cadI Resolved · high auto-curated
H37Rv Rv2641 · MTBC0 mtbc0_002811 ·
152 aa · 2989500–2989958 (+) ·
RefSeq NP_217157.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cadmium inducible protein CadI |
|---|---|
| MTBC0 PGAP re-annotation | cadmium-induced metalloenzyme CadI |
| Revised (this work) | Cadmium-induced metalloenzyme CadI. Pfam: Glyoxalase (PF00903.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIR5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cadmium-induced protein CadI |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | cadI |
| eggNOG description | Glyoxalase bleomycin resistance protein dioxygenase |
| Orthologous group | COG0346 |
| Gene Ontology (6) |
GO:0008150, GO:0010035, GO:0010038, GO:0042221, GO:0046686, GO:0050896
|
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 | 0.651 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Glyoxalase | PF00903.32 | 6.4e-16 | 5–114 | Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arsC (arsenic-transport integral membrane protein ArsC), high confidence from genomic context alone (score 817 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 965 | 817 ctx | neighborhood:756 textmining:820 |
Rv2640c |
ArsR family transcriptional regulator | 872 | 812 ctx | neighborhood:665 cooccurence:453 |
Rv2642 |
ArsR family transcriptional regulator | 762 | 753 ctx | neighborhood:703 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 676 | 656 | coexpression:645 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 531 | 512 | coexpression:498 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 526 | 505 | coexpression:502 |
Rv1171 hyp |
hypothetical protein | 452 | 453 ctx | cooccurence:452 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 440 | 429 | coexpression:427 |
Rv0306 bluB |
oxidoreductase | 440 | 428 | coexpression:418 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 448 | 427 | coexpression:414 |
Rv3131 |
NAD(P)H nitroreductase | 437 | 425 | coexpression:415 |
Rv2032 acg |
NAD(P)H nitroreductase | 437 | 425 | coexpression:415 |
Rv3127 hyp |
hypothetical protein | 436 | 424 | coexpression:414 |
Rv3368c |
oxidoreductase | 436 | 424 | coexpression:414 |
Rv0828c |
deaminase | 432 | 418 | coexpression:418 |
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: cadmium inducible protein CadI
- MTBC0 PGAP product: cadmium-induced metalloenzyme CadI
- Pfam (hmmscan --cut_ga): Glyoxalase PF00903.32 (E=6e-16)
- (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_217157.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyoxalase (PF00903.32)
- 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
COG0346 - Curated reference: UniProt P9WIR5 (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 —
41 functional partner(s); context anchor
arsC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002811|Rv2641|cadI MSRVQLALNVDDLEAAITFYSRLFNAEPAKRKPGYANFAIADPPLKLVLLENPGTGGTLNHLGVEVGSSNTVHAEIARLTEAGLVTEKEIGTTCCFATQDKVWVTGPGGERWEVYTVLADSETFGSGPRHNDTSDGEASMCCDGQVAVGASG