esxU Resolved · high auto-curated
H37Rv Rv3445c · MTBC0 mtbc0_003664 ·
105 aa · 3888832–3889149 (-) ·
RefSeq NP_217962.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESAT-6 like protein EsxU |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-4 protein EsxU |
| Revised (this work) | Type VII secretion system ESX-4 protein EsxU. Pfam: WXG100 (PF06013.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y3I6
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESAT-6-like protein EsxU |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | esxU |
| eggNOG description | Belongs to the WXG100 family |
| Orthologous group | COG4842 |
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 | 0.338 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
WXG100 | PF06013.19 | 1.2e-13 | 7–91 | Proteins of 100 residues with WXG |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: esxT (ESAT-6 like protein EsxT), high confidence from genomic context alone (score 974 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3444c esxT |
ESAT-6 like protein EsxT | 998 | 974 ctx | neighborhood:857 coexpression:827 textmining:948 |
Rv3447c eccC4 |
ESX-4 secretion system protein EccC4 | 946 | 939 ctx | neighborhood:811 experimental:677 |
Rv3446c hyp |
hypothetical protein | 861 | 822 ctx | neighborhood:811 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 828 | 822 | experimental:815 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 815 | 789 ctx | neighborhood:733 |
Rv3449 mycP4 |
membrane-anchored mycosin | 900 | 766 ctx | neighborhood:733 textmining:592 |
Rv3903c cpnT hyp |
hypothetical protein | 736 | 737 | coexpression:732 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 791 | 705 | experimental:677 |
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 732 | 698 | experimental:677 |
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 731 | 696 | experimental:677 |
Rv3443c rplM |
50S ribosomal protein L13 | 523 | 523 ctx | neighborhood:520 |
Rv3442c rpsI |
30S ribosomal protein S9 | 522 | 523 ctx | neighborhood:520 |
Rv3441c mrsA |
phosphoglucosamine mutase | 406 | 406 ctx | neighborhood:402 |
Rv0287 esxG |
ESAT-6 like protein EsxG | 628 | 392 | textmining:414 |
Rv3020c esxS |
ESAT-6 like protein EsxS | 467 | 390 |
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: ESAT-6 like protein EsxU
- MTBC0 PGAP product: type VII secretion system ESX-4 protein EsxU
- Pfam (hmmscan --cut_ga): WXG100 PF06013.19 (E=1e-13)
- (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_217962.2)
- Domains: Pfam-A via hmmscan --cut_ga — WXG100 (PF06013.19)
- 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
COG4842 - Curated reference: UniProt I6Y3I6 (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 —
28 functional partner(s); context anchor
esxT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003664|Rv3445c|esxU MSTPNTLNADFDLMRSVAGITDARNEEIRAMLQAFIGRMSGVPPSVWGGLAAARFQDVVDRWNAESTRLYHVLHAIADTIRHNEAALREAGQIHARHIAAAGGDL