Rv0309 Resolved · high auto-curated
H37Rv Rv0309 · MTBC0 mtbc0_000329 ·
218 aa · 381254–381910 (+) ·
RefSeq NP_214823.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | L%2CD-transpeptidase |
| Revised (this work) | L%2CD-transpeptidase. Pfam: YkuD (PF03734.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07236
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved exported protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | protein conserved in bacteria |
| Orthologous group | COG3786 |
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 | 0.655 · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
YkuD | PF03734.20 | 5.6e-06 | 87–215 | L,D-transpeptidase catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0308 (integral membrane protein), high confidence from genomic context alone (score 817 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) |
|---|---|---|---|---|
Rv0308 |
integral membrane protein | 817 | 817 ctx | neighborhood:771 |
Rv1303 hyp |
hypothetical protein | 717 | 718 ctx | cooccurence:717 |
Rv0307c hyp |
hypothetical protein | 685 | 685 ctx | neighborhood:684 |
Rv0185 hyp |
hypothetical protein | 575 | 576 ctx | cooccurence:573 |
Rv0184 hyp |
hypothetical protein | 524 | 524 ctx | cooccurence:521 |
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 474 | 475 ctx | cooccurence:474 |
Rv1702c hyp |
hypothetical protein | 461 | 461 ctx | cooccurence:460 |
Rv0450c mmpL4 |
transmembrane transport protein MmpL4 | 447 | 448 ctx | cooccurence:445 |
Rv2339 mmpL9 |
transmembrane transport protein MmpL9 | 442 | 443 ctx | cooccurence:441 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 440 | 441 ctx | cooccurence:437 |
Rv1598c hyp |
hypothetical protein | 432 | 433 ctx | cooccurence:432 |
Rv1148c hyp |
hypothetical protein | 432 | 432 ctx | cooccurence:432 |
Rv2301 cut2 |
cutinase | 427 | 428 ctx | cooccurence:421 |
Rv1304 atpB |
ATP synthase subunit A | 427 | 428 ctx | cooccurence:423 |
Rv3467 hyp |
hypothetical protein | 423 | 423 ctx | cooccurence:423 |
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: L%2CD-transpeptidase
- Pfam (hmmscan --cut_ga): YkuD PF03734.20 (E=6e-06)
- (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_214823.1)
- Domains: Pfam-A via hmmscan --cut_ga — YkuD (PF03734.20)
- 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
COG3786 - Curated reference: UniProt O07236 (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 —
33 functional partner(s); context anchor
Rv0308 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000329|Rv0309| MSRLLALLCAAVCTGCVAVVLAPVSLAVVNPWFANSVGNATQVVSVVGTGGSTAKMDVYQRTAAGWQPLKTGITTHIGSAGMAPEAKSGYPATPMGVYSLDSAFGTAPNPGGGLPYTQVGPNHWWSGDDNSPTFNSMQVCQKSQCPFSTADSENLQIPQYKHSVVMGVNKAKVPGKGSAFFFHTTDGGPTAGCVAIDDATLVQIIRWLRPGAVIAIAK