Rv3753c Family assigned · medium auto-curated
H37Rv Rv3753c · MTBC0 - ·
166 aa · 4199721–4200221 (-) ·
RefSeq NP_218270.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Rv3753c (PF27101.1) 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 |
O69720
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein Rv3753c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | tRNA adenosine |
| Orthologous group | 2BM8T |
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 | 1.055 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
Rv3753c | PF27101.1 | 4.1e-57 | 11–154 | Rv3753c-like tRNA adenosine deaminase-associated protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tadA (cytidine/deoxycytidylate deaminase), high confidence from genomic context alone (score 873 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) |
|---|---|---|---|---|
Rv3752c tadA |
cytidine/deoxycytidylate deaminase | 873 | 873 ctx | neighborhood:867 |
Rv3013 hyp |
hypothetical protein | 763 | 763 ctx | cooccurence:763 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 759 | 759 ctx | neighborhood:758 |
Rv3311 hyp |
hypothetical protein | 743 | 744 ctx | cooccurence:742 |
Rv3438 hyp |
hypothetical protein | 717 | 718 ctx | cooccurence:715 |
Rv2446c |
integral membrane protein | 713 | 713 ctx | cooccurence:713 |
Rv3212 hyp |
hypothetical protein | 696 | 697 ctx | cooccurence:695 |
Rv2219 |
transmembrane protein | 691 | 692 ctx | cooccurence:690 |
Rv2980 hyp |
hypothetical protein | 689 | 689 ctx | cooccurence:689 |
Rv1332 |
transcriptional regulator | 686 | 687 ctx | cooccurence:685 |
Rv0358 hyp |
hypothetical protein | 678 | 678 ctx | cooccurence:677 |
Rv0863 hyp |
hypothetical protein | 676 | 676 ctx | cooccurence:675 |
Rv0990c hyp |
hypothetical protein | 665 | 665 ctx | cooccurence:665 |
Rv2170 |
GCN5-like N-acetyltransferase | 658 | 658 ctx | cooccurence:657 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 638 | 638 ctx | cooccurence:636 |
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): Rv3753c PF27101.1 (E=4e-57)
- (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_218270.3)
- Domains: Pfam-A via hmmscan --cut_ga — Rv3753c (PF27101.1)
- 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
2BM8T - Curated reference: UniProt O69720 (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 —
58 functional partner(s); context anchor
tadA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3753c| MQRPAADTPDGFGVAVVREEGRWRCSPMGPKALTSLRAAETELRELRSAGAVFGLLDVDDEFFVIVRPAPSGTRLLLSDATAALDYDIAAEVLDNLDAEIDPEDLEDADPFEEGDLGLLSDIGLPEAVLGVILDETDLYADEQLGRIAREMGFADQLSAVIDRLGR