eccD1 Family assigned · medium auto-curated
H37Rv Rv3877 · MTBC0 mtbc0_004111 ·
511 aa · 4379217–4380752 (+) ·
RefSeq NP_218394.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion system protein EccD1 |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 subunit EccD1 |
| Revised (this work) | Type VII secretion system ESX-1 subunit EccD1. Pfam: YukD (PF08817.17), EccD (PF19053.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNQ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion system protein EccD1 |
| 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 |
S Function unknown
|
|---|---|
| Preferred name | eccD1 |
| eggNOG description | WXG100 protein secretion system (Wss), protein YukD |
| Orthologous group | 2B6TZ |
| Gene Ontology (35) |
GO:0005575, GO:0005618, GO:0005623, GO:0008150, GO:0009605, GO:0009607, GO:0020012, GO:0030312, GO:0030682, GO:0040007, GO:0042783, GO:0043207 +23 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 | 2.248 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 18 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 |
|---|---|---|---|---|
YukD | PF08817.17 | 2.7e-18 | 23–107 | WXG100 protein secretion system (Wss), protein YukD |
EccD | PF19053.7 | 1.6e-32 | 154–508 | EccD-like transmembrane domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espI (ESX-1 secretion-associated protein EspI), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3876 espI |
ESX-1 secretion-associated protein EspI | 997 | 988 ctx | neighborhood:881 cooccurence:524 coexpression:798 textmining:808 |
Rv3875 esxA |
ESAT-6 protein EsxA | 971 | 893 ctx | neighborhood:570 cooccurence:754 textmining:745 |
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 974 | 867 ctx | cooccurence:733 textmining:815 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 980 | 857 ctx | cooccurence:772 textmining:869 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 929 | 802 ctx | cooccurence:768 textmining:657 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 960 | 796 ctx | cooccurence:579 textmining:814 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 933 | 784 ctx | cooccurence:774 textmining:704 |
Rv2542 hyp |
hypothetical protein | 836 | 768 ctx | cooccurence:765 |
Rv3878 espJ |
ESX-1 secretion-associated protein EspJ | 913 | 762 ctx | neighborhood:750 textmining:651 |
Rv0658c |
integral membrane protein | 721 | 722 ctx | cooccurence:719 |
Rv0341 iniB |
isoniazid inducible protein IniB | 719 | 720 ctx | cooccurence:719 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 879 | 701 ctx | cooccurence:573 textmining:613 |
Rv1157c hyp |
hypothetical protein | 691 | 691 ctx | cooccurence:689 |
Rv3365c hyp |
hypothetical protein | 633 | 634 ctx | cooccurence:632 |
Rv2608 PPE42 |
PPE family protein PPE42 | 631 | 631 ctx | cooccurence:631 |
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 EccD1
- MTBC0 PGAP product: type VII secretion system ESX-1 subunit EccD1
- Pfam (hmmscan --cut_ga): YukD PF08817.17 (E=3e-18), EccD PF19053.7 (E=2e-32)
- (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_218394.1)
- Domains: Pfam-A via hmmscan --cut_ga — YukD (PF08817.17), EccD (PF19053.7)
- 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
2B6TZ - Curated reference: UniProt P9WNQ7 (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 —
91 functional partner(s); context anchor
espI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004111|Rv3877|eccD1 MSAPAVAAGPTAAGATAARPATTRVTILTGRRMTDLVLPAAVPMETYIDDTVAVLSEVLEDTPADVLGGFDFTAQGVWAFARPGSPPLKLDQSLDDAGVVDGSLLTLVSVSRTERYRPLVEDVIDAIAVLDESPEFDRTALNRFVGAAIPLLTAPVIGMAMRAWWETGRSLWWPLAIGILGIAVLVGSFVANRFYQSGHLAECLLVTTYLLIATAAALAVPLPRGVNSLGAPQVAGAATAVLFLTLMTRGGPRKRHELASFAVITAIAVIAAAAAFGYGYQDWVPAGGIAFGLFIVTNAAKLTVAVARIALPPIPVPGETVDNEELLDPVATPEATSEETPTWQAIIASVPASAVRLTERSKLAKQLLIGYVTSGTLILAAGAIAVVVRGHFFVHSLVVAGLITTVCGFRSRLYAERWCAWALLAATVAIPTGLTAKLIIWYPHYAWLLLSVYLTVALVALVVVGSMAHVRRVSPVVKRTLELIDGAMIAAIIPMLLWITGVYDTVRNIRF