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138  structures 8160  species 0  interactions 32379  sequences 203  architectures

Family: GDP_Man_Dehyd (PF16363)

Summary: GDP-mannose 4,6 dehydratase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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GDP-mannose 4,6 dehydratase Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016040

This entry represents NAD- and NADP-binding domains with a core Rossmann-type fold, which consists of 3-layers alpha/beta/alpha, where the six beta strands are parallel in the order 321456. Many different enzymes contain an NAD/NADP-binding domain, including:

  • C-terminal domain of alcohol dehydrogenases [ PUBMED:15449945 ]
  • Tyrosine-dependent oxidoreductases (also known as short-chain dehydrogenases) [ PUBMED:9174344 ]
  • N-terminal domain of glyceraldehyde-3-phosphate dehydrogenase [ PUBMED:10448043 ]
  • NAD-binding domain of formate/glycerate dehydrogenases [ PUBMED:8114093 ]
  • N-terminal domain of sirohaem synthase [ PUBMED:14595395 ]
  • N-terminal domain of lactate dehydrogenase [ PUBMED:11276087 ]
  • N-terminal domain of 6-phosphogluconate dehydrogenase (the beta-sheet is extended to 8 strands) [ PUBMED:17222187 ]
  • C-terminal domain of amino acid dehydrogenases (an extra N-terminal helix displaces the C-terminal helix [ PUBMED:8591026 ]
  • NAD-binding domain of certain potassium channels [ PUBMED:11301020 ]
  • C-terminal domain of the transcriptional repressor Rex [ PUBMED:15642260 ]
  • Ornithine cyclodeaminase [ PUBMED:15518536 ]
  • CoA-binding N-terminal domain of the alpha chain of succinyl-CoA synthetase [ PUBMED:9917402 ]

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 206 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_ExoN CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1442 DUF1611_N DUF166 DUF1776 DUF2431 DUF268 DUF2855 DUF3410 DUF364 DUF43 DUF5129 DUF5130 DUF6094 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ fvmX7 G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecG GMC_oxred_N Gp_dh_N GRAS GRDA HcgC HI0933_like HIM1 IlvN ISPD_C K_oxygenase KR LCM Ldh_1_N LpxI_N Lycopene_cycl Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MOLO1 Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall Orbi_VP4 PALP PARP_regulatory PCMT PDH PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(223)
Full
(32379)
Representative proteomes UniProt
(142795)
RP15
(4887)
RP35
(16002)
RP55
(31391)
RP75
(51299)
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HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(223)
Full
(32379)
Representative proteomes UniProt
(142795)
RP15
(4887)
RP35
(16002)
RP55
(31391)
RP75
(51299)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(223)
Full
(32379)
Representative proteomes UniProt
(142795)
RP15
(4887)
RP35
(16002)
RP55
(31391)
RP75
(51299)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:O60547
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Eberhardt R
Number in seed: 223
Number in full: 32379
Average length of the domain: 298.30 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 85.42 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 332
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Selections

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the GDP_Man_Dehyd domain has been found. There are 138 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096QI23 View 3D Structure Click here
A0A0G2JZS4 View 3D Structure Click here
A0A0P0W9S9 View 3D Structure Click here
A0A0P0WJ20 View 3D Structure Click here
A0A0P0XAB6 View 3D Structure Click here
A0A0R0ERF2 View 3D Structure Click here
A0A0R0F370 View 3D Structure Click here
A0A0R0FH68 View 3D Structure Click here
A0A0R0FQT4 View 3D Structure Click here
A0A0R0H5T1 View 3D Structure Click here
A0A0R0IPL8 View 3D Structure Click here
A0A0R0JEC6 View 3D Structure Click here
A0A0R0KMW5 View 3D Structure Click here
A0A1D6GEP1 View 3D Structure Click here
A0A1D6GTV7 View 3D Structure Click here
A0A1D6HHQ0 View 3D Structure Click here
A0A1D6I244 View 3D Structure Click here
A0A1D6I245 View 3D Structure Click here
A0A1D6I688 View 3D Structure Click here
A0A1D6JEI4 View 3D Structure Click here
A0A1D6K005 View 3D Structure Click here
A0A1D6K005 View 3D Structure Click here
A0A1D6KLI4 View 3D Structure Click here
A0A1D6L333 View 3D Structure Click here
A0A1D6L6K8 View 3D Structure Click here
A0A1D6LKP7 View 3D Structure Click here
A0A1D6LWB6 View 3D Structure Click here
A0A1D6M0H1 View 3D Structure Click here
A0A1D6M1Z5 View 3D Structure Click here
A0A1D6M3H2 View 3D Structure Click here
A0A1D6M5K4 View 3D Structure Click here
A0A1D6MS17 View 3D Structure Click here
A0A1D6MS17 View 3D Structure Click here
A0A1D6N7M5 View 3D Structure Click here
A0A1D6N7M5 View 3D Structure Click here
A0A1D6PCE2 View 3D Structure Click here
A0A1D6PCE2 View 3D Structure Click here
A0A1D8PCN0 View 3D Structure Click here
A0A1X7YIP9 View 3D Structure Click here
A0A368UHG2 View 3D Structure Click here
A0A368UIG2 View 3D Structure Click here
A0A368UIG2 View 3D Structure Click here
A4I2F0 View 3D Structure Click here
B4FAG0 View 3D Structure Click here
B4FF24 View 3D Structure Click here
B4FU63 View 3D Structure Click here
B4FYI0 View 3D Structure Click here
B6TQ45 View 3D Structure Click here
B6U0P4 View 3D Structure Click here
B7EIS5 View 3D Structure Click here
B7ZXP4 View 3D Structure Click here
C0HI30 View 3D Structure Click here
C0PN92 View 3D Structure Click here
C6T9D7 View 3D Structure Click here
C6THA9 View 3D Structure Click here
C6THZ0 View 3D Structure Click here
C6TKZ2 View 3D Structure Click here
F1Q5H4 View 3D Structure Click here
F1QPT3 View 3D Structure Click here
G5EF65 View 3D Structure Click here
I1J8M6 View 3D Structure Click here
I1JAE3 View 3D Structure Click here
I1JGU4 View 3D Structure Click here
I1K4B8 View 3D Structure Click here
I1K694 View 3D Structure Click here
I1KP71 View 3D Structure Click here
I1KTG8 View 3D Structure Click here
I1KY24 View 3D Structure Click here
I1L0L0 View 3D Structure Click here
I1L5R8 View 3D Structure Click here
I1L7V1 View 3D Structure Click here
I1L8M8 View 3D Structure Click here
I1LG74 View 3D Structure Click here
I1LI05 View 3D Structure Click here
I1LK43 View 3D Structure Click here
I1LQS4 View 3D Structure Click here
I1LVA7 View 3D Structure Click here
I1LYW8 View 3D Structure Click here
I1M2V7 View 3D Structure Click here
I1M4U9 View 3D Structure Click here
I1M9T9 View 3D Structure Click here
I1MI49 View 3D Structure Click here
I1MSX9 View 3D Structure Click here
K7L6B6 View 3D Structure Click here
K7MB71 View 3D Structure Click here
K7MR59 View 3D Structure Click here
K7MS59 View 3D Structure Click here
K7VJC9 View 3D Structure Click here
K7W6W9 View 3D Structure Click here
O45583 View 3D Structure Click here
O53634 View 3D Structure Click here
O60547 View 3D Structure Click here
O64749 View 3D Structure Click here
O95455 View 3D Structure Click here
P04397 View 3D Structure Click here
P0AC88 View 3D Structure Click here
P18645 View 3D Structure Click here
P71790 View 3D Structure Click here
P72050 View 3D Structure Click here
P93031 View 3D Structure Click here
P9WN65 View 3D Structure Click here
P9WN67 View 3D Structure Click here
Q10N92 View 3D Structure Click here
Q14376 View 3D Structure Click here
Q17556 View 3D Structure Click here
Q1ZXF7 View 3D Structure Click here
Q20697 View 3D Structure Click here
Q3MHS7 View 3D Structure Click here
Q42605 View 3D Structure Click here
Q4CM81 View 3D Structure Click here
Q4CNX9 View 3D Structure Click here
Q4CP59 View 3D Structure Click here
Q4CVL0 View 3D Structure Click here
Q4CVN3 View 3D Structure Click here
Q4CYB9 View 3D Structure Click here
Q4D941 View 3D Structure Click here
Q4DN47 View 3D Structure Click here
Q4DQ62 View 3D Structure Click here
Q4DUZ8 View 3D Structure Click here
Q4E0S3 View 3D Structure Click here
Q54WS6 View 3D Structure Click here
Q553X7 View 3D Structure Click here
Q564Q1 View 3D Structure Click here
Q59VY4 View 3D Structure Click here
Q5PQX0 View 3D Structure Click here
Q5QMG5 View 3D Structure Click here
Q5VPH2 View 3D Structure Click here
Q652A8 View 3D Structure Click here
Q6GMI9 View 3D Structure Click here
Q6I683 View 3D Structure Click here
Q6K2E1 View 3D Structure Click here
Q6ZDJ7 View 3D Structure Click here
Q75PK7 View 3D Structure Click here
Q79FN0 View 3D Structure Click here
Q8H0B2 View 3D Structure Click here
Q8H0B6 View 3D Structure Click here
Q8H930 View 3D Structure Click here
Q8IAX4 View 3D Structure Click here
Q8K0C9 View 3D Structure Click here
Q8LDN8 View 3D Structure Click here
Q8LNZ3 View 3D Structure Click here
Q8NBZ7 View 3D Structure Click here
Q8R059 View 3D Structure Click here
Q8S8T4 View 3D Structure Click here
Q8VDR7 View 3D Structure Click here
Q8VZC0 View 3D Structure Click here
Q8W3J0 View 3D Structure Click here
Q91XL3 View 3D Structure Click here
Q95XM5 View 3D Structure Click here
Q9C7W7 View 3D Structure Click here
Q9FI17 View 3D Structure Click here
Q9FIE8 View 3D Structure Click here
Q9HDU3 View 3D Structure Click here
Q9HDU4 View 3D Structure Click here
Q9LH76 View 3D Structure Click here
Q9LIS3 View 3D Structure Click here
Q9LPG6 View 3D Structure Click here
Q9LZI2 View 3D Structure Click here
Q9M0B6 View 3D Structure Click here
Q9SA77 View 3D Structure Click here
Q9SN58 View 3D Structure Click here
Q9SN95 View 3D Structure Click here
Q9SNY3 View 3D Structure Click here
Q9SUN3 View 3D Structure Click here
Q9SYM5 View 3D Structure Click here
Q9T0A7 View 3D Structure Click here
Q9VSE8 View 3D Structure Click here
Q9W0P5 View 3D Structure Click here
Q9Y7X5 View 3D Structure Click here
Q9ZV36 View 3D Structure Click here