yajC Family assigned · medium auto-curated
H37Rv Rv2588c · MTBC0 mtbc0_002755 ·
115 aa · 2939390–2939737 (-) ·
RefSeq NP_217104.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein secretion factor YajC |
|---|---|
| MTBC0 PGAP re-annotation | preprotein translocase subunit YajC |
| Revised (this work) | Preprotein translocase subunit YajC. Pfam: YajC (PF02699.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL75
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Sec translocon accessory complex subunit YajC |
| Curated function | The SecYEG-SecDF-YajC-YidC holo-translocon (HTL) protein secretase/insertase is a supercomplex required for protein secretion, insertion of proteins into membranes, and assembly of membrane protein complexes. While the SecYEG complex is essential for assembly of a number of proteins and complexes, the SecDF-YajC-YidC subcomplex facilitates these functions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | yajC |
| eggNOG description | Preprotein translocase |
| Orthologous group | COG1862 |
| KEGG orthology |
K03210
|
| KEGG pathways |
map02024, map03060, map03070
|
| KEGG modules |
M00335
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 0.305 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
YajC | PF02699.21 | 2.0e-18 | 6–81 | Preprotein translocase subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: secD (protein translocase subunit SecD), high confidence from genomic context alone (score 918 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0638 secE1 |
preprotein translocase SecE | 984 | 940 | coexpression:426 database:900 textmining:745 |
Rv0732 secY |
preprotein translocase SecY | 971 | 931 | database:900 textmining:601 |
Rv1440 secG |
protein-export membrane protein SecG | 979 | 922 | database:900 textmining:745 |
Rv2587c secD |
protein translocase subunit SecD | 990 | 918 ctx | neighborhood:768 coexpression:659 textmining:887 |
Rv3921c yidC |
membrane protein insertase YidC | 939 | 918 | database:900 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 977 | 916 | database:900 textmining:740 |
Rv2916c ffh |
signal recognition particle protein | 983 | 904 | database:900 textmining:838 |
Rv3240c secA1 |
protein translocase subunit SecA | 991 | 903 | database:900 textmining:921 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 984 | 903 | database:900 textmining:848 |
Rv2586c secF |
protein translocase subunit SecF | 935 | 863 ctx | neighborhood:768 coexpression:432 textmining:553 |
Rv2585c |
lipoprotein | 800 | 800 ctx | neighborhood:768 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 965 | 769 ctx | neighborhood:768 textmining:858 |
Rv2584c apt |
adenine phosphoribosyltransferase | 740 | 733 ctx | neighborhood:699 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 733 | 733 ctx | neighborhood:682 |
Rv1307 atpH |
ATP synthase subunit b/delta | 710 | 710 | coexpression:661 |
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 secretion factor YajC
- MTBC0 PGAP product: preprotein translocase subunit YajC
- Pfam (hmmscan --cut_ga): YajC PF02699.21 (E=2e-18)
- (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_217104.1)
- Domains: Pfam-A via hmmscan --cut_ga — YajC (PF02699.21)
- 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
COG1862 - Curated reference: UniProt P9WL75 (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 —
85 functional partner(s); context anchor
secD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002755|Rv2588c|yajC MESFVLFLPFLLIMGGFMYFASRRQRRAMQATIDLHDSLQPGERVHTTSGLEATIVAIADDTIDLEIAPGVVTTWMKLAIRDRILPDDDIDEELNEDLDKDVDDVAGERRVTNDS