SUPERFAMILY 1.75 HMM library and genome assignments server


Transthyretin (synonym: prealbumin) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Prealbumin-like [ 49451] (7)
Superfamily:   Transthyretin (synonym: prealbumin) [ 49472]
Families:   Transthyretin (synonym: prealbumin) [ 49473]


Superfamily statistics
Genomes (1,045) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,339 6,947 27
Proteins 1,333 6,941 27


Functional annotation
General category General
Detailed category General

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular component organization or biogenesis0.003750.02117Least InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0027130.0002493Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.010830.002026Moderately InformativeInherited
Biological Process (BP)protein oligomerization0.023080.009191InformativeInherited
Biological Process (BP)protein homooligomerization5.312e-077.22e-09Highly InformativeDirect
Biological Process (BP)protein tetramerization1.914e-073.218e-10Highly InformativeDirect
Molecular Function (MF)binding0.0022520.02632Least InformativeInherited
Molecular Function (MF)hormone binding3.505e-127.215e-13Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular component organization or biogenesis 0.02117 Least Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.0002493 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.002026 Moderately Informative Inherited
Biological Process (BP) protein oligomerization 0.009191 Informative Inherited
Biological Process (BP) protein homooligomerization 7.22e-09 Highly Informative Direct
Biological Process (BP) protein tetramerization 3.218e-10 Highly Informative Direct
Molecular Function (MF) binding 0.02632 Least Informative Inherited
Molecular Function (MF) hormone binding 7.215e-13 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)In cyclic amides0InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)In cyclic amides0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1.865e-09Least InformativeDirect
Biological processPurine metabolism0Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentPeriplasm6.751e-07InformativeDirect
DomainSignal0Least InformativeDirect
Post-translational modificationHydrolase1.348e-06Least InformativeDirect
Post-translational modificationHormone0Highly InformativeDirect
Post-translational modificationGlycoprotein0.0002103Least InformativeDirect
Post-translational modificationGamma-carboxyglutamic acid0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)nitrogen metabolism0Moderately InformativeDirect
UniPathway (UP)purine metabolism0Moderately InformativeDirect
UniPathway (UP)purine base metabolism0InformativeDirect
UniPathway (UP)ureide metabolism0InformativeDirect
UniPathway (UP)purine degradation0InformativeDirect
UniPathway (UP)urate degradation0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR000895 SSF49472 Protein matches
Abstract

Transthyretin (formerly prealbumin) is one of 3 thyroid hormone-binding proteins found in the blood of vertebrates [PubMed1833190]. It is produced in the liver and circulates in the bloodstream, where it binds retinol and thyroxine (T4) [PubMed4054629]. It differs from the other 2 hormone-binding proteins (T4-binding globulin and albumin) in 3 distinct ways: (1) the gene is expressed at a high rate in the brain choroid plexus; (2) it is enriched in cerebrospinal fluid; and (3) no genetically caused absence has been observed, suggesting an essential role in brain function, distinct from that played in the bloodstream [PubMed1833190]. The protein consists of around 130 amino acids, which assemble as a homotetramer that contains an internal channel in which T4 is bound. Within this complex, T4 appears to be transported across the blood-brain barrier, where, in the choroid plexus, the hormone stimulates further synthesis of transthyretin. The protein then diffuses back into the bloodstream, where it binds T4 for transport back to the brain [PubMed1833190].


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-quality) · Gene Ontology (high-coverage) · 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 4 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 Transthyretin (synonym: prealbumin) 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 4 hidden Markov models representing the Transthyretin (synonym: prealbumin) 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]