Rv3768 Family assigned · medium auto-curated
H37Rv Rv3768 · MTBC0 mtbc0_003992 ·
119 aa · 4238191–4238550 (+) ·
RefSeq NP_218285.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | nuclear transport factor 2 family protein |
| Revised (this work) | Nuclear transport factor 2 family protein. Pfam: SnoaL_2 (PF12680.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P72035
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | SnoaL-like domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | SnoaL-like domain |
| Orthologous group | COG4319 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
SnoaL_2 | PF12680.14 | 9.6e-13 | 18–109 | SnoaL-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2561 (Rv2561, (MTCY9C4.07c), len: 97 aa. Conserved hypothetical protein, highly similar in part (and longer 33 aa) to upstream ORF AAK46951|RV2562), medium confidence from genomic context alone (score 552 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) |
|---|---|---|---|---|
Rv3899c hyp |
hypothetical protein | 677 | 677 ctx | cooccurence:676 |
Rv1060 hyp |
hypothetical protein | 560 | 560 ctx | cooccurence:560 |
Rv2561 |
Rv2561, (MTCY9C4.07c), len: 97 aa. Conserved hypothetical protein, highly similar in part (and longer 33 aa) to upstream ORF AAK46951|RV2562 | 552 | 552 ctx | cooccurence:551 |
Rv3767c |
S-adenosylmethionine-dependent methyltransferase | 549 | 549 ctx | neighborhood:549 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 549 | 549 ctx | cooccurence:549 |
Rv3769 hyp |
hypothetical protein | 518 | 519 ctx | neighborhood:515 |
Rv1837c glcB |
malate synthase | 528 | 498 | coexpression:430 |
Rv0256c PPE2 |
PPE family protein PPE2 | 475 | 476 ctx | cooccurence:471 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 442 | 443 ctx | cooccurence:440 |
Rv2557 hyp |
hypothetical protein | 440 | 440 ctx | cooccurence:436 |
Rv2487c PE_PGRS42 |
PE-PGRS family protein PE_PGRS42 | 439 | 439 ctx | cooccurence:439 |
Rv1576c |
phage capsid protein | 433 | 434 ctx | cooccurence:432 |
Rv2423 hyp |
hypothetical protein | 425 | 425 ctx | cooccurence:417 |
Rv1057 hyp |
hypothetical protein | 406 | 406 | |
Rv2558 hyp |
hypothetical protein | 405 | 405 ctx | cooccurence:401 |
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: nuclear transport factor 2 family protein
- Pfam (hmmscan --cut_ga): SnoaL_2 PF12680.14 (E=1e-12)
- (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_218285.1)
- Domains: Pfam-A via hmmscan --cut_ga — SnoaL_2 (PF12680.14)
- 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
COG4319 - Curated reference: UniProt P72035 (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 —
20 functional partner(s); context anchor
Rv2561 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003992|Rv3768| MGSTPPRTPQEVFAHHGQALAAGDLDEIVADYADDSFVITPAGIARGKEGIRQLFVKLLDDIPNALWDLKTQIFEGDILFLEWTANSAVSRVDDGVDTFVFRDGTIWAHTVRYTPHPKT