arfC Family assigned · medium auto-curated
H37Rv Rv0901 · MTBC0 mtbc0_000955 ·
175 aa · 1007171–1007698 (+) ·
RefSeq NP_215416.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains ArfC (PF27542.1) 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.
Curated reference (UniProt)
| UniProt |
P9WJG5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized membrane protein ArfC |
| Curated function | Required for wild-type expression of ArfA and ammonia secretion, not however part of an ammonia transporter. Is highly immunogenic and may play a role in virulence. |
UniProt still lists this protein as Uncharacterized membrane protein ArfC; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DDPV |
|---|---|
| KEGG orthology |
K16193
|
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 | 0.698 · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
ArfC | PF27542.1 | 5.8e-25 | 107–167 | ArfC |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arfA (peptidoglycan-binding protein ArfA), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0899 arfA |
peptidoglycan-binding protein ArfA | 986 | 905 ctx | neighborhood:869 textmining:861 |
Rv0900 arfB |
membrane protein | 984 | 885 ctx | neighborhood:882 textmining:870 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 654 | 654 ctx | cooccurence:654 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 610 | 610 ctx | cooccurence:610 |
Rv0898c hyp |
hypothetical protein | 605 | 606 ctx | neighborhood:606 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 577 | 577 ctx | cooccurence:577 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 570 | 571 ctx | cooccurence:570 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 569 | 569 ctx | cooccurence:568 |
Rv0341 iniB |
isoniazid inducible protein IniB | 561 | 561 ctx | cooccurence:561 |
Rv3737 |
transmembrane protein | 546 | 547 ctx | cooccurence:544 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 544 | 544 ctx | cooccurence:544 |
Rv1226c |
transmembrane protein | 528 | 528 ctx | cooccurence:526 |
Rv2209 |
integral membrane protein | 519 | 520 ctx | cooccurence:517 |
Rv0897c |
oxidoreductase | 519 | 519 ctx | neighborhood:514 |
Rv2608 PPE42 |
PPE family protein PPE42 | 517 | 517 ctx | cooccurence:514 |
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: membrane protein
- MTBC0 PGAP product: hypothetical protein
- Pfam (hmmscan --cut_ga): ArfC PF27542.1 (E=6e-25)
- (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_215416.1)
- Domains: Pfam-A via hmmscan --cut_ga — ArfC (PF27542.1)
- 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
2DDPV - Curated reference: UniProt P9WJG5 (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 —
41 functional partner(s); context anchor
arfA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000955|Rv0901|arfC MEHVHWWLAGLAFTLGMVLTSTLMVRPVEHQVLVKKSVRGSSAKSKPPTARKPAVKSGTKREESPTAKTKVATESAAEQIPVAGEPAAEPIPVAGEPAARIPVVPYAPYGPGSARAGADGSGPQGWLVKGRSDTRLYYTPEDPTYDPTVAQVWFQDEESAARAFFTPWRKSTRRT