Rv1879 Family assigned · medium auto-curated
H37Rv Rv1879 · MTBC0 mtbc0_001993 ·
378 aa · 2147416–2148552 (+) ·
RefSeq NP_216395.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | amidohydrolase family protein |
| Revised (this work) | Amidohydrolase family protein. Pfam: Amidohydro_2 (PF04909.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07751
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Amidohydrolase-related domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | amidohydrolase |
| Orthologous group | COG2159 |
| KEGG orthology |
K07045
|
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, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.31% of strains (446) · 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 |
|---|---|---|---|---|
Amidohydro_2 | PF04909.21 | 3.8e-12 | 186–375 | Amidohydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glnA3 (glutamine synthetase GlnA), high confidence from genomic context alone (score 995 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) |
|---|---|---|---|---|
Rv1878 glnA3 |
glutamine synthetase GlnA | 998 | 995 ctx | neighborhood:881 fusion:862 cooccurence:697 textmining:654 |
Rv2222c glnA2 |
glutamine synthetase | 893 | 893 ctx | fusion:889 |
Rv1877 |
MFS-type transporter | 820 | 808 ctx | neighborhood:806 |
Rv1876 bfrA |
bacterioferritin BfrA | 738 | 738 ctx | neighborhood:732 |
Rv2860c glnA4 |
glutamine synthetase | 563 | 563 ctx | fusion:489 |
Rv1260 |
oxidoreductase | 497 | 472 | |
Rv1117 hyp |
hypothetical protein | 403 | 404 | |
Rv2220 glnA1 |
glutamine synthetase | 430 | 312 | |
Rv1870c hyp |
hypothetical protein | 480 | 274 | |
Rv1841c hyp |
hypothetical protein | 805 | 55 | textmining:803 |
Rv0072 |
glutamine ABC transporter permease | 518 | 55 | textmining:511 |
Rv1395 |
HTH-type transcriptional regulator | 552 | 47 | textmining:550 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 436 | 46 | textmining:434 |
Rv0071 |
maturase | 433 | 46 | textmining:431 |
Rv0095c hyp |
hypothetical protein | 433 | 44 | textmining:432 |
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: amidohydrolase family protein
- Pfam (hmmscan --cut_ga): Amidohydro_2 PF04909.21 (E=4e-12)
- (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_216395.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidohydro_2 (PF04909.21)
- 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
COG2159 - Curated reference: UniProt O07751 (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 —
15 functional partner(s); context anchor
glnA3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001993|Rv1879| MADSAGSDLTRHTAEVPLIDQHVHGCWLTEGNRRRFENALNEANTEPLADFDSGFDSQLGFAVRNHCAPILGLPRHVDPQTYWDRRSQFSEAELARRFLQAAGVTDWLVETGIGYDVSGMASVAGLGELSGSHAHEVVRLEQVAEQAVQASGDYASAFNEILRRRAATAVATKSILAYRGGFDGDLTEPPAAQVAEAAKRWRDRGGVRLQDRVLLRFGLHQALRLGKPLQFHVGFGDRDADLHKANPLYLLDFLRQSGNTPIVLLHCYPYEREAGYLAQAFNNVYLDGGLSVHYLGARSPAFIGRLLELAPFRKIVYSSDGFGPAELHFLGATLWRSGIQRVLRGFVERDDWCETDALRVVDLIAHGTAARIYRLGDR