cdd Resolved · high auto-curated
H37Rv Rv3315c · MTBC0 mtbc0_003525 ·
133 aa · 3725602–3726003 (-) ·
RefSeq NP_217832.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytidine deaminase |
|---|---|
| MTBC0 PGAP re-annotation | cytidine deaminase |
| Revised (this work) | Cytidine deaminase. Pfam: dCMP_cyt_deam_2 (PF08211.19), dCMP_cyt_deam_1 (PF00383.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPH3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cytidine deaminase |
| EC (curated) |
EC 3.5.4.5
|
| Curated function | Recycles cytidine and 2-deoxycytidine for uridine and 2-deoxyuridine synthesis, respectively. Catalyzes the hydrolytic deamination of cytidine and 2-deoxycytidine to form, respectively, uridine and 2-deoxyuridine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | cdd |
| eggNOG description | cytidine deaminase |
| Orthologous group | COG0295 |
| EC number |
EC 3.5.4.5
|
| KEGG orthology |
K01489
|
| KEGG pathways |
map00240, map00983, map01100
|
| Gene Ontology (95) |
GO:0003674, GO:0003824, GO:0004126, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006139, GO:0006206 +83 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
dCMP_cyt_deam_2 | PF08211.19 | 1.7e-06 | 8–61 | Cytidine and deoxycytidylate deaminase zinc-binding region |
dCMP_cyt_deam_1 | PF00383.30 | 5.0e-13 | 13–101 | Cytidine and deoxycytidylate deaminase zinc-binding region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: deoA (thymidine phosphorylase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3314c deoA |
thymidine phosphorylase | 999 | 999 ctx | neighborhood:881 fusion:530 cooccurence:750 coexpression:431 database:900 textmining:885 |
Rv3307 deoD |
purine nucleoside phosphorylase | 971 | 971 ctx | cooccurence:600 database:924 |
Rv3313c add |
adenosine deaminase | 976 | 915 ctx | neighborhood:881 textmining:731 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 753 | 754 ctx | neighborhood:746 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 751 | 751 ctx | neighborhood:746 |
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 765 | 734 ctx | cooccurence:590 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 680 | 680 ctx | neighborhood:677 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 679 | 679 ctx | neighborhood:677 |
Rv2357c glyS |
glycine--tRNA ligase | 650 | 651 | coexpression:631 |
Rv3312A mtp |
pilin | 643 | 601 ctx | neighborhood:597 |
Rv3393 iunH |
nucleoside hydrolase | 620 | 575 | database:500 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 591 | 572 | database:522 |
Rv3339c icd1 |
isocitrate dehydrogenase | 557 | 557 | database:553 |
Rv0480c |
amidohydrolase | 576 | 556 | database:522 |
Rv2364c era |
GTPase Era | 559 | 556 | coexpression:514 |
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: cytidine deaminase
- MTBC0 PGAP product: cytidine deaminase
- Pfam (hmmscan --cut_ga): dCMP_cyt_deam_2 PF08211.19 (E=2e-06), dCMP_cyt_deam_1 PF00383.30 (E=5e-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_217832.1)
- Domains: Pfam-A via hmmscan --cut_ga — dCMP_cyt_deam_2 (PF08211.19), dCMP_cyt_deam_1 (PF00383.30)
- 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
COG0295 - Curated reference: UniProt P9WPH3 (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 —
25 functional partner(s); context anchor
deoA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003525|Rv3315c|cdd MPDVDWNMLRGNATQAAAGAYVPYSRFAVGAAALVDDGRVVTGCNVENVSYGLTLCAECAVVCALHSTGGGRLLALACVDGHGSVLMPCGRCRQVLLEHGGSELLIDHPVRPRRLGDLLPDAFGLDDLPRERR