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
 
Glycogene class
A3GALT2
A4GALT
A4GNT
ABO
ALG1
ALG10
ALG10B
ALG11
ALG12
ALG13
ALG14
ALG1L
ALG1L2
ALG2
ALG3
ALG5
ALG6
ALG8
ALG9
AMDHD2
B3GALNT1
B3GALNT2
B3GALT1
B3GALT2
B3GALT4
B3GALT5
B3GALT6
B3GAT1
B3GAT2
B3GAT3
B3GLCT
B3GNT2
B3GNT3
B3GNT4
B3GNT5
B3GNT6
B3GNT7
B3GNT8
B4GALNT1
B4GALNT2
B4GALNT3
B4GALNT4
B4GALT1
B4GALT2
B4GALT3
B4GALT4
B4GALT5
B4GALT6
B4GALT7
C1GALT1
C1GALT1C1
CALR
CANX
CEMIP2
CHPF
CHPF2
CHST1
CHST10
CHST11
CHST12
CHST13
CHST14
CHST15
CHST2
CHST3
CHST4
CHST5
CHST6
CHST7
CHST8
CHST9
CHSY1
CHSY3
CMAS
CSGALNACT1
CSGALNACT2
CTBS
DAD1
DDOST
DPAGT1
DPM1
DPM2
DPM3
DPY19L1
DPY19L2
DPY19L3
DPY19L4
DSE
DSEL
EDEM1
EDEM2
EDEM3
ENGASE
EOGT
EXT1
EXT2
EXTL1
EXTL2
EXTL3
FAM20B
FCSK
FKRP
FKTN
FPGT
FUCA1
FUCA2
FUT1
FUT10
FUT11
FUT2
FUT3
FUT4
FUT5
FUT6
FUT7
FUT8
FUT9
G6PC1
GAL3ST1
GAL3ST2
GAL3ST3
GAL3ST4
GALC
GALE
GALK1
GALK2
GALNS
GALNT1
GALNT10
GALNT11
GALNT12
GALNT13
GALNT14
GALNT15
GALNT16
GALNT17
GALNT18
GALNT2
GALNT3
GALNT4
GALNT5
GALNT6
GALNT7
GALNT8
GALNT9
GALNTL6
GALT
GANAB
GANC
GBA
GBGT1
GCK
GCNT1
GCNT2
GCNT3
GCNT4
GCNT7
GFPT1
GFPT2
GLA
TMEM2
GLB1
GLCE
GMDS
GMPPA
GMPPB
GNE
GNPDA1
GNPDA2
GNPNAT1
GNPTAB
GNPTG
GNS
GPAA1
GPI
GUSB
GXYLT1
GXYLT2
HAS1
HAS2
HAS3
HEXA
HEXB
HK1
HK2
HK3
HPSE
HGSNAT
HS2ST1
HS3ST1
HS3ST2
HS3ST3A1
HS3ST3B1
HS3ST4
HS3ST5
HS3ST6
HS6ST1
HS6ST2
HS6ST3
HYAL1
HYAL2
HYAL3
HYAL4
IDS
IDUA
LFNG
MAN1A1
MAN1A2
MAN1B1
MAN1C1
MAN2A1
MAN2A2
MAN2B1
MAN2B2
MAN2C1
MANBA
MANEA
MANEAL
MFNG
MGAT1
MGAT2
MGAT3
MGAT4A
MGAT4B
MGAT4C
MGAT4D
MGAT5
MGAT5B
MOGS
MPI
MPPE1
NAGA
NAGK
NAGLU
NAGPA
NANS
NDST1
NDST2
NDST3
NDST4
NEU1
NEU2
NEU3
NEU4
OGT
PAPSS1
PAPSS2
PGAP4
PGM1
PGM2
PGM3
PIGA
PIGB
PIGC
PIGF
PIGG
PIGH
PIGK
PIGL
PIGM
PIGN
PIGO
PIGP
PIGQ
PIGS
PIGT
PIGU
PIGV
PIGW
PIGX
PIGY
PMM1
PMM2
POFUT1
POFUT2
POGLUT1
POGLUT2
POGLUT3
POMGNT1
POMGNT2
POMT1
POMT2
PRKCSH
RENBP
RFNG
RPN1
RPN2
RXYLT1
SGSH
SLC2A1
SLC2A10
SLC2A12
SLC2A2
SLC2A3
SLC2A4
SLC2A5
SLC2A8
SLC35A1
SLC35A2
SLC35A3
SLC35B2
SLC35B3
SLC35B4
SLC35C1
SLC35D1
SLC35D2
ST3GAL1
ST3GAL2
ST3GAL3
ST3GAL4
ST3GAL5
ST3GAL6
ST6GAL1
ST6GAL2
ST6GALNAC1
ST6GALNAC2
ST6GALNAC3
ST6GALNAC4
ST6GALNAC5
ST6GALNAC6
ST8SIA1
ST8SIA2
ST8SIA3
ST8SIA4
ST8SIA5
ST8SIA6
STT3A
STT3B
SULF1
SULF2
TMTC1
TMTC2
TMTC3
TMTC4
TSTA3
UAP1
UGCG
UGDH
UGGT1
UGGT2
UGP2
UGT1A1
UGT1A10
UGT1A3
UGT1A4
UGT1A5
UGT1A6
UGT1A7
UGT1A8
UGT1A9
UGT2A1
UGT2A2
UGT2A3
UGT2B10
UGT2B11
UGT2B15
UGT2B17
UGT2B28
UGT2B4
UGT2B7
UGT3A1
UGT3A2
UGT8
UST
UXS1
XXYLT1
XYLT1
XYLT2
AGA
ARSK
ARSB
GAA
CMAHP
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}
miRNA Name Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
hsa-miR-4493 307-314 -0.598 99.0 -0.598 99.0 noncon
hsa-miR-1199-3p 134-141 -0.581 99.0 -0.581 99.0 noncon
hsa-miR-6859-3p 717-724 -0.581 99.0 -0.161 85.0 noncon
hsa-miR-4423-3p 925-932 -0.577 99.0 -0.16 88.0 noncon
hsa-miR-4706 38-45 -0.556 98.0 -0.556 98.0 noncon
hsa-miR-4749-5p 38-45 -0.546 98.0 -0.546 99.0 noncon
hsa-miR-4750-3p 719-726 -0.467 99.0 -0.133 89.0 noncon
hsa-miR-4465 272-279 -0.463 99.0 -0.463 99.0 con
hsa-miR-6742-5p 428-435 -0.462 98.0 -0.131 83.0 noncon
hsa-miR-4734 40-47 -0.444 97.0 -0.444 98.0 noncon
hsa-miR-1297 272-279 -0.442 99.0 -0.442 99.0 con
hsa-miR-26a-5p 272-279 -0.434 99.0 -0.434 99.0 con
hsa-miR-26b-5p 272-279 -0.434 99.0 -0.434 99.0 con
hsa-miR-4799-3p 936-943 -0.433 99.0 -0.124 89.0 noncon
hsa-miR-5588-5p 936-943 -0.433 99.0 -0.124 89.0 noncon
hsa-miR-4720-5p 936-943 -0.428 99.0 -0.123 89.0 noncon
hsa-miR-6126 308-315 -0.419 99.0 -0.419 99.0 noncon
hsa-miR-874-5p 304-310 -0.417 97.0 -0.417 98.0 noncon
hsa-miR-6796-5p 429-436 -0.416 97.0 -0.12 78.0 noncon
hsa-miR-3144-5p 416-423 -0.416 97.0 -0.12 75.0 noncon
hsa-miR-4517 331-338 -0.413 99.0 -0.413 99.0 noncon
hsa-miR-6751-3p 1005-1011 -0.412 98.0 0.0 29.0 noncon
hsa-miR-1199-5p 1005-1011 -0.408 98.0 0.0 34.0 noncon
hsa-miR-4670-5p 200-206 -0.405 91.0 -0.405 93.0 noncon
hsa-miR-3609 266-273 -0.402 99.0 -0.402 99.0 noncon
hsa-miR-548ah-5p 266-273 -0.399 99.0 -0.399 99.0 noncon
hsa-miR-4758-3p 303-309 -0.399 98.0 -0.399 98.0 noncon
hsa-miR-4725-5p 368-375 -0.389 97.0 -0.113 75.0 noncon
hsa-miR-6502-3p 342-348 -0.388 99.0 -0.388 99.0 noncon
hsa-miR-4256 720-727 -0.362 97.0 -0.105 82.0 noncon
hsa-miR-1205 616-623 -0.36 99.0 -0.105 88.0 noncon
hsa-miR-6749-3p 625-632 -0.343 96.0 -0.1 78.0 noncon
hsa-miR-889-5p 909-915 -0.341 97.0 -0.1 80.0 noncon
hsa-miR-30c-1-3p 388-395 -0.338 98.0 -0.099 87.0 noncon
hsa-miR-30c-2-3p 388-395 -0.338 98.0 -0.099 86.0 noncon
hsa-miR-4724-3p 738-745 -0.335 98.0 -0.098 91.0 noncon
hsa-miR-551b-3p 198-204 -0.334 92.0 -0.334 95.0 noncon
hsa-miR-551a 198-204 -0.334 92.0 -0.334 95.0 noncon
hsa-miR-6878-5p 387-394 -0.334 97.0 -0.098 76.0 noncon
hsa-miR-6788-5p 388-395 -0.33 98.0 -0.097 85.0 noncon
hsa-miR-6810-5p 417-424 -0.324 97.0 -0.095 82.0 noncon
hsa-miR-1-3p 761-768 -0.311 96.0 -0.092 82.0 noncon
hsa-miR-3130-3p 54-61 -0.31 98.0 -0.31 98.0 noncon
hsa-miR-525-5p 600-607 -0.308 97.0 -0.091 80.0 noncon
hsa-miR-613 761-768 -0.305 96.0 -0.09 80.0 noncon
hsa-miR-1257 263-269 -0.304 97.0 -0.304 98.0 noncon
hsa-miR-4659a-5p 767-774 -0.303 96.0 -0.09 81.0 noncon
hsa-miR-6847-5p 224-231 -0.302 98.0 -0.302 98.0 noncon
hsa-miR-520a-5p 600-607 -0.3 97.0 -0.089 80.0 noncon
hsa-miR-3173-3p 548-555 -0.295 97.0 -0.087 81.0 noncon
hsa-miR-206 761-768 -0.295 95.0 -0.087 81.0 noncon
hsa-miR-4659b-5p 767-774 -0.282 96.0 -0.084 81.0 noncon
hsa-miR-513c-5p 703-710 -0.277 98.0 -0.082 90.0 noncon
hsa-miR-514b-5p 703-710 -0.277 98.0 -0.082 90.0 noncon
hsa-miR-4733-3p 585-592 -0.276 96.0 -0.082 80.0 noncon
hsa-miR-449c-3p 357-363 -0.276 94.0 -0.112 84.0 noncon
hsa-miR-3146 358-364 -0.273 97.0 -0.081 82.0 noncon
hsa-miR-3144-5p 99-105 -0.271 90.0 -0.271 93.0 noncon
hsa-miR-8070 258-264 -0.268 96.0 -0.268 97.0 noncon
hsa-miR-3622a-5p 925-931 -0.267 97.0 -0.08 84.0 noncon
hsa-miR-8075 967-973 -0.259 92.0 -0.077 68.0 noncon
hsa-miR-605-3p 308-314 -0.257 92.0 -0.257 94.0 noncon
hsa-miR-484 801-807 -0.255 97.0 -0.076 88.0 noncon
hsa-miR-3622b-5p 935-941 -0.254 93.0 -0.076 74.0 noncon
hsa-miR-6891-5p 548-555 -0.253 95.0 -0.076 78.0 noncon
hsa-miR-1233-3p 675-681 -0.25 94.0 -0.075 75.0 noncon