ureA Family assigned · medium auto-curated
H37Rv Rv1848 · MTBC0 mtbc0_001961 ·
100 aa · 2115386–2115688 (+) ·
RefSeq NP_216364.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | urease subunit gamma |
|---|---|
| MTBC0 PGAP re-annotation | urease subunit gamma |
| Revised (this work) | Urease subunit gamma. Pfam: Urease_gamma (PF00547.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFE7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Urease subunit gamma |
| EC (curated) |
EC 3.5.1.5
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | ureA |
| eggNOG description | Belongs to the urease gamma subunit family |
| Orthologous group | COG0831 |
| EC number |
EC 3.5.1.5
|
| KEGG orthology |
K01430
|
| KEGG pathways |
map00220, map00230, map00791, map01100, map01120
|
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 | 0.343 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Urease_gamma | PF00547.24 | 1.2e-47 | 1–99 | Urease, gamma subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ureB (urease subunit beta), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1849 ureB |
urease subunit beta | 999 | 1000 ctx | neighborhood:882 fusion:899 cooccurence:774 coexpression:880 experimental:927 database:900 textmining:845 |
Rv1850 ureC |
urease subunit alpha | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:774 coexpression:860 experimental:928 database:900 |
Rv1852 ureG |
urease accessory protein UreG | 993 | 991 ctx | neighborhood:874 cooccurence:774 coexpression:716 |
Rv1851 ureF |
urease accessory protein UreF | 985 | 982 ctx | neighborhood:882 coexpression:785 |
Rv1853 ureD |
urease accessory protein UreD | 973 | 967 ctx | neighborhood:874 coexpression:709 |
Rv1847 |
esterase | 806 | 806 ctx | neighborhood:804 |
Rv2678c hemE |
uroporphyrinogen decarboxylase | 519 | 520 | coexpression:504 |
Rv1846c blaI |
transcriptional repressor BlaI | 402 | 402 | |
Rv2747 argA |
L-glutamate alpha-N-acetyltranferase | 662 | 56 | textmining:657 |
Rv1885c |
chorismate mutase | 804 | 47 | textmining:803 |
Rv2883c pyrH |
uridylate kinase | 551 | 47 | textmining:549 |
Rv2537c aroD |
3-dehydroquinate dehydratase | 755 | 44 | textmining:755 |
Rv3859c gltB |
glutamate synthase large subunit | 622 | 42 | textmining:622 |
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 subunit gamma
- MTBC0 PGAP product: urease subunit gamma
- Pfam (hmmscan --cut_ga): Urease_gamma PF00547.24 (E=1e-47)
- (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_216364.1)
- Domains: Pfam-A via hmmscan --cut_ga — Urease_gamma (PF00547.24)
- 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
COG0831 - Curated reference: UniProt P9WFE7 (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 —
13 functional partner(s); context anchor
ureB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001961|Rv1848|ureA MRLTPHEQERLLLSYAAELARRRRARGLRLNHPEAIAVIADHILEGARDGRTVAELMASGREVLGRDDVMEGVPEMLAEVQVEATFPDGTKLVTVHQPIA