pyrH Resolved · high auto-curated
H37Rv Rv2883c · MTBC0 mtbc0_003065 ·
261 aa · 3213201–3213986 (-) ·
RefSeq NP_217399.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | uridylate kinase |
|---|---|
| MTBC0 PGAP re-annotation | UMP kinase |
| Revised (this work) | UMP kinase. Pfam: AA_kinase (PF00696.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHK5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uridylate kinase |
| EC (curated) |
EC 2.7.4.22
|
| Curated function | Catalyzes the reversible phosphorylation of UMP to UDP. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | pyrH |
| eggNOG description | Catalyzes the reversible phosphorylation of UMP to UDP |
| Orthologous group | COG0528 |
| EC number |
EC 2.7.4.22
|
| KEGG orthology |
K09903
|
| KEGG pathways |
map00240, map01100
|
| Gene Ontology (91) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006213, GO:0006220, GO:0006221, GO:0006225 +79 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 | 0.709 · 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 |
|---|---|---|---|---|
AA_kinase | PF00696.34 | 1.2e-33 | 32–239 | Amino acid kinase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: frr (ribosome recycling factor), high confidence from genomic context alone (score 968 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2882c frr |
ribosome recycling factor | 988 | 968 ctx | neighborhood:744 coexpression:862 textmining:652 |
Rv3309c upp |
uracil phosphoribosyltransferase | 962 | 951 | coexpression:453 database:900 |
Rv1307 atpH |
ATP synthase subunit b/delta | 950 | 948 | coexpression:940 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 938 | 919 | database:900 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 935 | 916 | database:900 |
Rv2889c tsf |
elongation factor EF-Ts | 930 | 910 | coexpression:855 |
Rv1385 pyrF |
orotidine 5'-phosphate decarboxylase | 945 | 909 | database:900 textmining:431 |
Rv2890c rpsB |
30S ribosomal protein S2 | 902 | 872 | coexpression:841 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 901 | 870 ctx | neighborhood:728 cooccurence:442 |
Rv0641 rplA |
50S ribosomal protein L1 | 827 | 801 | coexpression:706 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 808 | 778 ctx | cooccurence:607 coexpression:456 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 887 | 741 | coexpression:703 textmining:583 |
Rv2462c tig |
trigger factor | 729 | 730 | coexpression:721 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 867 | 721 | coexpression:674 textmining:543 |
Rv2906c trmD |
tRNA (guanine-N1)-methyltransferase | 760 | 713 | coexpression:649 |
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: uridylate kinase
- MTBC0 PGAP product: UMP kinase
- Pfam (hmmscan --cut_ga): AA_kinase PF00696.34 (E=1e-33)
- (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_217399.1)
- Domains: Pfam-A via hmmscan --cut_ga — AA_kinase (PF00696.34)
- 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
COG0528 - Curated reference: UniProt P9WHK5 (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 —
166 functional partner(s); context anchor
frr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003065|Rv2883c|pyrH MTEPDVAGAPASKPEPASTGAASAAQLSGYSRVLLKLGGEMFGGGQVGLDPDVVAQVARQIADVVRGGVQIAVVIGGGNFFRGAQLQQLGMERTRSDYMGMLGTVMNSLALQDFLEKEGIVTRVQTAITMGQVAEPYLPLRAVRHLEKGRVVIFGAGMGLPYFSTDTTAAQRALEIGADVVLMAKAVDGVFAEDPRVNPEAELLTAVSHREVLDRGLRVADATAFSLCMDNGMPILVFNLLTDGNIARAVRGEKIGTLVTT