cobL Resolved · high auto-curated
H37Rv Rv2072c · MTBC0 mtbc0_002206 ·
390 aa · 2357587–2358759 (-) ·
RefSeq NP_216588.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | precorrin-6Y C(5,15)-methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | bifunctional cobalt-precorrin-7 (C(5))-methyltransferase/cobalt-precorrin-6B (C(15))-methyltransferase |
| Revised (this work) | Bifunctional cobalt-precorrin-7 (C(5))-methyltransferase/cobalt-precorrin-6B (C(15))-methyltransferase. Pfam: TP_methylase (PF00590.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGA9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Precorrin-6Y C(5,15)-methyltransferase [decarboxylating] |
| EC (curated) |
EC 2.1.1.132
|
| Curated function | Catalyzes the methylation of both C-5 and C-15 in precorrin-6Y to form precorrin-8X. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | cobL |
| eggNOG description | Precorrin-6Y C5,15-methyltransferase (Decarboxylating) |
| Orthologous group | COG2241 |
| EC number |
EC 2.1.1.132
|
| KEGG orthology |
K00595
|
| KEGG pathways |
map00860, map01100
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, 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) pseudogene candidate
| pN/pS | 0.633 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 11.96% of strains (17361) · clonal |
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 |
|---|---|---|---|---|
TP_methylase | PF00590.26 | 1.5e-16 | 1–183 | Tetrapyrrole (Corrin/Porphyrin) Methylases |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cobIJ (bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 999 | 1000 ctx | neighborhood:544 cooccurence:774 coexpression:997 textmining:850 |
Rv2070c cobK |
precorrin-6A reductase | 999 | 999 ctx | neighborhood:881 cooccurence:774 coexpression:665 database:900 textmining:850 |
Rv2065 cobH |
precorrin-8X methylmutase | 999 | 999 ctx | cooccurence:774 coexpression:972 database:900 textmining:578 |
Rv2071c cobM |
precorrin-4 C(11)-methyltransferase | 999 | 998 ctx | neighborhood:881 cooccurence:735 coexpression:924 textmining:888 |
Rv2073c |
oxidoreductase | 943 | 943 ctx | neighborhood:796 coexpression:732 |
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 995 | 923 ctx | cooccurence:723 coexpression:648 textmining:949 |
Rv2848c cobB |
cobyrinic acid A,C-diamide synthase | 934 | 822 ctx | cooccurence:699 textmining:647 |
Rv2236c cobD |
cobalamin biosynthesis transmembrane protein CobD | 977 | 794 ctx | cooccurence:564 coexpression:404 textmining:896 |
Rv2064 cobG |
precorrin-3B synthase | 939 | 774 ctx | cooccurence:737 textmining:745 |
Rv0255c cobQ1 |
cobyric acid synthase | 885 | 754 | coexpression:513 textmining:553 |
Rv2850c |
magnesium chelatase | 834 | 733 ctx | neighborhood:544 cooccurence:432 textmining:407 |
Rv2074 |
pyridoxamine 5'-phosphate oxidase | 731 | 731 ctx | neighborhood:731 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 901 | 708 ctx | neighborhood:544 textmining:676 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 906 | 647 ctx | neighborhood:544 textmining:745 |
Rv2208 cobS |
adenosylcobinamide-GDP ribazoletransferase | 857 | 585 | textmining:672 |
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: precorrin-6Y C(5,15)-methyltransferase
- MTBC0 PGAP product: bifunctional cobalt-precorrin-7 (C(5))-methyltransferase/cobalt-precorrin-6B (C(15))-methyltransferase
- Pfam (hmmscan --cut_ga): TP_methylase PF00590.26 (E=1e-16)
- (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_216588.1)
- Domains: Pfam-A via hmmscan --cut_ga — TP_methylase (PF00590.26)
- 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
COG2241 - Curated reference: UniProt P9WGA9 (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 —
46 functional partner(s); context anchor
cobIJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002206|Rv2072c|cobL MIIVVGIGADGMTGLSEHSRSELRRATVIYGSKRQLALLDDTVTAERWEWPTPMLPAVQGLSPDGADLHVVASGDPLLHGIGSTLIRLFGHDNVTVLPHVSAVTLACARMGWNVYDTEVISLVTAQPHTAVRRGGRAIVLSGDRSTPQALAVLLTEHGRGDSKFSVLEQLGGPAERRRDGTARAWACDPPLDVDELNVIAVRYLPDERTSWAPDEAFAHDGQITKHPIRVLTLAALAPRPGQRLWDVGAGSGAIAVQWCRSWPGCTAVAFERDERRRRNIGFNAAAFGVSVDVRGDAPDAFDDAARPSVIFLGGGVTQPGLLEACLDSLPAGGNLVANAVTVESEAALAHAYSRLGGELRRFQHYLGEPLGGFTGWRPQLPVTQWSVTKR