ureF Resolved · high auto-curated
H37Rv Rv1851 · MTBC0 mtbc0_001964 ·
211 aa · 2117732–2118367 (+) ·
RefSeq NP_216367.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | urease accessory protein UreF |
|---|---|
| MTBC0 PGAP re-annotation | urease accessory protein UreF |
| Revised (this work) | Urease accessory protein UreF. Pfam: UreF (PF01730.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFE5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Urease accessory protein UreF |
| Curated function | Required for maturation of urease via the functional incorporation of the urease nickel metallocenter. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | ureF |
| eggNOG description | Urease accessory protein UreF |
| Orthologous group | COG0830 |
| KEGG orthology |
K03188
|
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 | 0.8 · 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 |
|---|---|---|---|---|
UreF | PF01730.22 | 8.0e-18 | 36–171 | UreF |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ureD (urease accessory protein UreD), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1853 ureD |
urease accessory protein UreD | 999 | 999 ctx | neighborhood:874 cooccurence:774 coexpression:657 experimental:919 textmining:604 |
Rv1852 ureG |
urease accessory protein UreG | 999 | 997 ctx | neighborhood:874 coexpression:871 experimental:810 textmining:625 |
Rv1850 ureC |
urease subunit alpha | 996 | 991 ctx | neighborhood:882 coexpression:887 textmining:625 |
Rv1848 ureA |
urease subunit gamma | 985 | 982 ctx | neighborhood:882 coexpression:785 |
Rv1849 ureB |
urease subunit beta | 988 | 971 ctx | neighborhood:882 coexpression:654 textmining:625 |
Rv1847 |
esterase | 801 | 801 ctx | neighborhood:801 |
Rv0339c iniR |
transcriptional regulator | 601 | 602 ctx | cooccurence:596 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 569 | 569 ctx | cooccurence:567 |
Rv0342 iniA |
isoniazid inductible protein IniA | 560 | 560 ctx | cooccurence:560 |
Rv2709 |
transmembrane protein | 558 | 558 ctx | cooccurence:556 |
Rv3903c cpnT hyp |
hypothetical protein | 441 | 442 ctx | cooccurence:436 |
Rv1648 |
transmembrane protein | 438 | 439 ctx | cooccurence:437 |
Rv2164c hyp |
hypothetical protein | 429 | 430 ctx | cooccurence:426 |
Rv1524 |
glycosyltransferase | 421 | 422 ctx | cooccurence:413 |
Rv1526c |
glycosyltransferase | 406 | 407 ctx | cooccurence: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: urease accessory protein UreF
- MTBC0 PGAP product: urease accessory protein UreF
- Pfam (hmmscan --cut_ga): UreF PF01730.22 (E=8e-18)
- (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_216367.1)
- Domains: Pfam-A via hmmscan --cut_ga — UreF (PF01730.22)
- 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
COG0830 - Curated reference: UniProt P9WFE5 (SwissProt, reviewed; Inferred from homology)
- 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 —
15 functional partner(s); context anchor
ureD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001964|Rv1851|ureF MTSLAVLLTLADSRLPTGAHVHSGGIEEAIAAGMVTGLATLEAFLKRRVRTHGLLTASIAAAVHRGELAVDDADRETDARTPAPAARHASRSQGRGLIRLARRVWPDSGWEELGPRPHLAVVAGRVGALSGLAPEHNALHLVYITMTGSAIAAQRLLALDPAEVTVVTFQLSELCEQIAQEATAGLADLSDPLLDTLAQRHDERVRPLFVS