ligD Resolved · high auto-curated
H37Rv Rv3730c · MTBC0 mtbc0_003955 ·
346 aa · 4204801–4205841 (-) ·
RefSeq NP_218247.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | non-homologous end-joining DNA ligase |
| Revised (this work) | Non-homologous end-joining DNA ligase. Pfam: LigD_Prim-Pol (PF21686.4), DNA_primase_S (PF01896.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69697
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA ligase D polymerase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ligD |
| eggNOG description | DNA primase |
| Orthologous group | COG3285 |
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 | 0.552 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
LigD_Prim-Pol | PF21686.4 | 5.5e-88 | 33–287 | LigD, primase-polymerase domain |
DNA_primase_S | PF01896.26 | 4.1e-10 | 138–260 | DNA primase small subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ligC (DNA ligase C), high confidence from genomic context alone (score 995 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3731 ligC |
DNA ligase C | 996 | 995 ctx | neighborhood:789 fusion:895 cooccurence:773 |
Rv0937c mku |
non-homologous end joining protein Ku | 927 | 864 ctx | cooccurence:773 coexpression:404 textmining:489 |
Rv3062 ligB |
DNA ligase | 739 | 647 ctx | cooccurence:633 |
Rv2828A hyp |
hypothetical protein | 456 | 456 ctx | cooccurence:455 |
Rv3296 lhr |
ATP-dependent helicase | 439 | 439 ctx | cooccurence:434 |
Rv3732 hyp |
hypothetical protein | 421 | 420 ctx | neighborhood:415 |
Rv3014c ligA |
DNA ligase A | 413 | 44 | textmining:412 |
Rv2737c recA |
recombinase A | 407 | 44 | textmining:406 |
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: hypothetical protein
- MTBC0 PGAP product: non-homologous end-joining DNA ligase
- Pfam (hmmscan --cut_ga): LigD_Prim-Pol PF21686.4 (E=5e-88), DNA_primase_S PF01896.26 (E=4e-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_218247.1)
- Domains: Pfam-A via hmmscan --cut_ga — LigD_Prim-Pol (PF21686.4), DNA_primase_S (PF01896.26)
- 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
COG3285 - Curated reference: UniProt O69697 (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 —
8 functional partner(s); context anchor
ligC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003955|Rv3730c|ligD MAAAAEELDVDGIAVRLTSPDRMYFPKLGSHGTKRRLVEYYFAVAGGPMLTALRDRPTHLQRFPDGVDGEQIYQKRIPRHRPDYLQTCRVTFPSGRMADALKVTHPAAIVWAAQMGTITLHPWQVRCPDTEHPDELRIDLDPQPGTGFVEARTVAVDVLRSVLDDLGLVGYPKTSGGRGIHVFLRIATDWDFVEVRRAGIALAREVERRAPDAVTTSWWKEERGARIFIDFNQNARDRTMASAYSVRPTPIATVSMPLTWEELAGADPDDYTMTTVPELVKIRDDPWAGMDDVAQSIAPLLDLAAADEERGLGDMPYPPNYPKMPGEPKRVQPSRDTDLKGGNTSK