cobB Resolved · high auto-curated
H37Rv Rv1151c · MTBC0 mtbc0_001237 ·
237 aa · 1287345–1288058 (-) ·
RefSeq NP_215667.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NAD-dependent protein deacylase |
|---|---|
| MTBC0 PGAP re-annotation | NAD-dependent protein deacylase |
| Revised (this work) | NAD-dependent protein deacylase. Pfam: SIR2 (PF02146.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGG3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NAD-dependent protein deacylase |
| EC (curated) |
EC 2.3.1.286
|
| Curated function | NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form..; FUNCTION: Reactivates acetylated acetyl-CoA synthetase (ACS) through an NAD-dependent deacetylation. Is able to auto-ADP-ribosylate. Deacetylates acetylated HupB..; FUNCTION: Probably desuccinylates succinylated HupB..; FUNCTION: Involved in non-homologous end joining (NHEJ) repair of blunt, 5' overhang and 3' overhang DNA double strand breaks (DSB). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | cobB |
| eggNOG description | NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form |
| Orthologous group | COG0846 |
| KEGG orthology |
K12410
|
| Gene Ontology (59) |
GO:0000726, GO:0003674, GO:0003824, GO:0003953, GO:0005575, GO:0005618, GO:0005623, GO:0006139, GO:0006259, GO:0006281, GO:0006302, GO:0006303 +47 more
|
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 | 0.331 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
SIR2 | PF02146.24 | 8.5e-57 | 8–184 | Sir2 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1152 (transcriptional regulator), high confidence from genomic context alone (score 923 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0212c nadR |
transcriptional regulator NadR | 984 | 984 | coexpression:845 database:900 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 963 | 926 | database:900 textmining:529 |
Rv1152 |
transcriptional regulator | 923 | 923 ctx | neighborhood:789 coexpression:651 |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 927 | 917 | database:900 |
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 947 | 915 | database:900 textmining:408 |
Rv2713 sthA |
pyridine nucleotide transhydrogenase | 919 | 914 | database:900 |
Rv3199c nudC |
NADH pyrophosphatase | 941 | 912 | database:900 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 923 | 906 | database:900 |
Rv3307 deoD |
purine nucleoside phosphorylase | 935 | 904 | database:900 |
Rv3393 iunH |
nucleoside hydrolase | 909 | 904 | database:900 |
Rv0156 pntAb |
NAD(P) transhydrogenase subunit alpha PntAb | 909 | 904 | database:900 |
Rv0155 pntAa |
NAD(P) transhydrogenase subunit alpha PntAa | 909 | 904 | database:900 |
Rv0157 pntB |
NAD(P) transhydrogenase subunit beta PntB | 904 | 904 | database:900 |
Rv3840 |
transcriptional regulator | 862 | 862 | coexpression:860 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 866 | 861 | coexpression:861 |
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: NAD-dependent protein deacylase
- MTBC0 PGAP product: NAD-dependent protein deacylase
- Pfam (hmmscan --cut_ga): SIR2 PF02146.24 (E=8e-57)
- (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_215667.1)
- Domains: Pfam-A via hmmscan --cut_ga — SIR2 (PF02146.24)
- 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
COG0846 - Curated reference: UniProt P9WGG3 (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 —
164 functional partner(s); context anchor
Rv1152 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001237|Rv1151c|cobB MRVAVLSGAGISAESGVPTFRDDKNGLWARFDPYELSSTQGWLRNPERVWGWYLWRHYLVANVEPNDGHRAIAAWQDHAEVSVITQNVDDLHERAGSGAVHHLHGSLFEFRCARCGVPYTDALPEMPEPAIEVEPPVCDCGGLIRPDIVWFGEPLPEEPWRSAVEATGSADVMVVVGTSAIVYPAAGLPDLALARGTAVIEVNPEPTPLSGSATISIRESASQALPGLLERLPALLK