurence:758 |
Rv3828c |
resolvase | 894 | 891 ctx | cooccurence:759 coexpression:553 |
Rv2978c tnpB |
transposase | 861 | 861 | coexpression:860 |
Rv2792c |
resolvase | 850 | 847 ctx | cooccurence:761 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 816 | 817 | coexpression:815 |
Rv3827c |
transposase | 801 | 801 | coexpression:799 |
Rv2977c thiL |
thiamine-monophosphate kinase | 798 | 799 | coexpression:798 |
Rv2791c tnpB |
transposase | 782 | 782 | coexpression:780 |
Rv0921 |
resolvase | 777 | 771 ctx | cooccurence:761 |
Rv1765c hyp |
hypothetical protein | 731 | 731 | coexpression:731 |
Rv0336 hyp |
hypothetical protein | 731 | 731 | coexpression:731 |
Rv2887 |
HTH-type transcriptional regulator | 576 | 576 ctx | neighborhood:572 |
Rv2015c hyp |
hypothetical protein | 533 | 533 | coexpression:533 |
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): transposase
- Pfam (hmmscan --cut_ga): HTH_OrfB_IS605 PF12323.15 (E=4e-08), OrfB_IS605 PF01385.26 (E=9e-28), Cas12f1-like_TNB PF07282.19 (E=1e-15)
- (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_217401.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_OrfB_IS605 (PF12323.15), OrfB_IS605 (PF01385.26), Cas12f1-like_TNB (PF07282.19)
- 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
COG0675 - Curated reference: UniProt P9WL37 (SwissProt, reviewed; Inferred from homology)
- 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 —
20 functional partner(s); context anchor
Rv2979c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2885c| MMARLKVPEGWCVQAFRFTLNPTQTQAASLARHFGARRKAFNWTVTALKADIKAWRADGTESAKPSLRVLRKRWNTVKDQVCVNAQTGQVWWPECSKEAYADGIAGAVDAYWNWQSCRAGKRAGKTVGVPRFKKKGRDADRVCFTTGAMRVEPDRRHLTLPVIGTIRTYENTRRVERLIAKGRARVLAITVRRNGTRLDASVRVLVQRPQQRRVALPDSRVGVDVGVRRLATVADAEGTVLEQVPNPRPLDAALRGLRRVSRARSRCTKGSRRYCERTTELSRLHRRVNDVRTHHLHVLTTRLAKTHGRIVVEGLDAAGMLRQKGLPGARARRRALSDAALATPRRHLSYKTGWYGSSLVVADRWFPSSKTCHACRHVQDIGWDEKWQCDGCSITHQRDDNAAINLARYEEPPSVVGPVGAAVKRGADRKTGPGPAGGREARKATGHPAGEQPRDGVQVK