Rv3712 Family assigned · medium auto-curated
H37Rv Rv3712 · MTBC0 mtbc0_003935 ·
413 aa · 4181102–4182343 (+) ·
RefSeq NP_218229.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ligase |
|---|---|
| MTBC0 PGAP re-annotation | Mur ligase family protein |
| Revised (this work) | Mur ligase family protein. Pfam: Mur_ligase_M (PF08245.19), MurT_C (PF08353.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y4C7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lipid II isoglutaminyl synthase |
| EC (curated) |
EC 6.3.5.13
|
| Curated function | The lipid II isoglutaminyl synthase complex catalyzes the formation of alpha-D-isoglutamine in the cell wall lipid II stem peptide. The MurT subunit catalyzes the ATP-dependent amidation of D-glutamate residue of lipid II, converting it to an isoglutamine residue. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | UDP-N-acetylmuramyl tripeptide synthase |
| Orthologous group | COG0769 |
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 | 0.447 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 6 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 |
|---|---|---|---|---|
Mur_ligase_M | PF08245.19 | 1.7e-14 | 56–185 | Mur ligase middle domain |
MurT_C | PF08353.16 | 1.8e-22 | 303–401 | MurT ligase C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cobQ2 (cobyric acid synthase CobQ), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3713 cobQ2 |
cobyric acid synthase CobQ | 999 | 1000 ctx | neighborhood:882 fusion:872 cooccurence:774 experimental:817 database:900 textmining:907 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 961 | 956 | coexpression:416 database:900 |
Rv3711c dnaQ |
DNA polymerase III subunit epsilon | 903 | 741 ctx | neighborhood:739 textmining:641 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 741 | 668 | coexpression:649 |
Rv2155c murD |
UDP-N-acetylmuramoylalanine--D-glutamate ligase | 676 | 633 | coexpression:550 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 575 | 549 | coexpression:445 |
Rv1302 rfe |
decaprenyl-phosphate N-acetylglucosaminephosphotransferase | 513 | 467 | coexpression:449 |
Rv2156c murX |
phospho-N-acetylmuramoyl-pentappeptidetransferase | 512 | 466 | coexpression:448 |
Rv2864c |
penicillin-binding lipoprotein | 497 | 465 | coexpression:447 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 492 | 460 | coexpression:442 |
Rv2151c ftsQ |
cell division protein FtsQ | 717 | 453 | coexpression:422 textmining:504 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 717 | 453 | coexpression:422 textmining:505 |
Rv3802c |
membrane protein | 437 | 437 ctx | cooccurence:430 |
Rv2981c ddlA |
D-alanine--D-alanine ligase | 503 | 436 | coexpression:404 |
Rv3267 lcp1 hyp |
hypothetical protein | 409 | 407 |
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: ligase
- MTBC0 PGAP product: Mur ligase family protein
- Pfam (hmmscan --cut_ga): Mur_ligase_M PF08245.19 (E=2e-14), MurT_C PF08353.16 (E=2e-22)
- (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_218229.1)
- Domains: Pfam-A via hmmscan --cut_ga — Mur_ligase_M (PF08245.19), MurT_C (PF08353.16)
- 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
COG0769 - Curated reference: UniProt I6Y4C7 (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 —
30 functional partner(s); context anchor
cobQ2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003935|Rv3712| MVTTRARLALAAGAGARWASRVTGRGAGAMIGGLVAMTLDRSILRQLGMGRRTVVVTGTNGKSTTTRMTAAALGTLGAVATNAEGANMDAGLVAALAAHRDAELAVLEVDEMHVPHISDAVDPAVVVLLNLSRDQLDRVGEINVIERTLRAGLARHPDAVVVANCDDVLMTSAAYDSPNVVWVAAGGAWSNDSVSCPRSGEVIVRKAPSQEDHWYSTGADFKRPAPHWWFDDATLYGPDGLALPMRLALPGSVNRGNAAQAVAAAVALGADPAVAVAAVCQVDEVAGRYRTVRIGAHQARILLAKNPAGWQEALAMVDKHADGVVIAVNGRVPDGEDLSWLWDVRFEHFEKTRVVAAGERGTDLAVRLGYAGVEHTLVHDTVAAIASCPPGRVEVVANYTAFLQLQRALARRG