clpS Resolved · high auto-curated
H37Rv Rv1331 · MTBC0 mtbc0_001428 ·
101 aa · 1511363–1511668 (+) ·
RefSeq NP_215847.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP-dependent Clp protease adapter protein ClpS |
|---|---|
| MTBC0 PGAP re-annotation | ATP-dependent Clp protease adapter ClpS |
| Revised (this work) | ATP-dependent Clp protease adapter ClpS. Pfam: ClpS (PF02617.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPC1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP-dependent Clp protease adapter protein ClpS |
| Curated function | Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | clpS |
| eggNOG description | Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation |
| Orthologous group | COG2127 |
| KEGG orthology |
K06891
|
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 | 0.291 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
ClpS | PF02617.23 | 1.4e-21 | 25–95 | ATP-dependent Clp protease adaptor protein ClpS |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1332 (transcriptional regulator), high confidence from genomic context alone (score 897 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1332 |
transcriptional regulator | 910 | 897 ctx | neighborhood:881 |
Rv1333 |
hydrolase | 895 | 890 ctx | neighborhood:861 |
Rv1334 mec |
[CysO | 861 | 862 ctx | neighborhood:861 |
Rv3596c clpC1 |
ATP-dependent protease ATP-binding subunit ClpC | 955 | 851 | experimental:773 textmining:712 |
Rv0384c clpB |
chaperone protein ClpB | 864 | 850 | experimental:773 |
Rv2667 clpC2 |
ATP-dependent protease ATP-binding subunit ClpC | 903 | 849 | experimental:773 |
Rv1335 cysO |
sulfur carrier protein CysO | 845 | 835 ctx | neighborhood:833 |
Rv1337 |
integral membrane protein | 850 | 832 ctx | neighborhood:829 |
Rv1336 cysM |
O-phosphoserine sulfhydrylase | 837 | 830 ctx | neighborhood:829 |
Rv1338 murI |
glutamate racemase | 829 | 829 ctx | neighborhood:829 |
Rv1339 hyp |
hypothetical protein | 798 | 798 ctx | neighborhood:797 |
Rv1340 rphA |
ribonuclease PH | 784 | 784 ctx | neighborhood:783 |
Rv1330c pncB1 |
nicotinic acid phosphoribosyltransferase PncB1 | 789 | 781 ctx | neighborhood:780 |
Rv1341 rdgB |
non-canonical purine NTP pyrophosphatase | 747 | 747 ctx | neighborhood:746 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 658 | 658 ctx | cooccurence:656 |
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: ATP-dependent Clp protease adapter protein ClpS
- MTBC0 PGAP product: ATP-dependent Clp protease adapter ClpS
- Pfam (hmmscan --cut_ga): ClpS PF02617.23 (E=1e-21)
- (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_215847.1)
- Domains: Pfam-A via hmmscan --cut_ga — ClpS (PF02617.23)
- 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
COG2127 - Curated reference: UniProt P9WPC1 (SwissProt, reviewed; 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 —
43 functional partner(s); context anchor
Rv1332 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001428|Rv1331|clpS MAVVSAPAKPGTTWQRESAPVDVTDRAWVTIVWDDPVNLMSYVTYVFQKLFGYSEPHATKLMLQVHNEGKAVVSAGSRESMEVDVSKLHAAGLWATMQQDR