cobG Resolved · high auto-curated
H37Rv Rv2064 · MTBC0 mtbc0_002198 ·
363 aa · 2350064–2351155 (+) ·
RefSeq NP_216580.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | precorrin-3B synthase |
|---|---|
| MTBC0 PGAP re-annotation | precorrin-3B synthase |
| Revised (this work) | Precorrin-3B synthase. Pfam: NIR_SIR_ferr (PF03460.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q10675
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Precorrin-3B synthase CobG |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | cobG |
| eggNOG description | Precorrin-3B synthase |
| Orthologous group | COG0155 |
| EC number |
EC 1.14.13.83
|
| KEGG orthology |
K02229
|
| KEGG pathways |
map00860, map01100
|
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 | 0.501 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 |
|---|---|---|---|---|
NIR_SIR_ferr | PF03460.23 | 8.3e-13 | 21–76 | Nitrite/Sulfite reductase ferredoxin-like half domain |
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 997 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 | 998 | 997 ctx | neighborhood:876 cooccurence:760 database:900 textmining:529 |
Rv2065 cobH |
precorrin-8X methylmutase | 998 | 992 ctx | neighborhood:876 fusion:806 cooccurence:665 textmining:818 |
Rv1286 cysC |
adenylyl-sulfate kinase | 992 | 987 | coexpression:985 textmining:418 |
Rv2063A mazF7 |
mRNA interferase MazF7 | 897 | 897 ctx | neighborhood:882 |
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 952 | 853 ctx | neighborhood:639 cooccurence:604 textmining:690 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 882 | 825 | coexpression:799 |
Rv2063 mazE7 |
antitoxin MazE7 | 786 | 786 ctx | neighborhood:781 |
Rv2072c cobL |
precorrin-6Y C(5,15)-methyltransferase | 939 | 774 ctx | cooccurence:737 textmining:745 |
Rv2070c cobK |
precorrin-6A reductase | 910 | 759 ctx | cooccurence:744 textmining:644 |
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 744 | 720 | coexpression:663 |
Rv2398c cysW |
sulfate ABC transporter permease CysW | 744 | 711 | coexpression:694 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 893 | 690 | coexpression:647 textmining:670 |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 709 | 682 | coexpression:671 |
Rv2397c cysA1 |
sulfate ABC transporter ATP-binding protein CysA | 708 | 680 | coexpression:669 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 698 | 670 | coexpression:659 |
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-3B synthase
- MTBC0 PGAP product: precorrin-3B synthase
- Pfam (hmmscan --cut_ga): NIR_SIR_ferr PF03460.23 (E=8e-13)
- (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_216580.1)
- Domains: Pfam-A via hmmscan --cut_ga — NIR_SIR_ferr (PF03460.23)
- 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
COG0155 - Curated reference: UniProt Q10675 (TrEMBL, unreviewed; 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 —
45 functional partner(s); context anchor
cobIJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002198|Rv2064|cobG MAGTRDADACPGALRPHQAADGALARIRLPGGMITAAQLATLASVASDFGSATLELTARGNVQLRGIRDVAAVADAVAKAGLLPSATHERVRNIVASPLSGRAGGLADVRAWVGELDAAIRAEPRLAELGGRFWFGLDDGRADVSGLGADVGVQVFPDGPRLLLTGRDTGVRVADVAETLIEVALRFVKIRETAWRVTELADIGELQSGVELGPSVRPVTKTPVGWIPQDDSRVTLGAAVPLGVLPARVAECLAAIEAPLVITPWRSVLICDLDDATADAALRVLAPLGLVFDENSPWLNISACTGSPGCAHSAADVRADAARSLNVESAGHRHFVGCERACGSPPAGEVLVATGGGYRRLRP