cpsA Family assigned · medium auto-curated
H37Rv Rv3484 · MTBC0 mtbc0_003699 ·
512 aa · 3927660–3929198 (+) ·
RefSeq NP_218001.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | LCP family protein |
| Revised (this work) | LCP family protein. Pfam: LytR_cpsA_psr (PF03816.20), LytR_C (PF13399.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06347
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved protein CpsA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | cpsA |
| eggNOG description | transcriptional |
| Orthologous group | COG1316 |
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 | 0.117 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
LytR_cpsA_psr | PF03816.20 | 3.6e-40 | 109–281 | LytR_cpsA_psr family |
LytR_C | PF13399.12 | 2.5e-12 | 379–464 | LytR cell envelope-related transcriptional attenuator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsdA (anti-sigma-D factor RsdA), medium confidence from genomic context alone (score 592 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) |
|---|---|---|---|---|
Rv3896c hyp |
hypothetical protein | 610 | 610 ctx | cooccurence:609 |
Rv3413c rsdA |
anti-sigma-D factor RsdA | 592 | 592 ctx | cooccurence:592 |
Rv3483c hyp |
hypothetical protein | 787 | 583 ctx | neighborhood:578 textmining:510 |
Rv0090 |
membrane protein | 503 | 503 ctx | cooccurence:503 |
Rv3482c |
membrane protein | 449 | 449 ctx | neighborhood:435 |
Rv1006 hyp |
hypothetical protein | 446 | 446 ctx | cooccurence:443 |
Rv2214c ephD |
oxidoreductase EphD | 429 | 429 ctx | cooccurence:427 |
Rv3840 |
transcriptional regulator | 929 | 423 | textmining:884 |
Rv1682 hyp |
hypothetical protein | 419 | 419 ctx | cooccurence:419 |
Rv1896c |
S-adenosyl-L-methionine-dependent methyltransferase | 412 | 412 ctx | cooccurence:410 |
Rv3718c hyp |
hypothetical protein | 406 | 406 ctx | cooccurence:406 |
Rv0180c |
transmembrane protein | 409 | 385 | |
Rv1868 hyp |
hypothetical protein | 406 | 385 | |
Rv2147c sepF |
cell division protein SepF | 427 | 343 | |
Rv2903c lepB |
signal peptidase | 564 | 244 | textmining:448 |
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: LCP family protein
- Pfam (hmmscan --cut_ga): LytR_cpsA_psr PF03816.20 (E=4e-40), LytR_C PF13399.12 (E=2e-12)
- (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_218001.1)
- Domains: Pfam-A via hmmscan --cut_ga — LytR_cpsA_psr (PF03816.20), LytR_C (PF13399.12)
- 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
COG1316 - Curated reference: UniProt O06347 (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 —
31 functional partner(s); context anchor
rsdA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003699|Rv3484|cpsA MARSEGNRPRHRAVPQPSRIRKRLSRGVMTLVSVVALLMTGAGYWVAHGALGGITISQALTPEDPRSSGNNMNILLIGLDSRKDQEGNDLPWSVLKQLHAGDSDDGGYNTNTLILVHVGADGKVVAFSIPRDDWVPFTGVPGYNHIKIKEAYGLTKQYVAEQLANQGVSDRKELETRGREAARAATLRAVRSLTGVPIDYFAEINLAGFYDLAQTLGGVDVCLNHAVYDSYSGADFPAGRQRLNAAQALAFVRQRHGLDNGDLDRTHRQQAFLSSVMRELQDSGTFTNLDRLDNLMAVARKDVVLSAGWDEDLFRRMGDLAGGNVEFRTLPVVRYDNIDGQDVNIIDPTAIRAEVAAAFGSAPPTSQTAAAAKPNPSTVVDVVNAGSISGLASQVSGALLKRGYTAGQVRDRESGDPFTTAIEYGAGAETDAQNVADLLGIDAPNHPDPAVAPGHIRVTVDTNFSLPAPDEATAAATSTETSTYPLYGGGTTTDPTPDQGAPIDGGGVPCVN