ndkA Resolved · high auto-curated
H37Rv Rv2445c · MTBC0 mtbc0_002604 ·
136 aa · 2769562–2769972 (-) ·
RefSeq NP_216961.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nucleoside diphosphate kinase |
|---|---|
| MTBC0 PGAP re-annotation | nucleoside-diphosphate kinase |
| Revised (this work) | Nucleoside-diphosphate kinase. Pfam: NDK (PF00334.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJH7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nucleoside diphosphate kinase |
| EC (curated) |
EC 2.7.4.6
|
| Curated function | Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | ndk |
| eggNOG description | Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate |
| Orthologous group | COG0105 |
| EC number |
EC 2.7.4.6
|
| KEGG orthology |
K00940
|
| KEGG pathways |
map00230, map00240, map00983, map01100, map01110, map01130, map04016
|
| KEGG modules |
M00049, M00050, M00052, M00053
|
| Gene Ontology (69) |
GO:0003674, GO:0003824, GO:0004518, GO:0004550, GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005886, GO:0006139, GO:0006163, GO:0006165 +57 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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
NDK | PF00334.25 | 2.5e-54 | 3–134 | Nucleoside diphosphate kinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplU (50S ribosomal protein L21), high confidence from genomic context alone (score 964 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0700 rpsJ |
30S ribosomal protein S10 | 994 | 995 | coexpression:794 experimental:847 database:844 |
Rv0682 rpsL |
30S ribosomal protein S12 | 994 | 994 | coexpression:769 experimental:845 database:844 |
Rv2785c rpsO |
30S ribosomal protein S15 | 993 | 994 | coexpression:728 experimental:859 database:844 |
Rv2890c rpsB |
30S ribosomal protein S2 | 993 | 993 | coexpression:696 experimental:858 database:844 |
Rv0683 rpsG |
30S ribosomal protein S7 | 993 | 993 | coexpression:729 experimental:845 database:844 |
Rv2909c rpsP |
30S ribosomal protein S16 | 992 | 992 | coexpression:558 experimental:887 database:844 |
Rv0053 rpsF |
30S ribosomal protein S6 | 991 | 992 | coexpression:666 experimental:851 database:844 |
Rv3459c rpsK |
30S ribosomal protein S11 | 991 | 991 | coexpression:655 experimental:845 database:844 |
Rv3442c rpsI |
30S ribosomal protein S9 | 987 | 987 | coexpression:491 experimental:850 database:844 |
Rv0721 rpsE |
30S ribosomal protein S5 | 986 | 986 | coexpression:452 experimental:847 database:844 |
Rv2442c rplU |
50S ribosomal protein L21 | 963 | 964 ctx | neighborhood:474 coexpression:701 experimental:789 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 957 | 957 | coexpression:469 experimental:780 database:662 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 957 | 957 | coexpression:470 experimental:780 database:662 |
Rv1307 atpH |
ATP synthase subunit b/delta | 946 | 945 | coexpression:931 |
Rv2441c rpmA |
50S ribosomal protein L27 | 944 | 944 | coexpression:649 experimental:789 |
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: nucleoside diphosphate kinase
- MTBC0 PGAP product: nucleoside-diphosphate kinase
- Pfam (hmmscan --cut_ga): NDK PF00334.25 (E=3e-54)
- (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_216961.1)
- Domains: Pfam-A via hmmscan --cut_ga — NDK (PF00334.25)
- 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
COG0105 - Curated reference: UniProt P9WJH7 (SwissProt, reviewed; Evidence at protein level)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
226 functional partner(s); context anchor
rplU - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002604|Rv2445c|ndkA MTERTLVLIKPDGIERQLIGEIISRIERKGLTIAALQLRTVSAELASQHYAEHEGKPFFGSLLEFITSGPVVAAIVEGTRAIAAVRQLAGGTDPVQAAAPGTIRGDFALETQFNLVHGSDSAESAQREIALWFPGA