ureD Resolved · high auto-curated
H37Rv Rv1853 · MTBC0 - ·
208 aa · 2101022–2101648 (+) ·
RefSeq NP_216369.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | urease accessory protein UreD |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Urease accessory protein UreD. Pfam: UreD (PF01774.23). |
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 |
P95161
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable urease accessory protein UreD |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | ureD |
| eggNOG description | urease accessory protein |
| Orthologous group | COG0829 |
| KEGG orthology |
K03190
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
UreD | PF01774.23 | 2.3e-15 | 29–162 | UreD urease accessory protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ureF (urease accessory protein UreF), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1851 ureF |
urease accessory protein UreF | 999 | 999 ctx | neighborhood:874 cooccurence:774 coexpression:657 experimental:919 textmining:604 |
Rv1852 ureG |
urease accessory protein UreG | 992 | 983 ctx | neighborhood:882 coexpression:728 experimental:446 textmining:590 |
Rv1849 ureB |
urease subunit beta | 987 | 971 ctx | neighborhood:874 coexpression:747 textmining:592 |
Rv1848 ureA |
urease subunit gamma | 973 | 967 ctx | neighborhood:874 coexpression:709 |
Rv1850 ureC |
urease subunit alpha | 961 | 925 ctx | neighborhood:874 coexpression:431 textmining:513 |
Rv0339c iniR |
transcriptional regulator | 749 | 750 ctx | cooccurence:745 |
Rv1847 |
esterase | 712 | 712 ctx | neighborhood:711 |
Rv0538 |
membrane protein | 668 | 669 ctx | cooccurence:664 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 668 | 668 ctx | cooccurence:667 |
Rv0342 iniA |
isoniazid inductible protein IniA | 656 | 656 ctx | cooccurence:656 |
Rv2164c hyp |
hypothetical protein | 646 | 647 ctx | cooccurence:645 |
Rv2709 |
transmembrane protein | 629 | 629 ctx | cooccurence:629 |
Rv1648 |
transmembrane protein | 626 | 627 ctx | cooccurence:625 |
Rv3254 hyp |
hypothetical protein | 607 | 608 ctx | cooccurence:600 |
Rv3909 hyp |
hypothetical protein | 587 | 587 ctx | cooccurence:586 |
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): urease accessory protein UreD
- Pfam (hmmscan --cut_ga): UreD PF01774.23 (E=2e-15)
- (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_216369.1)
- Domains: Pfam-A via hmmscan --cut_ga — UreD (PF01774.23)
- 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
COG0829 - Curated reference: UniProt P95161 (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 —
36 functional partner(s); context anchor
ureF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1853|ureD MVASPNRLPRIDCRGGVQARRTAPDTVHLVSAAATPLGGDTMRIRVIVERGAQLRLRSAAATVALPGVDTLTSHAHWEIDVTGTLDVDLEPTVVAASARHLSHATLRLHDDGRVRLRERVQIGRCNEREGFWSSSLQADRHGRPLLRHRVELGAGSLADDVIAAPRATISELRYPATAFTDAIDARSTVLALAGGGTLSTWQADRLPG