rpfD Resolved · high auto-curated
H37Rv Rv2389c · MTBC0 mtbc0_002542 ·
154 aa · 2707441–2707905 (-) ·
RefSeq NP_216905.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | resuscitation-promoting factor RpfD |
|---|---|
| MTBC0 PGAP re-annotation | resuscitation-promoting factor protein RpfD |
| Revised (this work) | Resuscitation-promoting factor protein RpfD. Pfam: Transglycosylas (PF06737.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG27
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Resuscitation-promoting factor RpfD |
| EC (curated) |
EC 3.-.-.-
|
| Curated function | Factor that stimulates resuscitation of dormant cells. Has peptidoglycan (PG) hydrolytic activity. Active in the pM concentration range. Has little to no effect on actively-growing cells. PG fragments could either directly activate the resuscitation pathway of dormant bacteria or serve as a substrate for endogenous Rpf, resulting in low molecular weight products with resuscitation activity..; FUNCTION: Stimulates growth of stationary phase M.bovis (a slow-growing Mycobacterium), reduces the lag phase of diluted fast-growers M.smegmatis and Micrococcus luteus. Sequential gene disruption indicat. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | rpfD |
| eggNOG description | Transglycosylase-like domain |
| Orthologous group | COG1388 |
| KEGG orthology |
K21690
|
| CAZy family |
GH23
|
| Gene Ontology (29) |
GO:0005575, GO:0005576, GO:0008150, GO:0009892, GO:0009893, GO:0010468, GO:0010604, GO:0010605, GO:0010628, GO:0010629, GO:0019222, GO:0022611 +17 more
|
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) | 1 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Transglycosylas | PF06737.20 | 1.9e-32 | 49–121 | Transglycosylase-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hemN (oxygen-independent coproporphyrinogen III oxidase), medium confidence from genomic context alone (score 642 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2390c hyp |
hypothetical protein | 922 | 895 ctx | neighborhood:882 |
Rv1954A |
Rv1954A, len: 100 aa. Hypothetical unknown protein. | 870 | 870 | coexpression:443 experimental:769 |
Rv2388c hemN |
oxygen-independent coproporphyrinogen III oxidase | 726 | 642 ctx | neighborhood:640 |
Rv0007 |
membrane protein | 498 | 498 | coexpression:498 |
Rv2466c hyp |
hypothetical protein | 466 | 466 ctx | cooccurence:466 |
Rv2286c hyp |
hypothetical protein | 458 | 458 ctx | cooccurence:453 |
Rv3268 hyp |
hypothetical protein | 446 | 446 ctx | cooccurence:443 |
Rv2771c hyp |
hypothetical protein | 444 | 423 | coexpression:423 |
Rv0819 mshD |
mycothiol acetyltransferase | 430 | 423 ctx | cooccurence:418 |
Rv0925c hyp |
hypothetical protein | 444 | 422 | coexpression:422 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 443 | 415 | coexpression:409 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 440 | 412 | coexpression:408 |
Rv3641c fic |
cell filamentation protein Fic | 402 | 403 | coexpression:403 |
Rv1052 hyp |
hypothetical protein | 401 | 402 | coexpression:402 |
Rv3669 |
transmembrane protein | 401 | 401 |
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: resuscitation-promoting factor RpfD
- MTBC0 PGAP product: resuscitation-promoting factor protein RpfD
- Pfam (hmmscan --cut_ga): Transglycosylas PF06737.20 (E=2e-32)
- (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_216905.1)
- Domains: Pfam-A via hmmscan --cut_ga — Transglycosylas (PF06737.20)
- 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
COG1388 - Curated reference: UniProt P9WG27 (SwissProt, reviewed; 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 —
23 functional partner(s); context anchor
hemN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002542|Rv2389c|rpfD MTPGLLTTAGAGRPRDRCARIVCTVFIETAVVATMFVALLGLSTISSKADDIDWDAIAQCESGGNWAANTGNGLYGGLQISQATWDSNGGVGSPAAASPQQQIEVADNIMKTQGPGAWPKCSSCSQGDAPLGSLTHILTFLAAETGGCSGSRDD