Rv3553 Resolved · high auto-curated
H37Rv Rv3553 · MTBC0 mtbc0_003770 ·
355 aa · 4015298–4016365 (+) ·
RefSeq NP_218070.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | nitronate monooxygenase |
| Revised (this work) | Nitronate monooxygenase. Pfam: IMPDH (PF00478.32), NMO (PF03060.22), FMN_dh (PF01070.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71847
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (3aS,4S,5R,7aS)-5-hydroxy-7a-methyl-1-oxo-octahydro-1H-indene-4-carboxyl-CoA dehydrogenase |
| EC (curated) |
EC 1.3.1.-
|
| Curated function | Involved in the final steps of cholesterol and steroid degradation. Probably catalyzes the introduction of a double bound into the C ring of 5OH-HIC-CoA, leading to the formation of (5R,7aS)-5-hydroxy-7a-methyl-1-oxo-3,5,6,7-tetrahydro-2H-indene-4-carboxyl-CoA (Probable). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | fabK |
| eggNOG description | 2-nitropropane dioxygenase |
| Orthologous group | COG2070 |
| EC number |
EC 1.13.12.16
|
| KEGG orthology |
K00459
|
| KEGG pathways |
map00910
|
| Gene Ontology (148) |
GO:0000166, GO:0001775, GO:0002252, GO:0002263, GO:0002274, GO:0002275, GO:0002283, GO:0002366, GO:0002376, GO:0002443, GO:0002444, GO:0002446 +136 more
|
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 | 0.186 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 |
|---|---|---|---|---|
IMPDH | PF00478.32 | 9.8e-10 | 2–205 | IMP dehydrogenase / GMP reductase domain |
NMO | PF03060.22 | 5.1e-103 | 5–341 | Nitronate monooxygenase |
FMN_dh | PF01070.25 | 3.1e-06 | 111–200 | FMN-dependent dehydrogenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3551 (CoA-transferase subunit alpha), high confidence from genomic context alone (score 981 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3551 |
CoA-transferase subunit alpha | 996 | 981 ctx | neighborhood:773 cooccurence:454 coexpression:860 textmining:803 |
Rv3552 |
CoA-transferase subunit beta | 980 | 981 ctx | neighborhood:773 cooccurence:446 coexpression:860 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 988 | 979 ctx | neighborhood:773 coexpression:864 textmining:472 |
Rv3549c |
short-chain type dehydrogenase/reductase | 982 | 955 ctx | neighborhood:713 coexpression:815 textmining:625 |
Rv3559c |
oxidoreductase | 962 | 933 | coexpression:813 database:500 textmining:462 |
Rv3548c |
short-chain type dehydrogenase/reductase | 979 | 895 ctx | neighborhood:449 coexpression:751 textmining:812 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 843 | 836 | coexpression:737 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 914 | 825 | coexpression:751 textmining:532 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 912 | 813 | coexpression:736 textmining:552 |
Rv3561 fadD3 |
fatty-acid--CoA ligase FadD3 | 909 | 808 | coexpression:805 textmining:547 |
Rv3554 fdxB |
electron transfer protein FdxB | 798 | 780 ctx | neighborhood:779 |
Rv2524c fas |
fatty acid synthase | 780 | 746 | coexpression:710 |
Rv0243 fadA2 |
acetyl-CoA acetyltransferase FadA | 534 | 534 | database:500 |
Rv1074c fadA3 |
beta-ketoacyl CoA thiolase FadA | 528 | 528 | database:500 |
Rv3541c chsH1 hyp |
hypothetical protein | 526 | 527 ctx | cooccurence:504 |
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: oxidoreductase
- MTBC0 PGAP product: nitronate monooxygenase
- Pfam (hmmscan --cut_ga): IMPDH PF00478.32 (E=1e-09), NMO PF03060.22 (E=5e-103), FMN_dh PF01070.25 (E=3e-06)
- (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_218070.1)
- Domains: Pfam-A via hmmscan --cut_ga — IMPDH (PF00478.32), NMO (PF03060.22), FMN_dh (PF01070.25)
- 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
COG2070 - Curated reference: UniProt P71847 (SwissProt, reviewed; 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 —
42 functional partner(s); context anchor
Rv3551 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003770|Rv3553| MRLRTPLTELIGIEHPVVQTGMGWVAGARLVSATANAGGLGILASATMTLDELAAAITKVKAVTDKPFGVNIRADAADAGDRVELMIREGVRVASFALAPKQQLIARLKEAGAVVIPSIGAAKHARKVAAWGADAMIVQGGEGGGHTGPVATTLLLPSVLDAVAGTGIPVIAAGGFFDGRGLAAALCYGAAGVAMGTRFLLTSDSTVPDAVKRRYLQAGLDGTVVTTRVDGMPHRVLRTELVEKLESGSRARGFAAALRNAGKFRRMSQMTWRSMIRDGLTMRHGKELTWSQVLMAANTPMLLKAGLVDGNTEAGVLASGQVAGILDDLPSCKELIESIVLDAITHLQTASALVE