PPE45 Family assigned · medium

Annotation: from legacy to revised

Curation note: 2026-10-02 (mtbc/Rv2892c project, back-propagation P52.2, destination C1, status: preprint, not peer-reviewed). PE-PPE proteins reach the type VII machinery as heterodimers: in the crystal structure of PE25-PPE41 bound to the chaperone EspG5, EspG recognises the PPE domain, and most PE-PPE proteins are predicted to use EspG5 and ESX-5 (Ekiert and Cox 2014; Chen et al. 2017, whose structures 4w4l and 5xfs appear among the Foldseek hits of this record). PPE45 is not named in the main text of either paper: a full-text search of Europe PMC on 2026-10-02, with a positive control on EspG, returns no mention of PPE45 or Rv2892c (supplementary files were not searched). It was therefore neither tested nor excluded as an EspG5 substrate. The ESX-5 assignment in the pe_ppe layer above is a class-level rule for orphan PPE genes, not a measurement on PPE45, and the empty cognate_partners field means that no PE partner is known, not that none exists: the dedicated project found no PE gene adjacent to PPE45, but characterised PE-PPE pairs are not always adjacent in the genome. Source: literature review of the dedicated project mtbc/Rv2892c (2026-09-13), rechecked here against the full texts. 2026-10-02 (mtbc/Rv2892c project, back-propagation P52.2, destination C1, status: preprint, not peer-reviewed). Position of the L6-fixed stop-gained variant (W75*, NC_000962.3:3201795:C:T, the single nonsense site counted above) relative to the domains listed on this record: it falls inside the PPE domain (residues 2 to 165) after 74 residues, and the whole PPE-SVP region (residues 325 to 404) lies downstream and is lost. An ESMFold prediction run by the dedicated project gives a mean pLDDT of 0.845 for residues 1 to 74 in the full-length model and 0.592 when the 74-residue fragment is folded alone (a drop of 0.253, present at all 74 positions). This is a drop in predicted folding confidence, not a measurement, and no control with isolated N-terminal fragments of comparable length from other PPE proteins was run, so part of the drop may reflect how the model treats short isolated sequences. Whether the truncated product is made, stable or functional is unknown: the dedicated project knows of no expression data for this locus in L6 or in any other lineage. 2026-10-02 (mtbc/Rv2892c project, back-propagation P52.2, destination C1, status: preprint, not peer-reviewed). Mappability and paralogy check of the stop-gained site (NC_000962.3:3201795:C:T), dedicated project, rerun with per-hit logging on 2026-09-16 (resultats/phase1_mappability_ppe45/paralogs_detail.tsv). A 101 bp window centred on the site matches six other PPE genes (PPE18, PPE19, PPE25, PPE27, PPE32, PPE60) at 80.5 to 83.3% identity over 57 to 82 bp, and the project's blastn test classes the site PARALOG-RISK, as it does the esxV positive control. The pattern differs from esxV (four paralogues at 96.0 to 100% identity over the full 101 bp, a near-identical duplicate): here the matches reflect the conserved N-terminal PPE motif shared by the family, not a duplicated copy. The variant call is therefore not obviously a mapping artefact, but the usual short-read mapping caveat for PE/PPE genes is reduced, not removed. P52.5 (2026-09-30): fiche flagged as hand-reviewed at the closure of the dedicated project mtbc/clos/Rv2892c (iteration 8, state of 2026-09-20). The project's findings were compared with this fiche (P52.1, 2026-09-29) and no divergence was found. P16.23 (phase135, 2026-08-17): couche tss ajoutee (leaderless=False). P49.1 (phase233, 2026-09-15): couche tss re-clee (leaderless=False). P59 (2026-09-22, cross-project signal from the sister project mtbc/Rv2892c, which characterised the L6-fixed stop-gained loss of PPE45 on eight independent axes): three empty layers on this fiche are VERIFIED absences, not unchecked gaps. mutant_phenotypes={}: seven Europe PMC queries (all aliases -- PPE45, Rv2892c, MMAR_1905, Mb2916c -- crossed with knockout/complementation/mutant) return zero admissible hits, and the local MtbTnDB compendium (data/mtbtndb/standardized.tsv, 146 conditions) shows 0/146 at q<0.05 for this gene, hypoxia and in-vivo mouse infection included. string={}: absent from the precomputed local STRING network and from the official STRING API (get_string_ids resolves the gene; interaction_partners returns empty at every confidence threshold), while its immediate genomic neighbours (Rv2891, Rv2893) are present -- not an artefact of a blanket PE/PPE exclusion. regulation={}: absent from RegPrecise's DosR core regulon, and absent from both tables of Rustad et al. 2008 (PLoS ONE, DOI 10.1371/journal.pone.0001502) -- the core regulon (Table S1, 49 loci) and the Enduring Hypoxic Response (Table S2, 230 genes) -- including among its immediate genomic neighbours. Source detail: ../Rv2892c/etat_des_decouvertes.md §2 and cahier_de_labo.md (2026-09-13 to 2026-09-22).

Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).

In the literature (TB corpus sweep) named in the literature

1 TB publication mentions this gene. One study characterises a variant of this gene: Gómez-González et al. 2023 (Frontiers in Microbiology, PMID 37876785) table 1 ("Lineage- or clade-specific variants") lists ppe45 [W75*(*)] as an L6-specific variant. That is the same stop-gained substitution (residue 75/408, NC_000962.3:3201795:C:T) independently characterised as fixed in lineage 6 (allele frequency 0.972, 0.000 elsewhere in the MTBC) by the dedicated project mtbc/Rv2892c (bioRxiv preprint BIORXIV/2026/753459, DOI pending, deposited 2026-09-22). This gene is therefore not absent from the literature: the earlier label rested on a title/abstract sweep (`full`) and a full-text alias sweep (`epmc_fulltext`) that, between them, did not attribute this table-only mention to the gene (P59.1, cross-project signal from the sister session, verified independently against the PMC full text before this edit). No functional claim beyond the variant table entry is made from this citation.

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`.

This layer CITES the literature and adds context; it does not change the verdict or the function stated elsewhere in this fiche. This distinguishes a gene that is dark because nobody has looked from one that is dark despite having been studied. Source: PubMed (whole): H37Rv locus tag + GENE NAME + ortholog identifiers (Mb…, MMAR_…, MSMEG_…, ML…, MAB_…), under a mycobacterial context filter; hits verified against the abstract text. Species-context counts distinguish M. tuberculosis literature from literature on other mycobacteria. phase76/phase77, 2026-07-13.

Intrinsic disorder (sequence + structure) highly disordered

carries a substantial disordered region (185/408 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).

Genomic-neighbour overlap (structural caveat) antiparallel · 18 % of gene

antiparallel overlap: this gene may inherit essentiality/conservation signal from its neighbour through shared TA sites or promoter constraint, without any protein of its own being produced (cf. Rv2438A/nadE) Signals attributed to this gene (Tn-seq essentiality via shared TA sites, conservation via promoter constraint) should be cross-checked against the neighbour before being read as its own. P20.1, derived from GFF3 gene coordinates, 2026-08-03.

Transcriptional start site (informative, coordinates unchanged)

Primary TSS at position 3202434 (- strand), 426 bp 5'UTR. TSS-derived candidate start codon: 3202008 (108 bp from the annotated start) -- 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 0.54 (95% CI -1.52 to 3.44). 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=0.385 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 Uncharacterized PPE family protein PPE45; 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)

Read the disruption percentage against its ceiling, not against 100%. The strain collection is deeply imbalanced by clade, so a loss fixed in an entire lineage still shows a small overall fraction: a gene disrupted in every L6 strain caps at 0.96% of the collection, in every M. caprae strain at 0.20%, in every M. microti strain at 0.02%. Of the 705 clades in this collection, 689 have a ceiling below 1%. A figure of "0.15% of strains" is therefore uninterpretable on its own — it can be noise or a complete, lineage-defining loss. Use the clade attribution row above, which gives the sub-clade sizes, and never read the percentage alone.

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) Mycobacterium

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.

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. For most detected proteins, what the count does establish, at any value, is that the product exists. This locus belongs to the PE/PPE family, whose long, low-complexity repeat domains carry few tryptic peptides usable for MS identification: median 5 peptides (7–30 aa, in-silico trypsin digest) per detected PE/PPE protein in this atlas, against 13 for the rest of the detected proteome (Mann-Whitney p < 10^-30, n=103 vs n=3,388). A detection here can therefore rest on very few peptides: the existence claim still holds, but it is weaker than the same count would be outside this family.

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)

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

No experimental structure is deposited for this gene: showing the AlphaFold DB predicted model (mean pLDDT 64.3, low), 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.

Genomic context (neighbours & predicted operon)

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.

PE/PPE family context (subfamily & T7SS secretion) PPE-SVP

Subfamily: PE / PE_PGRS from the Mycobrowser gene name/product; PPE refined to PPE-MPTR / PPE-SVP / PPE-PPW when a dedicated Pfam domain is present (plain PPE otherwise) -- Ates 2020 defines this four-subfamily framework, and the PPE-MPTR mapping (Pfam "Pentapeptide_2") is corroborated gene-by-gene against the literature (PPE10, PPE13), not an invented rule. T7SS locus and secretion status derived from this atlas's own gene nomenclature (the eccA/B/C/D/E and mycP genes already named on the corresponding fiches), not a hard-coded coordinate table. Orphan PE/PPE genes are trans-secreted by ESX-5 (Abdallah et al. 2009). Part of P42 (2026-08-28/29).

Functional interaction network (STRING v12)

This gene was queried against the STRING v12 network of M. tuberculosis H37Rv and has no partner at or above medium confidence (combined score ≥ 400). This is a verified absence, not a gap in the pipeline: an isolated node at this threshold is itself informative, and frequently the case for short or lineage-restricted proteins.

Evidence

• Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): PPE family protein PPE45
• Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=2e-68), PPE-SVP PF12484.14 (E=8e-19)
• (initial automatic assignment: auto-curated by rules from PGAP + Pfam + Foldseek; superseded by hand review)

Ancestral MTBC0 protein sequence

>H37Rv|Rv2892c|PPE45
MDFGVLPPEINSGRMYAGPGSGPMMAAAAAWDSLAAELGLAAGGYRLAISELTGAYWAGPAAASMVAAVTPYVAWLSATAGQAEQAGMQARAAAAAYELAFAMTVPPPVVVANRALLVALVATNFFGQNTPAIAATEAQYAEMWAQDAAAMYAYAGSAAIATELTPFTAAPVTTSPAALAGQAAATVSSTVPPLATTAAVPQLLQQLSSTSLIPWYSALQQWLAENLLGLTPDNRMTIVRLLGISYFDEGLLQFEASLAQQAIPGTPGGAGDSGSSVLDSWGPTIFAGPRASPSVAGGGAVGGVQTPQPYWYWALDRESIGGSVSAALGKGSSAGSLSVPPDWAARARWANPAAWRLPGDDVTALRGTAENALLRGFPMASAGQSTGGGFVHKYGFRLAVMQRPPFAG