Rv0500B Family assigned · low auto-curated · to review
H37Rv Rv0500B · MTBC0 ·
33 aa ·
591475–591576 H37Rv
(+) ·
RefSeq
Genomic neighbourhood (genome browser)
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Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Conserved hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Component of the small ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Binds rRNA |
| Functional category (TubercuList) | conserved hypotheticals |
Curation note: Added P16.5d: Mycobrowser-annotated gene absent from RefSeq NC_000962.3 (the atlas' original 3906-CDS reference). Foundation record from the Mycobrowser release + translated H37Rv sequence; heavy enrichment layers (structure, orthology, conservation, interaction) pending.
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
In the literature (TB corpus sweep)
This distinguishes a gene that is dark because nobody has looked from one that is dark despite having been studied. Source: .
CRISPRi vulnerability
Vulnerability index -5.88 (95% CI -20.70 to 11.07). A more negative index = more vulnerable to knockdown (better drug-target quality); indicative threshold VI ≤ -6 = highly vulnerable.
Quantitative CRISPRi knockdown, graded (finer than binary Tn-seq essentiality). Source: CRISPRi vulnerability index (Bosch 2021, supplementary Table S2 'mmc3.xlsx', bulk import via Europe PMC -- supersedes the per-gene pebble.rockefeller.edu scrape of phase46_crispri_vulnerability.py).
Caveat on this estimate. Bosch et al. flag this gene's vulnerability estimate as NOT certain, and here that call has a mechanical cause visible in the library itself: every guide targeting this gene is >=21 nt (str_span=0.000 on a 0-1 scale, near the genome floor), and guide repression strength saturates from 21 nt on -- so the library never sampled a partial knockdown for this gene, only the near-maximal repression plateau. The dose-response fit (and this VI) is therefore essentially unconstrained by data, not merely uncertain -- a limitation of the CRISPRi library design for the non-essential class (Bosch et al. 2021), not a defect in this specific measurement. n_guides=1 is descriptive only and does not predict this. Do not cite this VI as a standalone vulnerability claim.
Legacy record & comparison (Mycobrowser)
| Mycobrowser function | Function unknown |
|---|
The legacy Mycobrowser record is shown for verification. Mycobrowser is no longer maintained; its EC numbers predate recent nomenclature revisions, so a class change usually reflects re-numbering, not a conflict.
Curated reference (UniProt)
| UniProt |
P9WKT5
SwissProt · reviewed
|
|---|---|
| UniProt name | Small ribosomal subunit protein bS22 |
| Curated function | Component of the small ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Binds rRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Mitochondrial domain of unknown function (DUF1713) |
| Orthologous group | 2DEN5 |
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, 142 601 strains, snapshot of 2026-09-29)
| pN/pS | 0.325 · quasi-invariant (2 sites), pN/pS underpowered |
|---|---|
| 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.
Essentiality (transposon mutagenesis)
| DeJesus 2017 call | NE · non-essential |
|---|---|
| What the call means | non-essential |
| TA sites (Himar1) |
2 in the ORF —
0 in the essential state,
0 growth-defect,
2 non-essential,
0 growth-advantage.
Saturation 1.000,
mean read count 134.5.
A region of the protein devoid of TA sites is invisible to this assay: nothing can be
inferred about it, in either direction.
All 2 sites lie in this ORF alone (no overlapping CDS shares any), so the call is attributable to this gene. |
| Caveat | Statistically thin call: only 2 TA (Himar1) sites in the whole ORF (atlas median 13; genes under 300 nt typically have very few). A DeJesus 2017 call built on so few independent observations is less robust than the same call on a longer gene, in either direction. Cross-check against the CRISPRi vulnerability index (independent of TA-site density) and, if this gene overlaps a neighbour (see Genomic-neighbour overlap section below), verify how many of its TA sites actually fall inside its own ORF. (P20.3) |
Genome-wide Himar1 transposon essentiality in H37Rv (DeJesus 2017). An essential call (ES/ESD/GD) is strong, independent evidence that a "hypothetical" locus encodes a functional, selectively required gene — orthogonal to intra-species conservation.
Proteomics (mass spectrometry) not detected
Not detected in the mass-spectrometry datasets integrated by PaxDb. This is not evidence of absence, and this atlas can say which bias dominates, because it measured it on its own 482 undetected proteins. Size is the main factor: undetected proteins have a median length of 145 aa against 295 aa for detected ones, and 25.3 % of them are shorter than 100 aa against 6.0 %. Predicted localisation matters far less than usually assumed: detection rates are 89.3 % for globular, 84.9 % for transmembrane, 88.0 % for lipoproteins and 77.8 % for signal-peptide proteins — so a short protein is under-sampled whatever its predicted compartment, and hydrophobicity alone is a weak excuse. Condition-specific expression and few tryptic peptides (PE/PPE repeats) add to this.
Predicted localisation (DeepTMHMM + lipobox) no export signal, no TM helix
| Prediction | no signal peptide, no TM helix (DeepTMHMM class GLOB) |
|---|---|
| DeepTMHMM class | GLOB |
A verified absence of signals, which is not a compartment. No Sec/Tat signal peptide, no transmembrane helix and no lipobox were found on this sequence. The predictor reports topology and export signals; it does not measure where the protein ends up, so this page draws no cytoplasmic conclusion from it. In M. tuberculosis that reservation is not theoretical: the 12 Esx paralogues of this atlas — EsxA/ESAT-6 and EsxB/CFP-10 among them, the best-established secreted proteins of the species — carry this very call, because substrates of the type VII (ESX) secretion system leave no recognisable signal. « Secreted » and « no signal peptide » are true together here.
Transmembrane topology and signal peptide from DeepTMHMM (deep-learning reference predictor); lipoproteins from a (myco)bacterial lipobox motif. A sequence-based prediction of subcellular context.
Physico-chemical properties (computed, ProtParam)
| Length | 33 aa |
|---|---|
| Molecular weight | 4.1 kDa |
| Theoretical pI | 12.0 |
| GRAVY | -1.736 (hydrophilic) |
| Aliphatic index | 64.8 |
| Aromaticity | 0.0 |
| Instability index | 90.4 (unstable) |
Computed from the ancestral MTBC0 sequence with the ExPASy ProtParam method (Biopython). Descriptive biophysical context: a positive GRAVY flags a hydrophobic (often membrane) protein, a high instability index (>40) predicts a short in-vitro half-life, an extreme pI hints at compartment or binding partner.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
COX24_C | PF08213 | n/a | – | COX24_C |
3D structure (interactive — Mol*/pdbe-molstar)
Experimental structure 5v93 (PDBe), the strongest available structural
evidence for this gene. Drag to rotate, scroll to zoom; hetero-groups (ligands, ions, waters hidden by default)
shown as sticks.
Experimental structures (Protein Data Bank) 1 solved
| PDB | Method | Resolution | Coverage |
|---|---|---|---|
5v93 |
Electron Microscopy | 4.0 Å | 100% |
Experimentally solved structures mapped from the UniProt accession via PDBe/SIFTS (1 total; up to 8 shown, ranked by sequence coverage then resolution). An experimental structure is direct proof of the folded product and the strongest structural evidence — superseding the predicted ESMFold/AlphaFold models below for any covered region.
Functional interaction network (STRING v12, guilt-by-association)
Explore full network →Node colour = verdict, dashed = still uncharacterised; edge colour = evidence (green experimental, orange genomic-context, grey co-expression), width ∝ score. Click a partner to open its page; "Explore full network" to walk the graph.
Showing the 15 strongest of this gene's 66 partners at medium confidence (61 at high confidence). The table is an extract, not a neighbourhood: across the proteome the real median degree is 34 while the served median is 15, so no hub, degree distribution or centrality may be read on this table. None of the 66 partners rests on an interaction measured in M. tuberculosis itself.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0683 rpsG exp (transferred) |
30S ribosomal protein S7 | 999 | 999 | experimental:999 |
Rv2890c rpsB exp (transferred) |
30S ribosomal protein S2 | 999 | 999 | experimental:999 |
Rv3458c rpsD exp (transferred) |
30S ribosomal protein S4 | 999 | 999 | experimental:999 |
Rv0703 rplW exp (transferred) |
50S ribosomal protein L23 | 999 | 999 | experimental:999 |
Rv0708 rplP exp (transferred) |
50S ribosomal protein L16 | 999 | 999 | experimental:999 |
Rv0640 rplK exp (transferred) |
50S ribosomal protein L11 | 999 | 999 | experimental:999 |
Rv0705 rpsS exp (transferred) |
30S ribosomal protein S19 | 999 | 999 | experimental:999 |
Rv0053 rpsF exp (transferred) |
30S ribosomal protein S6 | 999 | 999 | experimental:999 |
Rv0718 rpsH exp (transferred) |
30S ribosomal protein S8 | 999 | 999 | experimental:999 |
Rv3924c rpmH exp (transferred) |
50S ribosomal protein L34 | 999 | 999 | experimental:999 |
Rv2904c rplS exp (transferred) |
50S ribosomal protein L19 | 999 | 999 | experimental:999 |
Rv0704 rplB exp (transferred) |
50S ribosomal protein L2 | 999 | 999 | experimental:999 |
Rv0055 rpsR1 exp (transferred) |
30S ribosomal protein S18 | 999 | 999 | experimental:999 |
Rv0709 rpmC exp (transferred) |
50S ribosomal protein L29 | 999 | 999 | experimental:999 |
Rv0721 rpsE exp (transferred) |
30S ribosomal protein S5 | 999 | 999 | experimental:999 |
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.
Where the experimental evidence comes from, and why it matters here. STRING's experimental channel fuses interactions measured in M. tuberculosis with interactions measured in another organism and transferred to this pair by orthology. The two are not equivalent for this atlas, whose standing rule is that better studied elsewhere is not a function established in M. tuberculosis. Measured on the served network: of the 38 229 partner pairs shown across the atlas, 13 483 partner rows carry a non-zero experimental channel, and only 106 pairs rest on an interaction measured in M. tuberculosis itself — 0.3 % of the network. Those 106 are long-established complexes (ESX-1/ESAT-6, RNA polymerase with CarD and RbpA, the Pup–Mpa proteasome, gyrase, Emb, GarA with PknB and PknG, the Rel modules); no still-uncharacterised gene is among them. The reason is not a gap in this atlas but in the literature: there is almost no experimental interactome of this bacterium, IntAct holding 134 curated protein pairs for a ~4 000-gene proteome. A exp (transferred) badge is therefore a lead, never a measurement, and an absence of badge is not evidence that the pair does not interact.
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 )
- Domains: Pfam-A via hmmscan --cut_ga — COX24_C (PF08213)
- 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
2DEN5 - Curated reference: UniProt P9WKT5 (SwissProt, reviewed)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 142 601 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Genome-wide structure: AlphaFold DB model (Jumper et al. 2021, doi:10.1038/s41586-021-03819-2; Varadi et al. 2024, doi:10.1093/nar/gkad1011) searched vs PDB with Foldseek (mean pLDDT 92.0)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 66 functional partner(s)
- Essentiality: genome-wide transposon mutagenesis in H37Rv — DeJesus et al. 2017 (mBio, doi:10.1128/mBio.02133-16, CC BY)
- Functional category: TubercuList scheme (Cole et al. 1998, doi:10.1038/31159), via Mycobrowser (Kapopoulou et al. 2011, doi:10.1016/j.tube.2010.09.006)
- Experimental structures: PDBe/SIFTS UniProt→PDB mapping (Dana et al. 2019, doi:10.1093/nar/gky1114)
- Physico-chemical properties: ExPASy ProtParam method via Biopython (Gasteiger et al. 2005), computed from the MTBC0 sequence
- Predicted localisation: DeepTMHMM (Hallgren et al. 2022, doi:10.1101/2022.04.08.487609) for transmembrane topology and signal peptide
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>|Rv0500B|Rv0500B MGSVIKKRRKRMSKKKHRKLLRRTRVQRRKLGK
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