GlyClass

GlycoEnzDB
Comprehensive glycoEnzyme database and dynamic pathway generation

Description: The GlycoEnzDB is a manually curated glycoEnzyme database, primarily focused on humans. It covers 390 enzymes across 28 pathway maps. Facilities are also available to create custom glycosylation reaction pathways using experimental data in SBML format and for pathway simulation
Contacts: Sriram Neelamegham (neel@buffalo.edu), Yusen Zhou (yusenzho@buffalo.edu) or Ted Groth (tgroth@buffalo.edu).

GlycoEnzDB
Create glycosylation pathway
Custom database generation
Instructions/Reference
 
Pathway Map
GMDS



General Information
Gene Symbol:   
GMDS
Protein name:   
GDP-mannose 4,6 dehydratase
Enzyme Class:   
CAZy Family:   
E.C. No:   
4.2.1.47
Organs:   
Reaction (SNFG):   

GDP-Man → GDP-4-6-dehydro-6-deoxy-D-Mannose
Reaction (IUBMB):   
No specified reaction.
About

• Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose. (Verbatim UniProt)
• Intermediate enzyme for mannose metabolism for sugar nucleotide synthesis.

Related Pathway
KEGG ORTHOLOGY:   
KEGG Pathway:   
No Record 
Reactome:   
R-HSA-6787639
Related Database
Organism:   
Homo sapiens
Uniprot:   
O60547 
NCBI GeneID:   
2762
GlyMap GeneID:   
2762
DNA aRefSeq:   
NM_001253846.1 
Protein RefSeq:   
NP_001240775.1 
BRENDA:   
Kinetic info.
OMIM number:   
602884
GeneCards database:   
GMDS
Enzyme Specificity
Glycan Type:  
     
Compartment:  
     
Substrate:  
     GDP-Man
Product:  
     GDP-4-6-dehydro-6-deoxy-D-Mannose
Constraints:  
     None
Simulation Parameters
Mechaelis-Menten parameters (suggested)
VM:       (pmol/cell • hr)       KM:       (pM)
Relative conc of enzymes in compartment.(sum will be normalized to 1)
ER Cis- Medial- Trans- TGN










Expression Data in Tissue {ref. 5} Source from NCBI gene database
adrenal appendix bone marrow brain colon duodenum endometrium esophagus fat gall bladder heart kidney liver lung lymph node ovary pancreas placenta prostate salivary gland skin small intestine spleen stomach testis thyroid urinary bladder 10 8 6 4 2 0 RPKM
Expression Data in Cells {ref. 13} Source from Cancer Cell Line Encyclopedia database
Kidney Lung Breast Prostate Large intestine Ovary HL60 haematopoietic and lymphoid tissue Skin Central nervous system 786O A498 ACHN CAKI1 UO31 A549 EKVX HOP62 HOP92 NCIH226 NCIH23 NCIH322 NCIH460 NCIH522 SHP77 BT549 HS578T MCF7 MDAMB231 MDAMB468 T47D DU145 PC3 HCT116 HCT15 HT29 KM12 SW620 OVCAR4 OVCAR8 IGROV1 SKOV3 HL60 K562 RPMI8226 LOXIMVI MALME3M RPMI7951 SKMEL28 SKMEL5 UACC257 UACC62 SF268 SF295 SF539 SNB75 160 140 120 100 80 60 40 20 0 Transcripts per million (TPM)
Transcription factor {ref. 10}
Transcriptional start site (TSS) 0 200 -2000 -1800 -1600 -1400 -1200 -1000 -800 -600 -400 -200
ENST00000380815 ENST00000530927 ZNF317 ZNF146 FLI1 ELF3 ZNF449 GATA1 ZFAT RCOR1 FOXP1 SMARCC1 HOXC8 CUX1 ARID3A TEAD4 GATAD2A CEBPA ZBTB7B TEAD3 TEAD1 TEAD1 KMT2B KMT2B KMT2B RCOR2 ZBTB48 ZBTB48 NFIC ETV5 NFIA KLF10 MYBL2 MYBL2 NFIB CTCF CTCF MAX RXRB HINFP NFIL3 NFIL3 SMARCC2 SMARCC2 SMARCC2 KAT8 ELF1 ELF1 ELF1 ELF1 TCF3 TCF3 STAT5A STAT5A ETV4 TSC22D4 SOX9 ARID4B NR2F6 NR2F6 ZNF83 HOMEZ HOMEZ KLF9 ATF1 TCF12 TCF12 TCF4 MYOD1 SCRT1 GLIS1 ZNF644 ZEB2 ZEB2 ZEB2 OSR2 OSR2 ZNF280D TFAP4 ASCL1 SP2 YY1 NFYC IRF1 ZNF35 TCF3 GATA3 NFE2 FEZF1 FEZF1 TAF1 DMAP1 LHX2 KLF4 ZBTB42 TCF4 E2F3 KLF5 ASCL1 VEZF1 MECOM RELB PPARG GRHL2 ZFX ZNF217 ELF3 ZNF263 GATA2 KLF6 TFAP2C KMT2A RUNX1 GATA1 RFX1 ATF2 SCRT1 CLOCK STAT2 BCL11A PPARG PPARG GATAD1 AEBP2 SMAD1 NR2F2 SCRT2 IKZF1 NR2F1 ZNF335 TFAP2A USF1 KDM5C KMT2A NR2F2 RUNX1 L3MBTL4 ERG PPARG ZFX ZBTB7A ZBTB7A BCL11A REST ZNF770 GLIS1 ZNF639 PBX3 NONO RUNX1 MAF CTCF SMAD5 TAF1 E2F6 KLF1 NFE2 TFAP4 TCF7L1 RFX5 ATF1 GATA1 KLF1 CREM KLF9 KLF9 FOS FOS PPARG REST FOXP2 SMAD2 SMAD2 TAF1 SP2 SP2 NFKB1 ZNF554 NFYB SP4 ARID3A USF2 ZBTB7A ZBTB7A EGR1 EGR1 POU5F1 MEIS2 KLF15 PPARG GLIS1 GLIS1 BCL6 MNT KLF6 SMAD4 MXD3 THAP11 TGIF2 ZSCAN22 HBP1
miRNA-GlycoEnzyme Interactome {ref. 9}
GMDS/hsa-miR-874-5p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'... UACACAACAAAUUG UGGGGCC U...
3'   AGAAUGGGACCACGC ACCCCGG C
 7mer-m8 304-310 -0.417 97.0 -0.417 98.0 noncon