espL Resolved · high auto-curated
H37Rv Rv3880c · MTBC0 mtbc0_004114 ·
115 aa · 4384445–4384792 (-) ·
RefSeq NP_218397.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion-associated protein EspL |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 associated protein EspL |
| Revised (this work) | Type VII secretion system ESX-1 associated protein EspL. Pfam: YbaB_DNA_bd (PF02575.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJB9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion-associated protein EspL |
| Curated function | Probably plays a role in host phagosome maturation arrest. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection |
| Orthologous group | 2B0QF |
| Gene Ontology (56) |
GO:0002682, GO:0002683, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0009605, GO:0009607, GO:0016020, GO:0030312, GO:0031347 +44 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 | 0.98 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
YbaB_DNA_bd | PF02575.22 | 6.8e-12 | 17–102 | YbaB/EbfC DNA-binding family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espB (ESX-1 secretion-associated protein EspB), high confidence from genomic context alone (score 978 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3881c espB |
ESX-1 secretion-associated protein EspB | 995 | 978 ctx | neighborhood:882 coexpression:822 textmining:817 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 889 | 766 ctx | neighborhood:763 textmining:547 |
Rv3715c recR |
recombination protein RecR | 776 | 748 | coexpression:734 |
Rv3883c mycP1 |
membrane-anchored mycosin | 824 | 653 ctx | neighborhood:648 textmining:514 |
Rv3614c espD |
ESX-1 secretion-associated protein EspD | 648 | 503 | experimental:500 |
Rv1307 atpH |
ATP synthase subunit b/delta | 463 | 464 | coexpression:448 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 498 | 451 | coexpression:432 |
Rv3644c |
DNA polymerase | 489 | 441 | coexpression:422 |
Rv2842c rimP |
ribosome maturation factor RimP | 440 | 441 | coexpression:422 |
Rv3443c rplM |
50S ribosomal protein L13 | 434 | 435 | coexpression:417 |
Rv0652 rplL |
50S ribosomal protein L7/L12 | 429 | 429 | coexpression:411 |
Rv1901 cinA |
competence damage-inducible protein CinA | 411 | 410 | |
Rv2461c clpP1 |
ATP-dependent CLP protease proteolytic subunit 1 | 417 | 395 | |
Rv2460c clpP2 |
ATP-dependent CLP protease proteolytic subunit 2 | 407 | 386 | |
Rv3867 espH |
ESX-1 secretion-associated protein EspH | 853 | 288 | textmining:803 |
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-associated protein EspL
- MTBC0 PGAP product: type VII secretion system ESX-1 associated protein EspL
- Pfam (hmmscan --cut_ga): YbaB_DNA_bd PF02575.22 (E=7e-12)
- (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_218397.1)
- Domains: Pfam-A via hmmscan --cut_ga — YbaB_DNA_bd (PF02575.22)
- 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
2B0QF - Curated reference: UniProt P9WJB9 (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 —
26 functional partner(s); context anchor
espB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004114|Rv3880c|espL MSMDELDPHVARALTLAARFQSALDGTLNQMNNGSFRATDEAETVEVTINGHQWLTGLRIEDGLLKKLGAEAVAQRVNEALHNAQAAASAYNDAAGEQLTAALSAMSRAMNEGMA