eccCb1 Family assigned · medium auto-curated
H37Rv Rv3871 · MTBC0 mtbc0_004104 ·
591 aa · 4373037–4374812 (+) ·
RefSeq NP_218388.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion system protein EccCb |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 FtsK/SpoIIIE family ATPase EccCb1 |
| Revised (this work) | Type VII secretion system ESX-1 FtsK/SpoIIIE family ATPase EccCb1. 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 |
P9WNB1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion system protein EccCb1 |
| 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). EccCb1 may link the cytosolic components of the system with the membrane components. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | eccCa |
| eggNOG description | DNA binding |
| 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 | 0.378 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 9 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 |
|---|---|---|---|---|
FtsK_SpoIIIE | PF01580.25 | 2.6e-35 | 71–289 | FtsK/SpoIIIE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccCa1 (ESX-1 secretion system protein EccCa), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 998 | 998 ctx | neighborhood:771 fusion:899 coexpression:860 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 998 | 992 | experimental:987 textmining:879 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 977 | 962 ctx | neighborhood:771 cooccurence:748 textmining:437 |
Rv3445c esxU |
ESAT-6 like protein EsxU | 828 | 822 | experimental:815 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 909 | 808 ctx | neighborhood:771 textmining:549 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 960 | 796 ctx | cooccurence:579 textmining:814 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 803 | 795 ctx | cooccurence:665 |
Rv3875 esxA |
ESAT-6 protein EsxA | 955 | 774 ctx | cooccurence:537 textmining:810 |
Rv3865 espF |
ESX-1 secretion-associated protein EspF | 752 | 748 ctx | neighborhood:736 |
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 810 | 744 ctx | neighborhood:736 |
Rv3450c eccB4 |
ESX-4 secretion system protein EccB4 | 736 | 718 ctx | cooccurence:575 |
Rv3873 PPE68 |
PPE family protein PPE68 | 868 | 660 ctx | neighborhood:643 textmining:628 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 809 | 660 ctx | cooccurence:475 textmining:463 |
Rv2542 hyp |
hypothetical protein | 652 | 652 ctx | cooccurence:650 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 779 | 626 ctx | neighborhood:406 textmining:435 |
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 EccCb
- MTBC0 PGAP product: type VII secretion system ESX-1 FtsK/SpoIIIE family ATPase EccCb1
- Pfam (hmmscan --cut_ga): FtsK_SpoIIIE PF01580.25 (E=3e-35)
- (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_218388.1)
- 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 P9WNB1 (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 —
42 functional partner(s); context anchor
eccCa1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004104|Rv3871|eccCb1 MTAEPEVRTLREVVLDQLGTAESRAYKMWLPPLTNPVPLNELIARDRRQPLRFALGIMDEPRRHLQDVWGVDVSGAGGNIGIGGAPQTGKSTLLQTMVMSAAATHSPRNVQFYCIDLGGGGLIYLENLPHVGGVANRSEPDKVNRVVAEMQAVMRQRETTFKEHRVGSIGMYRQLRDDPSQPVASDPYGDVFLIIDGWPGFVGEFPDLEGQVQDLAAQGLAFGVHVIISTPRWTELKSRVRDYLGTKIEFRLGDVNETQIDRITREIPANRPGRAVSMEKHHLMIGVPRFDGVHSADNLVEAITAGVTQIASQHTEQAPPVRVLPERIHLHELDPNPPGPESDYRTRWEIPIGLRETDLTPAHCHMHTNPHLLIFGAAKSGKTTIAHAIARAICARNSPQQVRFMLADYRSGLLDAVPDTHLLGAGAINRNSASLDEAVQALAVNLKKRLPPTDLTTAQLRSRSWWSGFDVVLLVDDWHMIVGAAGGMPPMAPLAPLLPAAADIGLHIIVTCQMSQAYKATMDKFVGAAFGSGAPTMFLSGEKQEFPSSEFKVKRRPPGQAFLVSPDGKEVIQAPYIEPPEEVFAAPPSAG