Rv1922 Resolved · high auto-curated
H37Rv Rv1922 · MTBC0 mtbc0_002036 ·
371 aa · 2193183–2194298 (+) ·
RefSeq NP_216438.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein |
|---|---|
| MTBC0 PGAP re-annotation | serine hydrolase |
| Revised (this work) | Serine hydrolase. Pfam: Beta-lactamase (PF00144.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95291
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved lipoprotein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | Beta-lactamase |
| Orthologous group | COG1680 |
| KEGG orthology |
K18372
|
| KEGG pathways |
map00640
|
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 | 0.856 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.18% of strains (259) · 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 |
|---|---|---|---|---|
Beta-lactamase | PF00144.30 | 1.2e-61 | 58–364 | Beta-lactamase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipD (lipase LipD), high confidence from genomic context alone (score 880 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1923 lipD |
lipase LipD | 880 | 880 ctx | neighborhood:773 cooccurence:491 |
Rv0074 hyp |
hypothetical protein | 450 | 451 ctx | cooccurence:450 |
Rv1921c lppF |
lipoprotein LppF | 444 | 444 ctx | neighborhood:436 |
Rv0907 hyp |
hypothetical protein | 470 | 292 | |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 421 | 69 | textmining:404 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 452 | 68 | textmining:437 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 440 | 50 | textmining:435 |
Rv2068c blaC |
beta-lactamase | 400 | 48 | |
Rv3677c |
beta lactamase | 810 | 47 | textmining:809 |
Rv1677 dsbF |
lipoprotein DsbF | 698 | 47 | textmining:697 |
Rv0406c |
beta lactamase-like protein | 814 | 46 | textmining:813 |
Rv1419 hyp |
hypothetical protein | 442 | 46 | textmining:440 |
Rv2864c |
penicillin-binding lipoprotein | 673 | 45 | textmining:672 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 460 | 45 | textmining:458 |
Rv2911 dacB2 |
penicillin-binding protein DacB2 | 671 | 43 | textmining:671 |
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: lipoprotein
- MTBC0 PGAP product: serine hydrolase
- Pfam (hmmscan --cut_ga): Beta-lactamase PF00144.30 (E=1e-61)
- (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_216438.1)
- Domains: Pfam-A via hmmscan --cut_ga — Beta-lactamase (PF00144.30)
- 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
COG1680 - Curated reference: UniProt P95291 (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 —
16 functional partner(s); context anchor
lipD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002036|Rv1922| MDSTVTASIRRMLGLLAATLLLGGCTGQHTTRTAASTTYTPHIKASSQDVLDGAINADEPGCSAAVGVEGKVIWSGVRGIADLASGAKITTDTVFDIASVSKQFTATAILLLVEAGKLTLDDPISQYVPELPDWAQTVTVEQLMHQTSGIPDYVALLAARGYQVSDRTIEAEARQALAAAPELQFKPGTRFDYSNSNYLLLGEIVHRASGQPLPEFLSAEIFQPLGLAMVVDPVGKVPNKAVSYEKGTGGNRSEYRVGNPAWEQIGDGGIQTTPSQLARWADNYRTGSVGGLKLLEAQLAGAVETEPGGGDRYGAGIVSRADGTLDHAGAWAGFVTAFHISSDRRTSVAISCNTDKPDPVAMADALGRLWM