yhjD Resolved · high auto-curated
H37Rv Rv3335c · MTBC0 mtbc0_003548 ·
289 aa · 3747716–3748585 (-) ·
RefSeq NP_217852.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | inner membrane protein YhjD |
| Revised (this work) | Inner membrane protein YhjD. Pfam: Virul_fac_BrkB (PF03631.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53385
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | yhjD |
| eggNOG description | PFAM ribonuclease |
| Orthologous group | COG1295 |
| KEGG orthology |
K07058
|
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 | 0.455 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 |
|---|---|---|---|---|
Virul_fac_BrkB | PF03631.21 | 2.8e-41 | 32–287 | Virulence factor BrkB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpS (tryptophan--tRNA ligase), high confidence from genomic context alone (score 861 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3336c trpS |
tryptophan--tRNA ligase | 861 | 861 ctx | neighborhood:857 |
Rv3013 hyp |
hypothetical protein | 670 | 670 ctx | cooccurence:574 |
Rv3337 |
Rv3337, (MTV016.37), len: 128 aa. Conserved hypothetical protein, equivalent to N-terminus of Q49926|ML0685 TPEA (putative hydrolase) from M | 587 | 586 ctx | neighborhood:585 |
Rv3338 |
Rv3338, (MTV016.38), len: 214 aa. Hypothetical protein, equivalent to C-termini of Q49926|ML0685 TPEA (putative hydrolase) from Mycobacteriu | 587 | 586 ctx | neighborhood:585 |
Rv3753c hyp |
hypothetical protein | 548 | 548 ctx | cooccurence:548 |
Rv2446c |
integral membrane protein | 500 | 500 ctx | cooccurence:493 |
Rv1332 |
transcriptional regulator | 497 | 497 ctx | cooccurence:492 |
Rv1224 tatB |
Sec-independent protein translocase protein TatB | 509 | 490 ctx | cooccurence:415 |
Rv1109c hyp |
hypothetical protein | 478 | 479 ctx | cooccurence:477 |
Rv2712c hyp |
hypothetical protein | 450 | 451 ctx | cooccurence:449 |
Rv1607 chaA |
ionic transporter integral membrane protein ChaA | 446 | 447 | coexpression:429 |
Rv0556 |
transmembrane protein | 441 | 441 ctx | cooccurence:428 |
Rv3205c hyp |
hypothetical protein | 427 | 428 ctx | cooccurence:421 |
Rv2289 cdh |
CDP-diacylglycerol pyrophosphatase | 426 | 427 ctx | cooccurence:426 |
Rv3092c |
integral membrane protein | 425 | 425 | coexpression:425 |
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: integral membrane protein
- MTBC0 PGAP product: inner membrane protein YhjD
- Pfam (hmmscan --cut_ga): Virul_fac_BrkB PF03631.21 (E=3e-41)
- (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_217852.1)
- Domains: Pfam-A via hmmscan --cut_ga — Virul_fac_BrkB (PF03631.21)
- 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
COG1295 - Curated reference: UniProt O53385 (TrEMBL, unreviewed; Predicted)
- 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 —
28 functional partner(s); context anchor
trpS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003548|Rv3335c|yhjD MGELAEPGVLDRLRARFGWLDHVVRAFTRFNDRNGSLFAAGLTYYTIFAIFPLLMVGFGVGGFALSRRPELLTTLEERIRTSVSGAVGQQLVDLMNSAIDARASVGVIGLATAAWVGLGWMWHLREALSQMWAHPVAPAGYLRTKLSDLAAMVGTFVVIVATIALTVLGHARPMAAVLRWLEIPQFSVFDEIFRGISVLVSVLVSWVLFTWMIGRLPREPVGLVTAARAGLMAAVGFELFKQVGAIYLQIVLRSPAGAVFGPVLGLMVFAFVTAWLILFATAWAATASA