secF Family assigned · medium auto-curated
H37Rv Rv2586c · MTBC0 mtbc0_002753 ·
442 aa · 2936227–2937555 (-) ·
RefSeq NP_217102.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | protein translocase subunit SecF |
|---|---|
| MTBC0 PGAP re-annotation | protein translocase subunit SecF |
| Revised (this work) | Protein translocase subunit SecF. Pfam: Sec_GG (PF07549.20), SecD_SecF_C (PF02355.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGN9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein translocase subunit SecF |
| Curated function | Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | secF |
| eggNOG description | Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA |
| Orthologous group | COG0341 |
| KEGG orthology |
K03072, K03074
|
| KEGG pathways |
map03060, map03070
|
| KEGG modules |
M00335
|
| Gene Ontology (26) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0006810, GO:0008104, GO:0008150, GO:0015031, GO:0015833, GO:0016020, GO:0016021 +14 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 | 0.722 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 10 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 |
|---|---|---|---|---|
Sec_GG | PF07549.20 | 5.8e-06 | 81–99 | SecD/SecF GG Motif |
SecD_SecF_C | PF02355.23 | 3.5e-60 | 168–354 | Protein export membrane protein SecD/SecF, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: secD (protein translocase subunit SecD), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2587c secD |
protein translocase subunit SecD | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:755 coexpression:963 experimental:790 database:900 textmining:870 |
Rv2585c |
lipoprotein | 885 | 884 ctx | neighborhood:881 |
Rv2588c yajC |
membrane protein secretion factor YajC | 935 | 863 ctx | neighborhood:768 coexpression:432 textmining:553 |
Rv3921c yidC |
membrane protein insertase YidC | 934 | 857 | experimental:790 textmining:560 |
Rv0732 secY |
preprotein translocase SecY | 970 | 820 | experimental:790 textmining:842 |
Rv2584c apt |
adenine phosphoribosyltransferase | 777 | 777 ctx | neighborhood:771 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 757 | 758 ctx | neighborhood:723 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 666 | 564 | coexpression:553 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 563 | 545 | coexpression:443 |
Rv1440 secG |
protein-export membrane protein SecG | 890 | 514 | experimental:474 textmining:783 |
Rv0638 secE1 |
preprotein translocase SecE | 965 | 506 | experimental:474 textmining:932 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 535 | 497 ctx | cooccurence:473 |
Rv0017c rodA |
cell division protein RodA | 491 | 491 ctx | cooccurence:436 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 447 | 446 ctx | neighborhood:438 |
Rv0979A rpmF |
50S ribosomal protein L32 | 444 | 445 | coexpression:413 |
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: protein translocase subunit SecF
- MTBC0 PGAP product: protein translocase subunit SecF
- Pfam (hmmscan --cut_ga): Sec_GG PF07549.20 (E=6e-06), SecD_SecF_C PF02355.23 (E=3e-60)
- (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_217102.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sec_GG (PF07549.20), SecD_SecF_C (PF02355.23)
- 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
COG0341 - Curated reference: UniProt P9WGN9 (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 —
47 functional partner(s); context anchor
secD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002753|Rv2586c|secF MASKAKTGRDDEATSAVELTEATESAVARTDGDSTTDTASKLGHHSFLSRLYTGTGAFEVVGRRRLWFGVSGAIVAVAIASIVFRGFTFGIDFKGGTTVSFPRGSTQVAQVEDVYYRALGSEPQSVVIVGAGASATVQIRSETLTSDQTAKLRDALFEAFGPKGTDGQPSKQAISDSAVSETWGGQITKKAVIALVVFLVLVALYITVRYERYMTISAITAMLFDLTVTAGVYSLVGFEVTPATVIGLLTILGFSLYDTVIVFDKVEENTHGFQHTTRRTFAEQANLAINQTFMRSINTSLIGVLPVLALMVVAVWLLGVGTLKDLALVQLIGIIIGTYSSIFFATPLLVTLRERTELVRNHTRRVLKRRNSGSPAGSEDASTDGGEQPAAADEQSLVGITQASSQSAPRAAQGSSKPAPGARPVRPVGTRRPTGKRNAGRR