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 457 1,076 44
Proteins 450 1,068 44


Functional annotation
General category Metabolism
Detailed category Energy

Document:
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 0.004727 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.004492 Least Informative Inherited
Biological Process (BP) biological adhesion 5.509e-09 Informative Direct
Biological Process (BP) cell adhesion 1.48e-07 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 1.227e-08 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 1.788e-12 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 adhesion1.511e-08InformativeDirect
Biological processLuminescence0Highly InformativeDirect
Cellular componentSecreted5.443e-07Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
Cellular componentBasement membrane0.0001374Highly InformativeDirect
Coding sequence diversityAlternative splicing0.0002295Least InformativeDirect
DomainSignal2.444e-05Least InformativeDirect
DomainRepeat8.041e-05Least InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionCalcium4.098e-09Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Post-translational modificationGlycoprotein4.069e-05Least InformativeDirect
Post-translational modificationDisulfide bond0.000186Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009017 SSF54511 Protein matches
Abstract

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 ]