ldtA Resolved · high auto-curated
H37Rv Rv0116c · MTBC0 mtbc0_000127 ·
251 aa · 140433–141188 (-) ·
RefSeq NP_214630.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | L,D-transpeptidase LdtA |
|---|---|
| MTBC0 PGAP re-annotation | L%2CD-transpeptidase LdtMt1 |
| Revised (this work) | L%2CD-transpeptidase LdtMt1. Pfam: Big_10 (PF17964.8), YkuD (PF03734.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53638
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | L,D-transpeptidase 1 |
| EC (curated) |
EC 2.3.2.-
|
| Curated function | Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems. Is thought to play a role in adaptation to the nonreplicative state of M.tuberculosis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | ErfK YbiS YcfS YnhG family protein |
| Orthologous group | COG1376 |
| Gene Ontology (50) |
GO:0000270, GO:0003674, GO:0003824, GO:0004180, GO:0004185, GO:0005575, GO:0005576, GO:0006022, GO:0006023, GO:0006024, GO:0006508, GO:0006807 +38 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 | 1.403 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 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 |
|---|---|---|---|---|
Big_10 | PF17964.8 | 6.6e-21 | 40–112 | Bacterial Ig domain |
YkuD | PF03734.20 | 4.7e-24 | 128–249 | L,D-transpeptidase catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: oxyS (oxidative stress response regulatory protein OxyS), high confidence from genomic context alone (score 751 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 750 | 751 ctx | neighborhood:748 |
Rv3015c hyp |
hypothetical protein | 627 | 627 ctx | cooccurence:627 |
Rv0017c rodA |
cell division protein RodA | 524 | 503 | database:500 |
Rv2413c hyp |
hypothetical protein | 408 | 409 ctx | cooccurence:407 |
Rv1140 |
integral membrane protein | 407 | 200 | |
Rv2911 dacB2 |
penicillin-binding protein DacB2 | 466 | 195 | |
Rv3778c |
aminotransferase | 461 | 84 | textmining:436 |
Rv0115 hddA |
D-alpha-D-heptose-7-phosphate kinase HddA | 440 | 50 | textmining:435 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 414 | 50 | textmining:409 |
Rv1863c |
integral membrane protein | 525 | 49 | textmining:522 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 660 | 47 | textmining:658 |
Rv2769c PE27 |
PE family protein PE27 | 511 | 41 | textmining:511 |
Rv2768c PPE43 |
PPE family protein PPE43 | 511 | 41 | textmining:511 |
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: L,D-transpeptidase LdtA
- MTBC0 PGAP product: L%2CD-transpeptidase LdtMt1
- Pfam (hmmscan --cut_ga): Big_10 PF17964.8 (E=7e-21), YkuD PF03734.20 (E=5e-24)
- (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_214630.1)
- Domains: Pfam-A via hmmscan --cut_ga — Big_10 (PF17964.8), YkuD (PF03734.20)
- 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
COG1376 - Curated reference: UniProt O53638 (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 —
13 functional partner(s); context anchor
oxyS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000127|Rv0116c|ldtA MRRVVRYLSVVVAITLMLTAESVSIATAAVPPLQPIPGVASVSPANGAVVGVAHPVVVTFTTPVTDRRAVERSIRISTPHNTTGHFEWVASNVVRWVPHRYWPPHTRVSVGVQELTEGFETGDALIGVASISAHTFTVSRNGEVLRTMPASLGKPSRPTPIGSFHAMSKERTVVMDSRTIGIPLNSSDGYLLTAHYAVRVTWSGVYVHSAPWSVNSQGYANVSHGCINLSPDNAAWYFDAVTVGDPIEVVG