murI Resolved · high auto-curated
H37Rv Rv1338 · MTBC0 mtbc0_001435 ·
271 aa · 1515777–1516592 (+) ·
RefSeq NP_215854.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamate racemase |
|---|---|
| MTBC0 PGAP re-annotation | glutamate racemase |
| Revised (this work) | Glutamate racemase. Pfam: Asp_Glu_race (PF01177.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPW9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamate racemase |
| EC (curated) |
EC 5.1.1.3
|
| Curated function | Provides the (R)-glutamate required for cell wall biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | murI |
| eggNOG description | Provides the (R)-glutamate required for cell wall biosynthesis |
| Orthologous group | COG0796 |
| EC number |
EC 5.1.1.3
|
| KEGG orthology |
K01776
|
| KEGG pathways |
map00471, map01100
|
| Gene Ontology (65) |
GO:0000270, GO:0003674, GO:0003824, GO:0004857, GO:0005575, GO:0005623, GO:0005886, GO:0006022, GO:0006023, GO:0006024, GO:0006807, GO:0008150 +53 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 | 0.378 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Asp_Glu_race | PF01177.28 | 1.7e-19 | 22–215 | Asp/Glu/Hydantoin racemase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysM (O-phosphoserine sulfhydrylase), high confidence from genomic context alone (score 973 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1336 cysM |
O-phosphoserine sulfhydrylase | 979 | 973 ctx | neighborhood:881 coexpression:785 |
Rv1341 rdgB |
non-canonical purine NTP pyrophosphatase | 960 | 960 ctx | neighborhood:632 fusion:890 |
Rv2155c murD |
UDP-N-acetylmuramoylalanine--D-glutamate ligase | 994 | 957 ctx | cooccurence:550 database:900 textmining:878 |
Rv1337 |
integral membrane protein | 966 | 907 ctx | neighborhood:881 textmining:650 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 901 | 902 | database:900 |
Rv1334 mec |
[CysO | 885 | 885 ctx | neighborhood:847 |
Rv1335 cysO |
sulfur carrier protein CysO | 882 | 882 ctx | neighborhood:876 |
Rv1333 |
hydrolase | 854 | 854 ctx | neighborhood:847 |
Rv1332 |
transcriptional regulator | 833 | 834 ctx | neighborhood:829 |
Rv1331 clpS |
ATP-dependent Clp protease adapter protein ClpS | 829 | 829 ctx | neighborhood:829 |
Rv1339 hyp |
hypothetical protein | 756 | 757 ctx | neighborhood:746 |
Rv1330c pncB1 |
nicotinic acid phosphoribosyltransferase PncB1 | 757 | 748 ctx | neighborhood:747 |
Rv1340 rphA |
ribonuclease PH | 743 | 743 ctx | neighborhood:714 |
Rv1329c dinG |
ATP-dependent helicase DinG | 587 | 588 ctx | neighborhood:577 |
Rv3455c truA |
tRNA pseudouridine synthase A | 462 | 462 | coexpression:431 |
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: glutamate racemase
- MTBC0 PGAP product: glutamate racemase
- Pfam (hmmscan --cut_ga): Asp_Glu_race PF01177.28 (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_215854.1)
- Domains: Pfam-A via hmmscan --cut_ga — Asp_Glu_race (PF01177.28)
- 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
COG0796 - Curated reference: UniProt P9WPW9 (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 —
50 functional partner(s); context anchor
cysM - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001435|Rv1338|murI MNSPLAPVGVFDSGVGGLTVARAIIDQLPDEDIVYVGDTGNGPYGPLTIPEIRAHALAIGDDLVGRGVKALVIACNSASSACLRDARERYQVPVVEVILPAVRRAVAATRNGRIGVIGTRATITSHAYQDAFAAARDTEITAVACPRFVDFVERGVTSGRQVLGLAQGYLEPLQRAEVDTLVLGCTHYPLLSGLIQLAMGENVTLVSSAEETAKEVVRVLTEIDLLRPHDAPPATRIFEATGDPEAFTKLAARFLGPVLGGVQPVHPSRIH