Top Level Name

  ⌊ Superfamily (core) Isoprenoid Synthase Type I

Family known
Total 100% <100% Family unknown
Functional domains 16579 0 79 16500
UniProtKB 57344 0 7506 49838
GI 104001 0 11446 92555
Structures 412
Reactions 0
Functional domains of this superfamily were last updated on March 22, 2017
New functional domains were last added to this superfamily on Aug. 2, 2014

The conserved chemistry of the Isoprenoid Synthase Type I superfamily involves the formation of a carbocation by release of a pyrophosphate group. A common DDXXD sequence motif is used to bind the diphosphate moiety of substrates via Mg2+, facilitating pyrophosphate release. Members share a common fold, termed the terpenoid synthase fold in SCOP. Many characterized enzymes in this superfamily are known to be promiscuous. Note: Some enzymes in this superfamily may also have a domain that is a member of the Isoprenoid Synthase Type II superfamily.

Christianson DW

Structural biology and chemistry of the terpenoid cyclases

▸ Abstract

Chem Rev 2006;106(8):3412-3442 | PubMed ID: 16895335

EFI

Sequence Similarity Networks

Download a Sequence Similarity Network of this superfamily (XGMML format ).

Network downloads are XGMML files that are readable by program such as Cytoscape. In these networks, nodes represent proteins and edges represent pairwise similarities better than a given bitscore cutoff. Additionally, these networks contain several attributes with data from the SFLD.

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Maximum number of edges:
250K 500K 750K ALL
bitscore cutoff

Full sequence similarity network is not available for this superfamily due to its size.
Repnet: 50% ID (1-Apr-2016)

List of files included in the download. A detailed list of included node attributes, their definitions, and their uses [revised: 1/24/2014].

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Although the download speed has improved please keep in mind that network files can be quite large. We are currently working on improving the network download and finding ways to make large networks manageable. Please see How to increase memory for Cytoscape.

Multiple Sequence Alignment

View the alignment of a representative set of sequences of this superfamily using

Multiple Sequence Alignment

Align one or multiple sequences to the alignment of a representative set of sequences of this superfamily.
Enter FASTA formatted sequence(s) : and view results using

Downloads

Data Type All (#) Known (#) Unknown (#)
Full length FASTA (16579) (79) (16500)
Complete annotation (.tsv) (16579) (79) (16500)
Annotation suitable for Excel ® (.tsv) (16579) (79) (16500)
Clear form

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To identify your sequence later, please make sure to provide a header line starting with '>' for each sequence. Empty headers are allowed, but a header line is always required.
Cutoff Value
The maximum bitscore at which pairwise similarities are included in the network.
XGMML format
Open in Cytoscape via:
 Menu
 →Import
 →Network (multiple file types)
Download the annotation of all sequences as shown in the table below as a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application.
Full length FASTA
Full length sequences in FASTA format.
Functional Domain FASTA
Sequences of the Functional Domain in FASTA format.
Complete annotation
Download complete annotation of sequences sets of this superfamily as a ͟Tab ͟Separated ͟Value (TSV) file. This file has all data but cell size can exceed the maximum supported by spreadsheet programs (such as Microsoft Excel ®).
Spreadsheet ready annotation
Annotation of sequences sets of this superfamily in a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application. Cells which exceed the allowed spreadsheet maximum (32.5K) are preceded by the word "Truncated" and clipped short.
Total number of functional domains in this group.
Number of Functional Domains that have been manually or automatically been assigned to a family.
Number of Functional Domains that have not been assigned to a family.
Number of structures available from the PDB for members of this group.
Number of Functional Domains with 100% of Conserved Residues
Number of Functional Domains with less than 100% Conserved Residues
Depth of the multi-level Subgroup hierarchy.