secE1 Resolved · high auto-curated
H37Rv Rv0638 · MTBC0 - ·
161 aa · 733737–734222 (+) ·
RefSeq YP_177743.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | preprotein translocase SecE |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Preprotein translocase SecE. Pfam: SecE (PF00584.26). |
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 |
P9WGN7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein translocase subunit SecE |
| Curated function | Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | secE |
| eggNOG description | Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation |
| Orthologous group | COG0690 |
| KEGG orthology |
K03073
|
| KEGG pathways |
map02024, map03060, map03070
|
| KEGG modules |
M00335
|
| Gene Ontology (16) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226, GO:0040007 +4 more
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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 |
|---|---|---|---|---|
SecE | PF00584.26 | 1.2e-18 | 107–160 | SecE/Sec61-gamma subunits of protein translocation complex |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nusG (transcription termination/antitermination protein NusG), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1440 secG |
protein-export membrane protein SecG | 999 | 998 | coexpression:668 experimental:928 database:900 textmining:965 |
Rv0732 secY |
preprotein translocase SecY | 999 | 996 | coexpression:520 experimental:928 database:900 textmining:979 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 996 | 994 ctx | neighborhood:835 coexpression:968 textmining:461 |
Rv0640 rplK |
50S ribosomal protein L11 | 996 | 994 ctx | neighborhood:775 coexpression:957 experimental:474 textmining:424 |
Rv0641 rplA |
50S ribosomal protein L1 | 986 | 978 ctx | neighborhood:719 coexpression:862 experimental:474 textmining:407 |
Rv3240c secA1 |
protein translocase subunit SecA | 996 | 977 | experimental:775 database:900 textmining:873 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 993 | 977 | experimental:775 database:900 textmining:724 |
Rv3921c yidC |
membrane protein insertase YidC | 980 | 957 | experimental:474 database:900 textmining:564 |
Rv2916c ffh |
signal recognition particle protein | 981 | 954 | experimental:446 database:900 textmining:622 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 989 | 946 | experimental:474 database:900 textmining:810 |
Rv2588c yajC |
membrane protein secretion factor YajC | 984 | 940 | coexpression:426 database:900 textmining:745 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 934 | 926 ctx | neighborhood:544 coexpression:729 experimental:446 |
Rv0701 rplC |
50S ribosomal protein L3 | 923 | 923 | coexpression:848 experimental:474 |
Rv0651 rplJ |
50S ribosomal protein L10 | 930 | 919 | coexpression:827 experimental:474 |
Rv3458c rpsD |
30S ribosomal protein S4 | 928 | 917 | coexpression:840 experimental:474 |
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): preprotein translocase SecE
- Pfam (hmmscan --cut_ga): SecE PF00584.26 (E=1e-18)
- (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_177743.1)
- Domains: Pfam-A via hmmscan --cut_ga — SecE (PF00584.26)
- 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
COG0690 - Curated reference: UniProt P9WGN7 (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 —
123 functional partner(s); context anchor
nusG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0638|secE1 MSDEGDVADEAVADGAENADSRGSGGRTALVTKPVVRPQRPTGKRSRSRAAGADADVDVEEPSTAASEATGVAKDDSTTKAVSKAARAKKASKPKARSVNPIAFVYNYLKQVVAEMRKVIWPNRKQMLTYTSVVLAFLAFMVALVAGADLGLTKLVMLVFG