cobT Resolved · high auto-curated
H37Rv Rv2207 · MTBC0 mtbc0_002343 ·
361 aa · 2497568–2498653 (+) ·
RefSeq NP_216723.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nicotinate-nucleotide-dimethylbenzimidazol phosphoribosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase |
| Revised (this work) | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase. Pfam: DBI_PRT (PF02277.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP85
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase |
| EC (curated) |
EC 2.4.2.21
|
| Curated function | Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | cobT |
| eggNOG description | Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6- dimethylbenzimidazole (DMB) |
| Orthologous group | COG2038 |
| EC number |
EC 2.4.2.21
|
| KEGG orthology |
K00768
|
| KEGG pathways |
map00860, map01100
|
| KEGG modules |
M00122
|
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 | 0.673 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
DBI_PRT | PF02277.23 | 2.9e-129 | 8–343 | Phosphoribosyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cobU (bifunctional cobinamide kinase/cobinamide phosphate guanylyltransferase), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0254c cobU |
bifunctional cobinamide kinase/cobinamide phosphate guanylyltransferase | 996 | 994 ctx | neighborhood:461 fusion:899 cooccurence:768 coexpression:557 textmining:421 |
Rv2208 cobS |
adenosylcobinamide-GDP ribazoletransferase | 995 | 992 ctx | neighborhood:882 cooccurence:772 coexpression:467 database:500 textmining:500 |
Rv0306 bluB |
oxidoreductase | 989 | 989 ctx | fusion:900 cooccurence:447 database:800 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 938 | 935 | database:900 |
Rv2848c cobB |
cobyrinic acid A,C-diamide synthase | 922 | 899 ctx | fusion:497 cooccurence:623 coexpression:440 |
Rv0255c cobQ1 |
cobyric acid synthase | 906 | 878 ctx | cooccurence:767 coexpression:426 |
Rv2236c cobD |
cobalamin biosynthesis transmembrane protein CobD | 852 | 806 ctx | cooccurence:761 |
Rv2206 |
transmembrane protein | 788 | 789 ctx | neighborhood:786 |
Rv2205c hyp |
hypothetical protein | 710 | 710 ctx | neighborhood:709 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 847 | 676 | coexpression:412 textmining:550 |
Rv2071c cobM |
precorrin-4 C(11)-methyltransferase | 747 | 669 ctx | cooccurence:568 |
Rv2204c hyp |
hypothetical protein | 667 | 668 ctx | neighborhood:663 |
Rv2209 |
integral membrane protein | 535 | 535 ctx | neighborhood:532 |
Rv2231c cobC |
aminotransferase | 554 | 507 | coexpression:424 |
Rv2065 cobH |
precorrin-8X methylmutase | 609 | 490 |
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: nicotinate-nucleotide-dimethylbenzimidazol phosphoribosyltransferase
- MTBC0 PGAP product: nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
- Pfam (hmmscan --cut_ga): DBI_PRT PF02277.23 (E=3e-129)
- (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_216723.1)
- Domains: Pfam-A via hmmscan --cut_ga — DBI_PRT (PF02277.23)
- 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
COG2038 - Curated reference: UniProt P9WP85 (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 —
30 functional partner(s); context anchor
cobU - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002343|Rv2207|cobT MIGFAPVSTPDAAAEAAARARQDSLTKPRGALGSLEDLSVWVASCQQRCPPRQFERARVVVFAGDHGVARSGVSAYPPEVTAQMVANIDAGGAAINALADVAGATVRVADLAVDADPLSERIGAHKVRRGSGNIATEDALTNDETAAAITAGQQIADEEVDAGADLLIAGDMGIGNTTAAAVLVAALTDAEPVAVVGFGTGIDDAGWARKTAAVRDALFRVRPVLPDPVGLLRCAGGADLAAIAGFCAQAAVRRTPLLLDGVAVTAAALVAERLAPGAHRWWQAGHRSSEPGHGLALAALGLDPIVDLHMRLGEGTGAAVALMVLRAAVAALSSMATFTEAGVSTRSVDGVDRTAPPAVSP