eccC2 Family assigned · medium auto-curated
H37Rv Rv3894c · MTBC0 mtbc0_004128 ·
1396 aa · 4400508–4404698 (-) ·
RefSeq NP_218411.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-2 type VII secretion system protein EccC |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-2 FtsK/SpoIIIE family ATPase EccC2 |
| Revised (this work) | Type VII secretion system ESX-2 FtsK/SpoIIIE family ATPase EccC2. 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 |
O05450
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein |
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
|
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 | 0.454 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 19 synonymous, 24 missense, 2 nonsense, 4 frameshift |
| Disruption | 6 distinct premature-stop/frameshift site(s); most common in 26.70% of strains (38765) · convergent |
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 | 6.0e-56 | 834–1096 | FtsK/SpoIIIE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccB5 (ESX-5 type VII secretion system protein EccB5), high confidence from genomic context alone (score 991 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 994 | 991 ctx | cooccurence:764 experimental:956 textmining:465 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 995 | 989 ctx | cooccurence:751 experimental:956 textmining:601 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 991 | 987 ctx | neighborhood:881 cooccurence:772 coexpression:409 textmining:410 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 907 | 894 | experimental:824 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 880 | 876 ctx | cooccurence:762 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 888 | 872 | experimental:821 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 921 | 827 ctx | cooccurence:640 experimental:513 textmining:562 |
Rv3896c hyp |
hypothetical protein | 818 | 818 ctx | neighborhood:776 |
Rv3899c hyp |
hypothetical protein | 784 | 785 ctx | cooccurence:689 |
Rv3445c esxU |
ESAT-6 like protein EsxU | 791 | 705 | experimental:677 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 784 | 690 | experimental:677 |
Rv1796 mycP5 |
membrane-anchored mycosin MycP | 779 | 682 ctx | cooccurence:664 |
Rv3886c mycP2 |
membrane-anchored mycosin | 686 | 646 ctx | cooccurence:548 |
Rv3888c |
membrane protein | 634 | 620 ctx | cooccurence:540 |
Rv2423 hyp |
hypothetical protein | 576 | 577 ctx | cooccurence:574 |
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-2 type VII secretion system protein EccC
- MTBC0 PGAP product: type VII secretion system ESX-2 FtsK/SpoIIIE family ATPase EccC2
- Pfam (hmmscan --cut_ga): FtsK_SpoIIIE PF01580.25 (E=6e-56)
- (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_218411.1)
- 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 O05450 (TrEMBL, unreviewed; 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 —
54 functional partner(s); context anchor
eccB5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004128|Rv3894c|eccC2 MSKKAFPINRVNIDPPKPVRVAPNPPIALPEREPRNIWVMIGVPALIVALIGTIVMLYVSGVRSLATGFFPLMGIGAFSMLAFSGRFGRARKITWGELEKGRRRYLRDLDTNRDEIQTAVCAQREWQNAVHSDPPGLGAIIGGPRMWERGRGDVDFLEVRVGTGVQHAPDSVLSVTWPDISSDEELEPVTGQALRDFILEQRKIRDIAKVVNLRSAPGFSFVSEDLDRVRSLMRSVLCSLAVFHNPRDVKLMVVTRNPEVWAWMVWLPHNLHDELFDACGWRRLIFATPEELEAALGAELHMKGKRGAWTPPTVASPTAMGSALETGQVGVDLGPHLVIVDDNTGSPDAWESVVGQVGKAGLTVLRIASRVGTGVGFAEDQVFEMAQRHGAATAVKAGRDGADADDDQRPAPLLRARGTFFAHADQLSIHRAYRYARAMARWSPTSRSEVTDSTSGAAELLRSLGISDPRELDVDRLWAERRGRGDDRWCEIPVGAKPNGELQNIILRAKDFGGFGFHSVVIGTSGSGKSELFLSLVYGIALTHSPETFNVIFVDMKFESAAQDILGIPHVVAALSNLGKDERHLAERMRRVIDGEIKQRYELFKSVGARDANDYEEIRLAGRDLPPVPVLLVIVDEYLELFANHKKWIDLIIHIGQEGRGANVFFMLGGQRLDLSSLQKVKSNIAFRIALRAESGDDSREVIGSDAAYHLPSKENGFALLKVGPRDLEPFRCFYLSAPFVVPKKKEVARTIDMTLTQPRLYDWQYQPLDAADAEALATAAAADAEPDEFLYYDDGFKKKKIVDVLRESLYNVPHRSPRRPWLAPLEDPEPVDRLVAAYRGKPWHVDYGQNPGLMFPVGVMDIPEESQQVVHAVDALRSNIIVVGAKQRGKTTTLMALMCSAATMYTPERVTFFCIGGATMAQIGSLPHVTDIVSPKDAEGIERILSTMDALIDAREEAFRRAKIDMDGFRERRFGIGGDGVGGTDPTDAFGDVFVVLDDYDDLYAKDTLLGDRIISLSSRGPEYGVHLMCSAGGWIHGQRQSLLQNVTARIQLRLADPGESQMGHLSIESREAARRTLNRPGFGLTESLHELRIGVPALADPGTGELVGITDVGARIADVAGVTKHASLQRLPQRVELSAIVEHEAVHQGGDDLSIAFAIGERHELGPVPIKLRESPGLMILGRQGCGKTTALVAIGEAVMNRFSPQQAQLTLIDPKTAPHGLRDLHAPGYVRAYAYDQDEIDEVITELAQQILLPRLPPKGLSQEELRALKPWEGPRHFVLIDDVQDLRPAQSYPQKPPVGAALWKLMERARQVGLHVFSTRNSANWATMPMDPWVKSQTSAKVAQLYMDNDPQNRINRSVRAQTLPPGRGLLVGADGDVEGILVGYPSVPGEQ