Rv3013 Family assigned · low auto-curated
H37Rv Rv3013 · MTBC0 mtbc0_003202 ·
218 aa · 3393124–3393780 (+) ·
RefSeq NP_217529.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | amino acid-binding protein |
| Revised (this work) | Amino acid-binding 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 |
O53260
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)
| COG category |
K TranscriptionT Signal transduction mechanisms
|
|---|---|
| eggNOG description | Amino acid-binding |
| Orthologous group | COG0317 |
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) | 5 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3458c rpsD |
30S ribosomal protein S4 | 849 | 842 | experimental:812 |
Rv0704 rplB |
50S ribosomal protein L2 | 836 | 836 | experimental:812 |
Rv1298 rpmE |
50S ribosomal protein L31 | 844 | 835 | experimental:791 |
Rv2785c rpsO |
30S ribosomal protein S15 | 832 | 832 | experimental:826 |
Rv0723 rplO |
50S ribosomal protein L15 | 831 | 831 | experimental:826 |
Rv0721 rpsE |
30S ribosomal protein S5 | 840 | 830 | experimental:812 |
Rv0719 rplF |
50S ribosomal protein L6 | 837 | 829 | experimental:828 |
Rv0716 rplE |
50S ribosomal protein L5 | 826 | 827 | experimental:826 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 826 | 827 | experimental:826 |
Rv1643 rplT |
50S ribosomal protein L20 | 833 | 826 | experimental:812 |
Rv0715 rplX |
50S ribosomal protein L24 | 820 | 821 | experimental:812 |
Rv3442c rpsI |
30S ribosomal protein S9 | 832 | 820 | experimental:812 |
Rv0053 rpsF |
30S ribosomal protein S6 | 826 | 820 | experimental:812 |
Rv2909c rpsP |
30S ribosomal protein S16 | 819 | 820 | experimental:812 |
Rv3443c rplM |
50S ribosomal protein L13 | 829 | 819 | experimental:812 |
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: amino acid-binding protein
- (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_217529.1)
- 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
COG0317 - Curated reference: UniProt O53260 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 149 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003202|Rv3013| MRSYLLRIELADRPGSLGSLAVALGSVGADILSLDVVERGNGYAIDDLVVELPPGAMPDTLITAAEALNGVRVDSVRPHTGLLEAHRELELLDHVAAAEGATARLQVLVNEAPRVLRVSWCTVLRSSGGELHRLAGSPGAPETRANSAPWLPIERAAALDGGADWVPQAWRDMDTTMVAAPLGDTHTAVVLGRPGPEFRPSEVARLGYLAGIVATMLR