Rv1155a Still unknown · low auto-curated
H37Rv Rv1155a · MTBC0 - ·
62 aa ·
1282030–1282218 H37Rv
(+) ·
RefSeq YP_009030031.1
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Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF5302. Function unknown. |
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) never studied
No TB publication mentions this locus tag in its title or abstract (sweep of a ~330k-abstract PubMed TB corpus). This gene is genuinely unstudied: its darkness reflects absence of investigation, not failure of investigation.
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) dark by construction (IDR-orphan)
| Predicted disorder | 100% of residues (metapredict) |
|---|---|
| Disordered regions | 1 IDR(s), longest 62 aa [0-62] |
both sequence (metapredict) and structure (low AlphaFold pLDDT) indicate little stable globular structure: this gene is dark BY CONSTRUCTION — there is no confident fold for structure/homology search to match, so its obscurity is expected, not a pipeline failure
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).
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Family of unknown function (DUF5302) |
| Orthologous group | 2EGF6 |
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.
Outgroup conservation (beyond the MTBC) Corynebacteriales
| Genus-wide presence (~53 non-MTBC Mycobacterium) |
present in 50/53 (94%) · mean identity 73.8%
· 4/4 closest MTBAP relatives conserved across the genus (present in 50/53 non-MTBC Mycobacterium genomes, incl. distant relatives) — an ancient core gene predating the genus radiation |
|---|---|
| Phylostratum (deepest detected homolog) |
MTBC-specific → Mycobacterium → Mycobacteriaceae → Corynebacteriales → Actinomycetia → Bacteria detected in 2/13 non-Mycobacterium reference genomes (down to Corynebacteriales) · mean identity 55.6% detected across the order Corynebacteriales (Corynebacterium/Nocardia/Rhodococcus/…) but not in more distant Actinomycetia — a Corynebacteriales-level gene |
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.
Proteomics (mass spectrometry) not detected
Not detected in the mass-spectrometry datasets integrated by PaxDb. This is not evidence of absence: low-abundance, condition-specific, or MS-refractory proteins (e.g. small, highly hydrophobic, or repetitive PE/PPE families with few tryptic peptides) are systematically under-sampled.
Physico-chemical properties (computed, ProtParam)
| Length | 62 aa |
|---|---|
| Molecular weight | 6.8 kDa |
| Theoretical pI | 10.35 |
| GRAVY | -1.674 (hydrophilic) |
| Aliphatic index | 17.4 |
| Aromaticity | 0.032 |
| Instability index | 102.9 (unstable) |
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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF5302 | PF17227.8 | 4.7e-21 | 12–62 | Family of unknown function (DUF5302) |
Genomic context (neighbours & predicted operon)
| Upstream (5' on genome) | Rv1155 (+ strand, 157 bp gap) |
|---|---|
| Downstream (3' on genome) | Rv1156 (+ strand, 87 bp gap) |
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).
Evidence
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DUF5302 PF17227.8 (E=5e-21)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq YP_009030031.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF5302 (PF17227.8)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
2EGF6 - Model confidence: ESMFold per-residue pLDDT (mean 58.5, low)
- Genomic context / operon: H37Rv annotation; operon predicted by co-directional intergenic distance (Salgado et al. 2000, doi:10.1073/pnas.030539397)
- Physico-chemical properties: ExPASy ProtParam method via Biopython (Gasteiger et al. 2005), computed from the MTBC0 sequence
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1155a| MGESKSPQESSSEGETKRKFREALDRKMAQSSSGSDHKDGGGKQSRAHGPVASRREFRRKSG
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