Rv0071 Family assigned · medium auto-curated
H37Rv Rv0071 · MTBC0 mtbc0_000078 ·
241 aa · 79631–80356 (+) ·
RefSeq NP_214585.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | maturase |
|---|---|
| MTBC0 PGAP re-annotation | reverse transcriptase domain-containing protein |
| Revised (this work) | Reverse transcriptase domain-containing protein. Pfam: RVT_1 (PF00078.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53616
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible maturase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Reverse transcriptase (RNA-dependent DNA polymerase) |
| Orthologous group | COG3344 |
| EC number |
EC 2.7.7.49
|
| KEGG orthology |
K00986
|
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 | 0.678 · 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 |
|---|---|---|---|---|
RVT_1 | PF00078.33 | 2.1e-15 | 77–192 | Reverse transcriptase (RNA-dependent DNA polymerase) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3428c (transposase), medium confidence from genomic context alone (score 670 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2816c cas2 |
CRISPR-associated endoribonuclease Cas2 | 819 | 806 | experimental:790 |
Rv3428c |
transposase | 670 | 670 ctx | cooccurence:657 |
Rv2424c |
transposase | 649 | 649 ctx | cooccurence:639 |
Rv2177c |
transposase | 623 | 623 ctx | cooccurence:614 |
Rv3427c istB |
transposase | 590 | 587 ctx | cooccurence:585 |
Rv2944 |
insertion sequence element IS1533 transposase | 445 | 440 ctx | cooccurence:436 |
Rv1034c |
Probable transposase (fragment); Rv1034c, (MTCY10G2.15), len: 129 aa. Probable IS1560 transposase fragment, similar to part of Rv3387|E12023 | 423 | 423 ctx | cooccurence:413 |
Rv3387 |
transposase | 423 | 423 ctx | cooccurence:413 |
Rv1366 hyp |
hypothetical protein | 416 | 417 | coexpression:417 |
Rv3638 |
transposase | 413 | 408 ctx | cooccurence:400 |
Rv3386 |
transposase | 404 | 405 | |
Rv2515c hyp |
hypothetical protein | 440 | 250 | |
Rv2979c |
resolvase | 425 | 199 | |
Rv0605 |
IS1536 family serine type transposase | 420 | 193 | |
Rv0921 |
resolvase | 419 | 190 |
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: maturase
- MTBC0 PGAP product: reverse transcriptase domain-containing protein
- Pfam (hmmscan --cut_ga): RVT_1 PF00078.33 (E=2e-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_214585.1)
- Domains: Pfam-A via hmmscan --cut_ga — RVT_1 (PF00078.33)
- 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
COG3344 - Curated reference: UniProt O53616 (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 —
33 functional partner(s); context anchor
Rv3428c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000078|Rv0071| MSSITVSVDPVDPVDPVDPVDPVDPVDPVDAVVAAGSDGLTVARIESEIGALEFLNELRTELKSGQFRPQPVRERKIPKPGGLGKVRRLGIPTVADRVVQAALKLVLEPIFETDFEPVSYGFRPARRAHDTIAEIHLFGTQEYRWVLDADIKACFDRIDHADLMDRVRHRIKDKRVLRLVNWQRIRHRWNWTDVRRWLTDPTGRWHPISADGITLFNPAAVPIRRYRYRGNTIPTPWTQAV