Rv0209 Family assigned · medium
H37Rv Rv0209 · MTBC0 mtbc0_000223 ·
361 aa · 249390–250475 (+) ·
RefSeq NP_214723.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | IniC/dynamin-like protein (isoniazid-induced, iniBAC-family large GTPase-like). RefSeq leaves it 'hypothetical protein'. Distinct locus from iniC/Rv0342. |
Curated reference (UniProt)
| UniProt |
P96391
TrEMBL · unreviewed
· Predicted
|
|---|---|
| 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)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | ATPase. Has a role at an early stage in the morphogenesis of the spore coat |
| Orthologous group | COG0699 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 9 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 94.9 (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 |
|---|---|---|---|---|
8xqp-assembly1_A |
1.00 | 0.42 | 2.0e-02 | 8xqp-assembly1_A Structure of human class T GPCR TAS2R14-Gustducin complex with Aristolochic acid A. |
7uxh-assembly1_d |
0.98 | 0.46 | 1.1e-01 | 7uxh-assembly1_d cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex |
1u0r-assembly1_C |
0.54 | 0.44 | 9.1e-01 | 1u0r-assembly1_C Crystal structure of Mycobacterium tuberculosis NAD kinase |
6y2k-assembly1_A |
0.28 | 0.34 | 1.2e+00 | 6y2k-assembly1_A Crystal structure of beta-galactosidase from the psychrophilic Marinomonas ef1 |
7kqa-assembly1_B |
0.23 | 0.24 | 3.9e-01 | 7kqa-assembly1_B Crystal Structure of Glucosamine-6-phosphate deanimase from Strenotrophomonas maltophilia |
7z0t-assembly1_G |
0.15 | 0.23 | 5.2e-01 | 7z0t-assembly1_G Structure of the Escherichia coli formate hydrogenlyase complex (aerobic preparation, composite structure) |
3hba-assembly1_A |
0.12 | 0.20 | 5.0e-01 | 3hba-assembly1_A Crystal structure of a putative phosphosugar isomerase (sden_2705) from shewanella denitrificans os217 at 2.00 A resolution |
3odp-assembly1_A-2 |
0.08 | 0.19 | 1.0e+00 | 3odp-assembly1_A-2 Crystal structure of a putative tagatose-6-phosphate ketose/aldose isomerase (NT01CX_0292) from CLOSTRIDIUM NOVYI NT at 2.35 A resolution |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trmB (tRNA (guanine-N(7)-)-methyltransferase), high confidence from genomic context alone (score 776 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) |
|---|---|---|---|---|
Rv0210 hyp |
hypothetical protein | 976 | 976 ctx | neighborhood:882 coexpression:806 |
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 776 | 776 ctx | neighborhood:775 |
Rv0207c hyp |
hypothetical protein | 730 | 730 ctx | neighborhood:729 |
Rv0211 pckA |
phosphoenolpyruvate carboxykinase | 714 | 715 ctx | neighborhood:713 |
Rv0206c mmpL3 |
transmembrane transport protein MmpL3 | 487 | 487 ctx | neighborhood:485 |
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
- Foldseek vs AFDB-SwissProt: isoniazid-induced protein IniC, TM 0.59, E 5e-9
- Structural homology vs AlphaFold-Swiss-Prot (Foldseek; 542k curated SwissProt structures), project 'Still unknown gene function' phase13, 2026-06-10. Fold/family-level, not a demonstrated function.
ESM Atlas signal (exploratory)
Ancestral protein hash 2b56ed1c2ea89436672f44b8e5b410ac ·
10 ESM-space neighbours (max similarity 0.935).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 13341 |
1.24 | P-loop GTPase G4 guanine-recognition subdomain |
| 2 | 2174 |
1.22 | P-loop GTPase coupling helix |
| 3 | 5138 |
1.18 | Canonical P-loop GTPase G-domain |
| 4 | 4409 |
1.12 | G-domain Walker A P-loop |
| 5 | 11953 |
0.99 | GTPase-flanking coiled-coil scaffolds |
| 6 | 8885 |
0.87 | Coiled-coil machine head domains |
| 7 | 1243 |
0.84 | P-loop NTPase Walker A/B |
| 8 | 10126 |
0.82 | Nucleotide-binding beta strand/loop |
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_214723.1)
- 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
COG0699 - Curated reference: UniProt P96391 (TrEMBL, unreviewed; Predicted)
- 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 94.9, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
5 functional partner(s); context anchor
trmB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000223|Rv0209| MRGQGHQIFVDELARFATSSADQRVVAIAQRAAEPLRVAVRGRPGVGCRTVARALQGAGSSSGMTVTPQARAADSDVDLVVYVTVEVVKPEDREAIAATRRPVVAVLNKADLAGPLSGAGPIVMAQARCAQFSTLLGVPMESMIGLLAVAALDDLDDTLRAALRALAAHPDGFDALDRAVAGFLAAALPVPTEVRLRLLDTLDLFGIALGMAAFRPGRPSRTPAQLRTLLRRVSGVDAVIDKVTAAGSEVRYRRLLDAVAELEALAAQAKEIGGPIGEFLRDDDTVLARMAAAVDVALAVGLDVGPLDDPAAHLPRAVRWHRYSLDNGDMHRTCGADIARGSLRLWSLAGGMPLHRYRKSS