SUPERFAMILY 1.75 HMM library and genome assignments server


RuBisCO, large subunit, small (N-terminal) domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   RuBisCO, large subunit, small (N-terminal) domain [ 54966]
Families:   Ribulose 1,5-bisphosphate carboxylase-oxygenase [ 54967]


Superfamily statistics
Genomes (499) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 748 70,714 27
Proteins 748 70,698 27


Functional annotation
General category Metabolism
Detailed category Photosynthesis

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases1Least InformativeInherited
Enzyme Commission (EC)Carboxy-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.02854Moderately InformativeInherited
Enzyme Commission (EC)Ribulose-bisphosphate carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Interconverting keto- and enol- groups0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxy-lyases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.02565InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processPhotosynthesis0InformativeDirect
Biological processMethionine biosynthesis3.168e-11Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentChloroplast0.0004635InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationMonooxygenase0Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)L-methionine biosynthesis0InformativeDirect
UniPathway (UP)L-methionine biosynthesis via salvage pathway0Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


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


Browse and view proteins in genomes which have different domain combinations including a RuBisCO, large subunit, small (N-terminal) domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 12 hidden Markov models representing the RuBisCO, large subunit, small (N-terminal) domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]