FlyBase Gene Report: Dmel\LysD

General Information

Symbol

Dmel\LysD

Species

D. melanogaster

Name

Lysozyme D

Annotation Symbol

CG9118

Feature Type

protein_coding_gene

FlyBase ID

FBgn0004427

Gene Model Status

Current

Stock Availability

1 publicly available

Enzyme Name (EC)

lysozyme (3.2.1.17)

Gene Summary

Unlikely to play an active role in the humoral immune defense. May have a function in the digestion of bacteria in the food. (UniProt, P83972)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

61F3-61F3

Sequence location

3L:1,210,717..1,211,196 [-]

Recombination map

3-0

RefSeq locus

NT_037436 REGION:1210717..1211196

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (4 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables chitinase activity

inferred from direct assay

(Regel et al., 1998)

enables lysozyme activity

inferred from direct assay

(Regel et al., 1998)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables lysozyme activity

inferred from electronic annotation with InterPro:IPR000974

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN004256961

(GO Reference Genome Project, 2011-)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in defense response to Gram-negative bacterium

inferred from sequence or structural similarity with UniProtKB:P00697

(Gene Ontology Curators, 2002-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in extracellular space

inferred from sequence or structural similarity with UniProtKB:C1BF55

(Gene Ontology Curators, 2002-)

Gene Group (FlyBase)

LYSOZYMES

Protein Family (UniProt)

Belongs to the glycosyl hydrolase 22 family. (P83972)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

lysozyme activity

Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl- D-glucosamine residues in chitodextrins (3.2.1.17)

Summaries

Gene Group (FlyBase)

LYSOZYMES -: Lysozymes belong to the glycoside hydrolase family 22. Lysozymes damage bacterial cell walls by hydrolyzing the β-(1,4)-glycosidic bond between N-acetyl-muraminic acid and N-acetyl-D-glucosamine of peptidoglycan, causing cell lysis. (Adapted from PMID:22581338, PMID:20413917, PMID:20049505).

Protein Function (UniProtKB)

Unlikely to play an active role in the humoral immune defense. May have a function in the digestion of bacteria in the food.

(UniProt, P83972)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\LysD for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry P83972)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.46

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

LysD-RA

FBtr0072634

NM_057475

480

140

Additional Transcript Data and Comments

Reported size (kB)

0.498 (longest cDNA)

(Daffre et al., 1994)

0.5 (northern blot)

(Kylsten et al., 1992)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

LysD-PA

FBpp0072530

15.6

140

5.58

P83972

NP_476823

AAF47450

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

140 (aa)

(Daffre et al., 1994, Kylsten et al., 1992)

Comments

External Data

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

P83972

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\LysD using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

LysD_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.37

Transcript Expression

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

embryonic/larval midgut

(Daffre et al., 1994)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

embryonic/larval anterior midgut

(Kylsten et al., 1992)

gastric caecum

(Kylsten et al., 1992)

larval stage & pupal stage & adult stage

(Kylsten et al., 1992)

adult stage

adult midgut | anterior

(Kylsten et al., 1992)

RNase protection, primer extension, SI map

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage & adult stage

(Daffre et al., 1994)

adult stage

adult midgut

(Daffre et al., 1994)

Additional Descriptive Data

LysD transcripts are detected in the feeding stages (larvae and adults) with maximal expression in third instar larvae.

(Daffre et al., 1994)

LysD transcripts are expressed at all feeding stages of development. Expression peaks in third instar larvae, declines then ceases in pupae and resumes in adults. Transcript levels are reduced after injection of bacteria. Strong epression is detected in the anterior region of the midgut by in situ hybridization in larvae and adults. In larvae, the anterior border of expressing tissue separates the proventriculus from the stomach. In adults, LysD expression starts at a point just caudal to the cardia. In both cases, strong staining is seen along the thoracic part of the midgut up to a discrete point in the abdomen where it abruptly ceases.

(Kylsten et al., 1992)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\LysD in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\LysD

View exonic expression by tissue for Dmel\LysD

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

38127/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0004427

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0004427

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of LysD

Transgenic constructs containing regulatory region of LysD

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)LysB-P-Δ

(Marra et al., 2021)

Inferred from location ( 10 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (9)

Hsap\LYZ

11 of 14

Yes

8 of 14

7 of 14

7 of 14

7 of 14

7 of 14

7 of 14

7 of 14

5 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (9)

Rnor\Lyz2

11 of 14

Yes

Rnor\RGD1306474

11 of 14

Yes

Rnor\Lyc2

10 of 14

Yes

7 of 14

7 of 14

7 of 14

7 of 14

6 of 14

5 of 14

Yes

Mus musculus (laboratory mouse) (9)

Mmus\9530003J23Rik

11 of 14

Yes

Mmus\Lyz1

11 of 14

Yes

Mmus\Lyz2

11 of 14

Yes

10 of 14

9 of 14

9 of 14

9 of 14

5 of 14

Yes

Mmus\Lyzl4

5 of 14

Xenopus tropicalis (Western clawed frog) (7)

Xtro\lyz

8 of 13

Yes

Xtro\LOC100493330

6 of 13

Yes

4 of 13

3 of 13

1 of 13

1 of 13

Yes

Xtro\spaca5

1 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\lyz

6 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (8)

Agam\LYSC3

12 of 12

Yes

Agam\LYSC5

12 of 12

Yes

Agam\LYSC8

12 of 12

Yes

8 of 12

8 of 12

5 of 12

5 of 12

3 of 12

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:LysD. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (12)

13 of 13

13 of 13

13 of 13

13 of 13

13 of 13

12 of 13

11 of 13

7 of 13

7 of 13

6 of 13

6 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

LYZ; lysozyme

11 of 14

LYSOZYME; LYZ

AMYLOIDOSIS, HEREDITARY SYSTEMIC 5; AMYLD5

SPACA5B; sperm acrosome associated 5B

8 of 14

LYZL1; lysozyme like 1

7 of 14

LYZL2; lysozyme like 2

7 of 14

612748

LYZL4; lysozyme like 4

7 of 14

612750

LYZL6; lysozyme like 6

7 of 14

612751

SPACA3; sperm acrosome associated 3

7 of 14

612749

SPACA5; sperm acrosome associated 5

7 of 14

300593

LALBA; lactalbumin alpha

5 of 14

149750

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

Interaction Browsers

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

63673

DroID - A comprehensive database of gene and protein interactions.

FBgn0004427

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.

Lactose synthesis

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Lactose synthesis

Class of Gene

gene_with_edited_transcript

(Graveley et al., 2011)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-0

Cytogenetic map

61F3-61F3

Sequence location

3L:1,210,717..1,211,196 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

61F3-61F3

Limits computationally determined from genome sequence between P{PZ}l(3)05967⁰⁵⁹⁶⁷ and P{PZ}l(3)02640⁰²⁶⁴⁰

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

61F1-61F4

(determined by in situ hybridisation)

(Kylsten et al., 1992)

61F-61F

(determined by in situ hybridisation)

(Kylsten et al., 1988)

Experimentally Determined Recombination Data

Location

3-0

(FlyBase, 2016)

3-1.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (1)

Aberrations including deletions of this gene Aberrations including duplications of this gene

VDRC

v110135

P{KK115910}VIE-260B

Genomic Clones (16)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (6)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

MIP14090

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

FBgn0004427

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004427

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

LysD enzyme has been purified and biochemically characterised.

(Regel et al., 1998)

Lysozymes are expressed at a high level mainly in the digestive tract, they are not a component of the haemolymph. Lysozyme is not induced by bacteria so is not part of the inducible immune response but instead has been recruited for digestion of symbiotic bacteria in the stomach.

(Daffre et al., 1994)

Isolated from a D.melanogaster genomic library using a lysozyme cDNA clone from H.cecropia as a probe.

(Kylsten et al., 1992)

LysD has been cloned, sequenced and its developmental expression pattern analysed. The transcription levels of LysD decrease after bacterial injections into the haemocoel. The LysD gene product is therefore not induced as part of the immune response, but instead appears to have a role in the digestion of bacteria present in fermenting food.

(Kylsten et al., 1992)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

CG9118

(Palu and Thummel, 2016, Cammarato et al., 2011, Keleman et al., 2009.8.5, Li et al., 2009)

Lys

(Gallo et al., 2022)

LysD

(Knop et al., 2025, Muita and Baxter, 2023, Marra et al., 2021, Zhou et al., 2021, Brown et al., 2014, Short and Lazzaro, 2013, Paré et al., 2012, Rynes et al., 2012, Li et al., 2009, Blanco et al., 2008, Kwon et al., 2008, Yan et al., 2008, Waterhouse et al., 2007, Roxstrom-Lindquist et al., 2004)

lysD

(Lemaitre, 2000.12.20)

Name Synonyms

Lysozyme D

(Cammarato et al., 2011, Hurlbut et al., 2009, Roxstrom-Lindquist et al., 2004)

lysozyme

(Hoffmann, 1997)

Secondary FlyBase IDs

FBgn0002575

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 30 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

38127

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

P83972

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

P83972

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

P83972

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

38127/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0004427

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0004427

FlyMine - An integrated database for Drosophila genomics

FBgn0004427

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG9118

MARRVEL_MODEL - MARRVEL (model organism gene)

38127

Linkouts

BioGRID - A database of protein and genetic interactions.

63673

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0004427

DroID - A comprehensive database of gene and protein interactions.

FBgn0004427

DRSC - Results frm RNAi screens

FBgn0004427

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

LysD_1

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004427

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0004427

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Lactose synthesis

Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.

Lactose synthesis

References (57)

The following external sites may use different assemblies or annotations than FlyBase.

-0.37

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