eccD5 Family assigned · medium auto-curated
H37Rv Rv1795 · MTBC0 mtbc0_001908 ·
503 aa · 2050251–2051762 (+) ·
RefSeq NP_216311.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-5 type VII secretion system protein EccD |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-5 subunit EccD5 |
| Revised (this work) | Type VII secretion system ESX-5 subunit EccD5. 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 |
P9WNP9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-5 secretion system protein EccD5 |
| Curated function | Part of the ESX-5 specialized secretion system, which is responsible for the secretion of EsxN and a number of PE_PGRS and PPE proteins, including PPE41. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | eccD5 |
| eggNOG description | Type VII secretion integral membrane protein EccD |
| Orthologous group | 28MNM |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.698 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 11 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 | 8.9e-14 | 22–103 | WXG100 protein secretion system (Wss), protein YukD |
EccD | PF19053.7 | 2.0e-42 | 145–501 | EccD-like transmembrane domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccC5 (ESX-5 type VII secretion system protein EccC5), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 999 | 1000 ctx | cooccurence:761 experimental:999 textmining:988 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 999 | 1000 ctx | cooccurence:773 experimental:999 textmining:979 |
Rv1796 mycP5 |
membrane-anchored mycosin MycP | 999 | 998 ctx | neighborhood:881 cooccurence:746 coexpression:730 experimental:800 textmining:671 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 995 | 989 ctx | cooccurence:751 experimental:956 textmining:601 |
Rv1797 eccE5 |
ESX-5 type VII secretion system protein EccE | 999 | 970 ctx | neighborhood:881 experimental:652 textmining:983 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 958 | 932 ctx | cooccurence:444 experimental:882 textmining:408 |
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 922 | 865 | experimental:821 textmining:453 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 855 | 849 ctx | cooccurence:771 |
Rv3447c eccC4 |
ESX-4 secretion system protein EccC4 | 868 | 848 | experimental:821 |
Rv1798 eccA5 |
ESX-5 type VII secretion system protein EccA | 931 | 844 ctx | neighborhood:780 textmining:579 |
Rv1794 espG5 hyp |
hypothetical protein | 886 | 734 ctx | neighborhood:721 textmining:591 |
Rv1006 hyp |
hypothetical protein | 709 | 709 ctx | cooccurence:705 |
Rv2423 hyp |
hypothetical protein | 706 | 706 ctx | cooccurence:706 |
Rv3899c hyp |
hypothetical protein | 705 | 706 ctx | cooccurence:704 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 794 | 674 | experimental:652 |
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-5 type VII secretion system protein EccD
- MTBC0 PGAP product: type VII secretion system ESX-5 subunit EccD5
- Pfam (hmmscan --cut_ga): YukD PF08817.17 (E=9e-14), EccD PF19053.7 (E=2e-42)
- (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_216311.1)
- 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
28MNM - Curated reference: UniProt P9WNP9 (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 —
90 functional partner(s); context anchor
eccC5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001908|Rv1795|eccD5 MTAVADAPQADIEGVASPQAVVVGVMAGEGVQIGVLLDANAPVSVMTDPLLKVVNSRLRELGEAPLEATGRGRWALCLVDGAPLRATQSLTEQDVYDGDRLWIRFIADTERRSQVIEHISTAVASDLSKRFARIDPIVAVQVGASMVATGVVLATGVLGWWRWHHNTWLTTIYTAVIGVLVLAVAMLLLMRAKTDADRRVADIMLMSAIMPVTVAAAAAPPGPVGSPQAVLGFGVLTVAAALALRFTGRRLGIYTTIVIIGALTMLAALARMVAATSAVTLLSSLLLICVVAYHAAPALSRRLAGIRLPVFPSATSRWVFEARPDLPTTVVVSGGSAPVLEGPSSVRDVLLQAERARSFLSGLLTGLGVMVVVCMTSLCDPHTGQRWLPLILAGFTSGFLLLRGRSYVDRWQSITLAGTAVIIAAAVCVRYALELSSPLAVSIVAAILVLLPAAGMAAAAHVPHTIYSPLFRKFVEWIEYLCLMPIFPLALWLMNVYAAIRYR