cfp6 Resolved · high auto-curated
H37Rv Rv3004 · MTBC0 - ·
112 aa · 3363348–3363686 (+) ·
RefSeq NP_217520.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | low molecular weight protein antigen 6 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Low molecular weight protein antigen 6. Pfam: bPH_6 (PF10756.16). |
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 |
P9WIR1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Low molecular weight protein antigen 6 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | cfp6 |
| eggNOG description | Bacterial PH domain |
| Orthologous group | 2EKMU |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 1.22 · diversifying/relaxed |
|---|---|
| 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 |
|---|---|---|---|---|
bPH_6 | PF10756.16 | 1.6e-20 | 39–109 | Bacterial PH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2520c (membrane protein), high confidence from genomic context alone (score 765 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2520c |
membrane protein | 765 | 765 ctx | cooccurence:764 |
Rv1109c hyp |
hypothetical protein | 763 | 763 ctx | cooccurence:761 |
Rv3311 hyp |
hypothetical protein | 760 | 761 ctx | cooccurence:759 |
Rv3212 hyp |
hypothetical protein | 759 | 760 ctx | cooccurence:759 |
Rv1222 rseA |
anti-sigma E factor RseA | 753 | 754 ctx | cooccurence:751 |
Rv0556 |
transmembrane protein | 749 | 750 ctx | cooccurence:749 |
Rv2980 hyp |
hypothetical protein | 740 | 740 ctx | cooccurence:740 |
Rv0010c |
membrane protein | 740 | 740 ctx | cooccurence:737 |
Rv1209 hyp |
hypothetical protein | 737 | 738 ctx | cooccurence:735 |
Rv2138 lppL |
lipoprotein LppL | 736 | 736 ctx | cooccurence:736 |
Rv3850 hyp |
hypothetical protein | 719 | 719 ctx | cooccurence:719 |
Rv2446c |
integral membrane protein | 715 | 716 ctx | cooccurence:713 |
Rv3839 hyp |
hypothetical protein | 712 | 712 ctx | cooccurence:712 |
Rv0358 hyp |
hypothetical protein | 711 | 712 ctx | cooccurence:711 |
Rv2091c |
membrane protein | 709 | 710 ctx | cooccurence:709 |
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): low molecular weight protein antigen 6
- Pfam (hmmscan --cut_ga): bPH_6 PF10756.16 (E=2e-20)
- (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_217520.1)
- Domains: Pfam-A via hmmscan --cut_ga — bPH_6 (PF10756.16)
- 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
2EKMU - Curated reference: UniProt P9WIR1 (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 —
95 functional partner(s); context anchor
Rv2520c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3004|cfp6 MAHFAVGFLTLGLLVPVLTWPVSAPLLVIPVALSASIIRLRTLADERGVTVRTLVGSRAVRWDDIDGLRFHRGSWARATLKDGTELRLPAVTFATLPHLTEASSGRVPNPYR