mce1A Family assigned · medium auto-curated
H37Rv Rv0169 · MTBC0 - ·
454 aa · 198534–199898 (+) ·
RefSeq YP_177701.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Mce family protein Mce1A |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Mce family protein Mce1A. Pfam: MlaD (PF02470.26), Mce4_CUP1 (PF11887.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
Q79FZ9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Mce-family protein Mce1A |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | mce1A |
| 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)
| pN/pS | 0.925 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 13 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 |
|---|---|---|---|---|
MlaD | PF02470.26 | 1.1e-13 | 44–125 | MlaD protein |
Mce4_CUP1 | PF11887.14 | 1.2e-75 | 131–329 | Cholesterol uptake porter CUP1 of Mce4, putative |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: yrbE1A (membrane protein), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0167 yrbE1A |
membrane protein | 999 | 997 ctx | neighborhood:882 cooccurence:729 coexpression:881 textmining:811 |
Rv0168 yrbE1B |
membrane protein | 999 | 995 ctx | neighborhood:799 cooccurence:757 coexpression:868 textmining:824 |
Rv0170 mce1B |
Mce family protein Mce1B | 998 | 993 ctx | neighborhood:794 cooccurence:772 coexpression:860 textmining:851 |
Rv0171 mce1C |
Mce family protein Mce1C | 998 | 993 ctx | neighborhood:790 cooccurence:774 coexpression:861 textmining:761 |
Rv0172 mce1D |
Mce family protein Mce1D | 998 | 993 ctx | neighborhood:784 cooccurence:774 coexpression:860 textmining:826 |
Rv0173 lprK |
Mce family lipoprotein LprK | 997 | 991 ctx | neighborhood:783 cooccurence:774 coexpression:836 textmining:717 |
Rv0174 mce1F |
Mce family protein Mce1F | 998 | 990 ctx | neighborhood:785 cooccurence:774 coexpression:805 textmining:828 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 964 | 888 ctx | cooccurence:692 experimental:431 textmining:699 |
Rv0166 fadD5 |
fatty-acid--CoA ligase FadD5 | 976 | 886 ctx | neighborhood:459 coexpression:798 textmining:804 |
Rv3500c yrbE4B |
integral membrane protein | 911 | 869 ctx | cooccurence:759 |
Rv1965 yrbE3B |
integral membrane protein | 901 | 869 ctx | cooccurence:747 |
Rv0588 yrbE2B hyp |
hypothetical protein | 892 | 862 ctx | cooccurence:754 |
Rv3501c yrbE4A |
integral membrane protein | 911 | 854 ctx | cooccurence:732 textmining:414 |
Rv0587 yrbE2A hyp |
hypothetical protein | 908 | 842 ctx | cooccurence:717 textmining:444 |
Rv1964 yrbE3A |
integral membrane protein | 895 | 839 ctx | cooccurence:699 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): Mce family protein Mce1A
- Pfam (hmmscan --cut_ga): MlaD PF02470.26 (E=1e-13), Mce4_CUP1 PF11887.14 (E=1e-75)
- (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 YP_177701.1)
- Domains: Pfam-A via hmmscan --cut_ga — MlaD (PF02470.26), Mce4_CUP1 (PF11887.14)
- 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 Q79FZ9 (TrEMBL, unreviewed; 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 —
79 functional partner(s); context anchor
yrbE1A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0169|mce1A MTTPGKLNKARVPPYKTAGLGLVLVFALVVALVYLQFRGEFTPKTQLTMLSARAGLVMDPGSKVTYNGVEIGRVDTISEVTRDGESAAKFILDVDPRYIHLIPANVNADIKATTVFGGKYVSLTTPKNPTKRRITPKDVIDVRSVTTEINTLFQTLTSIAEKVDPVKLNLTLSAAAEALTGLGDKFGESIVNANTVLDDLNSRMPQSRHDIQQLAALGDVYADAAPDLFDFLDSSVTTARTINAQQAELDSALLAAAGFGNTTADVFDRGGPYLQRGVADLVPTATLLDTYSPELFCTIRNFYDADPLAKAASGGGNGYSLRTNSEILSGIGISLLSPLALATNGAAIGIGLVAGLIAPPLAVAANLAGALPGIVGGAPNPYTYPENLPRVNARGGPGGAPGCWQPITRDLWPAPYLVMDTGASLAPYNHMEVGSPYAVEYVWGRQVGDNTINP