Rv0311 Family assigned · medium
H37Rv Rv0311 · MTBC0 mtbc0_000331 ·
409 aa · 382495–383724 (+) ·
RefSeq NP_214825.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Longin-like / alpha-beta-plait sensor (ligand-binding) domain; structural homology to DmpR/MopR aromatic-sensing transcriptional regulators, H-NOX gas sensors, and TRAPPC3; specific ligand undetermined RefSeq leaves this locus uncharacterised. |
Curated reference (UniProt)
| UniProt |
O07238
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28KAT |
|---|
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, 145 209 strains)
| pN/pS | 0.493 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 0 nonsense, 0 frameshift |
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.
Domains (Pfam, hmmscan --cut_ga)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 95.9 (very high). 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.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
5doe-assembly1_B |
0.13 | 0.27 | 7.2e-01 | 5doe-assembly1_B Crystal structure of the Human Cytomegalovirus UL53 (residues 72-292) |
5doc-assembly1_A |
0.08 | 0.23 | 1.2e+00 | 5doc-assembly1_A Crystal structure of the Human Cytomegalovirus UL53 subunit of the NEC |
7t7i-assembly2_H |
0.08 | 0.27 | 2.1e+00 | 7t7i-assembly2_H EBV nuclear egress complex |
5fki-assembly1_1A |
0.08 | 0.18 | 5.0e-01 | 5fki-assembly1_1A Pseudorabies virus (PrV) nuclear egress complex proteins fitted as a hexameric lattice into a sub-tomogram average derived from focused- ion beam milled lamellae electron cryo-microscopic data |
8g6d-assembly1_D |
0.08 | 0.24 | 1.3e+00 | 8g6d-assembly1_D HSV-1 Nuclear Egress Complex (SUP; UL31-R229L) |
5dob-assembly1_A |
0.07 | 0.23 | 1.7e+00 | 5dob-assembly1_A Crystal structure of the Human Cytomegalovirus Nuclear Egress Complex (NEC) |
5e8c-assembly1_A |
0.07 | 0.25 | 1.9e+00 | 5e8c-assembly1_A pseudorabies virus nuclear egress complex, pUL31, pUL34 |
5doc-assembly1_B |
0.06 | 0.26 | 3.0e+00 | 5doc-assembly1_B Crystal structure of the Human Cytomegalovirus UL53 subunit of the NEC |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0771 (4-carboxymuconolactone decarboxylase), high confidence from genomic context alone (score 820 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0310c hyp |
hypothetical protein | 896 | 896 ctx | neighborhood:645 cooccurence:718 |
Rv0771 |
4-carboxymuconolactone decarboxylase | 820 | 820 ctx | neighborhood:424 cooccurence:699 |
Rv0762c hyp |
hypothetical protein | 819 | 819 ctx | cooccurence:774 |
Rv0767c |
HTH-type transcriptional regulator | 818 | 819 ctx | cooccurence:774 |
Rv0765c |
oxidoreductase | 771 | 772 ctx | cooccurence:714 |
Rv0764c cyp51 |
lanosterol 14-alpha demethylase | 761 | 760 ctx | cooccurence:749 |
Rv0312 hyp |
hypothetical protein | 749 | 749 ctx | neighborhood:749 |
Rv0272c hyp |
hypothetical protein | 724 | 725 ctx | cooccurence:723 |
Rv3169 hyp |
hypothetical protein | 718 | 718 ctx | cooccurence:717 |
Rv0763c |
ferredoxin | 714 | 714 ctx | cooccurence:667 |
Rv0926c hyp |
hypothetical protein | 687 | 688 ctx | cooccurence:686 |
Rv0138 hyp |
hypothetical protein | 663 | 663 ctx | cooccurence:663 |
Rv1776c |
transcriptional regulator | 646 | 646 ctx | cooccurence:646 |
Rv3531c hyp |
hypothetical protein | 636 | 637 ctx | cooccurence:635 |
Rv1628c hyp |
hypothetical protein | 620 | 620 ctx | cooccurence:618 |
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.
Evidence
- HHpred (Neff 8.68): top hit 7YH3 TRAPPC3 longin 98.2% E3.2e-5; DmpR/MopR phenol-sensing regulators 97%; H-NOX NO/O2 sensors 95% - all share the longin/sensor alpha-beta-plait fold
- 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.
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 NP_214825.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
28KAT - Curated reference: UniProt O07238 (TrEMBL, unreviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 95.9, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
51 functional partner(s); context anchor
Rv0771 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000331|Rv0311| MSQSRYAGLSRSELAVLLPELLLIGQLIDRSGMAWCIQAFGRQEMLQIAIEEWAGASPIYTKRMQKALNFEGDDVPTIFKGLQLDIGAPPQFMDFRFTLHDRWHGEFHLDHCGALLDVEPMGDDYVVGMCHTIEDPTFDATAIATNPRAQVRPIHRPPRKPADRHPHCAWTVIIDESYPEAEGIPALDAVRETKAATWELDNVDASDDGLVDYSGPLVSDLDFGAFSHSALVRMADEVCLQMHLLNLSFAIAVRKRAKADAQLAISVNTRQLIGVAGLGAERIHRAMALPGGIEGALGVLELHPLLNPAGYVLAETSPDRLVVHNSPAHADGAWISLCTPASVQPLQAIATAVDPHLKVRISGTDTDWTAELIEADAPASELPEVLVAKVSRGSVFQFEPRRSLPLTVK