SUPERFAMILY 1.73 HMM library and genome assignments server


RuBisCo, C-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (141)
  Mainly parallel beta sheets (beta-alpha-beta units)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
  contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites
Superfamily:   RuBisCo, C-terminal domain [ 51649]
Families:   RuBisCo, large subunit, C-terminal domain [ 51650]
  N-terminal domain is alpha+beta


InterPro annotation
Cross references IPR000685 SSF51649 Protein matches
Abstract Ribulose bisphosphate carboxylase (RuBisCO) [PubMed6351728, PubMed12221984] catalyzes the initial step in Calvin's reductive pentose phosphate cycle in plants as well as purple and green bacteria. It consists of a large catalytic unit and a small subunit of undetermined function. In plants, the large subunit is coded by the chloroplastic genome while the small subunit is encoded in the nuclear genome. Molecular activation of RuBisCO by CO2 involves the formation of a carbamate with the epsilon-amino group of a conserved lysine residue. This carbamate is stabilized by a magnesium ion. One of the ligands of the magnesium ion is an aspartic acid residue close to the active site lysine [PubMed1969412].

InterPro database

Functional annotation
General category Metabolism
Detailed category Photosynthesis

Function annotation of SCOP domain superfamilies

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Internal database links

The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level. Click on the 'Genome Assignments' icon above to view the genome assignments for this superfamily.


Alignments of sequences to

Alignments of sequences to 12 models in this superfamily are available by clicking on the superfamily level 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequences may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own.


It is possible to browse and view the proteins in the genomes which have different combinations of domains including a RuBisCo, C-terminal domain domain. Click on the 'Domain Combinations' icon.


To view the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom click on the 'TaxViz' icon above. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Undirected domain occurrence networks are available for all superfamilies. Nodes in these networks represent genomes. Connections between nodes represent the presence of domain architectures, which contain the superfamily of interest, in both genomes.

There are 12 hidden Markov models representing the RuBisCo, C-terminal domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be viewed by clicking on the icon above.


Jump to [ Top of page · SCOP classification · InterPro annotation · Functional annotation · Internal database links ]