secY Family assigned · medium auto-curated
H37Rv Rv0732 · MTBC0 mtbc0_000774 ·
441 aa · 828993–830318 (+) ·
RefSeq NP_215246.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | preprotein translocase SecY |
|---|---|
| MTBC0 PGAP re-annotation | preprotein translocase subunit SecY |
| Revised (this work) | Preprotein translocase subunit SecY. Pfam: SecY (PF00344.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGN3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein translocase subunit SecY |
| Curated function | The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | secY |
| eggNOG description | The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently |
| Orthologous group | COG0201 |
| KEGG orthology |
K03076
|
| KEGG pathways |
map02024, map03060, map03070
|
| KEGG modules |
M00335
|
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, 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 | 1.015 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 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 |
|---|---|---|---|---|
SecY | PF00344.26 | 6.3e-111 | 75–424 | SecY |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplR (50S ribosomal protein L18), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0638 secE1 |
preprotein translocase SecE | 999 | 996 | coexpression:520 experimental:928 database:900 textmining:979 |
Rv0720 rplR |
50S ribosomal protein L18 | 997 | 996 ctx | cooccurence:666 coexpression:861 experimental:905 |
Rv0716 rplE |
50S ribosomal protein L5 | 996 | 995 ctx | cooccurence:611 coexpression:864 experimental:904 |
Rv0707 rpsC |
30S ribosomal protein S3 | 996 | 995 ctx | cooccurence:695 coexpression:859 experimental:881 |
Rv0719 rplF |
50S ribosomal protein L6 | 996 | 995 ctx | cooccurence:599 coexpression:864 experimental:904 |
Rv0706 rplV |
50S ribosomal protein L22 | 996 | 995 ctx | cooccurence:513 coexpression:860 experimental:918 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 995 | 995 ctx | cooccurence:677 coexpression:863 experimental:880 |
Rv1440 secG |
protein-export membrane protein SecG | 999 | 994 | experimental:928 database:900 textmining:947 |
Rv0721 rpsE |
30S ribosomal protein S5 | 995 | 994 ctx | cooccurence:614 coexpression:861 experimental:880 |
Rv0708 rplP |
50S ribosomal protein L16 | 995 | 994 ctx | cooccurence:554 coexpression:860 experimental:904 |
Rv0718 rpsH |
30S ribosomal protein S8 | 995 | 994 ctx | cooccurence:558 coexpression:864 experimental:879 |
Rv3459c rpsK |
30S ribosomal protein S11 | 995 | 994 ctx | cooccurence:556 coexpression:863 experimental:880 |
Rv1307 atpH |
ATP synthase subunit b/delta | 996 | 993 | coexpression:993 textmining:451 |
Rv0704 rplB |
50S ribosomal protein L2 | 995 | 993 ctx | cooccurence:408 coexpression:863 experimental:904 textmining:421 |
Rv0701 rplC |
50S ribosomal protein L3 | 994 | 993 ctx | cooccurence:404 coexpression:860 experimental:904 |
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: preprotein translocase SecY
- MTBC0 PGAP product: preprotein translocase subunit SecY
- Pfam (hmmscan --cut_ga): SecY PF00344.26 (E=6e-111)
- (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_215246.1)
- Domains: Pfam-A via hmmscan --cut_ga — SecY (PF00344.26)
- 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
COG0201 - Curated reference: UniProt P9WGN3 (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 —
205 functional partner(s); context anchor
rplR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000774|Rv0732|secY MLSAFISSLRTVDLRRKILFTLGIVILYRVGAALPSPGVNFPNVQQCIKEASAGEAGQIYSLINLFSGGALLKLTVFAVGVMPYITASIIVQLLTVVIPRFEELRKEGQAGQSKMTQYTRYLAIALAILQATSIVALAANGGLLQGCSLDIIADQSIFTLVVIVLVMTGGAALVMWMGELITERGIGNGMSLLIFVGIAARIPAEGQSILESRGGVVFTAVCAAALIIIVGVVFVEQGQRRIPVQYAKRMVGRRMYGGTSTYLPLKVNQAGVIPVIFASSLIYIPHLITQLIRSGSGVVGNSWWDKFVGTYLSDPSNLVYIGIYFGLIIFFTYFYVSITFNPDERADEMKKFGGFIPGIRPGRPTADYLRYVLSRITLPGSIYLGVIAVLPNLFLQIGAGGTVQNLPFGGTAVLIMIGVGLDTVKQIESQLMQRNYEGFLK