Top Level Name

  ⌊ Superfamily (core) Isoprenoid Synthase Type II

Family known
Total 100% <100% Family unknown
Functional domains 7645 0 0 7645
UniProtKB 9691 566 188 8937
GI 20452 1723 497 18232
Structures 227
Reactions 0
Functional domains of this superfamily were last updated on June 20, 2017
New functional domains were last added to this superfamily on June 20, 2017

The conserved chemistry of the Isoprenoid Synthase Class II superfamily involves the formation of a carbocation by protonating an epoxide or olefin. Members share a common fold, termed the alpha/alpha toroid fold in SCOP. Many characterized enzymes in this superfamily are known to be promiscuous. Note: Some enzymes may consist of two domains, where both domains are superfamily members. Additionally, some enzymes may have multiple domains where one or more are members of this superfamily and an additional domain is a member of the Isoprenoid Synthase Class I superfamily.

Christianson DW

Structural biology and chemistry of the terpenoid cyclases

▸ Abstract

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

Oldfield E, Lin FY

Terpene biosynthesis: modularity rules

▸ Abstract

Angew Chem Int Ed Engl 2012;51(5):1124-1137 | PubMed ID: 22105807

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 edge-score cutoff. The edge score is either a bit score for full networks or mean E values for a Repnet. Additionally, these networks contain several attributes with data from the SFLD.

No edge data is available for this network. Contact an SFLD curator to request this network.

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

Disclaimer
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.

Downloads

Data Type All (#) Known (#) Unknown (#)
Full length FASTA (7645) (0) (7645)
Complete annotation (.tsv) (7645) (0) (7645)
Annotation suitable for Excel ® (.tsv) (7645) (0) (7645)
Clear form

Some of these files can be quite large, please be patient during the download.

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 least significant edge-score at which pairwise similarities are included in the network. A bit score for the full network, or a mean E value for the Repnet.
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.