eccD4 Family assigned · medium auto-curated
H37Rv Rv3448 · MTBC0 mtbc0_003667 ·
467 aa · 3894237–3895640 (+) ·
RefSeq NP_217965.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-4 secretion system protein EccD4 |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-4 subunit EccD4 |
| Revised (this work) | Type VII secretion system ESX-4 subunit EccD4. 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 |
P9WNQ1
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | ESX-4 secretion system protein eccD4 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | eccD |
| eggNOG description | WXG100 protein secretion system (Wss), protein YukD |
| Orthologous group | 28MNM |
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, 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 | 0.899 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 | 2.2e-20 | 9–83 | WXG100 protein secretion system (Wss), protein YukD |
EccD | PF19053.7 | 1.3e-37 | 118–462 | EccD-like transmembrane domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccC4 (ESX-4 secretion system protein EccC4), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3447c eccC4 |
ESX-4 secretion system protein EccC4 | 997 | 996 ctx | neighborhood:778 cooccurence:758 coexpression:853 experimental:513 textmining:489 |
Rv3449 mycP4 |
membrane-anchored mycosin | 995 | 987 ctx | neighborhood:882 coexpression:850 textmining:645 |
Rv3446c hyp |
hypothetical protein | 989 | 981 ctx | neighborhood:778 cooccurence:428 coexpression:860 textmining:487 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 937 | 930 ctx | cooccurence:701 experimental:773 |
Rv3903c cpnT hyp |
hypothetical protein | 921 | 920 ctx | cooccurence:595 coexpression:805 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 917 | 907 ctx | cooccurence:607 experimental:773 |
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 882 | 870 ctx | cooccurence:734 experimental:513 |
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 887 | 843 ctx | cooccurence:681 experimental:513 |
Rv0292 eccE3 |
ESX-3 secretion system protein EccE | 850 | 841 | experimental:830 |
Rv2082 hyp |
hypothetical protein | 831 | 832 ctx | cooccurence:715 coexpression:432 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 921 | 827 ctx | cooccurence:640 experimental:513 textmining:562 |
Rv3450c eccB4 |
ESX-4 secretion system protein EccB4 | 827 | 821 ctx | cooccurence:770 |
Rv0603 hyp |
hypothetical protein | 803 | 803 | coexpression:803 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 802 | 802 | coexpression:802 |
Rv0022c whiB5 |
transcriptional regulator WhiB5 | 799 | 799 | coexpression:799 |
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-4 secretion system protein EccD4
- MTBC0 PGAP product: type VII secretion system ESX-4 subunit EccD4
- Pfam (hmmscan --cut_ga): YukD PF08817.17 (E=2e-20), EccD PF19053.7 (E=1e-37)
- (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_217965.1)
- 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 P9WNQ1 (SwissProt, reviewed; Inferred from homology)
- 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 —
134 functional partner(s); context anchor
eccC4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003667|Rv3448|eccD4 MPTSDPGLRRVTVHAGAQAVDLTLPAAVPVATLIPSIVDILGDRGASPATAARYQLSALGAPALPNATTLAQCGIRDGAVLVLHKSSAQPPTPRCDDVAEAVAAALDTTARPQCQRTTRLSGALAASCITAGGGLMLVRNALGTNVTRYSDATAGVVAAAGLAALLFAVIACRTYRDPIAGLTLSVIATIFGAVAGLLAVPGVPGVHSVLVAAMAAAATSVLAMRITGCGGITLTAVACCAVVVAAATLVGAITAAPVPAIGSLATLASFGLLEVSARMAVLLAGLSPRLPPALNPDDADALPTTDRLTTRANRADAWLTSLLAAFAASATIGAIGTAVATHGIHRSSMGGIALAAVTGALLLLRARSADTRRSLVFAICGITTVATAFTVAADRALEHGPWIAALTAMLAAVAMFLGFVAPALSLSPVTYRTIELLECLALIAMVPLTAWLCGAYSAVRHLDLTWT