Rv2943 Resolved · high auto-curated
H37Rv Rv2943 · MTBC0 - ·
413 aa · 3288464–3289705 (+) ·
RefSeq NP_217459.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | insertion sequence element IS1533 transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Insertion sequence element IS1533 transposase. Pfam: rve (PF00665.33), Mu-transpos_C_2 (PF22483.3). |
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 |
I6X5T4
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable transposase for insertion sequence element IS1533 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | PFAM Integrase catalytic |
| Orthologous group | COG4584 |
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 | 0.527 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
rve | PF00665.33 | 3.6e-10 | 116–228 | Integrase core domain |
Mu-transpos_C_2 | PF22483.3 | 4.7e-27 | 294–366 | Mu transposase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2943A (transposase), high confidence from genomic context alone (score 956 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2943A |
transposase | 958 | 956 ctx | neighborhood:785 cooccurence:774 |
Rv2944 |
insertion sequence element IS1533 transposase | 940 | 806 ctx | cooccurence:772 textmining:707 |
Rv3638 |
transposase | 804 | 797 ctx | cooccurence:773 |
Rv3427c istB |
transposase | 790 | 783 ctx | cooccurence:762 |
Rv3428c |
transposase | 710 | 711 ctx | cooccurence:708 |
Rv2014 |
Transposase; Rv2014, (MTCY39.03c), len: 196 aa. Transposase,similar to insertion elements; possibly made by frameshifting with respect to Rv | 770 | 57 | textmining:767 |
Rv3691 hyp |
hypothetical protein | 768 | 47 | textmining:767 |
Rv1227c |
transmembrane protein | 768 | 46 | textmining:767 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 768 | 46 | textmining:767 |
Rv2949c |
chorismate pyruvate-lyase | 543 | 46 | textmining:541 |
Rv2057c rpmG1 |
50S ribosomal protein L33 | 549 | 45 | textmining:548 |
Rv0255c cobQ1 |
cobyric acid synthase | 550 | 44 | textmining:549 |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 433 | 44 | textmining:432 |
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): insertion sequence element IS1533 transposase
- Pfam (hmmscan --cut_ga): rve PF00665.33 (E=4e-10), Mu-transpos_C_2 PF22483.3 (E=5e-27)
- (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_217459.1)
- Domains: Pfam-A via hmmscan --cut_ga — rve (PF00665.33), Mu-transpos_C_2 (PF22483.3)
- 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
COG4584 - Curated reference: UniProt I6X5T4 (TrEMBL, unreviewed; 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 —
13 functional partner(s); context anchor
Rv2943A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2943| MLTVEDWAEIRRLHRAEGLPIKMIARVLGISKNTVKSALESNQQPKYERAPQGSIVDAVEPRIRELLQAYPTMPATVIAERIGWERSIRVLSARVAELRPVYLPPDPASRTTYVAGEIAQCDFWFPPIELPVGFGQTRTAKQLPVLTMVCAYSRWLLAMLLPSRCAEDLFAGWWRLIEALGAVPRVLVWDGEGAIGRWRGGRSELTTECQAFRGTLAAKVLICRPADPEAKGLIERAHDYLERSFLPGRVFASPADFNAQLGAWLALVNTRTRRALGCAPTDRIGADRAAMLSLPPVAPATGWCTSLRLPRDHYVRCDSNDYSVHPGVIGHRVLVRADLERVHVFCDGELVADHERIWAVHQTVSDPAHVEAAKVLRRRHFSAASPVVEPQVQVRSLSDYDDALGVDIDGGVA