Rv1993c Family assigned · low auto-curated
H37Rv Rv1993c · MTBC0 mtbc0_002120 ·
90 aa · 2260916–2261188 (-) ·
RefSeq NP_216509.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF1490 family protein |
| Revised (this work) | DUF1490 family 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 |
P9WLP5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1993c |
UniProt still lists this protein as Uncharacterized protein Rv1993c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF1490) |
| Orthologous group | 2ET5E |
| 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)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
DUF1490 | PF07371.18 | 4.4e-39 | 1–86 | Protein of unknown function (DUF1490) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ctpG (cation transporter ATPase G), high confidence from genomic context alone (score 963 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1992c ctpG |
cation transporter ATPase G | 992 | 963 ctx | neighborhood:801 coexpression:820 textmining:802 |
Rv1994c cmtR |
HTH-type transcriptional regulator CmtR | 935 | 684 ctx | neighborhood:680 textmining:805 |
Rv1991c mazF6 |
mRNA interferase MazF6 | 550 | 550 ctx | neighborhood:536 |
Rv1991A mazE6 |
antitoxin MazE6 | 536 | 536 ctx | neighborhood:536 |
Rv1995 hyp |
hypothetical protein | 918 | 430 ctx | neighborhood:425 textmining:862 |
Rv1977 hyp |
hypothetical protein | 546 | 50 | textmining:542 |
Rv1333 |
hydrolase | 434 | 44 | textmining:433 |
Rv2075c hyp |
hypothetical protein | 650 | 41 | textmining:650 |
Rv1521 fadD25 |
fatty-acid--CoA ligase FadD25 | 517 | 41 | textmining:517 |
Rv1979c |
permease | 432 | 41 | 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
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: DUF1490 family protein
- Pfam (hmmscan --cut_ga): DUF1490 PF07371.18 (E=4e-39)
- (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_216509.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1490 (PF07371.18)
- 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
2ET5E - Curated reference: UniProt P9WLP5 (SwissProt, reviewed; Evidence at protein level)
- 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 —
10 functional partner(s); context anchor
ctpG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002120|Rv1993c| MVTHELLVKAAGAVLTGLVGVSAYETLRKALGTAPIRRASVTVMEWGLRGTRRAEAAAESARLTVADVVAEARGRIGEEAPLPAGARVDE