Rv2908c Family assigned · medium auto-curated
H37Rv Rv2908c · MTBC0 mtbc0_003090 ·
80 aa · 3237734–3237976 (-) ·
RefSeq NP_217424.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | RNA-binding protein |
| Revised (this work) | RNA-binding protein. Pfam: KH_KhpA-B (PF13083.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFM7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | RNA-binding protein KhpA |
| Curated function | A probable RNA-binding protein. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Belongs to the UPF0109 family |
| Orthologous group | COG1837 |
| KEGG orthology |
K06960
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 |
|---|---|---|---|---|
KH_KhpA-B | PF13083.14 | 1.7e-20 | 7–69 | KhpA/KhpB, KH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsP (30S ribosomal protein S16), high confidence from genomic context alone (score 989 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) |
|---|---|---|---|---|
Rv2909c rpsP |
30S ribosomal protein S16 | 990 | 989 ctx | neighborhood:882 coexpression:911 |
Rv2907c rimM |
16S rRNA processing protein RimM | 960 | 959 ctx | neighborhood:872 coexpression:692 |
Rv3920c hyp |
hypothetical protein | 992 | 931 | experimental:891 textmining:889 |
Rv3442c rpsI |
30S ribosomal protein S9 | 902 | 903 | coexpression:896 |
Rv2906c trmD |
tRNA (guanine-N1)-methyltransferase | 885 | 885 ctx | neighborhood:872 |
Rv2904c rplS |
50S ribosomal protein L19 | 862 | 863 | coexpression:840 |
Rv3458c rpsD |
30S ribosomal protein S4 | 830 | 830 | coexpression:827 |
Rv2785c rpsO |
30S ribosomal protein S15 | 831 | 826 | coexpression:823 |
Rv1643 rplT |
50S ribosomal protein L20 | 810 | 811 | coexpression:805 |
Rv1298 rpmE |
50S ribosomal protein L31 | 780 | 780 | coexpression:780 |
Rv2412 rpsT |
30S ribosomal protein S20 | 780 | 780 | coexpression:780 |
Rv0652 rplL |
50S ribosomal protein L7/L12 | 781 | 774 | coexpression:774 |
Rv3456c rplQ |
50S ribosomal protein L17 | 738 | 738 | coexpression:730 |
Rv0979A rpmF |
50S ribosomal protein L32 | 735 | 736 | coexpression:714 |
Rv2441c rpmA |
50S ribosomal protein L27 | 709 | 710 | coexpression:698 |
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: RNA-binding protein
- Pfam (hmmscan --cut_ga): KH_KhpA-B PF13083.14 (E=2e-20)
- (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_217424.1)
- Domains: Pfam-A via hmmscan --cut_ga — KH_KhpA-B (PF13083.14)
- 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
COG1837 - Curated reference: UniProt P9WFM7 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
59 functional partner(s); context anchor
rpsP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003090|Rv2908c| MSAVVVDAVEHLVRGIVDNPDDVRVDLITSRRGRTVEVHVHPDDLGKVIGRGGRTATALRTLVAGIGGRGIRVDVVDTDQ