eccB4 Family assigned · medium auto-curated
H37Rv Rv3450c · MTBC0 mtbc0_003669 ·
470 aa · 3896969–3898381 (-) ·
RefSeq NP_217967.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-4 secretion system protein EccB4 |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-4 subunit EccB4 |
| Revised (this work) | Type VII secretion system ESX-4 subunit EccB4. Pfam: T7SS_ESX1_EccB (PF05108.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNR1
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | ESX-4 secretion system ATPase EccB4 |
| EC (curated) |
EC 3.6.-.-
|
| Curated function | An ATPase (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | eccB |
| eggNOG description | Type VII secretion |
| Orthologous group | COG3266 |
| Gene Ontology (7) |
GO:0005575, GO:0005576, 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 | 0.455 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (224) · 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_ESX1_EccB | PF05108.19 | 1.7e-159 | 5–468 | Type VII secretion system ESX-1, transport TM domain B |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD4 (ESX-4 secretion system protein EccD4), high confidence from genomic context alone (score 821 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 827 | 821 ctx | cooccurence:770 |
Rv3447c eccC4 |
ESX-4 secretion system protein EccC4 | 829 | 810 ctx | cooccurence:725 |
Rv3657c |
membrane protein | 802 | 802 | coexpression:736 |
Rv3886c mycP2 |
membrane-anchored mycosin | 788 | 771 ctx | cooccurence:717 |
Rv3451 cut3 |
cutinase | 770 | 770 ctx | neighborhood:769 |
Rv1796 mycP5 |
membrane-anchored mycosin MycP | 755 | 735 ctx | cooccurence:675 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 736 | 718 ctx | cooccurence:575 |
Rv2474c hyp |
hypothetical protein | 711 | 712 ctx | cooccurence:710 |
Rv0358 hyp |
hypothetical protein | 738 | 692 ctx | cooccurence:688 |
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 711 | 678 ctx | cooccurence:554 |
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 699 | 672 ctx | cooccurence:507 |
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 677 | 641 ctx | cooccurence:501 |
Rv2732c |
transmembrane protein | 598 | 599 ctx | cooccurence:596 |
Rv1682 hyp |
hypothetical protein | 590 | 591 ctx | cooccurence:582 |
Rv3256c hyp |
hypothetical protein | 586 | 587 ctx | cooccurence:584 |
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 EccB4
- MTBC0 PGAP product: type VII secretion system ESX-4 subunit EccB4
- Pfam (hmmscan --cut_ga): T7SS_ESX1_EccB PF05108.19 (E=2e-159)
- (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_217967.1)
- Domains: Pfam-A via hmmscan --cut_ga — T7SS_ESX1_EccB (PF05108.19)
- 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
COG3266 - Curated reference: UniProt P9WNR1 (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 —
73 functional partner(s); context anchor
eccD4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003669|Rv3450c|eccB4 MPSPATTWLHVSGYRFLLRRIECALLFGDVCAATGALRARTTSLALGCVLAIVAAMGCAFVALLRPQSALGQAPIVMGRESGALYVRVDDVWHPVLNLASARLIAATNANPQPVSESELGHTKRGPLLGIPGAPQLLDQPLAGAESAWAICDSDNGGSTTVVVGPAEDSSAQVLTAEQMILVATESGSPTYLLYGGRRAVVDLADPAVVWALRLQGRVPHVVAQSLLNAVPEAPRITAPRIRGGGRASVGLPGFLVGGVVRITRASGDEYYVVLEDGVQRIGQVAADLLRFGDSQGSVNVPTVAPDVIRVAPIVNTLPVSAFPDRPPTPVDGSPGRAVTTLCVTWTPAQPGAARVAFLAGSGPPVPLGGVPVTLAQADGRGPALDAVYLPPGRSAYVAARSLSGGGTGTRYLVTDTGVRFAIHDDDVAHDLGLPTAAIPAPWPVLATLPSGPELSRANASVARDTVAPGP