secE2 Family assigned · medium auto-curated
H37Rv Rv0379 · MTBC0 - ·
71 aa · 455977–456192 (+) ·
RefSeq YP_177722.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | protein translocase subunit SecE |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Protein translocase subunit SecE. Pfam: Dodecin (PF07311.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
Q6MX43
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Calcium dodecin |
| Curated function | Binds calcium ions. May play a role in sequestering additional small ligands. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | secE2 |
| eggNOG description | Dodecin |
| Orthologous group | COG3360 |
| KEGG orthology |
K09165
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
Dodecin | PF07311.18 | 1.2e-20 | 3–65 | Dodecin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0377 (HTH-type transcriptional regulator), medium confidence from genomic context alone (score 667 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0377 |
HTH-type transcriptional regulator | 667 | 667 ctx | neighborhood:667 |
Rv0378 hyp |
hypothetical protein | 511 | 512 ctx | neighborhood:510 |
Rv3091 hyp |
hypothetical protein | 403 | 404 ctx | cooccurence:402 |
Rv0732 secY |
preprotein translocase SecY | 520 | 55 | textmining:513 |
Rv1440 secG |
protein-export membrane protein SecG | 718 | 51 | textmining:716 |
Rv2586c secF |
protein translocase subunit SecF | 719 | 47 | textmining:718 |
Rv2094c tatA |
Sec-independent protein translocase membrane-bound protein TatA | 414 | 47 | textmining:411 |
Rv0638 secE1 |
preprotein translocase SecE | 697 | 46 | textmining:696 |
Rv2587c secD |
protein translocase subunit SecD | 513 | 46 | textmining:511 |
Rv0559c hyp |
hypothetical protein | 751 | 41 | textmining:751 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): protein translocase subunit SecE
- Pfam (hmmscan --cut_ga): Dodecin PF07311.18 (E=1e-20)
- (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 YP_177722.1)
- Domains: Pfam-A via hmmscan --cut_ga — Dodecin (PF07311.18)
- 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
COG3360 - Curated reference: UniProt Q6MX43 (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 —
10 functional partner(s); context anchor
Rv0377 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0379|secE2 MSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR