ldtMt3 Resolved · high auto-curated
H37Rv Rv1433 · MTBC0 mtbc0_001533 ·
271 aa · 1620778–1621593 (+) ·
RefSeq NP_215949.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | L%2CD-transpeptidase LdtMt3 |
| Revised (this work) | L%2CD-transpeptidase LdtMt3. 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 |
O06825
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable L,D-transpeptidase 3 |
| EC (curated) |
EC 2.3.2.-
|
| Curated function | Probable L,D-transpeptidase that may perform as-yet-unknown cross-linking reactions in M.tuberculosis. Is not able to generate 3->3 cross-links in peptidoglycan, using tetrapeptide stems as acyl donor substrates. May function in the anchoring of proteins to peptidoglycan. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | L,D-transpeptidase catalytic domain |
| Orthologous group | COG1376 |
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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Big_10 | PF17964.8 | 1.1e-18 | 37–114 | Bacterial Ig domain |
YkuD | PF03734.20 | 1.3e-19 | 167–269 | L,D-transpeptidase catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1432 (dehydrogenase), medium confidence from genomic context alone (score 495 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) |
|---|---|---|---|---|
Rv3015c hyp |
hypothetical protein | 659 | 659 ctx | cooccurence:658 |
Rv1431 hyp |
hypothetical protein | 497 | 497 ctx | neighborhood:495 |
Rv1432 |
dehydrogenase | 495 | 495 ctx | neighborhood:495 |
Rv2525c hyp |
hypothetical protein | 434 | 412 | |
Rv2413c hyp |
hypothetical protein | 411 | 411 ctx | cooccurence:410 |
Rv3779 |
transmembrane protein | 403 | 403 | |
Rv0483 lprQ |
lipoprotein LprQ | 455 | 297 | |
Rv3915 cwlM |
peptidoglycan hydrolase | 454 | 275 | |
Rv2151c ftsQ |
cell division protein FtsQ | 628 | 237 | textmining:533 |
Rv3330 dacB1 |
penicillin-binding protein DacB | 433 | 231 | |
Rv2911 dacB2 |
penicillin-binding protein DacB2 | 438 | 219 | |
Rv1140 |
integral membrane protein | 434 | 204 | |
Rv3627c dacB hyp |
hypothetical protein | 464 | 195 | |
Rv3594 hyp |
hypothetical protein | 443 | 181 | |
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 549 | 119 | textmining:510 |
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: L%2CD-transpeptidase LdtMt3
- Pfam (hmmscan --cut_ga): Big_10 PF17964.8 (E=1e-18), YkuD PF03734.20 (E=1e-19)
- (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_215949.1)
- 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 O06825 (SwissProt, reviewed; Evidence at protein level)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
17 functional partner(s); context anchor
Rv1432 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001533|Rv1433|ldtMt3 MRAVFGCAIAVVGIAGSVVAGPADIHLVAAKQSYGFAVASVLPTRGQVVGVAHPVVVTFSAPITNPANRHAAERAVEVKSTPAMTGKFEWLDNDVVQWVPDRFWPAHSTVELSVGSLSSDFKTGPAVVGVASISQHTFTVSIDGVEEGPPPPLPAPHHRVHFGEDGVMPASMGRPEYPTPVGSYTVLSKERSVIMDSSSVGIPVDDPDGYRLSVDYAVRITSRGLYVHSAPWALPALGLENVSHGCISLSREDAEWYYNAVDIGDPVIVQE