Summary: Starch synthase catalytic domain
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Starch synthase catalytic domain Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||DUF3492 Glyco_transf_4 Glyco_trans_4_2 Glyco_trans_4_4|
|Similarity to PfamA using HHSearch:||Glyco_transf_4 Glyco_trans_4_2 Glyco_trans_4_4|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013534
This region represents the catalytic domain of glycogen (or starch) synthases that use ADP-glucose (EC), rather than UDP-glucose (EC) as in animals, as the glucose donor. This enzyme is found in bacteria and plants. Whether the name given is glycogen synthase or starch synthase depends on context, and therefore on substrate.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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This is the GT-B clan that contains diverse glycosyltransferases that possess a Rossmann like fold .
The clan contains the following 38 members:ALG11_N Alg14 Asp1 Capsule_synth DUF1205 DUF1972 DUF3492 DUF354 Epimerase_2 Glyco_tran_28_C Glyco_trans_1_2 Glyco_trans_1_3 Glyco_trans_1_4 Glyco_trans_4_2 Glyco_trans_4_3 Glyco_trans_4_4 Glyco_trans_4_5 Glyco_transf_20 Glyco_transf_28 Glyco_transf_4 Glyco_transf_41 Glyco_transf_5 Glyco_transf_56 Glyco_transf_9 Glyco_transf_90 Glycogen_syn Glycos_transf_1 Glycos_transf_N Glyphos_transf LpxB MGDG_synth Mito_fiss_Elm1 Phosphorylase PIGA PS_pyruv_trans SUA5 Sucrose_synth UDPGT
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Seed source:||Pfam-B_148 (Release 17.0)|
|Number in seed:||174|
|Number in full:||2745|
|Average length of the domain:||227.40 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||32.03 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Glyco_transf_5 domain has been found. There are 22 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 seqence.
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