pafC Family assigned · medium auto-curated
H37Rv Rv2095c · MTBC0 mtbc0_002229 ·
316 aa · 2381989–2382939 (-) ·
RefSeq NP_216611.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | proteasome accessory factor C |
|---|---|
| MTBC0 PGAP re-annotation | YafY family protein |
| Revised (this work) | YafY family protein. Pfam: HTH_PafC (PF19187.7), WYL (PF13280.13), WCX (PF25583.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIL9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein PafC |
| Curated function | Part of the pafABC operon, but PafC does not seem to be involved in pupylation or substrate degradation. Appears to play at least a small role in resistance to reactive nitrogen intermediates (RNI) in vitro. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | pafC |
| eggNOG description | WYL domain |
| Orthologous group | COG2378 |
| KEGG orthology |
K13573
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.494 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
HTH_PafC | PF19187.7 | 1.7e-41 | 6–119 | PafC helix-turn-helix domain |
WYL | PF13280.13 | 8.2e-18 | 140–204 | WYL domain |
WCX | PF25583.2 | 6.7e-19 | 235–307 | WCX domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pafB (proteasome accessory factor B), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2096c pafB |
proteasome accessory factor B | 999 | 997 ctx | neighborhood:882 fusion:899 cooccurence:760 textmining:907 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 928 | 897 | experimental:870 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 892 | 893 | experimental:870 |
Rv2097c pafA |
proteasome accessory factor PafA | 980 | 886 ctx | neighborhood:881 textmining:839 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 871 | 871 | experimental:870 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 877 | 870 | experimental:870 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 870 | 870 | experimental:870 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 870 | 870 | experimental:870 |
Rv2094c tatA |
Sec-independent protein translocase membrane-bound protein TatA | 807 | 797 ctx | neighborhood:796 |
Rv2092c helY |
ATP-dependent DNA helicase HelY | 735 | 735 ctx | neighborhood:722 |
Rv2099c PE21 |
Rv2099c, (MTCY49.39c), len: 58 aa. PE21, Member of the Mycobacterium tuberculosis PE family (see Brennan and Delogu, 2002); 5'-end of Rv2098 | 622 | 622 ctx | neighborhood:622 |
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 622 | 622 ctx | neighborhood:622 |
Rv2093c tatC |
Sec-independent protein translocase transmembrane protein TatC | 616 | 617 ctx | neighborhood:611 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 573 | 574 | experimental:571 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 438 | 439 ctx | cooccurence:437 |
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: proteasome accessory factor C
- MTBC0 PGAP product: YafY family protein
- Pfam (hmmscan --cut_ga): HTH_PafC PF19187.7 (E=2e-41), WYL PF13280.13 (E=8e-18), WCX PF25583.2 (E=7e-19)
- (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_216611.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_PafC (PF19187.7), WYL (PF13280.13), WCX (PF25583.2)
- 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
COG2378 - Curated reference: UniProt P9WIL9 (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 —
31 functional partner(s); context anchor
pafB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002229|Rv2095c|pafC MSALSTRLVRLLNMVPYFQANPRITRAEAAAELGVTAKQLEEDLNQLWMCGLPGYSPGDLIDFEFCGDTIEVTFSAGIDRPLKLTSPEATGLLVALRALADIPGVVDPQAARSAIAKIAAAAGAVAAVAEQAPTESPAAAAVRAAVRNSRALTIDYYAASHDTLTTRIVDPIRVLLIGGHSYLEAWSREAEGVRLFRFDRIVDAAELGEPAVPPESARQAPPDTSLFDGDLSLPSATLRVAPSASWMLEYYPIRELRQLPDGSCEVAMTYASEDWMTRLLLGFGSDVRVLAPESLAQRVRDAATAALDAYQAAAPP