rpfB Resolved · high auto-curated
H37Rv Rv1009 · MTBC0 - ·
362 aa · 1128091–1129179 (+) ·
RefSeq NP_215525.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | resuscitation-promoting factor RpfB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Resuscitation-promoting factor RpfB. Pfam: DUF348 (PF03990.21), G5 (PF07501.18), Transglycosylas (PF06737.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WG29
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Resuscitation-promoting factor RpfB |
| 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: Reduces lag phase and enhances the growth of quiescent (1 month-old culture) M.tuberculosis; works best between 8 and 128 pM. Increases the number of bacteria that can be recovered from a 3 month. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | rpfB |
| eggNOG description | Resuscitation-promoting factor rpfB |
| Orthologous group | COG3583 |
| KEGG orthology |
K21688
|
| 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 | 2.157 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 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 |
|---|---|---|---|---|
DUF348 | PF03990.21 | 2.9e-09 | 27–66 | G5-linked-Ubiquitin-like domain |
G5 | PF07501.18 | 1.1e-18 | 198–271 | G5 domain |
Transglycosylas | PF06737.20 | 1.6e-34 | 283–355 | Transglycosylase-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ksgA (rRNA small subunit methyltransferase A), high confidence from genomic context alone (score 975 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1010 ksgA |
rRNA small subunit methyltransferase A | 995 | 975 ctx | neighborhood:881 coexpression:797 textmining:830 |
Rv1008 tatD |
deoxyribonuclease TatD | 913 | 736 ctx | neighborhood:734 textmining:687 |
Rv1886c fbpB |
diacylglycerol acyltransferase/mycolyltransferase Ag85B | 843 | 733 | coexpression:733 textmining:437 |
Rv1011 ispE |
4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 804 | 638 ctx | neighborhood:633 textmining:480 |
Rv1007c metS |
methionine--tRNA ligase | 621 | 621 ctx | neighborhood:619 |
Rv3268 hyp |
hypothetical protein | 537 | 538 ctx | cooccurence:535 |
Rv1012 hyp |
hypothetical protein | 517 | 517 ctx | neighborhood:515 |
Rv1823 hyp |
hypothetical protein | 466 | 466 ctx | cooccurence:457 |
Rv0481c hyp |
hypothetical protein | 442 | 442 ctx | cooccurence:438 |
Rv3212 hyp |
hypothetical protein | 465 | 440 ctx | cooccurence:433 |
Rv0012 |
membrane protein | 430 | 431 ctx | cooccurence:424 |
Rv3915 cwlM |
peptidoglycan hydrolase | 609 | 427 | |
Rv1824 hyp |
hypothetical protein | 421 | 421 ctx | cooccurence:409 |
Rv0950c hyp |
hypothetical protein | 547 | 415 | |
Rv2518c ldtB |
L,D-transpeptidase LdtB | 443 | 414 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): resuscitation-promoting factor RpfB
- Pfam (hmmscan --cut_ga): DUF348 PF03990.21 (E=3e-09), G5 PF07501.18 (E=1e-18), Transglycosylas PF06737.20 (E=2e-34)
- (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_215525.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF348 (PF03990.21), G5 (PF07501.18), 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
COG3583 - Curated reference: UniProt P9WG29 (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 —
41 functional partner(s); context anchor
ksgA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1009|rpfB MLRLVVGALLLVLAFAGGYAVAACKTVTLTVDGTAMRVTTMKSRVIDIVEENGFSVDDRDDLYPAAGVQVHDADTIVLRRSRPLQISLDGHDAKQVWTTASTVDEALAQLAMTDTAPAAASRASRVPLSGMALPVVSAKTVQLNDGGLVRTVHLPAPNVAGLLSAAGVPLLQSDHVVPAATAPIVEGMQIQVTRNRIKKVTERLPLPPNARRVEDPEMNMSREVVEDPGVPGTQDVTFAVAEVNGVETGRLPVANVVVTPAHEAVVRVGTKPGTEVPPVIDGSIWDAIAGCEAGGNWAINTGNGYYGGVQFDQGTWEANGGLRYAPRADLATREEQIAVAEVTRLRQGWGAWPVCAARAGAR