Rv3472 Family assigned · medium auto-curated
H37Rv Rv3472 · MTBC0 mtbc0_003689 ·
168 aa · 3915302–3915808 (+) ·
RefSeq NP_217989.1
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_4 (PF13577.13), DUF4440 (PF14534.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YG83
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)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | SnoaL-like domain |
| Orthologous group | 2EQU1 |
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, 2 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_4 | PF13577.13 | 5.9e-26 | 12–126 | SnoaL-like domain |
DUF4440 | PF14534.13 | 2.9e-06 | 14–122 | Domain of unknown function (DUF4440) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espK (ESX-1 secretion-associated protein EspK), high confidence from genomic context alone (score 756 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) |
|---|---|---|---|---|
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 756 | 756 ctx | cooccurence:756 |
Rv0341 iniB |
isoniazid inducible protein IniB | 751 | 751 ctx | cooccurence:747 |
Rv0613c hyp |
hypothetical protein | 746 | 747 ctx | cooccurence:745 |
Rv0355c PPE8 |
PPE family protein PPE8 | 736 | 736 ctx | cooccurence:736 |
Rv3350c PPE56 |
PPE family protein PPE56 | 733 | 733 ctx | cooccurence:733 |
Rv0304c PPE5 |
PPE family protein PPE5 | 732 | 732 ctx | cooccurence:732 |
Rv3347c PPE55 |
PPE family protein PPE55 | 731 | 731 ctx | cooccurence:731 |
Rv1004c |
membrane protein | 723 | 723 ctx | cooccurence:722 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 715 | 715 ctx | cooccurence:715 |
Rv2209 |
integral membrane protein | 714 | 714 ctx | cooccurence:714 |
Rv1917c PPE34 |
PPE family protein PPE34 | 713 | 713 ctx | cooccurence:713 |
Rv3343c PPE54 |
PPE family protein PPE54 | 705 | 705 ctx | cooccurence:705 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 703 | 703 ctx | cooccurence:703 |
Rv2954c hyp |
hypothetical protein | 698 | 699 ctx | cooccurence:689 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 698 | 698 ctx | cooccurence:698 |
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_4 PF13577.13 (E=6e-26), DUF4440 PF14534.13 (E=3e-06)
- (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_217989.1)
- Domains: Pfam-A via hmmscan --cut_ga — SnoaL_4 (PF13577.13), DUF4440 (PF14534.13)
- 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
2EQU1 - Curated reference: UniProt I6YG83 (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 —
78 functional partner(s); context anchor
espK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003689|Rv3472| MRPVDEQWIEILRIQALCARYCLTIDTQDGEGWAGCFTEDGAFEFDGWVIRGRPALREYADAHARVVRGRHLTTDLLYEVDGDVATGRSASVVTLATAAGYKILGSGEYQDRLIKQDGQWRIAYRRLRNDRLVSDPSVAVNVADADVAAVVGHLLAAARRLGTQMSDT