cobN Family assigned · medium auto-curated
H37Rv Rv2062c · MTBC0 mtbc0_002195 ·
1194 aa · 2345782–2349366 (-) ·
RefSeq NP_216578.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cobalamin biosynthesis protein CobN |
|---|---|
| MTBC0 PGAP re-annotation | cobaltochelatase subunit CobN |
| Revised (this work) | Cobaltochelatase subunit CobN. Pfam: CobN-Mg_chel (PF02514.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53498
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cobalamin biosynthesis protein CobN |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | cobN |
| eggNOG description | cobaltochelatase, CobN subunit |
| Orthologous group | COG1429 |
| EC number |
EC 6.6.1.2
|
| KEGG orthology |
K02230
|
| 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 | 0.814 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 23 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 |
|---|---|---|---|---|
CobN-Mg_chel | PF02514.22 | 0.0e+00 | 104–1175 | CobN/Magnesium Chelatase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cobO (cob(I)alamin adenosyltransferase), high confidence from genomic context alone (score 969 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2849c cobO |
cob(I)alamin adenosyltransferase | 998 | 969 ctx | cooccurence:651 database:900 textmining:965 |
Rv2848c cobB |
cobyrinic acid A,C-diamide synthase | 982 | 965 ctx | cooccurence:507 database:900 textmining:519 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 969 | 926 ctx | neighborhood:672 cooccurence:759 textmining:608 |
Rv2072c cobL |
precorrin-6Y C(5,15)-methyltransferase | 995 | 923 ctx | cooccurence:723 coexpression:648 textmining:949 |
Rv2850c |
magnesium chelatase | 965 | 915 ctx | cooccurence:774 coexpression:480 textmining:610 |
Rv1314c |
cob(I)yrinic acid a,c-diamide adenosyltransferase | 933 | 907 | database:900 |
Rv2065 cobH |
precorrin-8X methylmutase | 935 | 897 ctx | neighborhood:633 cooccurence:696 textmining:400 |
Rv2064 cobG |
precorrin-3B synthase | 952 | 853 ctx | neighborhood:639 cooccurence:604 textmining:690 |
Rv2070c cobK |
precorrin-6A reductase | 960 | 749 ctx | cooccurence:704 textmining:851 |
Rv2061c hyp |
hypothetical protein | 612 | 612 ctx | neighborhood:607 |
Rv2063 mazE7 |
antitoxin MazE7 | 554 | 553 ctx | neighborhood:552 |
Rv2063A mazF7 |
mRNA interferase MazF7 | 600 | 552 ctx | neighborhood:552 |
Rv0958 |
magnesium chelatase | 542 | 481 | coexpression:451 |
Rv1234 |
transmembrane protein | 529 | 461 | coexpression:417 |
Rv1138c |
oxidoreductase | 517 | 454 | coexpression:436 |
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: cobalamin biosynthesis protein CobN
- MTBC0 PGAP product: cobaltochelatase subunit CobN
- Pfam (hmmscan --cut_ga): CobN-Mg_chel PF02514.22 (E=0e+00)
- (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_216578.1)
- Domains: Pfam-A via hmmscan --cut_ga — CobN-Mg_chel (PF02514.22)
- 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
COG1429 - Curated reference: UniProt O53498 (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 —
62 functional partner(s); context anchor
cobO - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002195|Rv2062c|cobN MPEPTVLLLSTSDTDLISARSSGKNYRWANPSRLSDLELTDLLAEASIVVIRILGGYRAWQSGIDTVIAGGVPAVLVSGEQAADAELTDRSTVAAGTALQAHIYLAHGGVDNLRELHAFLCDTVLMTGFGFTPPVATPTWGVLERPDAGKTGPTIAVLYYRAQHLAGNTGYVEALCRAIEDAGGRPLPLYCASLRTAEPRLLERLGGADAMVVTVLAAGGVKPAAASAGGDDDSWNVEHLAALDIPILQGLCLTSPRDQWCANDDGLSPLDVASQVAVPEFDGRIITVPFSFKEIDDDGLISYVADPERCARVAGLAVRHARLRQVAPADKRVALVFSAYPTKHARIGNAVGLDTPASAVALLQAMRQRGYRVGDLPGVESNDGDALIHALIECGGHDPDWLTEGQLAGNPIRVSAKEYRDWFATLPAELTDVVTAYWGPPPGELFVDRSHDPDGEIVIAALRAGNLVLMVQPPRGFGENPVAIYHDPDLPPSHHYLAAYRWLDTGFSNGFGAHAVVHLGKHGNLEWLPGKTLGMSASCGPDAALGDLPLIYPFLVNDPGEGTQAKRRAHAVLVDHLIPPMARAETYGDIARLEQLLDEHASVAALDPGKLPAIRQQIWTLIRAAKMDHDLGLTERPEEDSFDDMLLHVDGWLCEIKDVQIRDGLHILGQNPTGEQELDLVLAILRARQLFGGAHAIPGLRQALGLAEDGTDERATVDQTEAKARELVAALQATGWDPSAADRLTGNADAAAVLRFAATEVIPRLAGTATEIEQVLRALDGRFIPAGPSGSPLRGLVNVLPTGRNFYSVDPKAVPSRLAWEAGVALADSLLARYRDEHGRWPRSVGLSVWGTSAMRTAGDDIAEVLALLGVRPVWDDASRRVIDLAPMQPAELGRPRIDVTVRISGFFRDAFPHVVTMLDDAVRLVADLDEAAEDNYVRAHAQADLAHHGDQRRATTRIFGSKPGTYGAGLLQLIDSRSWRDDADLAQVYTAWGGFAYGRDLDGREAIDDMNRQYRRIAVAAKNTDTREHDIADSDDYFQYHGGMVATVRALTGQAPAAYIGDNTRPDAIRTRTLSEETTRVFRARVVNPRWMAAMRRHGYKGAFEMAATVDYLFGYDATAGVMADWMYEQLTQRYVLDAQNRTFMTESNPWALHGMAERLLEAAGRGLWAQPAPETLDGLRQVLLETEGDLEA