Rv1817 Family assigned · medium auto-curated
H37Rv Rv1817 · MTBC0 mtbc0_001931 ·
487 aa · 2077683–2079146 (+) ·
RefSeq NP_216333.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | flavoprotein |
|---|---|
| MTBC0 PGAP re-annotation | FAD-binding protein |
| Revised (this work) | FAD-binding protein. Pfam: FAD_binding_2 (PF00890.31), DAO (PF01266.31), FAD_oxidored (PF12831.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q50616
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible flavoprotein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | Succinate dehydrogenase fumarate reductase flavoprotein subunit |
| Orthologous group | COG1053 |
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 | 0.133 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 4 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 |
|---|---|---|---|---|
FAD_binding_2 | PF00890.31 | 4.1e-49 | 22–452 | FAD binding domain |
DAO | PF01266.31 | 5.5e-11 | 22–237 | FAD dependent oxidoreductase |
FAD_oxidored | PF12831.14 | 6.7e-07 | 22–66 | FAD dependent oxidoreductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hsaC (extradiol dioxygenase), high confidence from genomic context alone (score 833 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 962 | 959 | coexpression:650 experimental:707 database:621 |
Rv0760c hyp |
hypothetical protein | 947 | 946 ctx | cooccurence:476 database:900 |
Rv3537 kstD |
3-oxosteroid 1-dehydrogenase | 947 | 935 | database:900 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 937 | 918 | coexpression:894 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 881 | 875 | coexpression:486 experimental:454 database:578 |
Rv1553 frdB |
fumarate reductase iron-sulfur subunit | 881 | 875 | coexpression:487 experimental:454 database:578 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 881 | 875 | coexpression:484 experimental:454 database:578 |
Rv3568c hsaC |
extradiol dioxygenase | 848 | 833 ctx | cooccurence:710 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 811 | 797 | coexpression:647 experimental:430 |
Rv0310c hyp |
hypothetical protein | 785 | 773 ctx | cooccurence:582 coexpression:415 |
Rv3570c hsaA |
flavin-dependent monooxygenase oxygenase subunit HsaA | 770 | 750 ctx | cooccurence:710 |
Rv3526 kshA |
3-ketosteroid-9-alpha-monooxygenase oxygenase subunit | 738 | 725 ctx | cooccurence:714 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 723 | 701 | coexpression:646 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 723 | 701 | coexpression:650 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 721 | 699 | coexpression:652 |
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: flavoprotein
- MTBC0 PGAP product: FAD-binding protein
- Pfam (hmmscan --cut_ga): FAD_binding_2 PF00890.31 (E=4e-49), DAO PF01266.31 (E=5e-11), FAD_oxidored PF12831.14 (E=7e-07)
- (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_216333.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_2 (PF00890.31), DAO (PF01266.31), FAD_oxidored (PF12831.14)
- 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
COG1053 - Curated reference: UniProt Q50616 (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 —
85 functional partner(s); context anchor
hsaC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001931|Rv1817| MSTDIPATVSAETVTSWSDDVDVTVIGFGIAGGCAAVSAAAAGARVLVLERAAAAGGTTALAGGHFYLGGGTTVQLATGHPDSPEEMYKYLVAVSREPDHDKIRAYCDGSVEHFNWLEGLGFQFERSYFPGKAVIQPNTEGLMFTGNEKVWPFLELAVPAPRGHKVPVPGDTGGAAMVIDLLLKRAASLGIQIRYETGATELIVDGTGKVTGVMWKRFSETGAIKAKSVIIAAGGFVMNPDMVAKYTPKLAEKPFVLGNTYDDGLGIRLGVSAGGATQHMDQMFITAPPYPPSILLTGIIVNKLGQRFVAEDSYHSRTAGFIMEQPDSAAYLIVDEAHLEHPKMPLVPLIDGWETVVEMEAALGIPPGNLAATLDRYNAYAARGADPDFHKQPEFLAAQDNGPWGAFDMSLGKAMYAGFTLGGLATSVDGQVLRDDGAVVAGLYAVGACASNIAQDGKGYASGTQLGEGSFFGRRAGAHAAARAQGM