eccA2 Family assigned · medium auto-curated
H37Rv Rv3884c · MTBC0 mtbc0_004118 ·
619 aa · 4389225–4391084 (-) ·
RefSeq NP_218401.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-2 secretion system protein EccA |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-2 AAA family ATPase EccA2 |
| Revised (this work) | Type VII secretion system ESX-2 AAA family ATPase EccA2. Pfam: T7SS_EccA1_N (PF21545.4), AAA (PF00004.36), AAA_lid_6 (PF17866.9). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPH7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-2 secretion system protein EccA2 |
| Curated function | Shows ATPase activity. Could provide energy for export of ESX-2 substrates (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | Type VII secretion |
| Orthologous group | COG0464 |
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 | 1.439 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 12 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 5.93% of strains (8604) · 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 |
|---|---|---|---|---|
T7SS_EccA1_N | PF21545.4 | 6.7e-27 | 32–204 | T7SS, ESX-1 secretion system protein EccA1, N-terminal domain |
AAA | PF00004.36 | 2.3e-18 | 369–504 | ATPase family associated with various cellular activities (AAA) |
AAA_lid_6 | PF17866.9 | 4.1e-15 | 507–607 | AAA lid domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccE2 (ESX-2 secretion system protein EccE), high confidence from genomic context alone (score 954 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3885c eccE2 |
ESX-2 secretion system protein EccE | 954 | 954 ctx | neighborhood:794 coexpression:788 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 916 | 899 ctx | neighborhood:794 cooccurence:519 |
Rv3888c |
membrane protein | 876 | 850 ctx | neighborhood:794 |
Rv3886c mycP2 |
membrane-anchored mycosin | 845 | 835 ctx | neighborhood:794 |
Rv3696c glpK |
glycerol kinase | 752 | 752 | database:606 |
Rv3883c mycP1 |
membrane-anchored mycosin | 912 | 742 ctx | neighborhood:728 textmining:673 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 801 | 739 ctx | neighborhood:731 |
Rv2109c prcA |
proteasome subunit alpha | 754 | 739 | experimental:406 database:537 |
Rv2110c prcB |
proteasome subunit beta | 754 | 739 | experimental:406 database:537 |
Rv2115c mpa |
proteasome-associated ATPase | 697 | 698 | database:566 |
Rv1334 mec |
[CysO | 705 | 687 | database:502 |
Rv1273c |
drug ABC transporter ATP-binding protein | 686 | 666 | database:528 |
Rv1272c |
drug ABC transporter ATP-binding protein | 686 | 666 | database:528 |
Rv2299c htpG |
chaperone protein HtpG | 691 | 664 | database:604 |
Rv1348 irtA |
iron ABC transporter ATP-binding protein/permease IrtA | 705 | 663 | database:528 |
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 secretion system protein EccA
- MTBC0 PGAP product: type VII secretion system ESX-2 AAA family ATPase EccA2
- Pfam (hmmscan --cut_ga): T7SS_EccA1_N PF21545.4 (E=7e-27), AAA PF00004.36 (E=2e-18), AAA_lid_6 PF17866.9 (E=4e-15)
- (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_218401.1)
- Domains: Pfam-A via hmmscan --cut_ga — T7SS_EccA1_N (PF21545.4), AAA (PF00004.36), AAA_lid_6 (PF17866.9)
- 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
COG0464 - Curated reference: UniProt P9WPH7 (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 —
122 functional partner(s); context anchor
eccE2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004118|Rv3884c|eccA2 MSRMVDTMGDLLTARRHFDRAMTIKNGQGCVAALPEFVAATEADPSMADAWLGRIACGDRDLASLKQLNAHSEWLHRETTRIGRTLAAEVQLGPSIGITVTDASQVGLALSSALTIAGEYAKADALLANRELLDSWRNYQWHQLARAFLMYVTQRWPDVLSTAAEDLPPQAIVMPAVTASICALAAHAAAHLGQGRVALDWLDRVDVIGHSRSSGRFGADVLTAAIGPADIPLLVADLAYVRGMVYRQLHEEDKAQIWLSKATINGVLTDAAKEALADPNLRLIVTDERTIASRSDRWDASTAKSRDQLDDDNAAQRRGELLAEGRELLAKQVGLAAVKQAVSALEDQLEVRMMRLEHGLPVEGQTNHMLLVGPPGTGKTTTAEALGKIYAGMGIVRHPEIREVRRSDFCGHYIGESGPKTNELIEKSLGRIIFMDEFYSLIERHQDGTPDMIGMEAVNQLLVQLETHRFDFCFIGAGYEDQVDEFLTVNPGLAGRFNRKLRFESYSPVEIVEIGHRYATPRASQLDDAAREVFLDAVTTIRNYTTPSGQHGIDAMQNGRFARNVIERAEGFRDTRVVAQKRAGQPVSVQDLQIITATDIDAAIRSVCSDNRDMAAIVW