mce1D Family assigned · medium auto-curated
H37Rv Rv0172 · MTBC0 mtbc0_000185 ·
530 aa · 202824–204416 (+) ·
RefSeq NP_214686.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Mce family protein Mce1D |
|---|---|
| MTBC0 PGAP re-annotation | virulence factor Mce family protein |
| Revised (this work) | Virulence factor Mce family protein. 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.
Curated reference (UniProt)
| UniProt |
O07416
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Mce-family protein Mce1D |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | mce1D |
| 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 | 1.575 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 14 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 | 3.4e-15 | 46–121 | MlaD protein |
Mce4_CUP1 | PF11887.14 | 1.0e-12 | 128–290 | 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 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0167 yrbE1A |
membrane protein | 997 | 995 ctx | neighborhood:792 cooccurence:753 coexpression:871 textmining:467 |
Rv0168 yrbE1B |
membrane protein | 997 | 995 ctx | neighborhood:785 cooccurence:767 coexpression:860 textmining:534 |
Rv0169 mce1A |
Mce family protein Mce1A | 998 | 993 ctx | neighborhood:784 cooccurence:774 coexpression:860 textmining:826 |
Rv0170 mce1B |
Mce family protein Mce1B | 997 | 993 ctx | neighborhood:795 cooccurence:772 coexpression:860 textmining:645 |
Rv0173 lprK |
Mce family lipoprotein LprK | 996 | 993 ctx | neighborhood:782 cooccurence:774 coexpression:860 textmining:578 |
Rv0171 mce1C |
Mce family protein Mce1C | 983 | 979 ctx | neighborhood:795 coexpression:861 |
Rv0174 mce1F |
Mce family protein Mce1F | 977 | 974 ctx | neighborhood:787 coexpression:834 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 903 | 899 ctx | cooccurence:746 experimental:431 |
Rv3500c yrbE4B |
integral membrane protein | 878 | 874 ctx | cooccurence:766 |
Rv0588 yrbE2B hyp |
hypothetical protein | 873 | 868 ctx | cooccurence:765 |
Rv1965 yrbE3B |
integral membrane protein | 873 | 867 ctx | cooccurence:759 |
Rv3501c yrbE4A |
integral membrane protein | 894 | 864 ctx | cooccurence:751 |
Rv0166 fadD5 |
fatty-acid--CoA ligase FadD5 | 883 | 863 ctx | neighborhood:460 coexpression:757 |
Rv0587 yrbE2A hyp |
hypothetical protein | 936 | 858 ctx | cooccurence:746 textmining:570 |
Rv1964 yrbE3A |
integral membrane protein | 902 | 856 ctx | cooccurence:737 |
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 Mce1D
- MTBC0 PGAP product: virulence factor Mce family protein
- Pfam (hmmscan --cut_ga): MlaD PF02470.26 (E=3e-15), Mce4_CUP1 PF11887.14 (E=1e-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_214686.1)
- 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 O07416 (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
>mtbc0_000185|Rv0172|mce1D MSTIFDIRNLRLPQLSRASVVIGSLVVVLALAAGIVGVRLYQKLTNNTVVAYFTQANALYVGDKVQIMGLPVGSIDKIEPAGDKMKVTFHYQNKYKVPANASAVILNPTLVASRNIQLEPPYRGGPVLADNAVIPVERTQVPTEWDELRDSVSHIIDELGPTPEQPKGPFGEVIEAFADGLAGKGKQINTTLNSLSQALNALNEGRGDFFAVVRSLALFVNALHQDDQQFVALNKNLAEFTDRLTHSDADLSNAIQQFDSLLAVARPFFAKNREVLTHDVNNLATVTTTLLQPDPLDGLETVLHIFPTLAANINQLYHPTHGGVVSLSAFTNFANPMEFICSSIQAGSRLGYQESAELCAQYLAPVLDAIKFNYFPFGLNVASTASTLPKEIAYSEPRLQPPNGYKDTTVPGIWVPDTPLSHRNTQPGWVVAPGMQGVQVGPITQGLLTPESLAELMGGPDIAPPSSGLQTPPGPPNAYDEYPVLPPIGLQAPQVPIPPPPPGPDVIPGPVPPTPAPVGAPLPAEAGGGQ