Rv1043c Resolved · high auto-curated
H37Rv Rv1043c · MTBC0 mtbc0_001120 ·
341 aa · 1173119–1174144 (-) ·
RefSeq NP_215559.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | serine protease |
| Revised (this work) | Serine protease. Pfam: Trypsin (PF00089.33), Trypsin_2 (PF13365.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96358
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Serine protease |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | Trypsin |
| Orthologous group | COG0265 |
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 | 0.538 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.43% of strains (619) · 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 |
|---|---|---|---|---|
Trypsin | PF00089.33 | 1.5e-08 | 143–297 | Trypsin |
Trypsin_2 | PF13365.13 | 2.4e-17 | 145–293 | Trypsin-like peptidase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS28 (PE-PGRS family protein PE_PGRS28), high confidence from genomic context alone (score 736 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) |
|---|---|---|---|---|
Rv2115c mpa |
proteasome-associated ATPase | 824 | 813 | experimental:551 database:594 |
Rv3696c glpK |
glycerol kinase | 769 | 754 | experimental:402 database:589 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 736 | 736 ctx | cooccurence:728 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 736 | 736 ctx | cooccurence:728 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 733 | 733 ctx | cooccurence:725 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 729 | 729 ctx | cooccurence:721 |
Rv1004c |
membrane protein | 738 | 726 ctx | cooccurence:702 |
Rv0355c PPE8 |
PPE family protein PPE8 | 721 | 722 ctx | cooccurence:718 |
Rv3350c PPE56 |
PPE family protein PPE56 | 719 | 720 ctx | cooccurence:716 |
Rv3347c PPE55 |
PPE family protein PPE55 | 718 | 718 ctx | cooccurence:714 |
Rv2209 |
integral membrane protein | 721 | 714 ctx | cooccurence:712 |
Rv2082 hyp |
hypothetical protein | 713 | 714 ctx | cooccurence:712 |
Rv1334 mec |
[CysO | 710 | 700 | database:576 |
Rv1045 hyp |
hypothetical protein | 697 | 697 ctx | neighborhood:460 cooccurence:459 |
Rv0304c PPE5 |
PPE family protein PPE5 | 696 | 696 ctx | cooccurence:692 |
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: serine protease
- Pfam (hmmscan --cut_ga): Trypsin PF00089.33 (E=1e-08), Trypsin_2 PF13365.13 (E=2e-17)
- (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_215559.1)
- Domains: Pfam-A via hmmscan --cut_ga — Trypsin (PF00089.33), Trypsin_2 (PF13365.13)
- 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
COG0265 - Curated reference: UniProt P96358 (TrEMBL, unreviewed; Predicted)
- 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 —
284 functional partner(s); context anchor
PE_PGRS28 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001120|Rv1043c| MCAHQFFGLVHNPVVAAAIGKPEPPPVDSDIGLPTTVPFEPWSVADFSRYLSTLGLPAAGDAVTLHRILSSMERAGLLLPLGWDPRLPVMGQKYISQGAISKGQRGGNLWLSEVFGAELIIPSYNAVTVQLAGHDDAGNPVDSWGTGLVVDHNHVITNKHVVTGLAGTSAGLSVYPSSNHAEAELVNFSGTAHPHPTLDVAVIKFEMPEGKYIPRLGGMAFRDPDWADEVYVFGYPRVPMTAEMAITVQRGEVVNPAATTIPGRQKIFLYSAIARPGNSGGPIVAQDGRVIGLVVEDSAEAPSTGTGPNAAPFYRGIPSSEVIRALDELDFGGIVEMDTLP