Rv2699c Still unknown · low auto-curated

Annotation: from legacy to revised

Curation note: 2026-10-02 (mtbc/Rv2699c project, back-propagation P52.2, destination C1, status: in preparation, not peer-reviewed). Cortes et al. (2013) dRNA-seq maps: no primary TSS is called for Rv2699c in exponential growth, where its transcript is nonetheless detected (RPKM 7.79). After 24 h of nutrient starvation a primary TSS is called at NC_000962.3 position 3,015,010 (5'UTR of 45 nt, Shine-Dalgarno class, promoter expression 5.81) and the RPKM rises to 53.63 (supplementary tables mmc2 sheet 1C and mmc6 sheet 6B). 2026-10-02 (mtbc/Rv2699c project, back-propagation P52.2, destination C1, status: in preparation, not peer-reviewed). Same study, differential expression table (1,306 CDS called after 24 h of nutrient starvation, 611 induced): Rv2699c is induced 10.4-fold (adjusted p 3.2e-34), rank 31 of the 611 by fold change. Of the five CDS around it (Rv2696c to Rv2701c) only Rv2701c (suhB) is also called, repressed 0.40-fold. The transcription-factor edges under Regulation come from overexpression and do not say in which condition the gene responds; nutrient starvation is one such condition. 2026-10-02 (mtbc/Rv2699c project, back-propagation P52.2, destination C1, status: in preparation, not peer-reviewed). Rv2699c is one of the 230 genes of the Enduring Hypoxic Response (Table S2 of Rustad et al. 2008): median log2 ratios (hypoxia over log phase) of -0.49, +0.30, +0.74, +0.57, +1.21 and +2.63 at 4 h, 8 h, 12 h, 1 d, 4 d and 7 d, rank 67 of 230 at 7 days. It is not among the 49 genes of the DosR regulon (Table S1). Its divergent neighbour Rv2700 (cei) is also listed (+1.09 at 7 d). The article names the gene only in the supplementary table, not in its text. 2026-10-02 (mtbc/Rv2699c project, back-propagation P52.2, destination C1, status: in preparation, not peer-reviewed). Table S2 of Rustad et al. (2014) (206 transcription-factor overexpressions; the authors' thresholds: absolute log2 fold change at least 1, adjusted p below 0.01) lists three regulators that lower Rv2699c and are not shown under Regulation: Rv0238 (log2 -1.85, adjusted p 1.0e-05), Rv1358 (-1.57, 1.0e-03) and Rv0260c (-1.42, 1.2e-03), none with a ChIP-seq peak at this promoter in Minch et al. (2015). The Rv0678 edge shown there matches a peak at the start codon, but its overexpression response is +0.59 (adjusted p 0.25), below the thresholds: read it as binding evidence only. Rv1358 and Rv0260c are themselves induced in starvation (2.19- and 24.5-fold), so release from repression does not explain that induction. Thirteen genes are lowered by all three (pairwise regulon overlaps at the 95th to 99th percentile of the null): a weak inference of a module. 2026-10-02 (mtbc/Rv2699c project, back-propagation P52.2, destination C1, status: in preparation, not peer-reviewed). CRP binding site listed under Regulation (peak between Rv2699c and Rv2700, target undecided in the source): the canonical motif TGTGA-N6-TCACA has a single perfect match within 60 bp of the Minch et al. (2015) peak midpoint (3,015,072), at 3,015,065 to 3,015,080 (centre 3,015,072.5). Against the Rv2699c primary TSS measured in starvation (3,015,010, Cortes et al. 2013) the box lies 55 to 70 nt upstream (centre -62.5), against about 131 nt from the Rv2700 TSS (3,015,203, leaderless). A position, not a direction of effect: CRP overexpression changes Rv2699c by +0.18 log2 (adjusted p 0.91) in Rustad et al. (2014), and the reserve above (binding site only) stands. 2026-10-02 (mtbc/Rv2699c project, back-propagation P52.2, destination C1, status: in preparation, not peer-reviewed). Site-level audit of the DeJesus et al. (2017) call (Tables S2 and S3): the 4 TA sites are all permissive (motif recomputed on NC_000962.3) and empty in all 14 libraries (35,314,576 insertion events genome-wide); the call is a plurality of HMM states (4 of 4), not the small-ORF binomial rule (3 sites or fewer). Probability that the 4 sites of a dispensable gene all stay empty: 1.5e-6 at the saturation of high-coverage regions (96.5%), 4.3e-5 counting the 3 sites at least 15 bp apart, 6.1e-4 at the raw aggregate saturation (84.3%). Essential calls are rarer at 4 TA sites (10 of 152 ORFs, 6.6%) than above 10 sites (349 of 2,492, 14.0%), so the thin-call caveat above shows no excess of essential calls at this TA count. Reserve: 3 of the 4 sites lie in the first 30 bp of the coding sequence, inside the annotated promoter PROM-1495 (downstream of the starvation TSS), so a requirement for the protein cannot be formally separated from one for a cis element. 2026-10-02 (mtbc/Rv2699c project, back-propagation P52.2, destination C1, status: in preparation, not peer-reviewed). Context anchor RbpA: the edge (combined 0.783) is carried by phylogenetic co-occurrence (0.773); experiments, database, text-mining, neighbourhood and fusion are 0, co-expression 0.086. In RbpA's own STRING neighbourhood co-occurrence does not track interaction: 6 of its 10 partners with an experimental score of at least 0.5 score exactly 0 on it (median 0.000), SigA included (complex solved at 2.20 A, PDB 4X8K). Both proteins being restricted to the Actinomycetota suffices to produce the score, and Rv2699c heads a flat plateau of 14 RbpA partners (co-occurrence 0.706 to 0.773) that includes SecG, a Sec translocon subunit, and GlnE. The 'high' confidence above is the STRING score band, here from co-occurrence alone, not evidence of an interaction. A paired-alignment mutual-information test failed its own positive control (RbpA-SigA Z 12.5, below negative controls at 35.8 and 60.2; test pair 77.4) and is uninformative; a calibrated Boltz-2 panel was not completed, so a direct interaction is untested. P16.14 TrEMBL-name audit (2026-07-11): UniProt TrEMBL name 'dUTPase' NOT corroborated and contradicted -- eggNOG assigns DUF4193 and Foldseek shows no dUTPase; the annotated dut (dUTPase) is the near neighbour Rv2697c, so the name is a mis-propagation. Kept dark. NB a real, important gene: essential (DeJesus ES), vulnerable at the median level of the genes with a reliable CRISPRi estimate (VI -6.8, 95% CI -7.6 to -5.9, flagged certain; Bosch et al. 2021; established targets sit lower, e.g. rpoB -9.6, inhA -9.9), DUF4193, conserved to Actinomycetia -- function still unknown.

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

In the literature (TB corpus sweep) unstudied by one source only

No TB publication mentions this locus tag in its title or abstract (sweep of a ~330k-abstract PubMed TB corpus). A second, independent source (tbmonitor) does however find 1 paper(s) naming this locus tag — see the second-source check below. The gene remains dark on function, but it is not unstudied, and this page no longer claims that it is.

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).

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) highly disordered

sequence-based disorder is high but AlphaFold folds it confidently (pLDDT>=70): treat the disorder call with caution (possible metapredict over-call)

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).

Candidate functional site (conserved residues clustered in space, hypothesis) supported (NOT confirmed)

metal-binding (donor geometry, Cys/His/Asp/Glu default BioMetAll set) — residues C73, C76, C95, C98 (conservation 99.7 %, 99.5 %, 98.8 %, 99.5 % on 4 684 aligned sequences).

Read with care. SUPPORTED, NOT CONFIRMED (anti-circularity guardrail, Rv1025 review): no holo-AF3/Boltz metal-docking run in this extension (CPU cost prohibitive at batch scale, deferred as an optional 3rd line for high-priority candidates). 'Metal-binding site' != 'metalloenzyme' -- catalysis is one hypothesis among several (structural, regulatory, cofactor). BioMetAll's default residue set (Asp/Cys/Glu/His) biases toward metal sites; a non-metal functional site (protein-protein interface, small-molecule pocket) would not be caught by this pipeline. phase183_p17_2_extension.py.

Binding-pocket screen (P2Rank, geometric prediction) detector blind at this length

Read with care. This protein (100 aa) is below the size where this detector has meaningful power: on proven enzymes, only 3.8% (1/26) under 200 aa reach this layer's P2Rank confidence threshold of best_probability >= 0.70, versus 60.5% (75/124) above it (P16.3b calibration, negative control EsxA/EsxB-scale panel). Both figures are recall AT 0.70, which is also the best separation this detector reaches on that panel (Youden J = 0.416) and whose false-positive rate above 200 aa is 18.9% (81.1% specificity); the looser 0.50 that appears elsewhere in this repository would raise recall above 200 aa to 74.2% and drop specificity to 64.9%. A negative or weak pocket result here should NOT be read as evidence against a ligand-binding role -- the test essentially has no power at this length, not that the protein lacks a site. The same holds in the other direction, and that half was missing here: a STRONG score at this length is not a result either. The same calibration panel does carry that other arm below 200 aa, and the two do not separate: the 3.8% above is matched by 6.6% (5/76) of proteins annotated as non-catalytic clearing 0.70 (Fisher p = 1.00; 15.4% against 11.8% at 0.50, p = 0.73). At this length the score therefore carries no measured information in either direction -- which is a stronger statement than untested power, and the reason a strong score here is not a result. P16.3e, calibration phase72b_pocket_calibration.py, 2026-08-03.

CRISPRi vulnerability

Vulnerability index -6.76 (95% CI -7.55 to -5.94). 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).

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)

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) essential

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.

Chemical-genetic target & druggability (PROSPECT) hypomorph tool strain

This gene is part of the PROSPECT collection of TetON transcriptional-knockdown (hypomorph) strains of essential M. tuberculosis genes, built as a sensitised background for chemical-genetic mechanism-of-action deconvolution. Being in the panel means the gene is an essential / vulnerable target for which a validated knockdown tool strain exists.

Panel membership reflects essentiality/vulnerability and the availability of a genetic tool, not a specific molecular function; it never changes the verdict here. Source: Bond AN et al., Nat Commun 2025;16:9673 (doi:10.1038/s41467-025-64662-x); PROSPECT chemical-genetic platform.

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 (best E=0.17, non-significant); small basic-peptide/zinc-finger promiscuity, consistent short-sequence artifact. Remains dark. top hits 4AYB_P/4QIW_P/5IP7_L RNA polymerase subunit-like hits (78.3-92.3%, E>=0.17), 8Q5B_A small CPxCG-related zinc finger (76.0%, E=2). 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 78.4, 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.

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.

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: rbpA (RNA polymerase-binding protein RbpA), high confidence (score 784, 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 49 partners at medium confidence (13 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 49 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: DUF4193 domain-containing protein
• Pfam (hmmscan --cut_ga): DUF4193 PF13834.12 (E=1e-45)
• (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)

Ancestral MTBC0 protein sequence

>mtbc0_002873|Rv2699c|
MPTDYDAPRRTETDDVSEDSLEELKARRNEAASAVVDVDESESAESFELPGADLSGEELSVRVVPKQADEFTCSSCFLVQHRSRLASEKNGVMICTDCAA