Rv3863 Family assigned · medium auto-curated
H37Rv Rv3863 · MTBC0 - ·
392 aa · 4338849–4340027 (+) ·
RefSeq NP_218380.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains MSMEG_6518_N (PF27182.1) domain(s); putative function inferred from the domain architecture. |
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 |
P96214
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | FHA domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | ATPase activity |
| Orthologous group | COG1716 |
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 | 0.418 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 8 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 |
|---|---|---|---|---|
MSMEG_6518_N | PF27182.1 | 5.6e-30 | 267–337 | MSMEG_6518 N-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espE (ESX-1 secretion-associated protein EspE), medium confidence from genomic context alone (score 500 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) |
|---|---|---|---|---|
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 870 | 500 ctx | neighborhood:493 textmining:751 |
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 482 | 456 ctx | neighborhood:444 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 452 | 449 ctx | neighborhood:438 |
Rv3865 espF |
ESX-1 secretion-associated protein EspF | 800 | 408 ctx | neighborhood:402 textmining:677 |
Rv3862c whiB6 |
transcriptional regulator WhiB6 | 408 | 408 | |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 838 | 382 | textmining:749 |
Rv3867 espH |
ESX-1 secretion-associated protein EspH | 791 | 361 | textmining:687 |
Rv3004 cfp6 |
low molecular weight protein antigen 6 | 431 | 41 | textmining:431 |
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): hypothetical protein
- Pfam (hmmscan --cut_ga): MSMEG_6518_N PF27182.1 (E=6e-30)
- (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_218380.1)
- Domains: Pfam-A via hmmscan --cut_ga — MSMEG_6518_N (PF27182.1)
- 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
COG1716 - Curated reference: UniProt P96214 (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 —
8 functional partner(s); context anchor
espE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3863| MAGERKVCPPSRLVPANKGSTQMSKAGSTVGPAPLVACSGGTSDVIEPRRGVAIIGHSCRVGTQIDDSRISQTHLRAVSDDGRWRIVGNIPRGMFVGGRRGSSVTVSDKTLIRFGDPPGGKALTFEVVRPSDSAAQHGRVQPSADLSDDPAHNAAPVAPDPGVVRAGAAAAARRRELDISQRSLAADGIINAGALIAFEKGRSWPRERTRAKLEEVLQWPAGTIARIRRGEPTEPATNPDASPGLRPADGPASLIAQAVTAAVDGCSLAIAALPATEDPEFTERAAPILADLRQLEAIAVQATRISRITPELIKALGAVRRHHDELMRLGATAPGATLAQRLYAARRRANLSTLETAQAAGVAEEMIVGAEAEEELPAEATEAIEALIRQIN