Rv0434 Family assigned · medium auto-curated
H37Rv Rv0434 · MTBC0 mtbc0_000456 ·
217 aa · 524879–525532 (+) ·
RefSeq NP_214948.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | LON peptidase substrate-binding domain-containing protein |
| Revised (this work) | LON peptidase substrate-binding domain-containing protein. Pfam: LON_substr_bdg (PF02190.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96280
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lon N-terminal domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | ATP-dependent protease |
| Orthologous group | COG2802 |
| EC number |
EC 3.4.21.53
|
| KEGG orthology |
K01338, K07157
|
| KEGG pathways |
map04112
|
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 | 0.552 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
LON_substr_bdg | PF02190.23 | 3.8e-33 | 8–204 | ATP-dependent protease La (LON) substrate-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0433 (carboxylate-amine ligase), high confidence from genomic context alone (score 827 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) |
|---|---|---|---|---|
Rv0433 |
carboxylate-amine ligase | 827 | 827 ctx | neighborhood:801 |
Rv0432 sodC |
superoxide dismutase | 804 | 804 ctx | neighborhood:801 |
Rv0431 |
tuberculin-like peptide | 760 | 760 ctx | neighborhood:758 |
Rv0430 hyp |
hypothetical protein | 740 | 741 ctx | neighborhood:739 |
Rv1277 hyp |
hypothetical protein | 699 | 683 | database:637 |
Rv1278 hyp |
hypothetical protein | 706 | 680 | database:637 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 705 | 676 | database:560 |
Rv0428c |
GCN5-like N-acetyltransferase | 665 | 665 ctx | neighborhood:609 |
Rv2337c hyp |
hypothetical protein | 658 | 645 | database:595 |
Rv3206c moeB1 |
adenylyltransferase/sulfurtransferase MoeZ | 658 | 645 | database:595 |
Rv2338c moeW |
molybdopterin biosynthesis protein MoeW | 657 | 645 | database:595 |
Rv0429c def |
polypeptide deformylase | 646 | 645 ctx | neighborhood:642 |
Rv3116 moeB2 |
molybdenum cofactor biosynthesis protein MoeB | 657 | 644 | database:595 |
Rv3196 hyp |
hypothetical protein | 657 | 644 | database:595 |
Rv1355c moeY |
molybdopterin biosynthesis protein MoeY | 656 | 643 | database:595 |
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: LON peptidase substrate-binding domain-containing protein
- Pfam (hmmscan --cut_ga): LON_substr_bdg PF02190.23 (E=4e-33)
- (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_214948.1)
- Domains: Pfam-A via hmmscan --cut_ga — LON_substr_bdg (PF02190.23)
- 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
COG2802 - Curated reference: UniProt P96280 (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 —
41 functional partner(s); context anchor
Rv0433 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000456|Rv0434| MADFAPVELAMFPLESAPLPDEDLPLHIFEPRYAALVRDCMDTADPRFGVVLISRGREVGGGDTRCDVGTLARITECADAGSGRYMLRCRVGERIRVCDWLPDDPYPRAKVRFWPDQPGHPVTAAQLLEVEDRVVALFERIAAARGVRLPAREVVLGYPVVDPADTGQRLYALACRVPMGPADRYAVLAAPSAADRLVRLGDALDSVAAMVEFELST