Rv3218 Family assigned · medium auto-curated
H37Rv Rv3218 · MTBC0 mtbc0_003424 ·
321 aa · 3616610–3617575 (+) ·
RefSeq NP_217734.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | diacylglycerol kinase family lipid kinase |
| Revised (this work) | Diacylglycerol kinase family lipid kinase. Pfam: DAGK_cat (PF00781.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05848
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 |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | diacylglycerol kinase, catalytic |
| Orthologous group | COG1597 |
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 | 0.264 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 |
|---|---|---|---|---|
DAGK_cat | PF00781.30 | 2.2e-24 | 2–119 | Diacylglycerol kinase catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3217c (integral membrane protein), high confidence from genomic context alone (score 748 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) |
|---|---|---|---|---|
Rv3217c |
integral membrane protein | 747 | 748 ctx | neighborhood:748 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 869 | 722 ctx | neighborhood:720 textmining:550 |
Rv0440 groEL2 |
molecular chaperone GroEL | 626 | 622 | database:608 |
Rv3417c groEL1 |
chaperonin GroEL | 625 | 621 | database:608 |
Rv0814c sseC2 hyp |
hypothetical protein | 482 | 483 ctx | cooccurence:482 |
Rv3118 sseC1 hyp |
hypothetical protein | 482 | 482 ctx | cooccurence:482 |
Rv1023 eno |
enolase | 446 | 446 | coexpression:446 |
Rv2844 hyp |
hypothetical protein | 425 | 426 ctx | cooccurence:422 |
Rv3231c hyp |
hypothetical protein | 421 | 422 ctx | cooccurence:420 |
Rv3752c tadA |
cytidine/deoxycytidylate deaminase | 415 | 77 | |
Rv1592c hyp |
hypothetical protein | 619 | 47 | textmining:617 |
Rv0022c whiB5 |
transcriptional regulator WhiB5 | 512 | 41 | textmining:512 |
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: diacylglycerol kinase family lipid kinase
- Pfam (hmmscan --cut_ga): DAGK_cat PF00781.30 (E=2e-24)
- (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_217734.1)
- Domains: Pfam-A via hmmscan --cut_ga — DAGK_cat (PF00781.30)
- 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
COG1597 - Curated reference: UniProt O05848 (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 —
12 functional partner(s); context anchor
Rv3217c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003424|Rv3218| MRAVLIVNPTATATTPAGRDLLAHALESRLQLTVEHTNHRGHGTELGQAAVADGVDLVVVHGGDGTVSAVVNGMLGRPGTTPVRPVPAVAVVPGGSANVLARALGISADPIAATNQLIQLLDDYGRHQQWRRIGLIDCGERWAVFNAGMGVDAEVVAAVEAERDKGGKVTAWRYIRAAVRAVLACTRREPALTLQLPNRDPITGVHFVFVSNSSPWTYANNRPVWTNPDCRFESGLGVFATTSMKVVPTLRVVRQMFAKQPKFEFNHVINNDDVACLRVTSMGPPIASQFDGDYLGVRETMTFRAVPDALAVVAPPARKRI