thiL Resolved · high auto-curated
H37Rv Rv2977c · MTBC0 mtbc0_003162 ·
333 aa · 3353960–3354961 (-) ·
RefSeq NP_217493.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | thiamine-monophosphate kinase |
|---|---|
| MTBC0 PGAP re-annotation | thiamine-phosphate kinase |
| Revised (this work) | Thiamine-phosphate kinase. Pfam: AIRS (PF00586.30), AIRS_C (PF02769.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG71
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Thiamine-monophosphate kinase |
| EC (curated) |
EC 2.7.4.16
|
| Curated function | Catalyzes the ATP-dependent phosphorylation of thiamine-monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | thiL |
| eggNOG description | Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1 |
| Orthologous group | COG0611 |
| EC number |
EC 2.7.4.16
|
| KEGG orthology |
K00946
|
| KEGG pathways |
map00730, map01100
|
| KEGG modules |
M00127
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.862 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 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 |
|---|---|---|---|---|
AIRS | PF00586.30 | 1.0e-21 | 42–152 | AIR synthase related protein, N-terminal domain |
AIRS_C | PF02769.28 | 2.0e-05 | 166–250 | AIR synthase related protein, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tnpB (transposase), high confidence from genomic context alone (score 978 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2978c tnpB |
transposase | 978 | 978 ctx | neighborhood:882 coexpression:824 |
Rv2979c |
resolvase | 967 | 967 ctx | neighborhood:882 coexpression:732 |
Rv3585 radA |
DNA repair protein RadA | 943 | 943 | coexpression:943 |
Rv0414c thiE |
thiamine-phosphate synthase | 944 | 908 | database:900 textmining:419 |
Rv0733 adk |
adenylate kinase | 902 | 902 | database:900 |
Rv3228 rsgA hyp |
hypothetical protein | 913 | 901 | database:900 |
Rv2976c ung |
uracil-DNA glycosylase | 851 | 852 ctx | neighborhood:836 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 801 | 802 | coexpression:801 |
Rv2885c |
transposase | 798 | 799 | coexpression:798 |
Rv0605 |
IS1536 family serine type transposase | 754 | 754 | coexpression:754 |
Rv3644c |
DNA polymerase | 733 | 734 | coexpression:733 |
Rv0185 hyp |
hypothetical protein | 732 | 732 | coexpression:732 |
Rv2791c tnpB |
transposase | 732 | 732 | coexpression:731 |
Rv2980 hyp |
hypothetical protein | 585 | 585 ctx | neighborhood:585 |
Rv2736c recX |
regulatory protein RecX | 559 | 560 | coexpression:524 |
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: thiamine-monophosphate kinase
- MTBC0 PGAP product: thiamine-phosphate kinase
- Pfam (hmmscan --cut_ga): AIRS PF00586.30 (E=1e-21), AIRS_C PF02769.28 (E=2e-05)
- (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_217493.1)
- Domains: Pfam-A via hmmscan --cut_ga — AIRS (PF00586.30), AIRS_C (PF02769.28)
- 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
COG0611 - Curated reference: UniProt P9WG71 (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 —
41 functional partner(s); context anchor
tnpB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003162|Rv2977c|thiL MTTKDHSLATESPTLQQLGEFAVIDRLVRGRRQPATVLLGPGDDAALVSAGDGRTVVSTDMLVQDSHFRLDWSTPQDVGRKAIAQNAADIEAMGARATAFVVGFGAPAETPAAQASALVDGMWEEAGRIGAGIVGGDLVSCRQWVVSVTAIGDLDGRAPVLRSGAKAGSVLAVVGELGRSAAGYALWCNGIEDFAELRRRHLVPQPPYGHGAAAAAVGAQAMIDVSDGLLADLRHIAEASGVRIDLSAAALAADRDALTAAATALGTDPWPWVLSGGEDHALVACFVGPVPAGWRTIGRVLDGPARVLVDGEEWTGYAGWQSFGEPDNQGSLG