cmk Resolved · high auto-curated
H37Rv Rv1712 · MTBC0 mtbc0_001822 ·
230 aa · 1951614–1952306 (+) ·
RefSeq NP_216228.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytidylate kinase |
|---|---|
| MTBC0 PGAP re-annotation | (d)CMP kinase |
| Revised (this work) | (d)CMP kinase. Pfam: Cytidylate_kin2 (PF13189.13), Cytidylate_kin (PF02224.25), AAA_18 (PF13238.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPA9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cytidylate kinase |
| EC (curated) |
EC 2.7.4.25
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | cmk |
| eggNOG description | Belongs to the cytidylate kinase family. Type 1 subfamily |
| Orthologous group | COG0283 |
| EC number |
EC 2.7.4.25
|
| KEGG orthology |
K00945
|
| KEGG pathways |
map00240, map01100
|
| KEGG modules |
M00052
|
| Gene Ontology (85) |
GO:0003674, GO:0003824, GO:0004127, GO:0004592, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006082, GO:0006139, GO:0006520 +73 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 | 0.126 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Cytidylate_kin2 | PF13189.13 | 1.2e-06 | 8–161 | Cytidylate kinase-like family |
Cytidylate_kin | PF02224.25 | 1.9e-83 | 9–223 | Cytidylate kinase |
AAA_18 | PF13238.13 | 1.5e-07 | 9–163 | AAA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: engA (GTPase Der), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1713 engA |
GTPase Der | 999 | 999 ctx | neighborhood:881 fusion:887 coexpression:849 textmining:917 |
Rv1711 |
RNA pseudouridine synthase | 997 | 995 ctx | neighborhood:882 fusion:592 coexpression:886 textmining:489 |
Rv1710 scpB |
segregation and condensation protein ScpB | 990 | 983 ctx | neighborhood:881 coexpression:829 textmining:489 |
Rv1709 scpA |
segregation and condensation protein ScpA | 983 | 970 ctx | neighborhood:881 coexpression:761 textmining:479 |
Rv1630 rpsA |
30S ribosomal protein S1 | 925 | 918 ctx | fusion:897 |
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 923 | 913 ctx | fusion:896 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 922 | 913 | database:900 |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 922 | 913 | database:900 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 931 | 910 | database:900 |
Rv3602c panC |
pantothenate synthetase | 908 | 908 ctx | fusion:900 |
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 913 | 904 | database:900 |
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 913 | 904 | database:900 |
Rv1981c nrdF1 |
ribonucleoside-diphosphate reductase subunit beta NrdF1 | 912 | 903 | database:900 |
Rv1708 |
initiation inhibitor protein | 888 | 889 ctx | neighborhood:881 |
Rv1707 |
transmembrane protein | 743 | 744 ctx | neighborhood:744 |
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: cytidylate kinase
- MTBC0 PGAP product: (d)CMP kinase
- Pfam (hmmscan --cut_ga): Cytidylate_kin2 PF13189.13 (E=1e-06), Cytidylate_kin PF02224.25 (E=2e-83), AAA_18 PF13238.13 (E=1e-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_216228.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cytidylate_kin2 (PF13189.13), Cytidylate_kin (PF02224.25), AAA_18 (PF13238.13)
- 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
COG0283 - Curated reference: UniProt P9WPA9 (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 —
98 functional partner(s); context anchor
engA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001822|Rv1712|cmk MSRLSAAVVAIDGPAGTGKSSVSRRLARELGARFLDTGAMYRIVTLAVLRAGADPSDIAAVETIASTVQMSLGYDPDGDSCYLAGEDVSVEIRGDAVTRAVSAVSSVPAVRTRLVELQRTMAEGPGSIVVEGRDIGTVVFPDAPVKIFLTASAETRARRRNAQNVAAGLADDYDGVLADVRRRDHLDSTRAVSPLQAAGDAVIVDTSDMTEAEVVAHLLELVTRRSEAVR