Rv1061 Resolved · high auto-curated
H37Rv Rv1061 · MTBC0 mtbc0_001141 ·
287 aa · 1191354–1192217 (+) ·
RefSeq NP_215577.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | class II glutamine amidotransferase |
| Revised (this work) | Class II glutamine amidotransferase. Pfam: GATase_4 (PF13230.12), GATase_6 (PF13522.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53409
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | glutamine amidotransferase |
| Orthologous group | COG0121 |
| EC number |
EC 3.5.1.118
|
| KEGG orthology |
K07008
|
| KEGG pathways |
map00340
|
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 | 0.854 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.18% of strains (255) · clonal |
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 |
|---|---|---|---|---|
GATase_4 | PF13230.12 | 7.7e-22 | 1–250 | Glutamine amidotransferases class-II |
GATase_6 | PF13522.12 | 5.7e-07 | 72–141 | Glutamine amidotransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD14 (fatty-acid--CoA ligase FadD14), high confidence from genomic context alone (score 714 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1062 hyp |
hypothetical protein | 908 | 908 ctx | neighborhood:882 |
Rv1060 hyp |
hypothetical protein | 853 | 853 ctx | neighborhood:832 |
Rv1059 hyp |
hypothetical protein | 804 | 804 ctx | neighborhood:772 |
Rv1058 fadD14 |
fatty-acid--CoA ligase FadD14 | 714 | 714 ctx | neighborhood:712 |
Rv1057 hyp |
hypothetical protein | 709 | 709 ctx | neighborhood:656 |
Rv0232 |
transcriptional regulator | 429 | 429 ctx | cooccurence:426 |
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: hypothetical protein
- MTBC0 PGAP product: class II glutamine amidotransferase
- Pfam (hmmscan --cut_ga): GATase_4 PF13230.12 (E=8e-22), GATase_6 PF13522.12 (E=6e-07)
- (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_215577.1)
- Domains: Pfam-A via hmmscan --cut_ga — GATase_4 (PF13230.12), GATase_6 (PF13522.12)
- 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
COG0121 - Curated reference: UniProt O53409 (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 —
6 functional partner(s); context anchor
fadD14 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001141|Rv1061| MCRLFGLHSGTDAVTATFWLLNASDSLAEQSRRNPDGTGLGVFDEHHQPRLHKQPIAAWQDADFATEAHELTGTTFVAHVRYATTGSLDIRNTHPFLQDGRIFAHNGVVEGLDVLDERLREVGADDLVLGQTDSERVFALITASIRARDGNESAGLIDALRWLAANVPIYAVNVLLSTATDVWALRYPESHELYILDRRGDGAPEFHLRSKRIRAHSTHLRERSSVVFATEPMDDNPRWRLLDAGELVHVDAALRVNRSLVLPDPPRHPIRREDLSEPVLHAQHTSA