eccCa1 Family assigned · medium auto-curated
H37Rv Rv3870 · MTBC0 mtbc0_004103 ·
747 aa · 4370638–4372881 (+) ·
RefSeq NP_218387.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion system protein EccCa |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 FtsK/SpoIIIE family ATPase EccCa1 |
| Revised (this work) | Type VII secretion system ESX-1 FtsK/SpoIIIE family ATPase EccCa1. 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 |
P9WNB3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion system protein EccCa1 |
| Curated function | Part of the ESX-1 specialized secretion system, which delivers several virulence factors to host cells during infection, including the key virulence factors EsxA (ESAT-6) and EsxB (CFP-10). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | eccCa |
| eggNOG description | FtsK/SpoIIIE family |
| Orthologous group | COG1674 |
| KEGG orthology |
K03466
|
| Gene Ontology (57) |
GO:0002790, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006810, GO:0008104, GO:0008150, GO:0009306, GO:0009405, GO:0009605, GO:0009607 +45 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) | 16 synonymous, 13 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.40% of strains (575) · 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 | 2.7e-53 | 430–637 | FtsK/SpoIIIE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccCb1 (ESX-1 secretion system protein EccCb), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 998 | 998 ctx | neighborhood:771 fusion:899 coexpression:860 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 997 | 992 ctx | neighborhood:881 cooccurence:766 coexpression:651 textmining:657 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 969 | 920 ctx | neighborhood:881 textmining:639 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 974 | 867 ctx | cooccurence:733 textmining:815 |
Rv3875 esxA |
ESAT-6 protein EsxA | 946 | 857 ctx | neighborhood:416 cooccurence:656 textmining:642 |
Rv3865 espF |
ESX-1 secretion-associated protein EspF | 832 | 833 ctx | neighborhood:825 |
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 885 | 832 ctx | neighborhood:825 |
Rv3867 espH |
ESX-1 secretion-associated protein EspH | 870 | 831 ctx | neighborhood:801 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 937 | 821 ctx | neighborhood:580 experimental:585 textmining:664 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 926 | 805 ctx | cooccurence:699 textmining:640 |
Rv2553c mltG |
membrane protein | 776 | 777 | coexpression:731 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 814 | 724 ctx | neighborhood:524 |
Rv2542 hyp |
hypothetical protein | 804 | 721 ctx | cooccurence:720 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 705 | 693 ctx | cooccurence:498 |
Rv3873 PPE68 |
PPE family protein PPE68 | 705 | 691 ctx | neighborhood:672 |
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-1 secretion system protein EccCa
- MTBC0 PGAP product: type VII secretion system ESX-1 FtsK/SpoIIIE family ATPase EccCa1
- Pfam (hmmscan --cut_ga): FtsK_SpoIIIE PF01580.25 (E=3e-53)
- (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_218387.1)
- 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 P9WNB3 (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 —
38 functional partner(s); context anchor
eccCb1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004103|Rv3870|eccCa1 MTTKKFTPTITRGPRLTPGEISLTPPDDLGIDIPPSGVQKILPYVMGGAMLGMIAIMVAGGTRQLSPYMLMMPLMMIVMMVGGLAGSTGGGGKKVPEINADRKEYLRYLAGLRTRVTSSATSQVAFFSYHAPHPEDLLSIVGTQRQWSRPANADFYAATRIGIGDQPAVDRLLKPAVGGELAAASAAPQPFLEPVSHMWVVKFLRTHGLIHDCPKLLQLRTFPTIAIGGDLAGAAGLMTAMICHLAVFHPPDLLQIRVLTEEPDDPDWSWLKWLPHVQHQTETDAAGSTRLIFTRQEGLSDLAARGPHAPDSLPGGPYVVVVDLTGGKAGFPPDGRAGVTVITLGNHRGSAYRIRVHEDGTADDRLPNQSFRQVTSVTDRMSPQQASRIARKLAGWSITGTILDKTSRVQKKVATDWHQLVGAQSVEEITPSRWRMYTDTDRDRLKIPFGHELKTGNVMYLDIKEGAEFGAGPHGMLIGTTGSGKSEFLRTLILSLVAMTHPDQVNLLLTDFKGGSTFLGMEKLPHTAAVVTNMAEEAELVSRMGEVLTGELDRRQSILRQAGMKVGAAGALSGVAEYEKYRERGADLPPLPTLFVVVDEFAELLQSHPDFIGLFDRICRVGRSLRVHLLLATQSLQTGGVRIDKLEPNLTYRIALRTTSSHESKAVIGTPEAQYITNKESGVGFLRVGMEDPVKFSTFYISGPYMPPAAGVETNGEAGGPGQQTTRQAARIHRFTAAPVLEEAPTP