yidC Resolved · high auto-curated
H37Rv Rv3921c · MTBC0 mtbc0_004155 ·
366 aa · 4433220–4434320 (-) ·
RefSeq NP_218438.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein insertase YidC |
|---|---|
| MTBC0 PGAP re-annotation | membrane protein insertase YidC |
| Revised (this work) | Membrane protein insertase YidC. Pfam: 60KD_IMP (PF02096.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIT5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Membrane protein insertase YidC |
| Curated function | Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | yidC |
| eggNOG description | Required for the insertion and or proper folding and or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins (By similarity) |
| Orthologous group | COG0706 |
| KEGG orthology |
K03217
|
| KEGG pathways |
map02024, map03060, map03070
|
| KEGG modules |
M00335
|
| Gene Ontology (14) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0040007, GO:0044425, GO:0044459 +2 more
|
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 | 0.63 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 10 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 |
|---|---|---|---|---|
60KD_IMP | PF02096.27 | 1.8e-50 | 38–277 | 60Kd inner membrane protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rnpA (ribonuclease P protein component), high confidence from genomic context alone (score 993 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3923c rnpA |
ribonuclease P protein component | 997 | 993 ctx | neighborhood:881 coexpression:947 textmining:683 |
Rv0732 secY |
preprotein translocase SecY | 996 | 989 ctx | cooccurence:426 experimental:790 database:900 textmining:670 |
Rv3922c yidD |
membrane protein insertion efficiency factor | 998 | 988 ctx | neighborhood:881 coexpression:881 textmining:845 |
Rv3920c hyp |
hypothetical protein | 987 | 986 ctx | neighborhood:792 coexpression:909 |
Rv1440 secG |
protein-export membrane protein SecG | 985 | 980 | experimental:792 database:900 |
Rv0638 secE1 |
preprotein translocase SecE | 980 | 957 | experimental:474 database:900 textmining:564 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 955 | 932 | database:900 |
Rv3240c secA1 |
protein translocase subunit SecA | 969 | 931 | database:900 textmining:570 |
Rv1297 rho |
transcription termination factor Rho | 933 | 926 | coexpression:922 |
Rv2588c yajC |
membrane protein secretion factor YajC | 939 | 918 | database:900 |
Rv2916c ffh |
signal recognition particle protein | 956 | 917 | database:900 textmining:496 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 954 | 914 | database:900 textmining:494 |
Rv2587c secD |
protein translocase subunit SecD | 957 | 902 | coexpression:488 experimental:792 textmining:585 |
Rv3924c rpmH |
50S ribosomal protein L34 | 953 | 887 ctx | neighborhood:816 coexpression:409 textmining:607 |
Rv0684 fusA1 |
elongation factor G | 881 | 874 | coexpression:807 |
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 insertase YidC
- MTBC0 PGAP product: membrane protein insertase YidC
- Pfam (hmmscan --cut_ga): 60KD_IMP PF02096.27 (E=2e-50)
- (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_218438.1)
- Domains: Pfam-A via hmmscan --cut_ga — 60KD_IMP (PF02096.27)
- 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
COG0706 - Curated reference: UniProt P9WIT5 (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 —
173 functional partner(s); context anchor
rnpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004155|Rv3921c|yidC MSLLFDFFSLDFIYYPVSWIMWVWYRLFAFVLGPSNFFAWALSVMFLVFTLRALLYKPFVRQIRTTRQMQELQPQIKALQKKYGKDRQRMALEMQKLQREHGFNPILGCLPMLAQIPVFLGLYHVLRSFNRTTGGFGQPHLSVIENRLTGNYVFSPVDVGHFLDANLFGAPIGAYMTQRSGLDAFVDFSRPALIAVGVPVMILAGIATYFNSRASIARQSAEAAANPQTAMMNKLALYVFPLGVVVGGPFLPLAIILYWFSNNIWTFGQQHYVFGMIEKEEEAKKQEAVRRRAANAPAPGAKPKRSPKTAPATNAAAPTEAGDTDDGAESDASTERPADTSNPARRNSGPSARTPRPGVRPKKRKR