yrbE3A Family assigned · medium auto-curated
H37Rv Rv1964 · MTBC0 mtbc0_002080 ·
265 aa · 2226817–2227614 (+) ·
RefSeq NP_216480.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter permease |
| Revised (this work) | ABC transporter permease. Pfam: MlaE (PF02405.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53965
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Conserved hypothetical integral membrane protein YrbE3A |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | yrbE3A |
| eggNOG description | ABC-type transport system involved in resistance to organic solvents, permease component |
| Orthologous group | COG0767 |
| KEGG orthology |
K02066
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00210, M00669, M00670
|
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) pseudogene candidate
| pN/pS | 0.363 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.16% of strains (1678) · 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 |
|---|---|---|---|---|
MlaE | PF02405.22 | 9.9e-53 | 49–257 | Permease MlaE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mce3F (Mce family protein Mce3F), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1971 mce3F |
Mce family protein Mce3F | 997 | 996 ctx | neighborhood:876 cooccurence:764 coexpression:815 textmining:412 |
Rv1968 mce3C |
Mce family protein Mce3C | 996 | 996 ctx | neighborhood:876 cooccurence:767 coexpression:831 |
Rv1967 mce3B |
Mce family protein Mce3B | 995 | 995 ctx | neighborhood:785 cooccurence:767 coexpression:863 |
Rv1966 mce3A |
Mce family protein Mce3A | 997 | 994 ctx | neighborhood:782 cooccurence:690 coexpression:878 textmining:602 |
Rv1970 lprM |
Mce family lipoprotein LprM | 993 | 993 ctx | neighborhood:777 cooccurence:752 coexpression:834 |
Rv1969 mce3D |
Mce family protein Mce3D | 991 | 991 ctx | neighborhood:777 cooccurence:742 coexpression:784 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 991 | 988 ctx | cooccurence:774 coexpression:450 experimental:505 database:800 |
Rv1965 yrbE3B |
integral membrane protein | 987 | 985 ctx | neighborhood:789 coexpression:860 |
Rv1972 |
Mce associated membrane protein | 946 | 946 ctx | neighborhood:747 cooccurence:492 coexpression:615 |
Rv3497c mce4C |
Mce family protein Mce4C | 883 | 881 ctx | cooccurence:768 |
Rv0590 mce2B |
Mce-family protein Mce2B; Rv0590, (MTCY19H5.32c), len: 275 aa. Mce2B; belongs to 24-membered Mycobacterium tuberculosis Mce protein family ( | 881 | 879 ctx | cooccurence:769 |
Rv3498c mce4B |
Mce family protein Mce4B | 875 | 873 ctx | cooccurence:769 |
Rv0170 mce1B |
Mce family protein Mce1B | 874 | 872 ctx | cooccurence:768 |
Rv3496c mce4D |
Mce family protein Mce4D | 876 | 871 ctx | cooccurence:765 |
Rv0592 mce2D |
Mce family protein Mce2D | 874 | 868 ctx | cooccurence:757 |
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: integral membrane protein
- MTBC0 PGAP product: ABC transporter permease
- Pfam (hmmscan --cut_ga): MlaE PF02405.22 (E=1e-52)
- (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_216480.1)
- Domains: Pfam-A via hmmscan --cut_ga — MlaE (PF02405.22)
- 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
COG0767 - Curated reference: UniProt O53965 (TrEMBL, unreviewed; Predicted)
- 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 —
50 functional partner(s); context anchor
mce3F - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002080|Rv1964|yrbE3A MVIVADKAAGRVADPVLRPVGALGDFFAMTLDTSVCMFKPPFAWREYLLQCWFVARVSTLPGVLMTIPWAVISGFLFNVLLTDIGAADFSGTGCAIFTVNQSAPIVTVLVVAGAGATAMCADLGARTIREELDALRVMGINPIQALAAPRVLAATTVSLALNSVVTATGLIGAFFCSVFLMHVSAGAWVTGLTTLTHTVDVVISMIKATLFGLMAGLIACYKGMSVGGGPAGVGRAVNETVVFAFIVLFVINIVVTAVGIPFMVS