Rv3194c Family assigned · medium auto-curated
H37Rv Rv3194c · MTBC0 mtbc0_003395 ·
340 aa · 3585396–3586418 (-) ·
RefSeq NP_217710.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | PDZ domain-containing protein |
| Revised (this work) | PDZ domain-containing protein. Pfam: PDZ_2 (PF13180.13), Lon_C (PF05362.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53340
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | endopeptidase La |
| EC (curated) |
EC 3.4.21.53
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | lon |
| eggNOG description | Belongs to the peptidase S16 family |
| Orthologous group | COG3480 |
| KEGG orthology |
K07177
|
| KEGG pathways |
map02024
|
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 | 1.031 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
PDZ_2 | PF13180.13 | 8.3e-10 | 135–193 | PDZ domain |
Lon_C | PF05362.20 | 1.7e-08 | 236–305 | Lon protease (S16) C-terminal proteolytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3193c (transmembrane protein), high confidence from genomic context alone (score 803 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) |
|---|---|---|---|---|
Rv3195 hyp |
hypothetical protein | 837 | 838 ctx | neighborhood:784 |
Rv3193c |
transmembrane protein | 804 | 803 ctx | neighborhood:778 |
Rv3196 hyp |
hypothetical protein | 567 | 566 ctx | neighborhood:566 |
Rv2145c wag31 |
cell wall synthesis protein Wag31 | 536 | 536 ctx | cooccurence:521 |
Rv1423 whiA |
transcriptional regulator WhiA | 527 | 527 ctx | cooccurence:527 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 530 | 430 ctx | cooccurence:430 |
Rv2413c hyp |
hypothetical protein | 416 | 416 | |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 640 | 414 ctx | cooccurence:414 textmining:411 |
Rv1830 |
HTH-type transcriptional regulator | 413 | 413 ctx | cooccurence:413 |
Rv2147c sepF |
cell division protein SepF | 404 | 404 ctx | cooccurence:404 |
Rv2965c kdtB |
phosphopantetheine adenylyltransferase | 400 | 363 | |
Rv2175c |
DNA-binding protein | 516 | 260 | |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 411 | 45 | textmining:409 |
Rv0814c sseC2 hyp |
hypothetical protein | 656 | 41 | textmining:656 |
Rv2672 |
protease | 541 | 41 | textmining:541 |
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: PDZ domain-containing protein
- Pfam (hmmscan --cut_ga): PDZ_2 PF13180.13 (E=8e-10), Lon_C PF05362.20 (E=2e-08)
- (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_217710.1)
- Domains: Pfam-A via hmmscan --cut_ga — PDZ_2 (PF13180.13), Lon_C (PF05362.20)
- 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
COG3480 - Curated reference: UniProt O53340 (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 —
20 functional partner(s); context anchor
Rv3193c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003395|Rv3194c| MNRRILTLMVALVPIVVFGVLLAVVTVPFVALGPGPTFDTLGEIDGKQVVQIVGTQTYPTSGHLNMTTVSQRDGLTLGEALALWLSGQEQLMPRDLVYPPGKSREEIENDNAADFKRSEAAAEYAALGYLKYPKAVTVASVMDPGPSVDKLQAGDAIDAVDGTPVGNLDQFTALLKNTKPGQEVTIDFRRKNEPPGIAQITLGKNKDRDQGVLGIEVVDAPWAPFAVDFHLANVGGPSAGLMFSLAVVDKLTSGHLVGSTFVAGTGTIAVDGKVGQIGGITHKMAAARAAGATVFLVPAKNCYEASSDSPPGLKLVKVETLSQAVDALHAMTSGSPTPSC