SUPERFAMILY 1.75 HMM library and genome assignments server

GFP-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   GFP-like [ 54510]
Superfamily:   GFP-like [ 54511] (2)
Families:   Fluorescent proteins [ 54512] (5)
  Domain G2 of nidogen-1 [ 64244]

Superfamily statistics
Genomes (147) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 427 1,076 44
Proteins 422 1,068 44

Functional annotation
General category Metabolism
Detailed category Energy

Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism cellular process 0.004811 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.004653 Least Informative Inherited
Biological Process (BP) biological adhesion 0.000000005522 Informative Direct
Biological Process (BP) cell adhesion 0.0000001433 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.00000001216 Highly Informative Direct
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 0.000000000002297 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell adhesion0.00000001523InformativeDirect
Biological processLuminescence0Highly InformativeDirect
Cellular componentSecreted0.0000005442Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
Cellular componentBasement membrane0.0001376Highly InformativeDirect
Coding sequence diversityAlternative splicing0.0002839Least InformativeDirect
DomainSignal0.00002445Least InformativeDirect
DomainRepeat0.00008137Least InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionCalcium0.000000004451Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Post-translational modificationGlycoprotein0.00004145Least InformativeDirect
Post-translational modificationDisulfide bond0.0001857Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009017 SSF54511 Protein matches

The green fluorescent-like protein family consists of fluorescent proteins and non-fluorescent chromoproteins, derived from several species of Cnidarians, as well as certain diazotrophic bacteria [PubMed11929996, PubMed12502888]. These proteins range in their absorption wavelength maximum, and are often classified by their colour: green, yellow, red and purple-blue. These colour differences arise from changes in the structure of the chromophore, which is generated internally by auto-catalysis. The chromophore comprises Ser65-Tyr66-Gly67 in Aequorea victoria, which forms a five-member ring after its modification. In the bioluminescent organism A. victoria, GFP acts to transform the blue light emitted from aequorin into green light. However, most organisms with GFP-like molecules are not bioluminescent, and in some cases are not even fluorescent. These proteins all display a beta-can structure, which surrounds the chromophore and acts to shield it against quenching agents.

The G2 domain of nidogen contains a beta-can structure that exhibits extraordinary similarity to GFP, even though their sequences show only low sequence identity [PubMed11427896]. Nidogen is a component of basement membranes, whose interactions with other basement membrane proteins contribute to the assembly and function of the basement membrane. The G2 domain serves as a protein-binding module. The structure is similar enough between GFP and the G2 domain of nidogen to suggest a common ancestral origin.

More information about this protein can be found at Protein of the Month: Green Fluorescent Protein.

InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

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 8 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 GFP-like 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 8 hidden Markov models representing the GFP-like 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]