nrdI Resolved · high auto-curated
H37Rv Rv3052c · MTBC0 mtbc0_003244 ·
150 aa · 3435542–3435994 (-) ·
RefSeq NP_217568.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NrdI protein |
|---|---|
| MTBC0 PGAP re-annotation | class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI |
| Revised (this work) | Class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI. Pfam: Flavodoxin_NdrI (PF07972.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIZ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein NrdI |
| Curated function | Probably involved in ribonucleotide reductase function. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | nrdI |
| eggNOG description | Probably involved in ribonucleotide reductase function |
| Orthologous group | COG1780 |
| KEGG orthology |
K03647
|
| Gene Ontology (29) |
GO:0000166, GO:0003674, GO:0005488, GO:0006464, GO:0006807, GO:0008150, GO:0008152, GO:0009987, GO:0010181, GO:0019538, GO:0032553, GO:0036094 +17 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 | 0.325 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Flavodoxin_NdrI | PF07972.17 | 1.1e-44 | 9–130 | NrdI Flavodoxin like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nrdH (glutaredoxin electron transport protein NrdH), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3053c nrdH |
glutaredoxin electron transport protein NrdH | 999 | 995 ctx | neighborhood:833 cooccurence:772 coexpression:887 textmining:798 |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 999 | 993 ctx | neighborhood:633 cooccurence:773 coexpression:924 textmining:896 |
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 998 | 982 ctx | cooccurence:774 coexpression:515 experimental:788 textmining:895 |
Rv1981c nrdF1 |
ribonucleoside-diphosphate reductase subunit beta NrdF1 | 992 | 975 ctx | cooccurence:774 coexpression:460 experimental:788 textmining:693 |
Rv3050c |
AsnC family transcriptional regulator | 919 | 920 ctx | neighborhood:709 coexpression:735 |
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 950 | 884 | coexpression:455 experimental:788 textmining:591 |
Rv1094 desA2 |
acyl-ACP desaturase DesA | 846 | 834 | coexpression:440 experimental:707 |
Rv0824c desA1 |
acyl-ACP desaturase DesA | 845 | 833 | coexpression:436 experimental:707 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 837 | 695 | coexpression:654 textmining:488 |
Rv3049c |
monooxygenase | 621 | 621 ctx | neighborhood:619 |
Rv0815c cysA2 |
thiosulfate sulfurtransferase CysA | 514 | 514 | coexpression:514 |
Rv2383c mbtB |
phenyloxazoline synthase | 443 | 443 | coexpression:443 |
Rv3198A |
glutaredoxin protein | 471 | 415 | |
Rv0508 hyp |
hypothetical protein | 470 | 413 | |
Rv1461 sufB hyp |
hypothetical protein | 403 | 400 |
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: NrdI protein
- MTBC0 PGAP product: class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI
- Pfam (hmmscan --cut_ga): Flavodoxin_NdrI PF07972.17 (E=1e-44)
- (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_217568.1)
- Domains: Pfam-A via hmmscan --cut_ga — Flavodoxin_NdrI (PF07972.17)
- 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
COG1780 - Curated reference: UniProt P9WIZ3 (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 —
27 functional partner(s); context anchor
nrdH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003244|Rv3052c|nrdI MDIAGRSLVYFSSVSENTHRFVQKLGIPATRIPLHGRIEVDEPYVLILPTYGGGRANPGLDAGGYVPKQVIAFLNNDHNRAQLRGVIAAGNTNFGAEFCYAGDVVSRKCSVPYLYRFELMGTEDDVAAVRTGLAEFWKEQTCHQPSLQSL