Rv2390c Family assigned · low auto-curated · to review
H37Rv Rv2390c · MTBC0 mtbc0_002543 ·
185 aa · 2707902–2708459 (-) ·
RefSeq NP_216906.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 8rta-assembly1_G Arches-protomer complex full-length structure (TrwJ/VirB8) from (prob 1.00, TM 0.65). Structure-based, putative. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
Curated reference (UniProt)
| UniProt |
P71754
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Mce associated membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2E5H4 |
|---|---|
| KEGG orthology |
K18481
|
| KEGG modules |
M00670
|
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) pseudogene candidate
| pN/pS | 0.491 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.05% of strains (1526) · 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 94.8 (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 |
|---|---|---|---|---|
8rta-assembly1_G |
1.00 | 0.65 | 1.2e-04 sig | 8rta-assembly1_G Arches-protomer complex full-length structure (TrwJ/VirB8) from the fully-assembled R388 type IV secretion system determined by cryo-EM. |
7q1v-assembly1_D |
1.00 | 0.64 | 1.9e-04 sig | 7q1v-assembly1_D Arches protomer (trimer of TrwG/VirB8peri) structure from the fully-assembled R388 type IV secretion system determined by cryo-EM. |
4l8p-assembly1_A |
1.00 | 0.65 | 2.3e-04 sig | 4l8p-assembly1_A Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.60 A resolution |
7o41-assembly1_E-5 |
1.00 | 0.50 | 3.8e-05 sig | 7o41-assembly1_E-5 Hexameric composite model of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system determined by cryo-EM. |
3b8l-assembly2_F |
1.00 | 0.66 | 9.4e-04 sig | 3b8l-assembly2_F CRYSTAL STRUCTURE OF A PUTATIVE AROMATIC RING HYDROXYLASE (SARO_3538) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM AT 1.75 A RESOLUTION |
8rtd-assembly1_S |
1.00 | 0.48 | 9.2e-05 sig | 8rtd-assembly1_S Stalk-Arches-IMC structure from the fully-assembled R388 type IV secretion system determined by cryo-EM. |
4akz-assembly1_A |
1.00 | 0.70 | 2.2e-03 sig | 4akz-assembly1_A CRYSTAL STRUCTURE OF VIRB8 FROM BRUCELLA SUIS |
6of8-assembly1_B-2 |
1.00 | 0.64 | 4.1e-04 sig | 6of8-assembly1_B-2 Structure of Thr354Asn, Glu355Gln, Thr412Asn, Ile414Met, Ile464His, and Phe467Met mutant human CamKII-alpha hub domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpfD (resuscitation-promoting factor RpfD), high confidence from genomic context alone (score 895 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) |
|---|---|---|---|---|
Rv2389c rpfD |
resuscitation-promoting factor RpfD | 922 | 895 ctx | neighborhood:882 |
Rv3492c |
Mce associated protein | 753 | 754 ctx | cooccurence:752 |
Rv1527c pks5 |
polyketide synthase | 763 | 735 | experimental:470 database:508 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 763 | 735 | experimental:470 database:508 |
Rv2048c pks12 |
polyketide synthase | 762 | 735 | experimental:470 database:508 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 762 | 734 | experimental:470 database:508 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 762 | 734 | experimental:470 database:508 |
Rv1691 hyp |
hypothetical protein | 742 | 731 | experimental:417 database:540 |
Rv2267c stf3 hyp |
hypothetical protein | 740 | 730 | experimental:417 database:540 |
Rv3529c hyp |
hypothetical protein | 740 | 729 | experimental:417 database:540 |
Rv1663 pks17 |
polyketide synthase | 739 | 729 | experimental:458 database:508 |
Rv1334 mec |
[CysO | 729 | 719 | experimental:404 database:546 |
Rv1277 hyp |
hypothetical protein | 704 | 705 | experimental:438 database:493 |
Rv3696c glpK |
glycerol kinase | 708 | 695 | database:502 |
Rv1389 gmk |
guanylate kinase | 701 | 689 | experimental:411 database:491 |
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: 8rta-assembly1_G Arches-protomer complex full-length structure (TrwJ/VirB8) from (prob 1.00, E=1e-04, TM=0.65)
- (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_216906.1)
- 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
2E5H4 - Curated reference: UniProt P71754 (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 94.8, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
278 functional partner(s); context anchor
rpfD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002543|Rv2390c| MAIFGRGHGASEPGGTGEPAETPGRGRLTRSVIGWVGAVAVVVSLAGSGWCGWVLFEKHQTDVAAGQALQAARSYVVKLATMDCERIDHNMRDILEGSTGEFKDKYGKSSAHLRQLLADNRVATHGTVVAASVKSATTNKVVVLMFIDQSVSNRNSPTPQIDRSRIKVIMDKVNGRWLASKVELL