Rv2812 Family assigned · low auto-curated
H37Rv Rv2812 · MTBC0 mtbc0_002992 ·
310 aa · 3139241–3140652 (+) ·
RefSeq NP_217328.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | DDE-type integrase/transposase/recombinase |
| Revised (this work) | Helix-turn-helix domain-containing protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71639
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable transposase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | PFAM Integrase, catalytic |
| Orthologous group | COG2801 |
| KEGG orthology |
K07497
|
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 | 1.591 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 4.28% of strains (6221) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3349c (transposase), medium confidence from genomic context alone (score 587 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2813 hyp |
hypothetical protein | 977 | 977 ctx | neighborhood:882 cooccurence:643 |
Rv3786c hyp |
hypothetical protein | 738 | 739 ctx | cooccurence:738 |
Rv2811 hyp |
hypothetical protein | 635 | 635 ctx | neighborhood:620 |
Rv1978 hyp |
hypothetical protein | 630 | 630 ctx | cooccurence:630 |
Rv3899c hyp |
hypothetical protein | 612 | 611 ctx | cooccurence:605 |
Rv3349c |
transposase | 587 | 587 ctx | cooccurence:581 |
Rv3604c |
transmembrane protein | 578 | 578 ctx | cooccurence:577 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 567 | 568 ctx | cooccurence:565 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 554 | 554 ctx | cooccurence:552 |
Rv3896c hyp |
hypothetical protein | 552 | 552 ctx | cooccurence:551 |
Rv0804 hyp |
hypothetical protein | 531 | 532 ctx | cooccurence:529 |
Rv1158c hyp |
hypothetical protein | 483 | 484 ctx | cooccurence:482 |
Rv2633c hyp |
hypothetical protein | 477 | 477 ctx | cooccurence:477 |
Rv1435c hyp |
hypothetical protein | 465 | 465 ctx | cooccurence:465 |
Rv2810c |
Probable transposase; Rv2810c, (MTCY16B7.33), len: 133 aa. Probable transposase for IS1555, similar to C-terminal domain of transposases for | 446 | 446 ctx | neighborhood:438 |
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: transposase
- MTBC0 PGAP product: helix-turn-helix domain-containing protein
- (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_217328.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2801 - Curated reference: UniProt P71639 (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 —
19 functional partner(s); context anchor
Rv3349c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002992|Rv2812| MAVGDDEEKVRAERARAIGLFRYQLIWEAADAAHSTKQRGKMVRELASREHTDPFGRRVRISRQTIDRWIRGWRAGGFDALVPNPRQCTPRTPAEVLELAVALRRENPQRTAAAIRRILRTQLGWAPDERTLQRNFHRLGLTGATTGSAPAVFGRFEAEHPNALWTGDVLHGIRIDLRKTYLFAFLDDHSRLVPGYRWGHAEDTVRLAAALRPALASRGVPNAVYVDNGSPYVDAWLLRACAKLGVRLVHSTPGRPQGRGKIERFFRTVREQFLVEITGEPDVVGRHYVADLAELNRLFTAWVETVYHRS