eccB1 Family assigned · medium auto-curated
H37Rv Rv3869 · MTBC0 mtbc0_004102 ·
480 aa · 4369196–4370638 (+) ·
RefSeq NP_218386.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion system protein EccB |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 subunit EccB1 |
| Revised (this work) | Type VII secretion system ESX-1 subunit EccB1. 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 |
P9WNR7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion system ATPase EccB1 |
| EC (curated) |
EC 3.6.-.-
|
| Curated function | An ATPase. 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 | eccB1 |
| eggNOG description | ATP binding |
| Orthologous group | COG3266 |
| Gene Ontology (29) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0008150, GO:0009605, GO:0009607, GO:0030312, GO:0035821, GO:0043207, GO:0044003, GO:0044403 +17 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 | 0.867 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 19 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (179) · 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 | 1.3e-171 | 4–464 | Type VII secretion system ESX-1, transport TM domain B |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccCa1 (ESX-1 secretion system protein EccCa), high confidence from genomic context alone (score 992 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 997 | 992 ctx | neighborhood:881 cooccurence:766 coexpression:651 textmining:657 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 977 | 962 ctx | neighborhood:771 cooccurence:748 textmining:437 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 957 | 905 ctx | neighborhood:881 textmining:575 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 980 | 857 ctx | cooccurence:772 textmining:869 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 974 | 834 ctx | cooccurence:767 textmining:851 |
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 924 | 831 ctx | neighborhood:825 textmining:569 |
Rv3865 espF |
ESX-1 secretion-associated protein EspF | 897 | 827 ctx | neighborhood:825 textmining:431 |
Rv3875 esxA |
ESAT-6 protein EsxA | 900 | 822 ctx | cooccurence:731 textmining:461 |
Rv3867 espH |
ESX-1 secretion-associated protein EspH | 849 | 809 ctx | neighborhood:800 |
Rv2542 hyp |
hypothetical protein | 848 | 740 ctx | cooccurence:740 textmining:440 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 848 | 734 ctx | neighborhood:608 textmining:454 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 843 | 727 ctx | neighborhood:550 textmining:450 |
Rv3883c mycP1 |
membrane-anchored mycosin | 842 | 717 ctx | cooccurence:654 textmining:466 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 896 | 714 ctx | cooccurence:714 textmining:652 |
Rv1157c hyp |
hypothetical protein | 711 | 701 ctx | cooccurence:693 |
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 EccB
- MTBC0 PGAP product: type VII secretion system ESX-1 subunit EccB1
- Pfam (hmmscan --cut_ga): T7SS_ESX1_EccB PF05108.19 (E=1e-171)
- (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_218386.1)
- 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 P9WNR7 (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 —
76 functional partner(s); context anchor
eccCa1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004102|Rv3869|eccB1 MGLRLTTKVQVSGWRFLLRRLEHAIVRRDTRMFDDPLQFYSRSIALGIVVAVLILAGAALLAYFKPQGKLGGTSLFTDRATNQLYVLLSGQLHPVYNLTSARLVLGNPANPATVKSSELSKLPMGQTVGIPGAPYATPVSAGSTSIWTLCDTVARADSTSPVVQTAVIAMPLEIDASIDPLQSHEAVLVSYQGETWIVTTKGRHAIDLTDRALTSSMGIPVTARPTPISEGMFNALPDMGPWQLPPIPAAGAPNSLGLPDDLVIGSVFQIHTDKGPQYYVVLPDGIAQVNATTAAALRATQAHGLVAPPAMVPSLVVRIAERVYPSPLPDEPLKIVSRPQDPALCWSWQRSAGDQSPQSTVLSGRHLPISPSAMNMGIKQIHGTATVYLDGGKFVALQSPDPRYTESMYYIDPQGVRYGVPNAETAKSLGLSSPQNAPWEIVRLLVDGPVLSKDAALLEHDTLPADPSPRKVPAGASGAP