mce3F Family assigned · medium auto-curated
H37Rv Rv1971 · MTBC0 mtbc0_002087 ·
437 aa · 2234374–2235687 (+) ·
RefSeq NP_216487.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Mce family protein Mce3F |
|---|---|
| MTBC0 PGAP re-annotation | MlaD family protein |
| Revised (this work) | MlaD family protein. Pfam: MlaD (PF02470.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53972
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Mce-family protein Mce3F |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | mce3F |
| eggNOG description | Virulence factor Mce family protein |
| Orthologous group | COG1463 |
| KEGG orthology |
K02067
|
| 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 | 0.72 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 5.19% of strains (7539) · 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 |
|---|---|---|---|---|
MlaD | PF02470.26 | 3.4e-17 | 42–116 | MlaD protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: yrbE3A (integral membrane protein), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1964 yrbE3A |
integral membrane protein | 997 | 996 ctx | neighborhood:876 cooccurence:764 coexpression:815 textmining:412 |
Rv1965 yrbE3B |
integral membrane protein | 995 | 995 ctx | neighborhood:799 cooccurence:771 coexpression:849 |
Rv1972 |
Mce associated membrane protein | 994 | 994 ctx | neighborhood:851 cooccurence:755 coexpression:860 |
Rv1967 mce3B |
Mce family protein Mce3B | 996 | 993 ctx | neighborhood:795 cooccurence:774 coexpression:860 textmining:566 |
Rv1966 mce3A |
Mce family protein Mce3A | 995 | 993 ctx | neighborhood:787 cooccurence:774 coexpression:860 textmining:443 |
Rv1970 lprM |
Mce family lipoprotein LprM | 994 | 993 ctx | neighborhood:789 cooccurence:774 coexpression:860 |
Rv1969 mce3D |
Mce family protein Mce3D | 998 | 992 ctx | neighborhood:786 cooccurence:774 coexpression:857 textmining:778 |
Rv1968 mce3C |
Mce family protein Mce3C | 990 | 988 ctx | neighborhood:881 coexpression:860 |
Rv1973 |
Mce associated membrane protein | 976 | 976 ctx | neighborhood:721 cooccurence:608 coexpression:801 |
Rv1974 |
membrane protein | 956 | 956 ctx | neighborhood:839 coexpression:738 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 940 | 900 ctx | cooccurence:759 experimental:431 textmining:424 |
Rv0168 yrbE1B |
membrane protein | 907 | 881 ctx | cooccurence:770 |
Rv3500c yrbE4B |
integral membrane protein | 902 | 875 ctx | cooccurence:772 |
Rv0588 yrbE2B hyp |
hypothetical protein | 901 | 874 ctx | cooccurence:770 |
Rv3501c yrbE4A |
integral membrane protein | 874 | 872 ctx | cooccurence:768 |
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: Mce family protein Mce3F
- MTBC0 PGAP product: MlaD family protein
- Pfam (hmmscan --cut_ga): MlaD PF02470.26 (E=3e-17)
- (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_216487.1)
- Domains: Pfam-A via hmmscan --cut_ga — MlaD (PF02470.26)
- 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
COG1463 - Curated reference: UniProt O53972 (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 —
47 functional partner(s); context anchor
yrbE3A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002087|Rv1971|mce3F MLHLPRRVIVQLAVFTVIAVGVLAITFLHFVRLPAMLFGVGRYTVTMELVEAGGLYRTGNVTYRGFEVGRVAAVRLTDTGVQAVLALKSGIDIPSDLKAEVHSHTAIGETYVELLPRNAASPPLKNGDVIALADTSVPPDINDLLSAANTALEAIPHENLQTVIDESYTAVAGLGLELSRLIKGSAELAIDARANLDPLVALIDRAGPVLDSQTHTSDAIAAWAAQLAAVTGQLQTHDSAVGDLIDRGGPALGETRQLLERLQPTVPILLANLVSVGQVALTYHNDIEQLLVVFPMAIAAEQAGILANLNTKQAYRGQYLSFNLNLNLPPPCTTGFLPAQQRRIPTFEDYPDRPAGDLYCRVPQDSPFNVRGARNIPCETVPGKRAPTVKLCESDEPYLPLNDGYNWKGDPNATVPGLGSGQDIPQTWQTMLLPPGS