Rv3668c Resolved · medium auto-curated
H37Rv Rv3668c · MTBC0 mtbc0_003887 ·
232 aa · 4133613–4134311 (-) ·
RefSeq NP_218185.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | protease |
|---|---|
| MTBC0 PGAP re-annotation | protease |
| Revised (this work) | Protease. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YGW2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible protease |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | endopeptidase activity |
| Orthologous group | COG5640 |
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 | 0.172 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3802c (membrane protein), high confidence from genomic context alone (score 779 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3802c |
membrane protein | 778 | 779 ctx | cooccurence:769 |
Rv1275 lprC |
lipoprotein LprC | 774 | 775 ctx | cooccurence:773 |
Rv1274 lprB |
lipoprotein LprB | 773 | 774 ctx | cooccurence:771 |
Rv3244c lpqB |
lipoprotein LpqB | 768 | 768 ctx | cooccurence:762 |
Rv0531 |
membrane protein | 765 | 765 ctx | cooccurence:764 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 763 | 764 ctx | cooccurence:763 |
Rv3035 hyp |
hypothetical protein | 763 | 763 ctx | cooccurence:761 |
Rv1476 |
membrane protein | 759 | 759 ctx | cooccurence:759 |
Rv0227c |
membrane protein | 756 | 756 ctx | cooccurence:756 |
Rv2525c hyp |
hypothetical protein | 769 | 755 ctx | cooccurence:752 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 754 | 755 ctx | cooccurence:754 |
Rv1754c hyp |
hypothetical protein | 769 | 754 ctx | cooccurence:601 |
Rv3669 |
transmembrane protein | 733 | 733 ctx | neighborhood:693 |
Rv1100 hyp |
hypothetical protein | 731 | 731 ctx | cooccurence:731 |
Rv0466 hyp |
hypothetical protein | 725 | 725 ctx | cooccurence:724 |
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: protease
- MTBC0 PGAP product: protease
- (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_218185.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG5640 - Curated reference: UniProt I6YGW2 (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 —
115 functional partner(s); context anchor
Rv3802c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003887|Rv3668c| MQTAHRRFAAAFAAVLLAVVCLPANTAAADDKLPLGGGAGIVVNGDTMCTLTTIGHDKNGDLIGFTSAHCGGPGAQIAAEGAENAGPVGIMVAGNDGLDYAVIKFDPAKVTPVAVFNGFAINGIGPDPSFGQIACKQGRTTGNSCGVTWGPGESPGTLVMQVCGGPGDSGAPVTVDNLLVGMIHGAFSDNLPSCITKYIPLHTPAVVMSINADLADINAKNRPGAGFVPVPA