PPE56 Family assigned · medium auto-curated

Annotation: from legacy to revised

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

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) 1 publication

1 TB publication mentions this gene. 1 publication discusses this gene (count verified against title and abstract text). Queried separately, 1 record carries a M. tuberculosis context and 1 a non-TB mycobacterial context (species named in the 1-record verified sample: M. smegmatis (1)). The three counts come from three distinct PubMed queries (the total is text-verified, the context counts are raw query volumes), so they neither partition the total nor need to add up to it.

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 (3123/3716 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).

CRISPRi vulnerability

Vulnerability index 1.02 (95% CI -1.34 to 4.75). 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=0.087 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=32 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)

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) MTBC-specific

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)

Conditional fitness of transposon-disruption mutants across 1 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.

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

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, 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-MPTR

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).

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.

Additional regulons (curated, outside the TFOE-derived TRN)

Curated from primary literature not covered by the ISB signed TRN (Minch 2015 / Rustad 2014): Zur regulon (Maciag et al. 2007, PMID 17098899), SigG regulon (Gaudion et al. 2013, PMID 23871545), LexA/SOS regulon (Smollett et al. 2012, PMID 22528497) — added P16.25 (2026-08-18); CRP regulon (Kahramanoglou et al. 2014, PMID 24957601) — added P16.25b (2026-09-27). Confidence and caveats are per-edge and carried from the source paper — read them before citing a specific gene as "regulated by" its listed TF. An entry reading "binding site only — direction not determined" is not a regulation claim: it records a measured ChIP-seq binding site for which the source reports no expression change, and the absence of such a change is not evidence of absent regulation.

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: cpnT (hypothetical protein), high confidence (score 787, all STRING channels except text-mining; the partner is chosen on its genomic-context evidence).

Showing the 15 strongest of this gene's 139 partners at medium confidence (50 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 139 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

• Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): PPE family protein PPE56
• Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=3e-59), Pentapeptide_2 PF01469.25 (E=2e-09)
• (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)

Ancestral MTBC0 protein sequence

>H37Rv|Rv3350c|PPE56
MEFPVLPPEINSVLMYSGAGSSPLLAAAAAWDGLAEELGSAAVSFGQVTSGLTAGVWQGAAAAAMAAAAAPYAGWLGSVAAAAEAVAGQARVVVGVFEAALAATVDPALVAANRARLVALAVSNLLGQNTPAIAAAEAEYELMWAADVAAMAGYHSGASAAAAALPAFSPPAQALGGGVGAFLTALFASPAKALSLNAGLGNVGNYNVGLGNVGVFNLGAGNVGGQNLGFGNAGGTNVGFGNLGNGNVGFGNSGLGAGLAGLGNIGLGNAGSSNYGFANLGVGNIGFGNTGTNNVGVGLTGNHLTGIGGLNSGTGNIGLFNSGTGNVGFFNSGTGNFGVFNSGNYNTGVGNAGTASTGLFNAGNFNTGVVNVGSYNTGSFNAGDTNTGGFNPGGVNTGWLNTGNTNTGIANSGNVNTGAFISGNFNNGVLWVGDYQGLFGVSAGSSIPAIPIGLVLNGDIGPITIQPIPILPTIPLSIHQTVNLGPLVVPDIVIPAFGGGIGIPINIGPLTITPITLFAQQTFVNQLPFPTFSLGKITIPQIQTFDSNGQLVSFIGPIVIDTTIPGPTNPQIDLTIRWDTPPITLFPNGISAPDNPLGLLVSVSISNPGFTIPGFSVPAQPLPLSIDIEGQIDGFSTPPITIDRIPLTVGGGVTIGPITIQGLHIPAAPGVGNTTTAPSSGFFNSGAGGVSGFGNVGAGSSGWWNQAPSALLGAGSGVGNVGTLGSGVLNLGSGISGFYNTSVLPFGTPAAVSGIGNLGQQLSGVSAAGTTLRSMLAGNLGLANVGNFNTGFGNVGDVNLGAANIGGHNLGLGNVGDGNLGLGNIGHGNLGFANLGLTAGAAGVGNVGFGNAGINNYGLANMGVGNIGFANTGTGNIGIGLVGDHRTGIGGLNSGIGNIGLFNSGTGNVGFFNSGTGNFGIGNSGRFNTGIGNSGTASTGLFNAGSFSTGIANTGDYNTGSFNAGDTNTGGFNPGGINTGWFNTGHANTGLANAGTFGTGAFMTGDYSNGLLWRGGYEGLVGVRVGPTISQFPVTVHAIGGVGPLHVAPVPVPAVHVEITDATVGLGPFTVPPISIPSLPIASITGSVDLAANTISPIRALDPLAGSIGLFLEPFRLSDPFITIDAFQVVAGVLFLENIIVPGLTVSGQILVTPTPIPLTLNLDTTPWTLFPNGFTIPAQTPVTVGMEVANDGFTFFPGGLTFPRASAGVTGLSVGLDAFTLLPDGFTLDTVPATFDGTILIGDIPIPIIDVPAVPGFGNTTTAPSSGFFNTGGGGGSGFANVGAGTSGWWNQGHDVLAGAGSGVANAGTLSSGVLNVGSGISGWYNTSTLGAGTPAVVSGIGNLGQQLSGFLANGTVLNRSPIVNIGWADVGAFNTGLGNVGDLNWGAANIGAQNLGLGNLGSGNVGFGNIGAGNVGFANSGPAVGLAGLGNVGLSNAGSNNWGLANLGVGNIGLANTGTGNIGIGLVGDYQTGIGGLNSGSGNIGLFNSGTGNVGFFNTGTGNFGLFNSGSFNTGIGNSGTGSTGLFNAGNFNTGIANPGSYNTGSFNVGDTNTGGFNPGDINTGWFNTGIMNTGTRNTGALMSGTDSNGMLWRGDHEGLFGLSYGITIPQFPIRITTTGGIGPIVIPDTTILPPLHLQITGDADYSFTVPDIPIPAIHIGINGVVTVGFTAPEATLLSALKNNGSFISFGPITLSNIDIPPMDFTLGLPVLGPITGQLGPIHLEPIVVAGIGVPLEIEPIPLDAISLSESIPIRIPVDIPASVIDGISMSEVVPIDASVDIPAVTITGTTISAIPLGFDIRTSAGPLNIPIIDIPAAPGFGNSTQMPSSGFFNTGAGGGSGIGNLGAGVSGLLNQAGAGSLVGTLSGLGNAGTLASGVLNSGTAISGLFNVSTLDATTPAVISGFSNLGDHMSGVSIDGLIAILTFPPAESVFDQIIDAAIAELQHLDIGNALALGNVGGVNLGLANVGEFNLGAGNVGNINVGAGNLGGSNLGLGNVGTGNLGFGNIGAGNFGFGNAGLTAGAGGLGNVGLGNAGSGSWGLANVGVGNIGLANTGTGNIGIGLTGDYRTGIGGLNSGTGNLGLFNSGTGNIGFFNTGTGNFGLFNSGSYSTGVGNAGTASTGLFNAGNFNTGLANAGSYNTGSLNVGSFNTGGVNPGTVNTGWFNTGHTNTGLFNTGNVNTGAFNSGSFNNGALWTGDYHGLVGFSFSIDIAGSTLLDLNETLNLGPIHIEQIDIPGMSLFDVHEIVEIGPFTIPQVDVPAIPLEIHESIHMDPIVLVPATTIPAQTRTIPLDIPASPGSTMTLPLISMRFEGEDWILGSTAAIPNFGDPFPAPTQGITIHTGPGPGTTGELKISIPGFEIPQIATTRFLLDVNISGGLPAFTLFAGGLTIPTNAIPLTIDASGALDPITIFPGGYTIDPLPLHLALNLTVPDSSIPIIDVPPTPGFGNTTATPSSGFFNSGAGGVSGFGNVGSNLSGWWNQAASALAGSGSGVLNVGTLGSGVLNVGSGVSGIYNTSVLPLGTPAVLSGLGNVGHQLSGVSAAGTALNQIPILNIGLADVGNFNVGFGNVGDVNLGAANLGAQNLGLGNVGTGNLGFANVGHGNIGFGNSGLTAGAAGLGNTGFGNAGSANYGFANQGVRNIGLANTGTGNIGIGLVGDNLTGIGGLNSGAGNIGLFNSGTGNIGFFNSGTGNFGIGNSGSFNTGIGNSGTGSTGLFNAGSFNTGVANAGSYNTGSFNAGDTNTGGFNPGTINTGWFNTGHTNTGIANSGNVGTGAFMSGNFSNGLLWRGDHEGLFSLFYSLDVPRITIVDAHLDGGFGPVVLPPIPVPAVNAHLTGNVAMGAFTIPQIDIPALTPNITGSAAFRIVVGSVRIPPVSVIVEQIINASVGAEMRIDPFEMWTQGTNGLGITFYSFGSADGSPYATGPLVFGAGTSDGSHLTISASSGAFTTPQLETGPITLGFQVPGSVNAITLFPGGLTFPATSLLNLDVTAGAGGVDIPAITWPEIAASADGSVYVLASSIPLINIPPTPGIGNSTITPSSGFFNAGAGGGSGFGNFGAGTSGWWNQAHTALAGAGSGFANVGTLHSGVLNLGSGVSGIYNTSTLGVGTPALVSGLGNVGHQLSGLLSGGSAVNPVTVLNIGLANVGSHNAGFGNVGEVNLGAANLGAHNLGFGNIGAGNLGFGNIGHGNVGVGNSGLTAGVPGLGNVGLGNAGGNNWGLANVGVGNIGLANTGTGNIGIGLTGDYQTGIGGLNSGAGNLGLFNSGAGNVGFFNTGTGNFGLFNSGSFNTGVGNSGTGSTGLFNAGSFNTGVANAGSYNTGSFNVGDTNTGGFNPGSINTGWLNAGNANTGVANAGNVNTGAFVTGNFSNGILWRGDYQGLAGFAVGYTLPLFPAVGADVSGGIGPITVLPPIHIPPIPVGFAAVGGIGPIAIPDISVPSIHLGLDPAVHVGSITVNPITVRTPPVLVSYSQGAVTSTSGPTSEIWVKPSFFPGIRIAPSSGGGATSTQGAYFVGPISIPSGTVTFPGFTIPLDPIDIGLPVSLTIPGFTIPGGTLIPTLPLGLALSNGIPPVDIPAIVLDRILLDLHADTTIGPINVPIAGFGGAPGFGNSTTLPSSGFFNTGAGGGSGFSNTGAGMSGLLNAMSDPLLGSASGFANFGTQLSGILNRGAGISGVYNTGALGVVTAAVVSGFGNVGQQLSGLLFTGVGP