Rv2901c Still unknown · low auto-curated
H37Rv Rv2901c · MTBC0 mtbc0_003083 ·
101 aa · 3232632–3232937 (-) ·
RefSeq NP_217417.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2469 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2469. Function unknown. Foldseek best (non-significant) hit: 4m7d-assembly1_C Crystal structure of Lsm2-8 complex bound to the RNA (prob 0.16, TM 0.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL27
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2901c |
UniProt still lists this protein as Uncharacterized protein Rv2901c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2469) |
| Orthologous group | 2AFXT |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF2469 | PF10611.15 | 3.5e-52 | 1–100 | Protein of unknown function (DUF2469) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 49.1 (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 |
|---|---|---|---|---|
4m7d-assembly1_C |
0.16 | 0.31 | 8.5e-01 | 4m7d-assembly1_C Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU |
3jcm-assembly1_d |
0.15 | 0.31 | 1.0e+00 | 3jcm-assembly1_d Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP |
6n7r-assembly1_M |
0.14 | 0.25 | 5.6e-01 | 6n7r-assembly1_M Saccharomyces cerevisiae spliceosomal E complex (ACT1) |
3bw1-assembly1_A |
0.13 | 0.29 | 6.7e-01 | 3bw1-assembly1_A Crystal structure of homomeric yeast Lsm3 exhibiting novel octameric ring organisation |
6j6g-assembly1_g |
0.11 | 0.26 | 1.1e+00 | 6j6g-assembly1_g Cryo-EM structure of the yeast B*-a2 complex at an average resolution of 3.2 angstrom |
8tew-assembly1_T |
0.07 | 0.42 | 6.0e+00 | 8tew-assembly1_T Human cytomegalovirus penton vertex, CVSC-bound configuration |
8fnl-assembly1_G |
0.07 | 0.24 | 1.4e+00 | 8fnl-assembly1_G Structure of E138K/Q148K HIV-1 intasome with Dolutegravir bound |
6g90-assembly1_u |
0.05 | 0.23 | 3.1e+00 | 6g90-assembly1_u Prespliceosome structure provides insight into spliceosome assembly and regulation (map A2) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rnhB (ribonuclease HII), high confidence from genomic context alone (score 821 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) |
|---|---|---|---|---|
Rv2902c rnhB |
ribonuclease HII | 821 | 821 ctx | neighborhood:809 |
Rv2903c lepB |
signal peptidase | 812 | 812 ctx | neighborhood:802 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 773 | 773 ctx | cooccurence:770 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 769 | 770 ctx | cooccurence:767 |
Rv2904c rplS |
50S ribosomal protein L19 | 751 | 752 ctx | neighborhood:748 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 735 | 736 ctx | cooccurence:732 |
Rv1440 secG |
protein-export membrane protein SecG | 732 | 733 ctx | cooccurence:729 |
Rv1830 |
HTH-type transcriptional regulator | 732 | 733 ctx | cooccurence:730 |
Rv3681c whiB4 |
transcriptional regulator WhiB4 | 710 | 711 ctx | cooccurence:709 |
Rv2900c fdhF |
formate dehydrogenase subunit alpha FdhF | 674 | 675 ctx | neighborhood:670 |
Rv2899c fdhD |
formate dehydrogenase accessory protein FdhD | 673 | 674 ctx | neighborhood:670 |
Rv3416 whiB3 |
redox-responsive transcriptional regulator WhiB3 | 670 | 671 ctx | cooccurence:669 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 658 | 658 ctx | cooccurence:656 |
Rv2413c hyp |
hypothetical protein | 658 | 658 ctx | cooccurence:658 |
Rv2708c hyp |
hypothetical protein | 635 | 635 ctx | cooccurence:630 |
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: DUF2469 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF2469 PF10611.15 (E=4e-52)
- Foldseek best: 4m7d-assembly1_C Crystal structure of Lsm2-8 complex bound to the RNA fragment C (prob 0.16, E=8e-01, TM=0.31)
- (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_217417.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2469 (PF10611.15)
- 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
2AFXT - Curated reference: UniProt P9WL27 (SwissProt, reviewed; 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 49.1, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
39 functional partner(s); context anchor
rnhB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003083|Rv2901c| MSAEDLEKYETEMELSLYREYKDIVGQFSYVVETERRFYLANSVEMVPRNTDGEVYFELRLADAWVWDMYRPARFVKQVRVVTFKDVNIEEVEKPELRLPE