eccC4 Family assigned · medium auto-curated
H37Rv Rv3447c · MTBC0 mtbc0_003666 ·
1236 aa · 3890413–3894123 (-) ·
RefSeq NP_217964.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-4 secretion system protein EccC4 |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-4 FtsK/SpoIIIE family ATPase EccC4 |
| Revised (this work) | Type VII secretion system ESX-4 FtsK/SpoIIIE family ATPase EccC4. Pfam: FtsK_SpoIIIE (PF01580.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNA7
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | ESX-4 secretion system protein EccC4 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | eccCa |
| eggNOG description | COG1674 DNA segregation ATPase FtsK SpoIIIE and related proteins |
| Orthologous group | COG1674 |
| KEGG orthology |
K03466
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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) pseudogene candidate
| pN/pS | 0.744 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 17 synonymous, 33 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.26% of strains (3275) · clonal |
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 |
|---|---|---|---|---|
FtsK_SpoIIIE | PF01580.25 | 7.9e-65 | 721–967 | FtsK/SpoIIIE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD4 (ESX-4 secretion system protein EccD4), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 997 | 996 ctx | neighborhood:778 cooccurence:758 coexpression:853 experimental:513 textmining:489 |
Rv3446c hyp |
hypothetical protein | 986 | 979 ctx | neighborhood:881 coexpression:831 |
Rv3449 mycP4 |
membrane-anchored mycosin | 967 | 965 ctx | neighborhood:778 coexpression:807 |
Rv3445c esxU |
ESAT-6 like protein EsxU | 946 | 939 ctx | neighborhood:811 experimental:677 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 931 | 921 ctx | cooccurence:553 experimental:824 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 927 | 917 ctx | cooccurence:515 experimental:824 |
Rv3444c esxT |
ESAT-6 like protein EsxT | 876 | 863 ctx | neighborhood:792 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 868 | 848 | experimental:821 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 849 | 828 | experimental:821 |
Rv2891 hyp |
hypothetical protein | 832 | 825 | coexpression:823 |
Rv3450c eccB4 |
ESX-4 secretion system protein EccB4 | 829 | 810 ctx | cooccurence:725 |
Rv3903c cpnT hyp |
hypothetical protein | 792 | 764 | coexpression:730 |
Rv0603 hyp |
hypothetical protein | 738 | 738 | coexpression:738 |
Rv0745 hyp |
hypothetical protein | 735 | 735 | coexpression:735 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 782 | 690 | experimental:677 |
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: ESX-4 secretion system protein EccC4
- MTBC0 PGAP product: type VII secretion system ESX-4 FtsK/SpoIIIE family ATPase EccC4
- Pfam (hmmscan --cut_ga): FtsK_SpoIIIE PF01580.25 (E=8e-65)
- (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_217964.1)
- Domains: Pfam-A via hmmscan --cut_ga — FtsK_SpoIIIE (PF01580.25)
- 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
COG1674 - Curated reference: UniProt P9WNA7 (SwissProt, reviewed; Inferred from homology)
- 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 —
41 functional partner(s); context anchor
eccD4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003666|Rv3447c|eccC4 MNSGPACATADILVAPPPELRRSEPSSLLIRLLPVVMSVATVGVMVTVFLPGSPATRHPTFLAFPMMMLVSLVVTAVTGRGRRHVSGIHNDRVDYLGYLSVLRTSVTQTAAAQHVSLNWTHPDPATLWTLIGGPRMWERRPGAADFCRIRVGVGSAPLATRLVVGQLPPAQRADPVTRAALRCFLAAHATIADAPIAIPLRVGGPIAIDGDPTKVRGLLRAMICQLAVWHSPEELLIAGVVSDRNRAHWDWLKWLPHNQHPNACDALGPAPMVYSTLAEMQNALAATVLAHVVAIVDTAERGNGAITGVITIEVGARRDGAPPVVRCAGEVTALACPDQLEPQDALVCARRLAAHRVGHSGRTFIRGSGWAELVGIGDVAAFDPSTLWRNVNQHDRLRVPIGVTPDGTAVQLDIKEAAEQGMGPHGLCVGATGSGKSELLRTIALGMMARNSPEVLNLLLVDFKGGATFLDLAGAPHVAAVITNLAEEAPLVARMQDALAGEMSRRQQLLRMAGHLVSVTAYQRARQTGAQLPCLPILFIVVDEFSELLSQHPEFVDVFLAIGRVGRSLGMHLLLASQRLDEGRLRGLETHLSYRMCLKTWSASESRNVLGTQDAYQLPNTPGAGLLQTGTGELIRFQTAFVSGPLRRASPSAVHPVAPPSVRPFTTHAAAPVTAGPVGGTAEVPTPTVLHAVLDRLVGHGPAAHQVWLPPLDEPPMLGALLRDAEPAQAELAVPIGIVDRPFEQSRVPLTIDLSGAAGNVAVVGAPQTGKSTALRTLIMALAATHDAGRVQFYCLDFGGGALAQVDELPHVGAVAGRAQPQLASRMLAELESAVRFREAFFRDHGIDSVARYRQLRAKSAAESFADIFLVIDGWASLRQEFAALEESIVALAAQGLSFGVHVALSAARWAEIRPSLRDQIGSRIELRLADPADSELDRRQAQRVPVDRPGRGLSRDGMHMVIALPDLDGVALRRRSGDPVAPPIPLLPARVDYDSVVARAGDELGAHILLGLEERRGQPVAVDFGRHPHLLVLGDNECGKTAALRTLCREIVRTHTAARAQLLIVDFRHTLLDVIESEHMGGYVSSPAALGAKLSSLVDLLQARMPAPDVSQAQLRARSWWSGPDIYVVVDDYDLVAVSSGNPLMVLLEYLPHARDLGLHLVVARRSGGAARALFEPVLASLRDLGCRALLMSGRPDEGALFGSSRPMPLPPGRGILVTGAGDEQLVQVAWSPPP