Rv3725 Resolved · high auto-curated
H37Rv Rv3725 · MTBC0 - ·
309 aa · 4170214–4171143 (+) ·
RefSeq NP_218242.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Oxidoreductase. Pfam: NmrA (PF05368.20), RmlD_sub_bind (PF04321.24), Epimerase (PF01370.28), Polysacc_synt_2 (PF02719.22), adh_short (PF00106.32), KR (PF08659.17), 3Beta_HSD (PF01073.26), GDP_Man_Dehyd (PF16363.12), NAD_binding_4 (PF07993.19), NAD_binding_10 (PF13460.13). |
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 |
O69692
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | Polysaccharide biosynthesis protein |
| Orthologous group | COG0451 |
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 | 1.259 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 62.18% of strains (90297) · reference-fixed |
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 |
|---|---|---|---|---|
NmrA | PF05368.20 | 1.5e-09 | 6–80 | NmrA-like family |
RmlD_sub_bind | PF04321.24 | 6.7e-07 | 6–122 | RmlD substrate binding domain |
Epimerase | PF01370.28 | 1.6e-21 | 8–236 | NAD dependent epimerase/dehydratase family |
Polysacc_synt_2 | PF02719.22 | 6.8e-08 | 8–125 | Polysaccharide biosynthesis protein |
adh_short | PF00106.32 | 1.9e-06 | 8–170 | short chain dehydrogenase |
KR | PF08659.17 | 3.9e-05 | 8–127 | KR domain |
3Beta_HSD | PF01073.26 | 2.5e-14 | 9–128 | 3-beta hydroxysteroid dehydrogenase/isomerase family |
GDP_Man_Dehyd | PF16363.12 | 1.4e-09 | 9–122 | GDP-mannose 4,6 dehydratase |
NAD_binding_4 | PF07993.19 | 2.4e-10 | 11–182 | Male sterility protein |
NAD_binding_10 | PF13460.13 | 3.8e-13 | 12–126 | NAD(P)H-binding |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0705 rpsS |
30S ribosomal protein S19 | 817 | 818 | experimental:463 database:574 |
Rv0682 rpsL |
30S ribosomal protein S12 | 814 | 806 | experimental:463 database:573 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 804 | 798 | experimental:463 database:578 |
Rv0707 rpsC |
30S ribosomal protein S3 | 803 | 796 | experimental:463 database:578 |
Rv0721 rpsE |
30S ribosomal protein S5 | 797 | 790 | experimental:463 database:575 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 790 | 790 | experimental:436 database:548 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 788 | 788 | experimental:436 database:548 |
Rv0718 rpsH |
30S ribosomal protein S8 | 794 | 787 | experimental:463 database:578 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 789 | 785 | experimental:463 database:557 |
Rv0702 rplD |
50S ribosomal protein L4 | 787 | 781 | experimental:463 database:575 |
Rv2785c rpsO |
30S ribosomal protein S15 | 783 | 781 | experimental:463 database:573 |
Rv2890c rpsB |
30S ribosomal protein S2 | 779 | 771 | experimental:463 database:573 |
Rv3459c rpsK |
30S ribosomal protein S11 | 776 | 768 | experimental:463 database:558 |
Rv3458c rpsD |
30S ribosomal protein S4 | 771 | 766 | experimental:463 database:555 |
Rv0683 rpsG |
30S ribosomal protein S7 | 772 | 764 | experimental:463 database:555 |
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): oxidoreductase
- Pfam (hmmscan --cut_ga): NmrA PF05368.20 (E=1e-09), RmlD_sub_bind PF04321.24 (E=7e-07), Epimerase PF01370.28 (E=2e-21), Polysacc_synt_2 PF02719.22 (E=7e-08), adh_short PF00106.32 (E=2e-06), KR PF08659.17 (E=4e-05), 3Beta_HSD PF01073.26 (E=3e-14), GDP_Man_Dehyd PF16363.12 (E=1e-09), NAD_binding_4 PF07993.19 (E=2e-10), NAD_binding_10 PF13460.13 (E=4e-13)
- (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_218242.1)
- Domains: Pfam-A via hmmscan --cut_ga — NmrA (PF05368.20), RmlD_sub_bind (PF04321.24), Epimerase (PF01370.28), Polysacc_synt_2 (PF02719.22), adh_short (PF00106.32), KR (PF08659.17), 3Beta_HSD (PF01073.26), GDP_Man_Dehyd (PF16363.12), NAD_binding_4 (PF07993.19), NAD_binding_10 (PF13460.13)
- 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
COG0451 - Curated reference: UniProt O69692 (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 — 76 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3725| MQNATMRVLVTGGTGFVGGWTAKAIADAGHSVRFLVRNPARLKTSVAKLGVDVSDFAVADISDRDSVREALNGCDAVVHSAALVATDPRETSRMLSTNMAGAQNVLGQAVELGMDPIVHVSSFTALFRPNLATLSADLPVAGGTDGYGQSKAQIEIYARGLQDAGAPVNITYPGMVLGPPVGDQFGEAGEGVRSALWMHVIPGRGAAWLIVDVRDVAALHAALLESGRGPRRYTAGGHRIPVPELAKILGGSPAPRCWPSRCPIPRCVSRDRCWIKPGPICLSILRSPRQVCSTTHRCRSPTIRRAKKN