secD Family assigned · medium auto-curated
H37Rv Rv2587c · MTBC0 mtbc0_002754 ·
573 aa · 2937559–2939280 (-) ·
RefSeq NP_217103.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | protein translocase subunit SecD |
|---|---|
| MTBC0 PGAP re-annotation | protein translocase subunit SecD |
| Revised (this work) | Protein translocase subunit SecD. Pfam: Sec_GG (PF07549.20), SecDF_P1_head (PF22599.3), 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 |
P9WGP1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein translocase subunit SecD |
| 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 | secD |
| 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 | COG0342 |
| KEGG orthology |
K03072
|
| KEGG pathways |
map03060, map03070
|
| KEGG modules |
M00335
|
| Gene Ontology (32) |
GO:0005575, GO:0005576, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005887, GO:0006810, GO:0008104, GO:0008150 +20 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 | 0.277 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 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 |
|---|---|---|---|---|
Sec_GG | PF07549.20 | 3.2e-04 | 39–57 | SecD/SecF GG Motif |
SecDF_P1_head | PF22599.3 | 5.6e-26 | 256–363 | SecDF, P1 head subdomain |
SecD_SecF_C | PF02355.23 | 5.4e-08 | 366–539 | Protein export membrane protein SecD/SecF, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: secF (protein translocase subunit SecF), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2586c secF |
protein translocase subunit SecF | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:755 coexpression:963 experimental:790 database:900 textmining:870 |
Rv2588c yajC |
membrane protein secretion factor YajC | 990 | 918 ctx | neighborhood:768 coexpression:659 textmining:887 |
Rv3921c yidC |
membrane protein insertase YidC | 957 | 902 | coexpression:488 experimental:792 textmining:585 |
Rv2585c |
lipoprotein | 884 | 885 ctx | neighborhood:881 |
Rv1440 secG |
protein-export membrane protein SecG | 979 | 848 | experimental:836 textmining:872 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 933 | 843 | experimental:830 textmining:594 |
Rv2584c apt |
adenine phosphoribosyltransferase | 839 | 839 ctx | neighborhood:771 |
Rv0638 secE1 |
preprotein translocase SecE | 968 | 834 | experimental:790 textmining:817 |
Rv0732 secY |
preprotein translocase SecY | 966 | 832 | experimental:790 textmining:809 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 772 | 764 ctx | neighborhood:746 |
Rv2555c alaS |
alanine--tRNA ligase | 714 | 715 | coexpression:691 |
Rv1308 atpA |
ATP synthase subunit alpha | 694 | 694 | coexpression:690 |
Rv2534c efp |
elongation factor P | 644 | 602 | coexpression:517 |
Rv0904c accD3 |
acetyl-CoAcarboxylase carboxyl transferase subunit beta | 533 | 534 | coexpression:490 |
Rv3201c adnB |
ATP-dependent DNA helicase | 544 | 516 ctx | cooccurence:507 |
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 SecD
- MTBC0 PGAP product: protein translocase subunit SecD
- Pfam (hmmscan --cut_ga): Sec_GG PF07549.20 (E=3e-04), SecDF_P1_head PF22599.3 (E=6e-26), SecD_SecF_C PF02355.23 (E=5e-08)
- (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_217103.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sec_GG (PF07549.20), SecDF_P1_head (PF22599.3), 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
COG0342 - Curated reference: UniProt P9WGP1 (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 —
79 functional partner(s); context anchor
secF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002754|Rv2587c|secD MASSSAPVHPARYLSVFLVMLIGIYLLVFFTGDKHTAPKLGIDLQGGTRVTLTARTPDGSAPSREALAQAQQIISARVNGLGVSGSEVVVDGDNLVITVPGNDGSEARNLGQTARLYIRPVLNSMPAQPAAEEPQPAPSAEPQPPGQPAAPPPAQSGAPASPQPGAQPRPYPQDPAPSPNPTSPASPPPAPPAEAPATDPRKDLAERIAQEKKLRQSTNQYMQMVALQFQATRCESDDILAGNDDPKLPLVTCSTDHKTAYLLAPSIISGDQIQNATSGMDQRGIGYVVDLQFKGPAANIWADYTAAHIGTQTAFTLDSQVVSAPQIQEAIPGGRTQISGGDPPFTAATARQLANVLKYGSLPLSFEPSEAQTVSATLGLSSLRAGMIAGAIGLLLVLVYSLLYYRVLGLLTALSLVASGSMVFAILVLLGRYINYTLDLAGIAGLIIGIGTTADSFVVFFERIKDEIREGRSFRSAVPRGWARARKTIVSGNAVTFLAAAVLYFLAIGQVKGFAFTLGLTTILDLVVVFLVTWPLVYLASKSSLLAKPAYNGLGAVQQVARERRAMARTGRG