Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|
| MTBC0 PGAP re-annotation | IS30 family transposase |
|---|
| Revised (this work) | IS30 family transposase. Pfam: HTH_38 (PF13936.13), HTH_23 (PF13384.13), rve (PF00665.33). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53337
TrEMBL · unreviewed
· Inferred from homology
|
|---|
| UniProt name | Probable transposase |
|---|
| Curated function | Required for the transposition of the insertion element. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|
| eggNOG description | PFAM Integrase |
|---|
| Orthologous group | COG2826 |
|---|
| KEGG orthology |
K07482
|
|---|
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 |
0.684 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 synonymous, 6 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 |
|---|
HTH_38 | PF13936.13 |
9.1e-16 | 7–48 |
Helix-turn-helix domain |
HTH_23 | PF13384.13 |
3.1e-08 | 9–50 |
Homeodomain-like domain |
rve | PF00665.33 |
1.1e-10 | 183–275 |
Integrase core domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv3003c ilvB1 |
acetolactate synthase large subunit IlvB |
442 |
59 |
textmining:432 |
Rv3221c TB7.3 |
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit |
545 |
46 |
textmining:543 |
Rv2621c |
transcriptional regulator |
436 |
46 |
textmining:434 |
Rv2882c frr |
ribosome recycling factor |
439 |
44 |
textmining:438 |
Rv2165c rsmH |
rRNA small subunit methyltransferase H |
540 |
41 |
textmining:540 |
Rv2618 hyp |
hypothetical protein |
434 |
41 |
textmining:434 |
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: IS30 family transposase
- Pfam (hmmscan --cut_ga): HTH_38 PF13936.13 (E=9e-16), HTH_23 PF13384.13 (E=3e-08), rve PF00665.33 (E=1e-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_217707.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_38 (PF13936.13), HTH_23 (PF13384.13), rve (PF00665.33)
- 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
COG2826
- Curated reference: UniProt
O53337
(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 —
6 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003390|Rv3191c|
MRQISSRYLSEEERINIADLRRSGLSIRKIADQLGRAPSTVSRELRRNSRRDGQYRPFEAHRWAVQRRVRRHRRRIDKNPDLCELIAELLAQRWSPQQIARHLRRKYPDDRSMWLCHESIYQAVYQPQSRLIRPPQVKSPHRGPLRTGRTHRRAHLRPGRRRPRFAQPMLSIHQRPFDPADRSEPGHWEGDLIVGKNQGSAIGTLVERQTRLIRLLHLPTHDAYCLRIAITETMSDLPVTLVRSITWDQGIEMARHIDITADLGAPVYFCDSRSPWQRASNENSNGLLRQYFPKGTSLSTYTPDHLRAVEYEINNRPRQVLGHRSPAELFTALLTSPDHQLLRR
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