Rv3843c Still unknown · low auto-curated
H37Rv Rv3843c · MTBC0 mtbc0_004073 ·
342 aa · 4339679–4340707 (-) ·
RefSeq NP_218360.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF4328 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF4328. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96235
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
N Cell motilityU Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4328) |
| Orthologous group | COG3170 |
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 | 0.685 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 13 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 |
|---|---|---|---|---|
DUF4328 | PF14219.12 | 1.4e-37 | 152–306 | Domain of unknown function (DUF4328) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glpQ1 (glycerophosphoryl diester phosphodiesterase), high confidence from genomic context alone (score 889 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3842c glpQ1 |
glycerophosphoryl diester phosphodiesterase | 889 | 889 ctx | neighborhood:882 |
Rv1610 |
membrane protein | 763 | 763 ctx | cooccurence:760 |
Rv3435c |
transmembrane protein | 743 | 744 ctx | cooccurence:743 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 741 | 741 ctx | cooccurence:741 |
Rv3166c hyp |
hypothetical protein | 728 | 728 ctx | cooccurence:728 |
Rv0713 |
transmembrane protein | 723 | 723 ctx | cooccurence:723 |
Rv2423 hyp |
hypothetical protein | 722 | 723 ctx | cooccurence:722 |
Rv2164c hyp |
hypothetical protein | 722 | 723 ctx | cooccurence:721 |
Rv1111c hyp |
hypothetical protein | 713 | 714 ctx | cooccurence:711 |
Rv0817c lmeA hyp |
hypothetical protein | 710 | 710 ctx | cooccurence:710 |
Rv1274 lprB |
lipoprotein LprB | 693 | 694 ctx | cooccurence:685 |
Rv3903c cpnT hyp |
hypothetical protein | 690 | 690 ctx | cooccurence:690 |
Rv0383c ttfA hyp |
hypothetical protein | 686 | 686 ctx | cooccurence:686 |
Rv1275 lprC |
lipoprotein LprC | 675 | 676 ctx | cooccurence:668 |
Rv3446c hyp |
hypothetical protein | 674 | 674 ctx | cooccurence:673 |
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: transmembrane protein
- MTBC0 PGAP product: DUF4328 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF4328 PF14219.12 (E=1e-37)
- (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_218360.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4328 (PF14219.12)
- 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
COG3170 - Curated reference: UniProt P96235 (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 —
138 functional partner(s); context anchor
glpQ1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004073|Rv3843c| MIQVCSQCGTRWNVRERQRVWCPRCRGMLLAPLADMPAEARWRTPARPQVPTASDTRRTPPRLPPGFRWIAVRPGAAPPPRHGPRLRGPTPRYAGIPRWGLTDHVDQAPVPASAKAGPSPAAVRTTLLVSLLVFSIAVVVFVVRYVLLVINRNTLLNSVVASASVWLGVLVSLAAIAAAGTTIVLLVRWLVARRAAAFMHQGLPERRSARELWAGCLLPMVNLLWAPLYVIELALVEDRYTRLRRPIVVWWIVWIVSNAISMFAFATSWVTDAQGIANNTTMMVLAYLCAAAAVAAAARVFEGFEQKPVERPAHRWVVVNTDGRSAPASSVAVELDGQEPAA