Rv3311 Family assigned · low auto-curated
H37Rv Rv3311 · MTBC0 mtbc0_003519 ·
420 aa · 3720259–3721521 (+) ·
RefSeq NP_217828.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | primosomal protein |
| Revised (this work) | Primosomal 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 |
O53362
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28NCS |
|---|
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 | 0.644 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sapM (acid phosphatase), high confidence from genomic context alone (score 779 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) |
|---|---|---|---|---|
Rv3310 sapM |
acid phosphatase | 817 | 779 ctx | neighborhood:779 |
Rv1109c hyp |
hypothetical protein | 775 | 775 ctx | cooccurence:770 |
Rv3212 hyp |
hypothetical protein | 774 | 775 ctx | cooccurence:774 |
Rv3438 hyp |
hypothetical protein | 773 | 773 ctx | cooccurence:773 |
Rv2520c |
membrane protein | 773 | 773 ctx | cooccurence:772 |
Rv2446c |
integral membrane protein | 772 | 772 ctx | cooccurence:771 |
Rv0863 hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:770 |
Rv1209 hyp |
hypothetical protein | 776 | 770 ctx | cooccurence:770 |
Rv0556 |
transmembrane protein | 770 | 770 ctx | cooccurence:769 |
Rv0996 |
transmembrane protein | 765 | 765 ctx | cooccurence:763 |
Rv0358 hyp |
hypothetical protein | 763 | 763 ctx | cooccurence:762 |
Rv2170 |
GCN5-like N-acetyltransferase | 763 | 763 ctx | cooccurence:763 |
Rv3004 cfp6 |
low molecular weight protein antigen 6 | 760 | 761 ctx | cooccurence:759 |
Rv2049c hyp |
hypothetical protein | 760 | 761 ctx | cooccurence:758 |
Rv1083 hyp |
hypothetical protein | 760 | 760 ctx | cooccurence:760 |
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: primosomal protein
- (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_217828.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
28NCS - Curated reference: UniProt O53362 (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 —
111 functional partner(s); context anchor
sapM - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003519|Rv3311| MVADLVPIRLSLSAGDRYTLWAPRWRDAGDEWEAFLGKDDDLYGFESVSDLVAFVRTDTENDLVDHPAWQDLTGAHAHNLNPAEDNQFDLVVVEELLAEKPTAESVAALAASLAIVSAIGSVCELAAVSKFFNGNPILGTVSGGLEHFTGKAGNKRWNSIAEVIGRSWDDVLAAIDEIISTPEVDAELSEKVAEELAEEPEGAEEVAAEVEATQDTQEAAESDDEEADAPGDSVVLGGDRDFWLQVGIDPIQIMTGTATFYTLRCYLDDRPIFLGRNGRISVFGSERALARYLADEHDHDLSDLSTYDDIRTAATDGSLAVAVTDDNVYVLSGLVDDFADGPDAVDREQLDLAVELLRDIGDYSEDSAVDKALETTRPLGQLVAYVLDPHSVGKPTAPYAAAVREWEKLERFVESRLRRE