Rv3103c Still unknown · low auto-curated
H37Rv Rv3103c · MTBC0 mtbc0_003299 ·
145 aa · 3492777–3493214 (-) ·
RefSeq NP_217619.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05780
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Hypothetical proline-rich protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2ATJE |
|---|
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 | 0.755 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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)
Closest characterised functional partner: Rv3104c (transmembrane protein), high confidence from genomic context alone (score 882 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) |
|---|---|---|---|---|
Rv3104c |
transmembrane protein | 883 | 882 ctx | neighborhood:882 |
Rv3105c prfB |
peptide chain release factor PrfB | 881 | 881 ctx | neighborhood:881 |
Rv3354 hyp |
hypothetical protein | 875 | 837 | experimental:814 |
Rv3106 fprA |
NADPH-ferredoxin reductase FprA | 717 | 718 ctx | neighborhood:718 |
Rv3101c ftsX |
cell division protein FtsX | 690 | 690 ctx | neighborhood:682 |
Rv3102c ftsE |
cell division ATP-binding protein FtsE | 689 | 689 ctx | neighborhood:682 |
Rv3100c smpB |
SsrA-binding protein | 708 | 682 ctx | neighborhood:682 |
Rv3099c hyp |
hypothetical protein | 633 | 634 ctx | neighborhood:634 |
Rv0393 hyp |
hypothetical protein | 618 | 594 | experimental:512 |
Rv1702c hyp |
hypothetical protein | 618 | 594 | experimental:512 |
Rv0297 PE_PGRS5 |
PE-PGRS family protein PE_PGRS5 | 618 | 594 | experimental:512 |
Rv0397 hyp |
hypothetical protein | 618 | 594 | experimental:512 |
Rv3653 PE_PGRS61 |
PE-PGRS family-related protein PE_PGRS61 | 618 | 594 | experimental:512 |
Rv1945 hyp |
hypothetical protein | 618 | 594 | experimental:512 |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 603 | 460 | experimental:421 |
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
- (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_217619.1)
- 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
2ATJE - Curated reference: UniProt O05780 (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 84.3, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
18 functional partner(s); context anchor
Rv3104c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003299|Rv3103c| MKLSNQKRHWPGYLFGRIRTSTLVLIAAFLAVWWIYETYRPQAPGPGDSPPTQVVPPGFVPDPDYTWVPRTRVQPPTVKATPTTTSSTPPVSPPETTTDSAVPPPFELPPPFGPGTTTPTPPAPLPQPGPGPTAGTYPKSEPPTR