Rv2778c Family assigned · medium auto-curated
H37Rv Rv2778c · MTBC0 mtbc0_002957 ·
156 aa · 3108128–3108598 (-) ·
RefSeq NP_217294.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SRPBCC family protein |
| Revised (this work) | SRPBCC family protein. Pfam: Polyketide_cyc2 (PF10604.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y1P2
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 |
S Function unknown
|
|---|---|
| eggNOG description | Polyketide cyclase / dehydrase and lipid transport |
| Orthologous group | COG3832 |
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) | 2 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (379) · clonal |
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 |
|---|---|---|---|---|
Polyketide_cyc2 | PF10604.16 | 1.4e-20 | 8–154 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2779c (Lrp/AsnC family transcriptional regulator), high confidence from genomic context alone (score 774 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) |
|---|---|---|---|---|
Rv2779c |
Lrp/AsnC family transcriptional regulator | 774 | 774 ctx | neighborhood:765 |
Rv0385 |
monooxygenase | 760 | 732 | coexpression:713 |
Rv2638 hyp |
hypothetical protein | 601 | 602 ctx | cooccurence:599 |
Rv2912c |
TetR family HTH-type transcriptional regulator | 582 | 582 ctx | cooccurence:578 |
Rv2777c hyp |
hypothetical protein | 560 | 560 ctx | neighborhood:471 |
Rv2776c |
oxidoreductase | 612 | 556 | |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 540 | 540 ctx | cooccurence:540 |
Rv1904 hyp |
hypothetical protein | 526 | 527 ctx | cooccurence:505 |
Rv0036c hyp |
hypothetical protein | 524 | 524 ctx | cooccurence:515 |
Rv2780 ald |
L-alanine dehydrogenase | 513 | 514 ctx | neighborhood:512 |
Rv1365c rsfA |
anti-sigma-F factor antagonist RsfA | 502 | 503 ctx | cooccurence:500 |
Rv0901 arfC |
membrane protein | 476 | 476 ctx | cooccurence:473 |
Rv1060 hyp |
hypothetical protein | 461 | 462 ctx | cooccurence:459 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 443 | 443 ctx | cooccurence:443 |
Rv0172 mce1D |
Mce family protein Mce1D | 414 | 414 ctx | cooccurence:406 |
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: SRPBCC family protein
- Pfam (hmmscan --cut_ga): Polyketide_cyc2 PF10604.16 (E=1e-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_217294.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polyketide_cyc2 (PF10604.16)
- 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
COG3832 - Curated reference: UniProt I6Y1P2 (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 —
18 functional partner(s); context anchor
Rv2779c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002957|Rv2778c| MPDPDGPSVTVTVEIDANPDLVYGLITDLPTLASLAEEVVAMQLRKGDDVRKGAVFVGRNENGGRRWTTTCTVTDADPGRVFAFDVRSGIIPISRWQYGIVATEHGCRVTESTWDRRPSWFRAVARMATGVKDRASVNTEHIRRTLQRLKDRAEAG