moeX Resolved · high auto-curated
H37Rv Rv1681 · MTBC0 mtbc0_001789 ·
330 aa · 1917265–1918257 (+) ·
RefSeq NP_216197.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | molybdopterin biosynthesis protein MoeX |
|---|---|
| MTBC0 PGAP re-annotation | radical SAM protein |
| Revised (this work) | Radical SAM protein. Pfam: Fer4_12 (PF13353.12), Radical_SAM (PF04055.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33183
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible molybdopterin biosynthesis protein MoeX |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | moeX |
| eggNOG description | 4Fe-4S single cluster domain |
| Orthologous group | COG0535 |
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 | 0.374 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Fer4_12 | PF13353.12 | 1.6e-04 | 75–151 | 4Fe-4S single cluster domain |
Radical_SAM | PF04055.28 | 2.8e-22 | 86–219 | Radical SAM superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE16 (acyl-CoA dehydrogenase FadE16), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1680 hyp |
hypothetical protein | 988 | 988 ctx | neighborhood:882 coexpression:863 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 984 | 985 ctx | neighborhood:879 coexpression:860 |
Rv1678 |
integral membrane protein | 977 | 978 ctx | neighborhood:879 coexpression:826 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 795 | 793 | coexpression:791 |
Rv2760c vapB42 |
antitoxin VapB42 | 765 | 765 | coexpression:765 |
Rv0273c |
transcriptional regulator | 761 | 761 | coexpression:757 |
Rv1033c trcR |
two component transcriptional regulator TrcR | 735 | 734 | coexpression:734 |
Rv0911 hyp |
hypothetical protein | 734 | 734 | coexpression:733 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 697 | 683 | coexpression:498 |
Rv1676 hyp |
hypothetical protein | 635 | 624 ctx | neighborhood:537 |
Rv0339c iniR |
transcriptional regulator | 561 | 562 | coexpression:560 |
Rv1682 hyp |
hypothetical protein | 555 | 555 ctx | neighborhood:497 |
Rv1677 dsbF |
lipoprotein DsbF | 543 | 543 ctx | neighborhood:522 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 504 | 498 | coexpression:493 |
Rv2488c |
LuxR family transcriptional regulator | 497 | 498 | coexpression:482 |
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: molybdopterin biosynthesis protein MoeX
- MTBC0 PGAP product: radical SAM protein
- Pfam (hmmscan --cut_ga): Fer4_12 PF13353.12 (E=2e-04), Radical_SAM PF04055.28 (E=3e-22)
- (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_216197.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fer4_12 (PF13353.12), Radical_SAM (PF04055.28)
- 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
COG0535 - Curated reference: UniProt O33183 (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 —
23 functional partner(s); context anchor
fadE16 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001789|Rv1681|moeX MIIELMRRVVGLAQGATAEVAVYGDRDRDLAERWCANTGNTLVRADVDQTGVGTLVVRRGHPPDPASVLGPDRLPGVRLWLYTNFHCNLCCDYCCVSSSPSTPHRELGAERIGRIVGEAARWGVRELFLTGGEPFLLPDIDTIIATCVKQLPTTVLTNGMVFKGRGRRALESLPRGLALQISLDSATPELHDAHRGAGTWVKAVAGIRLALSLGFRVRVAATVASPAPGELTAFHDFLDGLGIAPGDQLVRPIALEGAASQGVALTRESLVPEVTVTADGVYWHPVAATDERALVTRTVEPLTPALDMVSRLFAEQWTRAAEEAALFPCA