Rv1825 Resolved · medium

Annotation: from legacy to revised

Curation note: P16.23 (phase135, 2026-08-17): couche tss ajoutee (leaderless=True). P49.1 (phase233, 2026-09-15): couche tss re-clee (leaderless=False). 2026-10-18 (P62.30): co-folding sentences restated to what the Boltz-2 jobs carry (prediction without any measured interaction, scores stable but geometry bimodal, positive control from another model, 3-sample controls). Verdict and confidence unchanged.

In the literature (TB corpus sweep) named only in full text

No publication in PubMed mentions this gene in its title or abstract — not under its H37Rv locus tag, nor under any of its ortholog identifiers (M. bovis, M. marinum, M. smegmatis, M. leprae, M. abscessus). The atlas annotation rests on sequence/structure evidence, not on a primary study of this gene.

Scope of the sweep: What was actually swept: the H37Rv locus tag and the ortholog locus tags (M. bovis Mb…, M. marinum MMAR_…, M. smegmatis MSMEG_…, M. leprae ML…, M. abscessus MAB_…), plus the gene name where one exists. NOT swept: protein and enzyme names, including family shorthands such as Ldt(Mt4) or VapC28, and their orthographic variants. An absent locus-tag mention is therefore evidence about the TAG, and only indirect evidence about the protein (P18.14). Extended on 2026-08-10 (P18.20): the UniProt protein name and its spelling variants were swept as well; the result is in `protein_name_sweep`.

A verified absence of literature is itself information: it flags an annotation with no primary study behind it. 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: 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/phase75, 2026-07-13.

Intrinsic disorder (sequence + structure) partially disordered

carries a substantial disordered region (58/292 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 8.9

disruption sensitises to Ethambutol, Vancomycin (cell-envelope / intrinsic drug tolerance); mixed in vivo signal: required in 3 of 6 significant measurements, disruption advantageous in 3 — the data supports no single direction; predicted membrane protein.

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.

CRISPRi vulnerability

Vulnerability index 1.44 (95% CI -0.74 to 4.48). 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=0.222 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=8 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 UPF0749 protein Rv1825; 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 9 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. `marP_KO_vs_marP_WT` carries no source in MtbTnDB's own metadata (col_desc.tsv leaves paper_title/paper_URL empty). Traced by the `Rv0537c` companion project (2026-09-12): Weizhen Xu, PhD thesis, Weill Cornell Medicine, 2017, hdl:1813/64728 ("Genetic Screening In Mycobacterium Tuberculosis Utilizing Transposon Insertion Sequencing"), whose abstract describes a TnSeq genetic-interaction screen naming marP. Never published as a peer-reviewed article.

Provenance note on a condition above. This gene's displayed phenotypes include both `marP_KO_vs_marP_WT` and a drug-exposure condition from Xu et al. 2017 (AAC 61(12):e01334-17). Both trace to the same experimenter (Weizhen Xu) and very likely the same transposon insertion library -- read them as ONE handle, not two independent ones, when assessing convergence for an `integrative_lead` flip.

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)

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)

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

Experimental structure 3gmg (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

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.

Structural neighbours (Foldseek on the ESMFold model, exploratory)

ESMFold model confidence: mean pLDDT 86.4 (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.

Structural search (AlphaFold DB model, Foldseek vs PDB — genome-wide) pLDDT 79.8

Foldseek search of the AlphaFold DB model (mean pLDDT 79.8, gated at 70) against the PDB — a genome-wide extension of the ESMFold dark-gene search that also covers proteins beyond the single-sequence length limit. Confident structural neighbours (E < 0.01) shown.

Genomic context (neighbours & predicted operon) operon of 5

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.

Transcriptional regulation (signed TRN: ChIP-seq + TFOE)

Regulatory edges from the ISB signed transcriptional regulatory network (TF ChIP-seq binding, Minch 2015 + TF-overexpression response, Rustad 2014). An edge is regulatory evidence (binding and/or expression change), not necessarily direct. For a "hypothetical", membership in a known regulon (e.g. DosR dormancy, PhoP virulence) is a physiological-context lead, not a function.

Condition: Condition-blind by construction. These edges come from transcription-factor OVEREXPRESSION in a single laboratory condition, so a listed regulator is not a claim that it governs this gene in every circumstance. Measured counter-examples exist within this atlas (see Rv2516c, where the DosR regulon collapses under moxifloxacin while the gene itself rises). Read a regulator as 'capable of shifting this gene', and look for the condition before building a hypothesis on it.

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: Rv1824 (hypothetical protein), high confidence (score 978, all STRING channels except text-mining; the partner is chosen on its genomic-context evidence).

Showing the 15 strongest of this gene's 17 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 17 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.

Evidence

• HHpred: self-hit PDB 3GMG (Rv1825 own structure) 100% E9e-37; then divisome convergence Cg1604 96.5% E0.18, FtsB/FtsL 95-96% E0.1-0.22 (better E than the de-novo coiled-coil designs at 88-91% E>=0.58), + cell-wall hydrolases NlpC/P60/RipA/M23/CHAP. DUF881 (COG3879). Cross-check: 1-TM coiled-coil membrane; STRING Rv1824/Rv1823(paralog)/pgsA2/Rv0012/secA2 = cell-division/membrane context. Consistent with Rv1823 (paralog, already family_assigned divisome).
• HHpred web (MPI Bioinformatics Toolkit, profile-profile remote homology), interpreted in project 'Still unknown gene function', 2026-06-10. A fold/family-level assignment, not a demonstrated function.
• SigF regulon (Williams 2007, Hartkoorn 2012 ChIP-on-chip+microarray): induction demonstrated only at OPERON level (Rv1823-Rv1826, promoter upstream of Rv1823); no probe/primer in either study resolves Rv1825 individually -- gene-level regulation not established.
• Independent computational corroboration of the cell-envelope/divisome context (Doerks 2012, comparative genomic-context annotation, method independent of this atlas's own HHpred/STRING pipeline): Rv1823/Rv1825 annotated 'hypothetical cell wall associated gene products' functionally linked to pgsA2 in a conserved actinobacterial operon.
• Candidate UDP-binding site (Bhagavat 2017, PocketMatch PMSmax 0.46) refuted on two independent fronts: sub-threshold in the source study's own candidate table (its stated significance cutoff is PMSmax >=0.5), and no structural convergence to the UDP-glycosyltransferase template (PDB 3T7M) on Foldseek re-analysis (e-value ~2-3, TM-score ~0.07-0.08, site-residue conservation p=0.63 vs null) -- consolidates, without contradicting, the divisome/FtsB-FtsL fold assignment.
• Clade-restricted missense variant p.Arg53Trp (NC_000962.3:2071191:C:T, 0-based) fixed at 100% across 1415 strains spanning 7 subgroups of the MTBC basal African clade (animal-adapted lineages + L6/L9/L10), 0% among 123,789 strains of the strict human lineages (L1-L4, L7, L8, M. canettii). Independently corroborated by a second, unrelated phylogenomic reconstruction (Chiner-Oms et al. 2022, Dataset S8, >9000 genomes, distinct tree-building pipeline): the same substitution is placed on the ancestral branch of lineages A1+lineage6, with no recurrent homoplasy detected in either tree.
• A second missense variant at the same locus (p.Pro181Ser, NC_000962.3:2071575:C:T) flagged as destabilising in CHOPIN (Ochoa-Montano 2015) is unrelated to the above: an independent L4 sub-lineage marker (~12-13% of L4, 0% in the basal African clade), confirmed on two independent strain panels (local curated database and an ~256,000-genome external corpus) and by the same Chiner-Oms 2022 dataset.
• Operon synteny (pgsA2-Rv1823-Rv1824-Rv1825) conserved beyond the genus Mycobacterium: intact and ordered in all 51/51 local MTBC+NTM+outgroup genomes, then in Rhodococcus (Corynebacteriales, 2/2, ~52% id) and, at greater phylogenetic distance, in Streptomyces coelicolor, Bifidobacterium longum and Cutibacterium acnes (33-35% id, 4/4 ordered); orthology confirmed by reciprocal BLAST against the full H37Rv proteome. Method transposed from Goodall et al. 2023 (PLOS Genetics), independently applied here for the first time to this operon (tblastn e-5 on 71 local genomes, project Rv1825 P2.13, cahier 2026-09-18).
• Predicted, not measured, physical association: local Boltz-2 co-folding of Rv1825 with each of its two immediate operon neighbours, one job and one MSA-server run per pair. Rv1825xRv1824: ipTM 0.71-0.80 and minimum inter-chain PAE 2.9-5.0 A over 15 diffusion samples (0.74-0.78 and 3.1-4.2 A in the first 3-sample run); Rv1825xRv1823: ipTM 0.61-0.63 and minimum inter-chain PAE 0.9-1.3 A over 15 samples (0.62-0.64 and 1.1-1.2 A over 3). PAE is the minimum over the inter-chain block (best residue pair), the project's convention, not a mean. 'Reproducible' means that these confidence scores are stable across diffusion samples; the geometry is not: the distance from residue 53 to Rv1824 falls in two groups (10/15 samples at 3.4-9.6 A, 5/15 at 17-23 A), i.e. at least two poses. The reference positive control (Rv1025-divIC/FtsB-ftsQ, ipTM 0.38, minimum PAE 5.1 A, KB tuberculosis.md 2026-07-05) was run in AlphaFold3, not Boltz-2: it is a reference point, not a calibration of these scores. The specificity controls are 3-sample Boltz-2 runs (a 3-sample run reversed the R53W result once 15 samples were drawn, project Rv1825 P2.16): gcvH (genomic neighbour, not a coiled-coil) is unstable, ipTM 0.27-0.67, PAE 6.2-16.4 A; Rv1682 (SMC-like ATPase, soluble, unrelated to the divisome) gives ipTM 0.34-0.40, which equals the reference positive control, with PAE 8.3-12.7 A. Rv1823 is a DUF881 paralogue of Rv1825, so generic packing between related coiled-coils is not excluded for that pair. No experimental support: STRING has no experimental or curated-database evidence for either pair (neighbourhood, co-occurrence, co-expression and text-mining channels only); the Humphreys 2024 predicted interactome lists Rv1825-Rv1824 (AF_score 0.92) and not Rv1825-Rv1823 (a filtered set, so the absence is not informative). Project Rv1825 P2.14 and P2.16, cahier 2026-09-18/19 and 2026-09-20; caveat on coiled-coil specificity controls versioned to KB tuberculosis.md (2026-09-19).
• Published serodiagnostic antigen, independently of any divisome function: Zhou et al. 2015 (dedicated protein-array screen) identify Rv1825 among 8 'newly identified' antigens; Zhou et al. 2021 (same group, explicit follow-up) test it individually among 9 antigens with published numbers (sensitivity 15.6%, 95%CI 9.8-23.1; specificity 95.3%, 95%CI 86.9-99.0). Demonstrates expression and immune exposure of the protein; orthogonal to, and not counted toward, the functional-flip threshold above (project Rv1825 P2.1, cahier 2026-09-19).

Ancestral MTBC0 protein sequence

>mtbc0_001939|Rv1825|
MSENRPEPVAAETSAATTARHSQADAGAHDAVRRGRHELPADHPRSKVGPLRRTRLTEILRGGRSRLVFGTLAILLCLVLGVAIVTQVRQTDSGDSLETARPADLLVLLDSLRQREATLNAEVIDLQNTLNALQASGNTDQAALESAQARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPVK