Rv3483c Family assigned · medium auto-curated
H37Rv Rv3483c · MTBC0 mtbc0_003698 ·
220 aa · 3926732–3927394 (-) ·
RefSeq NP_218000.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | LppP/LprE family lipoprotein |
| Revised (this work) | LppP/LprE family lipoprotein. Pfam: Lipoprotein_21 (PF14041.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X7F2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible exported protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | LppP/LprE lipoprotein |
| Orthologous group | 2DTE8 |
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 | 1.756 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 24.30% of strains (35292) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Lipoprotein_21 | PF14041.12 | 4.5e-26 | 118–204 | LppP/LprE lipoprotein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3482c (membrane protein), high confidence from genomic context alone (score 839 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) |
|---|---|---|---|---|
Rv3482c |
membrane protein | 839 | 839 ctx | neighborhood:821 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 662 | 649 | database:530 |
Rv0153c ptbB |
phosphotyrosine protein phosphatase | 651 | 637 | experimental:629 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 647 | 629 | experimental:629 |
Rv0434 hyp |
hypothetical protein | 610 | 611 | database:561 |
Rv0832 PE_PGRS12 |
PE-PGRS family protein PE_PGRS12 | 601 | 598 | database:543 |
Rv3036c TB22.2 hyp |
hypothetical protein | 601 | 598 | database:543 |
Rv2328 PE23 |
PE family protein PE23 | 601 | 598 | database:543 |
Rv3812 PE_PGRS62 |
PE-PGRS family protein PE_PGRS62 | 601 | 598 | database:543 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 596 | 596 | database:530 |
Rv3360 hyp |
hypothetical protein | 595 | 595 | database:530 |
Rv0019c fhaB |
FHA domain-containing protein FhaB | 595 | 595 | database:530 |
Rv1827 garA |
glycogen accumulation regulator GarA | 595 | 595 | database:530 |
Rv3484 cpsA hyp |
hypothetical protein | 787 | 583 ctx | neighborhood:578 textmining:510 |
Rv1277 hyp |
hypothetical protein | 559 | 559 | database:544 |
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: LppP/LprE family lipoprotein
- Pfam (hmmscan --cut_ga): Lipoprotein_21 PF14041.12 (E=4e-26)
- (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_218000.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lipoprotein_21 (PF14041.12)
- 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
2DTE8 - Curated reference: UniProt I6X7F2 (TrEMBL, unreviewed; 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 —
69 functional partner(s); context anchor
Rv3482c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003698|Rv3483c| MSDEIDPDWPAPAYQPSDDVDTTPPAPGGSWPTAWLVALVVLACVAAAVVAYAGMHRVRPGANQAAPATTSAPARPTSPASQVGPCGPDEATAVRAALAQLAPDSKTGRPWNSTPEDSNYDPCADLSAVLVTVQDATNSSPDQALMFHRGTFVGTATPRAYPFTNLIGPASTNDIVVLSYRTRQSCDGCQDGILTIVGFAWRGDHVQILDSLPELFDAPP