scpA Resolved · high auto-curated
H37Rv Rv1709 · MTBC0 mtbc0_001819 ·
278 aa · 1949328–1950164 (+) ·
RefSeq NP_216225.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | segregation and condensation protein ScpA |
|---|---|
| MTBC0 PGAP re-annotation | segregation/condensation protein A |
| Revised (this work) | Segregation/condensation protein A. Pfam: SMC_ScpA (PF02616.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33208
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Segregation and condensation protein A |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | scpA |
| eggNOG description | Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpB that pull DNA away from mid-cell into both cell halves |
| Orthologous group | COG1354 |
| KEGG orthology |
K05896
|
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 | 0.939 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 |
|---|---|---|---|---|
SMC_ScpA | PF02616.20 | 4.7e-94 | 40–264 | Segregation and condensation protein ScpA |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: scpB (segregation and condensation protein ScpB), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1710 scpB |
segregation and condensation protein ScpB | 999 | 1000 ctx | neighborhood:881 cooccurence:773 coexpression:944 experimental:928 textmining:957 |
Rv1708 |
initiation inhibitor protein | 976 | 974 ctx | neighborhood:881 coexpression:736 |
Rv1712 cmk |
cytidylate kinase | 983 | 970 ctx | neighborhood:881 coexpression:761 textmining:479 |
Rv2922c smc |
chromosome partition protein Smc | 983 | 952 ctx | cooccurence:764 experimental:788 textmining:670 |
Rv1711 |
RNA pseudouridine synthase | 964 | 932 ctx | neighborhood:881 coexpression:451 textmining:505 |
Rv1713 engA |
GTPase Der | 937 | 928 ctx | neighborhood:881 |
Rv3769 hyp |
hypothetical protein | 827 | 805 | experimental:788 |
Rv2731 hyp |
hypothetical protein | 820 | 801 | experimental:788 |
Rv1707 |
transmembrane protein | 744 | 745 ctx | neighborhood:744 |
Rv1703c |
methyltransferase | 679 | 680 ctx | neighborhood:544 |
Rv3602c panC |
pantothenate synthetase | 523 | 523 | coexpression:484 |
Rv3102c ftsE |
cell division ATP-binding protein FtsE | 533 | 515 | coexpression:499 |
Rv1714 |
oxidoreductase | 497 | 497 ctx | neighborhood:476 |
Rv1716 hyp |
hypothetical protein | 484 | 484 ctx | neighborhood:476 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 483 | 483 ctx | neighborhood:476 |
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: segregation and condensation protein ScpA
- MTBC0 PGAP product: segregation/condensation protein A
- Pfam (hmmscan --cut_ga): SMC_ScpA PF02616.20 (E=5e-94)
- (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_216225.1)
- Domains: Pfam-A via hmmscan --cut_ga — SMC_ScpA (PF02616.20)
- 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
COG1354 - Curated reference: UniProt O33208 (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 —
39 functional partner(s); context anchor
scpB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001819|Rv1709|scpA MNGLQNSLANGGTAPENGYSAGFRVRLTNFEGPFDLLLQLIFAHQLDVTEVALHQVTDDFIAYTKAIGARLELEETTAFLVIAATLLDLKAARLLPAGQVDDEEDLALLEVRDLLFARLLQYRAFKHVAEMFAELEATALRSYPRAVSLEDGFVGLLPEVMLGVDAHRFAEIAAIALTPRPAPTVATEHLHELMVSVPEQAEHLLAMLKARGSGQWASFSELVADCTAPIEIVGRFLALLELYRTRAVAFEQSEPLGALQVSWTGDDAERSDEKERRL