secA1 Family assigned · medium auto-curated
H37Rv Rv3240c · MTBC0 - ·
949 aa · 3617682–3620531 (-) ·
RefSeq YP_177950.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | protein translocase subunit SecA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Protein translocase subunit SecA. Pfam: SecA_DEAD (PF07517.21), SecA_PP_bind (PF01043.27), P-loop_SecA (PF21090.4), SecA_SW (PF07516.19). |
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 |
P9WGP5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein translocase subunit SecA 1 |
| EC (curated) |
EC 7.4.2.8
|
| Curated function | Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | secA |
| eggNOG description | Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane |
| Orthologous group | COG0653 |
| KEGG orthology |
K03070
|
| KEGG pathways |
map02024, map03060, map03070
|
| KEGG modules |
M00335
|
| Gene Ontology (80) |
GO:0000166, GO:0003674, GO:0003824, GO:0005215, GO:0005488, GO:0005524, GO:0005575, GO:0005576, GO:0005618, GO:0005622, GO:0005623, GO:0005737 +68 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 | 0.397 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 |
|---|---|---|---|---|
SecA_DEAD | PF07517.21 | 1.9e-125 | 5–382 | SecA DEAD-like domain |
SecA_PP_bind | PF01043.27 | 1.0e-38 | 232–339 | SecA preprotein cross-linking domain |
P-loop_SecA | PF21090.4 | 1.8e-89 | 398–611 | SecA P-loop domain |
SecA_SW | PF07516.19 | 9.8e-72 | 613–833 | SecA Wing and Scaffold domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: secY (preprotein translocase SecY), high confidence from genomic context alone (score 990 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0732 secY |
preprotein translocase SecY | 999 | 990 ctx | cooccurence:562 experimental:788 database:900 textmining:955 |
Rv1440 secG |
protein-export membrane protein SecG | 996 | 978 | experimental:785 database:900 textmining:855 |
Rv0638 secE1 |
preprotein translocase SecE | 996 | 977 | experimental:775 database:900 textmining:873 |
Rv3921c yidC |
membrane protein insertase YidC | 969 | 931 | database:900 textmining:570 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 933 | 922 | database:900 |
Rv2588c yajC |
membrane protein secretion factor YajC | 991 | 903 | database:900 textmining:921 |
Rv2916c ffh |
signal recognition particle protein | 986 | 903 | database:900 textmining:862 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 983 | 901 | database:900 textmining:839 |
Rv3241c raiA hyp |
hypothetical protein | 796 | 796 ctx | neighborhood:787 |
Rv1643 rplT |
50S ribosomal protein L20 | 743 | 734 ctx | cooccurence:540 experimental:431 |
Rv1629 polA |
DNA polymerase I | 849 | 718 | coexpression:639 textmining:487 |
Rv3237c hyp |
hypothetical protein | 696 | 696 ctx | neighborhood:694 |
Rv3236c |
integral membrane transport protein | 694 | 694 ctx | neighborhood:694 |
Rv0706 rplV |
50S ribosomal protein L22 | 710 | 679 ctx | cooccurence:421 experimental:434 |
Rv2904c rplS |
50S ribosomal protein L19 | 689 | 675 ctx | cooccurence:427 experimental:431 |
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 SecA
- Pfam (hmmscan --cut_ga): SecA_DEAD PF07517.21 (E=2e-125), SecA_PP_bind PF01043.27 (E=1e-38), P-loop_SecA PF21090.4 (E=2e-89), SecA_SW PF07516.19 (E=1e-71)
- (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_177950.1)
- Domains: Pfam-A via hmmscan --cut_ga — SecA_DEAD (PF07517.21), SecA_PP_bind (PF01043.27), P-loop_SecA (PF21090.4), SecA_SW (PF07516.19)
- 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
COG0653 - Curated reference: UniProt P9WGP5 (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
secY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3240c|secA1 MLSKLLRLGEGRMVKRLKKVADYVGTLSDDVEKLTDAELRAKTDEFKRRLADQKNPETLDDLLPEAFAVAREAAWRVLDQRPFDVQVMGAAALHLGNVAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVHRFLGLQVGVILATMTPDERRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRDKDYIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHEIYKLGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRGGVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDELMRRFNGAALETLLTRLNLPDDVPIEAKMVTRAIKSAQTQVEQQNFEVRKNVLKYDEVMNQQRKVIYAERRRILEGENLKDQALDMVRDVITAYVDGATGEGYAEDWDLDALWTALKTLYPVGITADSLTRKDHEFERDDLTREELLEALLKDAERAYAAREAELEEIAGEGAMRQLERNVLLNVIDRKWREHLYEMDYLKEGIGLRAMAQRDPLVEYQREGYDMFMAMLDGMKEESVGFLFNVTVEAVPAPPVAPAAEPAELAEFAAAAAAAAQQRSAVDGGARERAPSALRAKGVASESPALTYSGPAEDGSAQVQRNGGGAHKTPAGVPAGASRRERREAARRQGRGAKPPKSVKKR