FlyBase Gene Report: Dmel\LysS

General Information

Symbol

Dmel\LysS

Species

D. melanogaster

Name

Lysozyme S

Annotation Symbol

CG1165

Feature Type

protein_coding_gene

FlyBase ID

FBgn0004430

Gene Model Status

Current

Stock Availability

3 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, P37160)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

61F4-61F4

Sequence location

3L:1,227,747..1,228,238 [+]

Recombination map

3-0

RefSeq locus

NT_037436 REGION:1227747..1228238

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

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Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (3 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables lysozyme activity

inferred from sequence or structural similarity with UniProtKB:P00697

(FlyBase Curators, 2008-)

inferred from sequence or structural similarity

(Daffre et al., 1994)

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

(FlyBase Curators, 2008-)

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

(FlyBase Curators, 2008-)

Gene Group (FlyBase)

LYSOZYMES

Protein Family (UniProt)

Belongs to the glycosyl hydrolase 22 family. (P37160)

Protein Signatures (InterPro)

Catalytic Activity (EC)

Experimental Evidence

Predictions / Assertions

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, P37160)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\LysS 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 New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry P37160)

If you don't see the viewer to the right, 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.

Comments on Gene Model

Gene model reviewed during 5.46

Gene model reviewed during 5.48

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

LysS-RA

FBtr0072631

NM_057481

492

140

Additional Transcript Data and Comments

Reported size (kB)

0.482 (longest cDNA)

(Daffre et al., 1994)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

LysS-PA

FBpp0072527

15.7

140

4.45

NP_476829

AAF47453

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)

139 (aa)

(Daffre et al., 1994)

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

P37160

Mapped Features

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

External Data

Crossreferences

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

LysS_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

RNase protection, primer extension, SI map

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

gastric caecum

(Daffre et al., 1994)

Additional Descriptive Data

LysS transcripts are detected in larvae with the highest level at the third instar stage. They are detected mainly in the epithelium of the gastric caecae by in situ hybridization. The levels of LysS transcripts are drastically reduced after bacterial injection.

(Daffre et al., 1994)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\LysS in GBrowse 2

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

View exonic expression by developmental stage for Dmel\LysS

View exonic expression by tissue for Dmel\LysS

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0004430

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

38130/tissue=All

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

FBgn0004430

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004430

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

FBgn0004430

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG1165

Flygut - An atlas of the Drosophila adult midgut

FBgn0004430

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 ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of LysS

Transgenic constructs containing regulatory region of LysS

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

viable, with Scer\GAL4^Mef2.PR

LysS^GD5939

viable, with Scer\GAL4^pnr-MD237

LysS^GD5939

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (9)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\LYZ

11 of 15

Yes

7 of 15

7 of 15

7 of 15

6 of 15

6 of 15

6 of 15

5 of 15

4 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (9)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Lyz1

11 of 15

Yes

Mmus\Lyz2

11 of 15

Yes

Mmus\9530003J23Rik

10 of 15

Mmus\Lyzl1

8 of 15

Yes

8 of 15

8 of 15

8 of 15

5 of 15

4 of 15

Yes

Rattus norvegicus (Norway rat) (9)

Rnor\Lyz2

11 of 13

Yes

Rnor\RGD1306474

10 of 13

Yes

Rnor\Lyc2

9 of 13

Yes

Rnor\Lyzl6

7 of 13

Yes

7 of 13

6 of 13

6 of 13

5 of 13

5 of 13

Xenopus tropicalis (Western clawed frog) (6)

Xtro\MGC89221

4 of 12

Yes

Xtro\LOC100493166

2 of 12

Yes

Xtro\LOC100493330

2 of 12

Yes

Xtro\LOC101730983

2 of 12

Yes

Xtro\lyz

2 of 12

Yes

Xtro\spaca5

2 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\lyz

5 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (0)

No records found.

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (12)

Gene Symbol

Score

Source

Alignment

8 of 10

7 of 10

7 of 10

7 of 10

7 of 10

6 of 10

6 of 10

6 of 10

5 of 10

5 of 10

4 of 10

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

LYZ; lysozyme

model of familial visceral amyloidosis

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v8.0 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 15

153450

AMYLOIDOSIS, FAMILIAL VISCERAL

familial visceral amyloidosis

LYZL1; lysozyme like 1

7 of 15

LYZL2; lysozyme like 2

7 of 15

612748

SPACA3; sperm acrosome associated 3

7 of 15

612749

LYZL4; lysozyme like 4

6 of 15

612750

LYZL6; lysozyme like 6

6 of 15

612751

SPACA5B; sperm acrosome associated 5B

6 of 15

LALBA; lactalbumin alpha

5 of 15

149750

SPACA5; sperm acrosome associated 5

4 of 15

300593

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

esyN Network Diagram

Interactions Browser

Summary of Genetic Interactions

esyN Network Diagram

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0004430

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

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

FBgn0004430

External Data

Linkouts

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-0

Cytogenetic map

61F4-61F4

Sequence location

3L:1,227,747..1,228,238 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

61F4-61F4

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

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 (3)

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

Bloomington

58077

y¹ v¹; P{TRiP.HMJ21969}attP40/CyO

VDRC

v108488

P{KK111657}VIE-260B

v13886

w¹¹¹⁸; P{GD5939}v13886

Genomic Clones (16)

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

cDNA Clones (11)

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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

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.

FBgn0004430

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004430

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

38130

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for database merge of

Source for merge of: LysS BcDNA:LP06719

(FlyBase, 1996-)

Additional comments

Source for merge of LysS BcDNA:LP06719 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Other Comments

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)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 38 )

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.

38130

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.

P37160

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

P37160

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.

P37160

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0004430

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

FBgn0004430

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

38130/tissue=All

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

FBgn0004430

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

LysS_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004430

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

FBgn0004430

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG1165

Flygut - An atlas of the Drosophila adult midgut

FBgn0004430

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

FBgn0004430

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

38130

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

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

Dmel_CG1165

MARRVEL_MODEL - MARRVEL (model organism gene)

38130

modMine - A data warehouse for the modENCODE project

FBgn0004430

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0004430

DRSC - Results frm RNAi screens

FBgn0004430

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004430

FlyMine - An integrated database for Drosophila genomics

FBgn0004430

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

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

BcDNA:LP06719

CG1165

(Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Li et al., 2009)

LysS

(Štětina et al., 2019, Paré et al., 2012, Seong et al., 2011, Li et al., 2009, Blanco et al., 2008, Yan et al., 2008, Waterhouse et al., 2007, Greene et al., 2005)

lysS

(Faisal et al., 2014, Zsindely et al., 2009, Lemaitre, 2000.12.20)

Name Synonyms

Lysozyme S

lysozyme S

(Faisal et al., 2014)

Secondary FlyBase IDs

FBgn0002575
FBgn0063108

Datasets (2)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (2)

Result

Result Type

Title

scRNAseq_2020_Cho_NI96HL_seq_clustering

cell clustering analysis

Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI120HL_seq_clustering

cell clustering analysis

Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying

References (42)

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

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