ssd Resolved · high auto-curated
H37Rv Rv3660c · MTBC0 mtbc0_003878 ·
350 aa · 4121926–4122978 (-) ·
RefSeq NP_218177.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | septum site-determining protein Ssd |
| Revised (this work) | Septum site-determining protein Ssd. Pfam: Rv3660c_N (PF26563.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKX7
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3660c |
| Curated function | May play a role in septum formation. |
UniProt still lists this protein as Uncharacterized protein Rv3660c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | cpaE |
| eggNOG description | bacterial-type flagellum organization |
| Orthologous group | COG0455 |
| Gene Ontology (10) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0008150, GO:0040007, GO:0044424, GO:0044444, GO:0044464
|
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 | 1.449 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (157) · clonal |
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 |
|---|---|---|---|---|
Rv3660c_N | PF26563.1 | 1.4e-35 | 1–109 | Rv3660c-like, CheY-like N-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3659c (conjugal transfer protein), high confidence from genomic context alone (score 954 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) |
|---|---|---|---|---|
Rv3659c |
conjugal transfer protein | 977 | 954 ctx | neighborhood:773 coexpression:806 textmining:531 |
Rv3657c |
membrane protein | 980 | 903 ctx | neighborhood:754 cooccurence:599 textmining:810 |
Rv3658c |
transmembrane protein | 875 | 871 ctx | neighborhood:773 |
Rv3656c hyp |
hypothetical protein | 950 | 758 ctx | neighborhood:754 textmining:803 |
Rv0990c hyp |
hypothetical protein | 754 | 754 ctx | cooccurence:740 |
Rv3654c hyp |
hypothetical protein | 858 | 722 ctx | neighborhood:720 textmining:511 |
Rv2862c hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:539 |
Rv3780 bpa hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:539 |
Rv3655c hyp |
hypothetical protein | 540 | 528 ctx | neighborhood:521 |
Rv3118 sseC1 hyp |
hypothetical protein | 509 | 509 ctx | cooccurence:509 |
Rv0814c sseC2 hyp |
hypothetical protein | 509 | 509 ctx | cooccurence:509 |
Rv3286c sigF |
RNA polymerase sigma factor SigF | 545 | 505 | coexpression:420 |
Rv0051 |
transmembrane protein | 474 | 474 ctx | cooccurence:471 |
Rv1332 |
transcriptional regulator | 470 | 471 ctx | cooccurence:469 |
Rv1211 hyp |
hypothetical protein | 459 | 459 ctx | cooccurence:459 |
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: septum site-determining protein Ssd
- Pfam (hmmscan --cut_ga): Rv3660c_N PF26563.1 (E=1e-35)
- (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_218177.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv3660c_N (PF26563.1)
- 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
COG0455 - Curated reference: UniProt P9WKX7 (SwissProt, reviewed; Evidence at transcript 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 —
29 functional partner(s); context anchor
Rv3659c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003878|Rv3660c|ssd MLTDPGLRDELDRVAAAVGVRVVHLGGRHPVSRKTWSAAAAVVLDHAAADRCGRLALPRRTHVSVLTGTEAATATWAAAITVGAQHVLRMPEQEGELVRELAEAAESARDDGICGAVVAVIGGRGGAGASLFAVALAQAAADALLVDLDPWAGGIDLLVGGETAPGLRWPDLALQGGRLNWSAVRAALPRPRGISVLSGTRRGYELDAGPVDAVIDAGRRGGVTVVCDLPRRLTDATQAALDAADLVVLVSPCDVRACAAAATMAPVLTAINPNLGLVVRGPSPGGLRAAEVADVAGVPLLASMRAQPRLAEQLEHGGLRLRRRSVLASAARRVLGVLPRAGSGRHGRAA