Curator's Entrance

Top Level Name

  ⌊ Superfamily (core) RuBisCO


9RUB (ribulose-1,5-bisphosphate carboxylase)
Family known
Total 100% <100% Family unknown
Functional domains 42603 581 1 42021
UniProtKB 49386 758 0 48628
GI 62817 1960 7 60850
Structures 74
Reactions 0
Functional domains of this superfamily were last updated on June 28, 2017
New functional domains were last added to this superfamily on March 23, 2015

Structurally characterized enzymes in the RuBisCO superfamily are dimers with an active site located at the interface of the N-terminal alpha+beta domain of one polypeptide and the C-terminal TIM beta/alpha-barrel of the second polypeptide. Though most of the enzymes in the superfamily are thought to function as D-Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), a smaller number of enzymes, termed the RuBisCO-like proteins, do not catalyze carboxylation reactions. Despite these differences, superfamily enzymes share a common active site architecture used to stabilize an enolate intermediate.

Imker HJ, Singh J, Warlick BP, Tabita FR, Gerlt JA

Mechanistic Diversity in the RuBisCO Superfamily: A Novel Isomerization Reaction Catalyzed by the RuBisCO-like Protein from Rhodospirillum rubrum

▸ Abstract

Biochemistry 2008;47(43):11171-11173 | PubMed ID: 18826254

Taylor TC, Andersson I

The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate

▸ Abstract

J Mol Biol 1997;265(4):432-444 | PubMed ID: 9034362

No notes.

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.

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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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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.
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Downloads

Data Type All (#) Known (#) Unknown (#)
Full length FASTA (42603) (582) (42021)
Complete annotation (.tsv) (42603) (582) (42021)
Annotation suitable for Excel ® (.tsv) (42603) (582) (42021)
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 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:
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 →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
Subgroup ▸ Legend T K C U S
RuBisCO 25157 0 0 25157 57
RuBisCO-like proteins 1147 582 581 565 12
┗ 2,3-diketo-5-methylthiopentyl-1-phosphate enolase 508 508 507 6
┗ 5-methylthio-D-ribulose 1-phosphate isomerase 74 74 74 1
Depth of the multi-level Subgroup hierarchy.