Rv2898c Family assigned · low auto-curated
H37Rv Rv2898c · MTBC0 mtbc0_003080 ·
128 aa · 3228771–3229157 (-) ·
RefSeq NP_217414.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YraN family protein |
| Revised (this work) | YraN family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFM9
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | UPF0102 protein Rv2898c |
UniProt still lists this protein as UPF0102 protein Rv2898c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | yraN |
| eggNOG description | Belongs to the UPF0102 family |
| Orthologous group | COG0792 |
| KEGG orthology |
K07460
|
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, 1 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 |
|---|---|---|---|---|
UPF0102 | PF02021.24 | 1.8e-28 | 16–108 | Uncharacterised protein family UPF0102 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: viuB (mycobactin utilization protein ViuB), high confidence from genomic context alone (score 837 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) |
|---|---|---|---|---|
Rv2897c hyp |
hypothetical protein | 965 | 963 ctx | neighborhood:882 cooccurence:676 |
Rv2896c dprA hyp |
hypothetical protein | 938 | 939 ctx | neighborhood:882 |
Rv2895c viuB |
mycobactin utilization protein ViuB | 837 | 837 ctx | neighborhood:836 |
Rv2899c fdhD |
formate dehydrogenase accessory protein FdhD | 729 | 729 ctx | neighborhood:726 |
Rv1364c |
sigma factor regulatory protein | 677 | 678 | coexpression:667 |
Rv1354c hyp |
hypothetical protein | 639 | 640 | coexpression:628 |
Rv2594c ruvC |
crossover junction endodeoxyribonuclease RuvC | 606 | 606 ctx | cooccurence:592 |
Rv2894c xerC |
tyrosine recombinase XerC | 599 | 600 ctx | neighborhood:598 |
Rv2900c fdhF |
formate dehydrogenase subunit alpha FdhF | 577 | 576 ctx | neighborhood:570 |
Rv2903c lepB |
signal peptidase | 497 | 497 | |
Rv2901c hyp |
hypothetical protein | 479 | 480 ctx | neighborhood:473 |
Rv2414c hyp |
hypothetical protein | 475 | 475 | |
Rv2904c rplS |
50S ribosomal protein L19 | 471 | 471 | |
Rv2926c hyp |
hypothetical protein | 463 | 463 ctx | cooccurence:446 |
Rv2902c rnhB |
ribonuclease HII | 438 | 438 ctx | neighborhood:430 |
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: YraN family protein
- Pfam (hmmscan --cut_ga): UPF0102 PF02021.24 (E=2e-28)
- (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_217414.1)
- Domains: Pfam-A via hmmscan --cut_ga — UPF0102 (PF02021.24)
- 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
COG0792 - Curated reference: UniProt P9WFM9 (SwissProt, reviewed; Inferred from homology)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
27 functional partner(s); context anchor
viuB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003080|Rv2898c| MTTLKTMTRVQLGAMGEALAVDYLTSMGLRILNRNWRCRYGELDVIACDAATRTVVFVEVKTRTGDGYGGLAHAVTERKVRRLRRLAGLWLADQEERWAAVRIDVIGVRVGPKNSGRTPELTHLQGIG