yidD Resolved · high auto-curated
H37Rv Rv3922c · MTBC0 mtbc0_004156 ·
120 aa · 4434304–4434666 (-) ·
RefSeq NP_218439.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein insertion efficiency factor |
|---|---|
| MTBC0 PGAP re-annotation | membrane protein insertion efficiency factor YidD |
| Revised (this work) | Membrane protein insertion efficiency factor YidD. Pfam: YidD (PF01809.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFL9
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative membrane protein insertion efficiency factor |
| Curated function | Could be involved in insertion of integral membrane proteins into the membrane. |
UniProt still lists this protein as Putative membrane protein insertion efficiency factor; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | ytjA |
| eggNOG description | Could be involved in insertion of integral membrane proteins into the membrane |
| Orthologous group | COG0759 |
| KEGG orthology |
K08998
|
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 | 0.663 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
YidD | PF01809.24 | 5.1e-28 | 22–86 | Putative membrane protein insertion efficiency factor |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rnpA (ribonuclease P protein component), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3923c rnpA |
ribonuclease P protein component | 999 | 996 ctx | neighborhood:881 coexpression:968 textmining:885 |
Rv3921c yidC |
membrane protein insertase YidC | 998 | 988 ctx | neighborhood:881 coexpression:881 textmining:845 |
Rv3920c hyp |
hypothetical protein | 955 | 955 ctx | neighborhood:792 coexpression:794 |
Rv3924c rpmH |
50S ribosomal protein L34 | 966 | 876 ctx | neighborhood:816 textmining:739 |
Rv1297 rho |
transcription termination factor Rho | 857 | 857 | coexpression:825 |
Rv0704 rplB |
50S ribosomal protein L2 | 782 | 783 | coexpression:783 |
Rv0702 rplD |
50S ribosomal protein L4 | 774 | 774 | coexpression:774 |
Rv0638 secE1 |
preprotein translocase SecE | 746 | 746 | coexpression:746 |
Rv3834c serS |
serine--tRNA ligase | 728 | 728 | coexpression:719 |
Rv3918c parA |
chromosome partitioning protein ParA | 697 | 697 ctx | neighborhood:688 |
Rv2966c rsmD |
methyltransferase | 700 | 695 | coexpression:685 |
Rv3917c parB |
chromosome partitioning protein ParB | 662 | 663 ctx | neighborhood:642 |
Rv0684 fusA1 |
elongation factor G | 617 | 617 | coexpression:615 |
Rv3919c gid |
16S rRNA (guanine(527)-N(7))-methyltransferase RsmG | 605 | 606 ctx | neighborhood:501 |
Rv0979A rpmF |
50S ribosomal protein L32 | 557 | 537 | coexpression:537 |
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 insertion efficiency factor
- MTBC0 PGAP product: membrane protein insertion efficiency factor YidD
- Pfam (hmmscan --cut_ga): YidD PF01809.24 (E=5e-28)
- (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_218439.1)
- Domains: Pfam-A via hmmscan --cut_ga — YidD (PF01809.24)
- 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
COG0759 - Curated reference: UniProt P9WFL9 (SwissProt, reviewed; Inferred from homology)
- 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
rnpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004156|Rv3922c|yidD MSLSRQSCGRVVRVTGRASARGLIFVIQVYRHMLSPLRPASCRFVPTCSQYAVDALTEYGLLRGSWLTMIRLAKCGPWHRGGWDPIPEGLTTGRSCQTDVDGANDDWNPASKRGERESFV