ligB Resolved · high auto-curated
H37Rv Rv3062 · MTBC0 mtbc0_003254 ·
507 aa · 3446948–3448471 (+) ·
RefSeq NP_217578.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | ATP-dependent DNA ligase |
| Revised (this work) | ATP-dependent DNA ligase. Pfam: DNA_ligase_A_N (PF04675.20), DNA_ligase_A_M (PF01068.27), DNA_ligase_A_C (PF04679.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNV5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA ligase B |
| EC (curated) |
EC 6.5.1.1
|
| Curated function | DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | lig |
| eggNOG description | DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair |
| Orthologous group | COG1793 |
| EC number |
EC 6.5.1.1, EC 6.5.1.6, EC 6.5.1.7
|
| KEGG orthology |
K10747
|
| KEGG pathways |
map03030, map03410, map03420, map03430
|
| Gene Ontology (56) |
GO:0000287, GO:0003674, GO:0003824, GO:0003909, GO:0003910, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0006139 +44 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 | 1.141 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.69% of strains (997) · 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 |
|---|---|---|---|---|
DNA_ligase_A_N | PF04675.20 | 1.7e-10 | 70–140 | DNA ligase N terminus |
DNA_ligase_A_M | PF01068.27 | 4.2e-51 | 186–380 | ATP dependent DNA ligase domain |
DNA_ligase_A_C | PF04679.22 | 5.4e-10 | 399–492 | ATP dependent DNA ligase C terminal region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE22 (acyl-CoA dehydrogenase FadE22), high confidence from genomic context alone (score 771 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3014c ligA |
DNA ligase A | 993 | 902 | database:900 textmining:932 |
Rv2116 lppK |
lipoprotein LppK | 892 | 886 | experimental:629 database:609 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 892 | 885 | experimental:629 database:609 |
Rv1629 polA |
DNA polymerase I | 901 | 842 | experimental:454 database:569 textmining:405 |
Rv2090 |
5'-3' exonuclease | 834 | 823 | experimental:429 database:569 |
Rv3061c fadE22 |
acyl-CoA dehydrogenase FadE22 | 771 | 771 ctx | neighborhood:770 |
Rv3063 cstA |
carbon starvation protein A | 787 | 758 ctx | neighborhood:756 |
Rv0114 gmhB |
D-glycero-alpha-D-manno-heptose-1,7-bisphosphate 7-phosphatase | 762 | 738 | database:597 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 725 | 698 | database:644 |
Rv1278 hyp |
hypothetical protein | 714 | 683 | database:611 |
Rv1329c dinG |
ATP-dependent helicase DinG | 706 | 679 | database:604 |
Rv1277 hyp |
hypothetical protein | 709 | 677 | database:611 |
Rv0937c mku |
non-homologous end joining protein Ku | 889 | 674 ctx | cooccurence:578 textmining:674 |
Rv0269c hyp |
hypothetical protein | 769 | 648 ctx | cooccurence:635 |
Rv3730c ligD hyp |
hypothetical protein | 739 | 647 ctx | cooccurence:633 |
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: DNA ligase
- MTBC0 PGAP product: ATP-dependent DNA ligase
- Pfam (hmmscan --cut_ga): DNA_ligase_A_N PF04675.20 (E=2e-10), DNA_ligase_A_M PF01068.27 (E=4e-51), DNA_ligase_A_C PF04679.22 (E=5e-10)
- (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_217578.1)
- Domains: Pfam-A via hmmscan --cut_ga — DNA_ligase_A_N (PF04675.20), DNA_ligase_A_M (PF01068.27), DNA_ligase_A_C (PF04679.22)
- 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
COG1793 - Curated reference: UniProt P9WNV5 (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 —
72 functional partner(s); context anchor
fadE22 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003254|Rv3062|ligB MLLHDVAITSMDVAATSSRLTKVARIAALLHRAAPDTQLVTIIVSWLSGELPQRHIGVGWAALRSLPPPAPQPALTVTGVDATLSKIGTLSGKGSQAQRAALVAELFSAATEAEQTFLLRLLGGELRQGAKGGIMADAVAQAAGLPAATVQRAAMLGGDLAAAAAAGLSGAALDTFTLRVGRPIGPMLAQTATSVHDALERHGGTTIFEAKLDGARVQIHRANDQVRIYTRSLDDVTARLPEVVEATLALPVRDLVADGEAIALCPDNRPQRFQVTASRFGRSVDVAAARATQPLSVFFFDILHRDGTDLLEAPTTERLAALDALVPARHRVDRLITSDPTDAANFLDATLAAGHEGVMAKAPAARYLAGRRGAGWLKVKPVHTLDLVVLAVEWGSGRRRGKLSNIHLGARDPATGGFVMVGKTFKGMTDAMLDWQTTRFHEIAVGPTDGYVVQLRPEQVVEVALDGVQRSSRYPGGLALRFARVVRYRADKDPAEADTIDAVRALY