Rv2680 Still unknown · low

Annotation: from legacy to revised

Curation note: P16.24 (2026-08-17): le catalogue Ribo-RET de Smith et al. 2022 (classe "Isoform", traductome H37Rv en culture standard log-phase) place un site de demarrage a 2996003 au lieu du start annote 2996105 (delta -102 nt = 34 codon(s) en amont), MEME stop codon (2996737) donc MEME cadre de lecture -- candidat de mauvais START annote, PAS un changement de fonction (verdict dark maintenu). Aucune densite ribosomique ni peptide MS chiffres pour cette classe dans le supplement (colonnes vides pour "Isoform", contrairement a "Novel"): preuve = appel de pic Ribo-RET seul, non hierarchisable. Ribo-RET ne couvre qu'une condition de croissance : ceci ne dit rien sur les autres dark sans signal ici. Source: Smith C, Canestrari JG, Wang AJ et al., "Pervasive translation in Mycobacterium tuberculosis", eLife 2022;11:e73980 (doi:10.7554/eLife.73980; PMC9094748), Supplementary File 1A, classe "Isoform". P16.23 (phase135, 2026-08-17): couche tss ajoutee (leaderless=False). P49.1 (phase233, 2026-09-15): couche tss re-clee (leaderless=False).

In the literature (TB corpus sweep) variant mention only

1 TB publication mentions this gene. Appears in the TB literature ONLY as a variant in a genomic / drug-resistance screen (GWAS of second-line injectable drug resistance); no functional content — do not over-interpret. reformulation, not a quotation

An antigen status or a virulence phenotype is NOT a molecular function: the verdict stays unchanged. This layer adds the missing context, it does not requalify the gene. This distinguishes a gene that is dark because nobody has looked from one that is dark despite having been studied. Source: PubMed (whole), MULTI-ALIAS sweep of title+abstract: the H37Rv locus tag AND every ortholog identifier (M. bovis Mb…, M. marinum MMAR_…, M. smegmatis MSMEG_…, M. leprae ML…, M. abscessus MAB_…), each hit VERIFIED against the abstract text (word-boundary regex). phase73, 2026-07-13.

Intrinsic disorder (sequence + structure) partially disordered

carries a substantial disordered region (33/210 residues); disorder is a property, not a function

A property (biophysics), not a function. No LLPS/condensate claim is made from disorder alone. Verdict unchanged. Source: metapredict v3 (Emenecker/Holehouse) per-residue disorder + AlphaFold mean pLDDT (annotation_mtbc P16.13).

Phenotype-driven functional lead (hypothesis) priority 7.0

disruption confers tolerance to Ethambutol; required for fitness in vivo (virulence / persistence factor).

This locus is a "hypothetical" with a conditional Tn-seq phenotype. The statement above is a working hypothesis for its functional context, synthesised from the phenotype pattern and the corroborating layers on this page (conservation, STRING coupling, operon, regulon, localisation, structure) — a prioritised requalification candidate to validate, not an established function.

Integrative functional lead (multi-layer synthesis, hypothesis) 1 convergent handles

candidate accessory/associated component of the RNA-metabolism operon Rv2680-Rv2681 (rnd / RNase D), to validate — no nuclease activity of its own

Synthesised across all evidence layers (conservation, operon, STRING, regulon, phenotype, localisation, structure, vulnerability) under an anti-oversell decision checklist. A functional hypothesis to validate, not an established function. integrative multi-layer synthesis (P8), 2026-07-05.

Binding-pocket screen (P2Rank, geometric prediction) no confident pocket

Read with care. This protein (210 aa) is above the size where the detector reliably differentiates proven enzymes (60.5% confident-pocket rate) from proteins annotated as non-catalytic (18.9%, i.e. 81.1% specificity; P16.3b calibration). Both rates are measured at the threshold this layer applies, best_probability >= 0.70, which is the best separation the detector reaches on that panel (Youden J = 0.416): even at its optimum it misses 39.5% of proven enzymes. No candidate pocket at all was detected, which is consistent with a non-catalytic role, though it does not rule out a shallow or non-canonical binding site that this geometric detector misses. (Individual read at this confidence level; the GROUP-level dark-vs-non-catalytic contrast is NOT statistically significant at this size, p=0.285 -- read as modest evidence, not proof, cf. P16.3c.) P16.3e, calibration phase72b_pocket_calibration.py, 2026-08-03.

Conditional expression context (iModulons)

Member of 1 independently-modulated gene set(s): Rv1828/SigH (Rv1828 or sigH).

iModulon membership (independently-modulated gene sets from a 647-sample RNA-seq compendium): the conditional co-expression context. Co-expression is a regulatory context, NOT a molecular function. Source: iModulonDB / modulome_mtb (Yoo 2022).

Transcriptional start site (informative, coordinates unchanged)

Primary TSS at position 2996002 (+ strand), 154 bp 5'UTR. TSS-derived candidate start codon: 2996156 -- candidate only, not applied to this record's coordinates.

Genome-wide 5'-triphosphate-enriched RNA-seq TSS mapping (Cortes et al. 2013): informative context on transcript architecture only. reannotated_start_candidate is the authors' TSS-derived candidate start codon -- reported for information, NEVER applied to this atlas's start_mtbc0/end_mtbc0 coordinates (P19 MTBC0<->H37Rv anchoring). Row re-keyed to this locus by matching its genomic boundary against the H37Rv GFF3 (P49.1 (phase233, 2026-09-15), P49): the original ingestion (P16.23/phase135, 2026-08-17) trusted the source table's own gene-identity column, which was desynchronised from its own numeric columns on 547/651 checkable rows -- see P49 for the full diagnostic. A missing primary_tss here means this gene falls outside the 680-gene re-annotation-candidate subset the source table covers, not an absence of transcription. Source: Cortes et al. 2013 (Cell Reports), Table S3 (TSS mapping and re-annotation of start codons), 680-gene re-annotation-candidate subset of >4,000 genome-wide TSS -- row re-keyed to this locus by coordinate match (P49).

CRISPRi vulnerability

Vulnerability index -0.59 (95% CI -3.66 to 3.54). 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=0.249 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=6 is descriptive only and does not predict this. Do not cite this VI as a standalone vulnerability claim.

Legacy record & comparison (Mycobrowser)

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.

Orthologues (reciprocal best hits across mycobacteria)

Reciprocal-best-hit orthologues (DIAMOND) against the Mycobrowser reference proteomes. A missing species is informative: e.g. a gene absent from M. leprae was likely lost in its reductive genome evolution. Locus tags link to Mycobrowser.

Curated reference (UniProt)

As checked on 2026-09-23, UniProt listed this protein as Conserved protein; the revised annotation above goes beyond that record. UniProt may have been recurated since: check the live entry.

Functional vocabulary (eggNOG-mapper, orthology transfer)

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 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.

Outgroup conservation (beyond the MTBC) Actinomycetia

Two orthogonal outgroup signals. M. canettii (the immediate outgroup) gives a deep-divergence dN/dS (a low value confirms a constrained, real gene; shown as confident only at ≥8 substitutions, else flagged low-power). Genus-wide presence/absence (tblastn vs assembled non-MTBC genomes) places the gene on the ancient-core ↔ MTBC-specific axis: a gene absent even from the closest MTBAP relatives is a candidate MTBC-specific innovation (possible host-adaptation factor, to confirm by synteny). The phylostratum extends that axis outside the genus (tblastn vs 13 reference genomes spanning Mycobacteriaceae → Corynebacteriales → Actinomycetia → outside the phylum): it is the deepest clade in which a homolog is still detected, i.e. a proxy for gene age. Read it with the null model in mind: a shallow (young) stratum can also reflect homology-detection failure for short or fast-evolving ORFs, so it is a descriptive axis, not a proof of novelty.

Essentiality (transposon mutagenesis)

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.

Mutant phenotypes (conditional Tn-seq, MtbTnDB) in-vivo phenotype

Conditional fitness of transposon-disruption mutants across 5 significant condition(s) (|log2FC|≥1, q≤0.05), from the standardized MtbTnDB compendium. A negative log2FC means the mutant is depleted — the gene contributes to fitness in that condition. An in-vivo defect for a "hypothetical" is strong evidence it matters for infection, even without a known molecular function. Disruption (Tn insertion), not a clean deletion; genetic-interaction screens excluded.

Provenance note on a condition above. MtbTnDB labels this condition in vivo (Collaborative Cross mouse panel) and attributes it to Smith et al. 2022, eLife 74419. Both are wrong and for the same reason: its left arm, `mbio_H37Rv`, is the saturated H37Rv reference of DeJesus et al. 2017 (mBio 8(1):e02133-16, fourteen independent Tn libraries grown in standard medium), not a mouse strain, and the upstream generator read the token before `_vs_` as a mouse-strain name. The same sample is the in vitro control of six knockout screens in the same file. Measured here on rank correlation over 3971 genes: this condition tracks the other 81 first-order in vivo conditions at rho = +0.03, where those conditions track each other at +0.270 -- it does not behave like an infection measurement. What the comparison actually is could not be established, so it is reported as undetermined rather than renamed, and it is excluded from the in vivo count of this fiche.

Proteomics (mass spectrometry) detected

Detection by mass spectrometry is direct, experimental evidence that the protein product exists — orthogonal to sequence conservation and to Tn-seq essentiality, and especially decisive for a "hypothetical" locus. Read the dataset count as abundance, not as replication. Measured across this atlas (3,491 detected proteins), the number of datasets a protein appears in tracks its abundance almost monotonically: median 1.2 ppm at 1 dataset of 16, 27 ppm at 10, 392 ppm at 15, 1,325 ppm at 16 — three orders of magnitude. A high count therefore says the protein is abundant more than it says several independent experiments confirmed it. What the count does establish, at any value, is that the product exists.

Predicted localisation (DeepTMHMM + lipobox) no export signal, no TM helix

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)

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)

HHpred profile-profile (no confident hit): No confident hit, single trivial hit, pure noise. Consistent with this gene's already-documented zero-handle status (P8.6/P16.3j). Remains dark. top hits 3KFW_X structural-genomics unknown-function protein (19.2%, E=130). Remote homology search on the deep UniRef30 profile (MPI Toolkit), run for the residual dark set.

3D structure (interactive — Mol*/pdbe-molstar)

No experimental structure is deposited for this gene: showing the AlphaFold DB predicted model (mean pLDDT 86.3, confident), coloured by per-residue confidence (dark blue = very high, orange/red = low — treat low-confidence regions as unreliable, especially termini and loops). Drag to rotate, scroll to zoom.

Structural neighbours (Foldseek on the ESMFold model, exploratory)

ESMFold model confidence: mean pLDDT 88.0 (confident). A confident model makes the fold comparison meaningful.

Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.

Genomic context (neighbours & predicted operon) operon of 2

Neighbours from the H37Rv annotation (+ strand). The operon is predicted by co-directional intergenic distance (same strand, gaps ≤50 bp) — a transcription-unit hypothesis, not a mapped TSS. For a "hypothetical", co-transcription with a characterised operon is a concrete functional lead (complements the STRING neighborhood channel below).

Published operon evidence (two independent sources)

Two independent published operon maps, cited alongside the distance heuristic above: an association corroborating or contradicting the heuristic, never proof of shared function. REMap's RNA-seq coverage continuity is the most direct of the three signals; Roback's logistic regression and the intergenic-distance heuristic are statistical proxies.

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.

Closest characterised functional partner: Rv2681 (hypothetical protein), high confidence (score 975, all STRING channels except text-mining; the partner is chosen on its genomic-context evidence). Read this as a lead toward a shared pathway or operon, not as evidence of a physical complex: when this atlas co-folded 98 such context-only pairs, their predicted interfaces were no more confident than those of length-matched control pairs.

Showing the 15 strongest of this gene's 53 partners at medium confidence (9 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 53 partners rests on an interaction measured in M. tuberculosis itself.

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.

Partners predicted by a published screen (co-evolution + structure, prediction) predicted, not measured

Contact predicted by a published co-evolution and structure screen; this is a prediction, not a measured interaction; the authors validated 6 of the 12 predictions they tested experimentally (cases they chose), which is a ceiling on precision, not a floor.

Source: Humphreys et al. 2024, Nat Microbiol, DOI 10.1038/s41564-024-01791-x (PMID 39294458), Supplementary Data 1 (final table of 3613 high-confidence pairs) and the ModelArchive deposit 10.5452/ma-bak-evip; read on 2026-10-10. The authors validated experimentally 6 of the 12 predictions they tested (cases chosen by the authors): that rate is a ceiling for this channel, not a floor. The screen score is the screen's own confidence for the pair; no interface score is shown because none is calibrated for this atlas. A predicted partner orients a hypothesis and does not assign a function; it does not change the verdict of this gene or the partner chosen by the STRING section.

Evidence

• Legacy H37Rv annotation: hypothetical protein
• MTBC0 PGAP product: DUF3000 domain-containing protein
• Pfam (hmmscan --cut_ga): DUF3000 PF11452.14 (E=4e-72)
• Foldseek best: 8any-assembly1_f Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-s (prob 0.44, E=7e-02, TM=0.39)
• (initial automatic assignment: auto-curated by rules from PGAP + Pfam + Foldseek; superseded by hand review)
• Ribo-RET (Smith 2022, classe Isoform): site de demarrage alternatif a 2996003 vs start annote 2996105 (delta -102 nt, meme cadre, meme stop 2996737) -- candidat de mauvais START annote

Ancestral MTBC0 protein sequence

>mtbc0_002854|Rv2680|
MTSAGDDAERSDEEERRLTSAEPALFREAVAAMNAVTVRPEIELGPIRPPQRLAPYSYALGAEIKHPELDVIPERSEGDAFGRLIMLYDPDGSDAWDGTIRLVAYVQADLDSSEAVDPLLPEVAWSWLVDALTARTDQVRALGGTVTATTSVRYGDISGPPRAHQLELRASWTATTPDLGAHVQAFCDVLEHAAGLPPAGVTDLGSRSRA