Rv3600c Resolved · high auto-curated
H37Rv Rv3600c · MTBC0 mtbc0_003818 ·
272 aa · 4066745–4067563 (-) ·
RefSeq NP_218117.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | type III pantothenate kinase |
|---|---|
| MTBC0 PGAP re-annotation | type III pantothenate kinase |
| Revised (this work) | Type III pantothenate kinase. Pfam: Pan_kinase (PF03309.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPA1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Type III pantothenate kinase |
| EC (curated) |
EC 2.7.1.33
|
| Curated function | Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | coaX |
| eggNOG description | Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis |
| Orthologous group | COG1521 |
| EC number |
EC 2.7.1.33
|
| KEGG orthology |
K03525
|
| KEGG pathways |
map00770, map01100
|
| KEGG modules |
M00120
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.121 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
Pan_kinase | PF03309.21 | 1.6e-61 | 2–206 | Type III pantothenate kinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: panC (pantothenate synthetase), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3602c panC |
pantothenate synthetase | 999 | 997 ctx | neighborhood:882 coexpression:759 database:900 textmining:713 |
Rv3601c panD |
aspartate 1-decarboxylase | 987 | 979 ctx | neighborhood:882 coexpression:827 textmining:421 |
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 935 | 926 | database:900 |
Rv2965c kdtB |
phosphopantetheine adenylyltransferase | 950 | 919 | database:900 textmining:416 |
Rv1092c coaA |
pantothenate kinase | 945 | 900 | database:900 textmining:482 |
Rv3603c hyp |
hypothetical protein | 986 | 897 ctx | neighborhood:881 textmining:870 |
Rv3598c lysS |
lysine--tRNA ligase | 958 | 800 ctx | neighborhood:773 textmining:803 |
Rv3604c |
transmembrane protein | 741 | 741 ctx | neighborhood:740 |
Rv3597c lsr2 |
iron-regulated H-NS-like protein | 703 | 703 ctx | neighborhood:702 |
Rv3610c ftsH |
zinc metalloprotease FtsH | 678 | 677 ctx | neighborhood:657 |
Rv3609c folE |
GTP cyclohydrolase I | 666 | 666 ctx | neighborhood:661 |
Rv3608c folP1 |
dihydropteroate synthase | 678 | 663 ctx | neighborhood:661 |
Rv3607c folB |
dihydroneopterin aldolase | 663 | 663 ctx | neighborhood:661 |
Rv3605c hyp |
hypothetical protein | 661 | 661 ctx | neighborhood:661 |
Rv3606c folK |
2-amino-4-hydroxy-6-hydroxymethyldihydropteridinepyrophosphokinase | 596 | 597 ctx | neighborhood:594 |
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: type III pantothenate kinase
- MTBC0 PGAP product: type III pantothenate kinase
- Pfam (hmmscan --cut_ga): Pan_kinase PF03309.21 (E=2e-61)
- (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_218117.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pan_kinase (PF03309.21)
- 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
COG1521 - Curated reference: UniProt P9WPA1 (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 —
26 functional partner(s); context anchor
panC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003818|Rv3600c| MLLAIDVRNTHTVVGLLSGMKEHAKVVQQWRIRTESEVTADELALTIDGLIGEDSERLTGTAALSTVPSVLHEVRIMLDQYWPSVPHVLIEPGVRTGIPLLVDNPKEVGADRIVNCLAAYDRFRKAAIVVDFGSSICVDVVSAKGEFLGGAIAPGVQVSSDAAAARSAALRRVELARPRSVVGKNTVECMQAGAVFGFAGLVDGLVGRIREDVSGFSVDHDVAIVATGHTAPLLLPELHTVDHYDQHLTLQGLRLVFERNLEVQRGRLKTAR