murF Resolved · high auto-curated
H37Rv Rv2157c · MTBC0 mtbc0_002293 ·
510 aa · 2444851–2446383 (-) ·
RefSeq NP_216673.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase |
|---|---|
| MTBC0 PGAP re-annotation | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase |
| Revised (this work) | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. Pfam: Mur_ligase (PF01225.31), Mur_ligase_M (PF08245.19), Mur_ligase_C (PF02875.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJL1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase |
| EC (curated) |
EC 6.3.2.10
|
| Curated function | Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | murF |
| eggNOG description | Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein |
| Orthologous group | COG0770 |
| EC number |
EC 6.3.2.10
|
| KEGG orthology |
K01929
|
| KEGG pathways |
map00300, map00550, map01100, map01502
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.571 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 | PF01225.31 | 3.0e-08 | 34–84 | Mur ligase family, catalytic domain |
Mur_ligase_M | PF08245.19 | 2.0e-38 | 134–321 | Mur ligase middle domain |
Mur_ligase_C | PF02875.27 | 2.1e-19 | 344–487 | Mur ligase, glutamate ligase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: murX (phospho-N-acetylmuramoyl-pentappeptidetransferase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2156c murX |
phospho-N-acetylmuramoyl-pentappeptidetransferase | 999 | 1000 ctx | neighborhood:882 cooccurence:669 coexpression:909 database:900 textmining:609 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 999 | 1000 ctx | neighborhood:881 fusion:899 coexpression:712 database:900 textmining:803 |
Rv2155c murD |
UDP-N-acetylmuramoylalanine--D-glutamate ligase | 999 | 998 ctx | neighborhood:881 cooccurence:712 coexpression:942 textmining:957 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 999 | 996 ctx | neighborhood:876 cooccurence:703 coexpression:903 textmining:944 |
Rv2981c ddlA |
D-alanine--D-alanine ligase | 998 | 989 ctx | cooccurence:697 coexpression:426 database:900 textmining:910 |
Rv2154c ftsW |
lipid II flippase FtsW | 994 | 977 ctx | neighborhood:876 cooccurence:665 coexpression:429 textmining:756 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 993 | 969 ctx | neighborhood:876 coexpression:666 textmining:798 |
Rv2151c ftsQ |
cell division protein FtsQ | 984 | 961 ctx | neighborhood:876 coexpression:698 textmining:630 |
Rv3423c alr |
alanine racemase | 987 | 935 ctx | fusion:835 cooccurence:590 textmining:816 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 927 | 859 ctx | neighborhood:544 cooccurence:547 textmining:507 |
Rv2160A |
Rv2160A, len: 211 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator,similar to N-terminal half of AL51266 | 808 | 807 ctx | neighborhood:712 |
Rv2148c hyp |
hypothetical protein | 793 | 793 ctx | neighborhood:597 coexpression:508 |
Rv2147c sepF |
cell division protein SepF | 833 | 762 ctx | neighborhood:559 coexpression:412 |
Rv2150c ftsZ |
cell division protein FtsZ | 876 | 748 ctx | neighborhood:561 textmining:529 |
Rv2159c hyp |
hypothetical protein | 752 | 746 ctx | neighborhood:709 |
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: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
- MTBC0 PGAP product: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
- Pfam (hmmscan --cut_ga): Mur_ligase PF01225.31 (E=3e-08), Mur_ligase_M PF08245.19 (E=2e-38), Mur_ligase_C PF02875.27 (E=2e-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_216673.1)
- Domains: Pfam-A via hmmscan --cut_ga — Mur_ligase (PF01225.31), Mur_ligase_M (PF08245.19), Mur_ligase_C (PF02875.27)
- 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
COG0770 - Curated reference: UniProt P9WJL1 (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 —
62 functional partner(s); context anchor
murX - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002293|Rv2157c|murF MIELTVAQIAEIVGGAVADISPQDAAHRRVTGTVEFDSRAIGPGGLFLALPGARADGHDHAASAVAAGAAVVLAARPVGVPAIVVPPVAAPNVLAGVLEHDNDGSGAAVLAALAKLATAVAAQLVAGGLTIIGITGSSGKTSTKDLMAAVLAPLGEVVAPPGSFNNELGHPWTVLRATRRTDYLILEMAARHHGNIAALAEIAPPSIGVVLNVGTAHLGEFGSREVIAQTKAELPQAVPHSGAVVLNADDPAVAAMAKLTAARVVRVSRDNTGDVWAGPVSLDELARPRFTLHAHDAQAEVRLGVCGDHQVTNALCAAAVALECGASVEQVAAALTAAPPVSRHRMQVTTRGDGVTVIDDAYNANPDSMRAGLQALAWIAHQPEATRRSWAVLGEMAELGEDAIAEHDRIGRLAVRLDVSRLVVVGTGRSISAMHHGAVLEGAWGSGEATADHGADRTAVNVADGDAALALLRAELRPGDVVLVKASNAAGLGAVADALVADDTCGSVRP