Rv2114 Still unknown · low auto-curated
H37Rv Rv2114 · MTBC0 mtbc0_002246 ·
207 aa · 2401097–2401720 (+) ·
RefSeq NP_216630.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 8b6h-assembly1_ES Cryo-EM structure of cytochrome c oxidase dimer (com (prob 0.08, TM 0.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33249
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2D663 |
|---|
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 | 0.331 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.53% of strains (767) · clonal |
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 38.9 (very low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
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 |
|---|---|---|---|---|
8b6h-assembly1_ES |
0.08 | 0.34 | 3.6e+00 | 8b6h-assembly1_ES Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from respiratory supercomplex of Tetrahymena thermophila |
8gzu-assembly1_0G |
0.08 | 0.35 | 3.6e+00 | 8gzu-assembly1_0G Cryo-EM structure of Tetrahymena thermophila respiratory Megacomplex MC (IV2+I+III2+II)2 |
8dgf-assembly1_C |
0.02 | 0.21 | 7.2e+00 | 8dgf-assembly1_C Avs4 bound to phage PhiV-1 portal |
4yj2-assembly1_E |
0.01 | 0.18 | 8.1e+00 | 4yj2-assembly1_E Crystal structure of tubulin bound to MI-181 |
7xqx-assembly1_E |
0.01 | 0.18 | 7.6e+00 | 7xqx-assembly1_E Crystal structure of T2R-TTL-27a complex |
6o5n-assembly1_E |
0.01 | 0.18 | 9.1e+00 | 6o5n-assembly1_E Tubulin-RB3_SLD-TTL in complex with compound 10ab |
4yj3-assembly1_E |
0.01 | 0.18 | 9.1e+00 | 4yj3-assembly1_E Crystal structure of tubulin bound to compound 2 |
7dbd-assembly1_E |
0.01 | 0.18 | 9.1e+00 | 7dbd-assembly1_E 444 in complex with tubulin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2113 (integral membrane protein), high confidence from genomic context alone (score 924 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) |
|---|---|---|---|---|
Rv2113 |
integral membrane protein | 924 | 924 ctx | neighborhood:874 cooccurence:418 |
Rv1006 hyp |
hypothetical protein | 761 | 761 ctx | cooccurence:759 |
Rv1868 hyp |
hypothetical protein | 745 | 745 ctx | cooccurence:745 |
Rv1435c hyp |
hypothetical protein | 735 | 736 ctx | cooccurence:735 |
Rv2047c hyp |
hypothetical protein | 635 | 635 ctx | cooccurence:635 |
Rv3033 hyp |
hypothetical protein | 626 | 626 ctx | cooccurence:624 |
Rv0180c |
transmembrane protein | 611 | 611 ctx | cooccurence:610 |
Rv2112c dop |
pup deamidase/depupylase | 606 | 605 ctx | neighborhood:604 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 559 | 559 ctx | cooccurence:557 |
Rv1748 hyp |
hypothetical protein | 552 | 552 ctx | cooccurence:552 |
Rv1364c |
sigma factor regulatory protein | 546 | 546 ctx | cooccurence:546 |
Rv2598 hyp |
hypothetical protein | 501 | 502 ctx | cooccurence:500 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 489 | 489 ctx | cooccurence:489 |
Rv3899c hyp |
hypothetical protein | 475 | 476 ctx | cooccurence:474 |
Rv0258c hyp |
hypothetical protein | 451 | 451 ctx | cooccurence:451 |
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
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: hypothetical protein
- Foldseek best: 8b6h-assembly1_ES Cryo-EM structure of cytochrome c oxidase dimer (complex IV) f (prob 0.08, E=4e+00, TM=0.34)
- (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 NP_216630.1)
- 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
2D663 - Curated reference: UniProt O33249 (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 38.9, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
21 functional partner(s); context anchor
Rv2113 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002246|Rv2114| MSAPERVTGLSGQRYGEVLLVTPGEAGPQATVYNSFPLNDCPAELWSALDPQALATEHKAATALLNGPRYWLMNAIEKAPQGPPVTKTFGGIEMLQQATVLLSSMNPAPYTVSQVSRNTVFVFNAGEEVYELQDPKGQRWVMQTWSQVVDPNLSRADLPKLGERLNLPAGWSYHTRVLTSELRVDTTNREARVLQDDLTNSYSLVTA