FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\ppl
Open Close
General Information
Symbol
Dmel\ppl
Species
D. melanogaster
Name
pumpless
Annotation Symbol
CG7758
Feature Type
protein_coding_gene
FlyBase ID
FBgn0027945
Gene Model Status
Current
Stock Availability
17 publicly available
Gene Summary
pumpless (ppl) encodes the non-catalytic subunit of the mitochondrial glycine cleavage complex that catalyzes the decarboxylation and deamination of glycine into ammonia and carbon dioxide and converts tetrahydrofolate to N5,N10-methylene tetrahydrofolate (5,10-CH2-THF). ppl (known as protein H) transfers the methylamine group of glycine via its lipoamide cofactor from Gldc to Gcst in the second step of glycine cleavage. [Date last reviewed: 2026-02-19] (FlyBase Gene Snapshot)
All Summaries
Also Known As

l(3)78Cb

Key Links
Genomic Location
Cytogenetic map
78C4-78C4
Sequence location
Recombination map
3-47
RefSeq locus
NT_037436 REGION:21280491..21281506
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (6 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 molecular carrier activity
inferred from sequence or structural similarity with UniProtKB:P11183
(Gene Ontology Curators, 2002-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in glycine catabolic process
inferred from sequence or structural similarity with UniProtKB:P39726
(Gene Ontology Curators, 2002-)
involved_in glycine decarboxylation via glycine cleavage system
inferred from sequence or structural similarity with UniProtKB:P16048
(Gene Ontology Curators, 2002-)
inferred from electronic annotation with InterPro:IPR002930, InterPro:IPR017453
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN001711613
(GO Reference Genome Project, 2011-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of glycine cleavage complex
inferred from electronic annotation with InterPro:IPR002930, InterPro:IPR017453
(InterPro Project Members, 2004-)
inferred from sequence or structural similarity with UniProtKB:P16048
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN001711613
(GO Reference Genome Project, 2011-)
is_active_in mitochondrial matrix
inferred from sequence or structural similarity with UniProtKB:P16048
(Gene Ontology Curators, 2002-)
is_active_in mitochondrion
inferred from biological aspect of ancestor with PANTHER:PTN001711613
(GO Reference Genome Project, 2011-)
located_in mitochondrion
inferred from sequence or structural similarity with UniProtKB:P39726
(Gene Ontology Curators, 2002-)
Gene Group (FlyBase)
Pathway (FlyBase)
Protein Family (UniProt)
Belongs to the GcvH family. (Q9U616)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
pumpless (ppl) encodes the non-catalytic subunit of the mitochondrial glycine cleavage complex that catalyzes the decarboxylation and deamination of glycine into ammonia and carbon dioxide and converts tetrahydrofolate to N5,N10-methylene tetrahydrofolate (5,10-CH2-THF). ppl (known as protein H) transfers the methylamine group of glycine via its lipoamide cofactor from Gldc to Gcst in the second step of glycine cleavage. [Date last reviewed: 2026-02-19]
Gene Group (FlyBase)
GLYCINE CLEAVAGE COMPLEX -
The major pathway for the catabolism of glycine involves the oxidative cleavage of glycine to CO2, NH4+ and a methylene group, which is accepted by tetrahydrofolate in a reversible reaction catalyzed by the glycine cleavage system/complex (GCC). In animals and plants, the GCC is composed of four proteins (three enzymes and a carrier protein) that form a complex loosely associated with the mitochondrial inner membrane. The enzymes are: i) P-protein or glycine dehydrogenase (decarboxylating), ii) T-protein or aminomethyl-transferase, and iii) L-protein or dihydrolipoamide dehydrogenase. The carrier protein is called H-protein (a lipoic acid-containing protein). (Adapted from PMID:18941301.)
Pathway (FlyBase)
GLYCINE CLEAVAGE SYSTEM -
The catabolism of glycine via the glycine cleavage complex (GCS) occurs in the mitochondrion. It involves the decarboxylation and deamination of glycine into ammonia and carbon dioxide, and converts tetrahydrofolate to N5,N10-methylene tetrahydrofolate (5,10-CH2-THF). By producing the one carbon unit donor 10-CH2-THF, GCS is part of the tetrahydrofolate (one carbon) cycle. (Adapted from PMID:18941301 and PMID: 23615880.)
Protein Function (UniProtKB)
The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein (By similarity).
(UniProt, Q9U616)
Summary (Interactive Fly)

glycine cleavage system H protein - involved in appetite control

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\ppl 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 Q9U616)

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

Gene model reviewed during 6.61

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
ppl-RA
FBtr0078412
NM_079473
900
165
ppl-RB
FBtr0482697
774
165
Additional Transcript Data and Comments
Reported size (kB)

0.813 (sequence analysis)

(Zinke et al., 1999)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
ppl-PA
FBpp0078066
18.0
165
4.87
Q9U616
NP_524197
AAF51697
ppl-PB
FBpp0428617
18.0
165
4.87
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

165 aa isoforms: ppl-PA, ppl-PB
Additional Polypeptide Data and Comments
Reported size (kDa)

165 (aa)

(Zinke et al., 1999)
Comments
External Data
Subunit Structure (UniProtKB)

The glycine cleavage system is composed of four proteins: P, T, L and H.

(UniProt, Q9U616)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

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

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

2.68

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage & larval stage
embryonic/larval fat body
(Zinke et al., 1999)
embryonic stage 7 -- 8
anterior endoderm anlage
(Fisher et al., 2012)
embryonic stage 9 -- 10
anterior endoderm
(Fisher et al., 2012)
embryonic stage 11 -- 12
anterior midgut primordium
(Fisher et al., 2012)
fat body/gonad primordium
(Fisher et al., 2012)
posterior midgut primordium
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic/larval fat body
(Fisher et al., 2012)
embryonic stage 15 -- larval stage
embryonic/larval fat body
(Zinke et al., 1999)
embryonic stage 15 -- third instar larval stage
embryonic/larval fat body
(Zinke et al., 1999)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 17 -- late third instar larval stage

Comment: reference states 22-103 hrs AEL

(Zinke et al., 1999)
larval stage
organism
(Zinke et al., 1999)
Additional Descriptive Data

ppl transcripts are expressed exclusively in the embryonic and larval fat body. Levels increase during first and second instar larval stages and decrease at the end of the third instar.

(Zinke et al., 1999)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
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\ppl in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 9 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of ppl
Transgenic constructs containing regulatory region of ppl
Aberrations (Deficiencies and Duplications) ( 17 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\GCSH
14 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (2)
Rnor\Gcsh
14 of 14
Yes
Yes
Rnor\RGD1563099
11 of 14
No
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Gcsh
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\gcsh
7 of 13
Yes
Yes
Xtro\ythdc2
6 of 13
No
Yes
Danio rerio (Zebrafish) (2)
Drer\gcsha
13 of 14
Yes
Yes
Drer\gcshb
12 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\gcsh-1
14 of 14
Yes
Yes
Cele\gcsh-2
14 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP006548
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (3)
Atha\AT1G32470
12 of 13
Yes
Yes
Atha\AT2G35120
12 of 13
Yes
Yes
Atha\GDCH
11 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\GCV3
12 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\gcv3
12 of 12
Yes
Yes
Escherichia coli (enterobacterium) (1)
Ecol\gcvH
11 of 11
Yes
Yes
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:ppl. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
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?
    GCSH; glycine cleavage system protein H
    14 of 14
    238330
      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
      Summary of Genetic Interactions
      Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Bx
      enhanceable
      ppl
      (Bronstein et al., 2010)
      External Data
      Subunit Structure (UniProtKB)
      The glycine cleavage system is composed of four proteins: P, T, L and H.
      (UniProt, Q9U616 )
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      FlyBase
      GLYCINE CLEAVAGE SYSTEM
      External Links
      KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.
      External Data
      Linkouts
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Class of Gene
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3L
      Recombination map
      3-47
      Cytogenetic map
      78C4-78C4
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      78C4-78C4
      Limits computationally determined from genome sequence between P{PZ}ppl00217 and P{lacW}l(3)j1B10j1B10
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      78C-78C
      (Zinke, 1999.9.15, Zinke, 1999.11.4)
      78C3-78C4
      (determined by in situ hybridisation)
      (Spradling et al., 1999)
      78C3-78C4
      (BDGP Project Members, 1994-1999)
      Experimentally Determined Recombination Data
      Location

      3-47

      (FlyBase, 2016)

      3-43.8

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (17)
      Genomic Clones (18)
       

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

      cDNA Clones (53)
       

      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
      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.

      cDNA Clones, End Sequenced (ESTs)
      BDGP DGC clones
      Other clones
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments

          Area matching Drosophila EST AI257267. This EST has sequence similarity to Chick glycine cleavage system h protein. Probable intron in gene represented by EST AI257267.

          (Davies, 2001.3.15)

          Feeding wild type larvae high levels of amino acids can phenocopy the feeding and growth defects of ppl mutants.

          (Zinke et al., 1999)

          ppl mutant larvae do not feed, failing to pump food from the pharynx to the esophagous, but do not show the normal physiological response to starvation.

          (Zinke et al., 1999)
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: ppl l(3)78Cb

          (Zinke et al., 1999)
          Additional comments
          Nomenclature History
          Source for database identify of
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (5)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 57 )
          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.
          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.
          UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
          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.
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          FlyMine - An integrated database for Drosophila genomics
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
          KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          MIST (protein-protein) - An integrated Molecular Interaction Database
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.
          References (77)