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The AAA Protein Superfamily
Aldehyde dehydrogenase (ALDH)
Amyloid Precursor Protein
The CBS domain web page
Cholinesterases
The Chaperonin Home Page
Chromatin Structure & Function Page
Chromo shadow domain
CySPID -- The Cytoskeletal Protein Interactions Database
Cytochrome P450 family
Cytokines
Dictionary of Cytokines
Cytokines
The International Cytokine Society
Cytokine Family cDNA Database (dbCFC)
Cytokines Online Pathfinder Encyclopaedia (COPE)
The DExH/D protein family database
DNA repair
EF-Hand Calcium-Binding Proteins
Eph Receptor Tyrosine Kinases & Their Ligands
ESTHER - ESTerases and alpha/beta Hydrolase Enzymes and Relatives
Gene Family Database
G protein-coupled receptor database (GCRDb)
Globin Gene Server
Glucoamylases
Glycosyltransferases
GnRH Family
Histone, Histone Sequence Database
Homeobox
HOX DataBase
HOX Pro database
HSP100 Alignments
The Integrin Page
InBase, The New England Biolabs Intein Database
Ion Channel Network
Ion Channel Resources
Insulin gene family
Inteins - protein introns
The Kinesin Home Page
Kinesins
MADS-box Gene
MEROPS - The Peptidase Database
Metallothionein
MutS Protein Family
PAX family
Pentapeptide repeat
PHD-finger
PROMISE - The Prosthetic groups and Metal Ions in Protein Active Sites Database
Protein Kinase Database Project
The RecA Protein Family Web Site
The Ribonuclease P Database
SAND domain
SANT domain
SNF2 family of proteins
The Thyroid Hormone Receptor Resource
Topoisomerases
Transposases
Wnt and Frizzled gene Homepage
The AAA Protein Superfamily
The AAA (for ATPases Associated with various cellular Activities) protein
superfamily is characterized by a highly conserved module of approximately
230 amino acid residues including an ATP binding consensus, present in one
or two copies in the AAA proteins. AAA proteins are found in all organisms
(Archaea, Eubacteria, Eukaryota: Protista, Fungi, Plants, Animals) and are
essential for, e.g., cell cycle functions, vesicular transport,
mitochondrial functions, peroxisome assembly, and proteolysis.
Aldehyde dehydrogenase (ALDH)
Aldehyde dehydrogenase (ALDH), often in tandem with Alchohol
dehydrogenase, acts in detoxifying a wide variety of organic compounds,
toxins and pollutants. Defects in ALDH leads to Sjogren-Larsson
syndrome in humans.
Amyloid Precursor Protein
The amyloidogenic glycoprotein family consists of the amyloid precursor
protein (APP) and two other APP-like proteins of unknown function,
APPLP1 and APPLP2. Two of the major protein products of the APP gene,
arising from alternative splicing (APP751 and APP770), contain a domain
that is homologous to the Kunitz class of serine protease inhibitors.
The CBS domain web page
The CBS domain is widespread: found in all species. The CBS domain is named after
Cystathionine Beta Synthase. All CBS domains identified to date occur in the cytoplasm
or nucleus. The domain is about 60 residues long, and usually found in two or four copies per
protein.
Cholinesterases
Information on cholinesterases.
The Chaperonin Home Page
The Chaperonin Home Page is designed to be a repository for
information about the important class of heat shock proteins known
as chaperonins. It includes the GroEL/GroES mutation databases.
Chromatin Structure & Function Page
This site is intended to disseminate information regarding the rapidly
evolving and highly exciting field of chromatin structure, proteins that
modify chromatin structure, and the effects that these modifications have
on cell function.
Chromo shadow domain
The chromo domain was originally identified as a protein sequence motif
common to the Drosophila chromatin proteins, Polycomb (Pc) and
Heterochromatin protein 1 (HP1).
CySPID -- The Cytoskeletal Protein Interactions Database
CySPID is a database that holds properties and relationships among
cytoskeletal proteins and other entities in the database, such as
protein classes, genes, or macromolecular complexes.
Cytochrome P450 family
The family referred here to as FAD-dependent pyridine nucleotide reductases (FADPNR) includes FAD
flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione
reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase,
alkyl hydroperoxide reductase), iron-sulphur protein reductases involved in oxidative metabolism of a
variety of hydrocarbons.
Cytokines
This provides information about cytokines and their
receptors including topological, evolutionary and mechanistic
relationships between the molecules, and illustrations of known
three-dimensional structures.
Dictionary of Cytokines
A dictionary of cytokine alternative names, elated factors, signal transducers etc.
Links to other Cytokine-related sites.
Cytokines
This is a useful site for anyone interested in cytokines, adhesion molecules, growth factors and related agents.
The International Cytokine Society
Cytokine Family cDNA Database (dbCFC)
The Cytokine Family cDNA Database (dbCFC) is a collection of EST (Expressed Sequence
Tag) records of cytokines deposited in the NCBI GenBank. It provides information about
the identification of EST records to cytokine members and related data contained in other
databases including GenBank, dbEST, GDB, Online Mendelian Inheritance in Man (OMIM),
The Transgenic/Targeted Mutation Database (TBASE), Unique Human Gene Sequence
Collection (UniGene), Anatomical Expression Database of Human Genes (BodyMap), Mouse
Genome Database (MGD) and Human/Mouse Homology Relationships.
Cytokines Online Pathfinder Encyclopaedia (COPE)
COPE consists of 6000 WWW pages hypertexted with 43000 links and 14000
references and covers all aspects of Cytokine research.
The DExH/D protein family database
This is a database covering the putative RNA helicases of the DEAD,
DEAH, and DExH proteins.
DExH/D proteins are essential in all aspects of the RNA metabolism in the cell: they play important roles in
DNA repair
The maintenance of genetic stability is an essential task for all
organisms, ensuring the proper function of cellular systems and the
passage of information to the next generation. Two distinct pathways of
DNA repair exist whose roles are delineated by the type of DNA lesion
that they recognize and repair. Initial work in the bacterial and yeast
systems has laid the foundation for identifying the genes of these
pathways in mammals.
EF-Hand Calcium-Binding Proteins
The EF-Hand Calcium-Binding Proteins Data Library is a growing collection of published
sequence, structural, functional, and other information about EF-hand calcium-binding
proteins and their roles in cellular signal transduction.
Eph Receptor Tyrosine Kinases & Their Ligands
This is a database for the Eph family of receptor protein
tyrosine kinases and their ligands, the ephrins. Much excitement
regarding this new family results from their roles in developmental
neurobiology as molecular guides for axons. However, they may be
involved in many other processes; cancer, angiogenesis,
haematopoiesis, and kidney development. The expression patterns of
members in this family suggest that their functions during
development and in the adult organism is still relatively unknown.
ESTHER - ESTerases and alpha/beta Hydrolase Enzymes and Relatives
ESTHER (for esterases, [alpha]/[beta] hydrolase enzymes and relatives)
is a database aimed at collecting in one information system, sequence
data together with biological annotations and experimental biochemical
results related to the structure-function analysis of the enzymes of the
family.
FYVE finger
The FYVE finger is a novel zinc finger-like domain found in several
proteins involved in membrane trafficing. The basic motif consists of 8
Cysteins, 4 of which are part of the core motif R+HHC+XCG (where '+' is
a positively charged residue and 'X' is any aminoacid). This finger has
only been observed as a single copy in each of the proteins and it has
been shown to bind 2 zinc ions per finger.
Gene Family Database
A prototype database of gene families in the human and mouse that
contains both community contributed information and hypertext links to
various biological databases.
G protein-coupled receptor database (GCRDb)
GCRDb was started in 1989 to
keep track of all new sequence data of this biologically important class
of proteins. The systematic collection of these data has been a large
undertaking which has been aided by Amos Bairoich, Gert Vriend, Kevin
Lynch and others.
Globin Gene Server
This provides access to sequence alignments and experimental results for
the beta-like globin gene cluster of mammals
Glucoamylases
Glucoamylase (also known as amyloglucosidase) is an important industrial
enzyme used in saccharification steps in both in Starch Enzymatic
Conversion and in Alcohol Production.
Glycosyltransferases
This guide lists, and gives WWW links to sequence databases for:
1. Cloned eukaryotic glycosyltransferases involved in the biosynthesis of glycoproteins, glycolipids, glycosylphosphatidylinositols and other complex glycoconjugates (together with journal references)
2. Cloned prokaryotic glycosyltransferases involved in lipopolysaccharide biosynthesis
3. Cloned glucuronyltransferases and some yeast chitin synthases (Swissprot links only)
However, this guide does not cover glycosyltransferases involved in the metabolism of sucrose, trehalose, glucan or many other polysaccharides, nor does it list the many expressed sequence tags (ESTs) or predicted Caenorhabditis elegans glycosyltransferase sequences.
GnRH Family
The vertebrate gonadotropin-releasing hormone (GnRH) is a decapeptide
involved in regulating reproduction. The release of GnRH from the
hypothalamus regulates the production of gonadotropins in the pituitary
and these gonadotropins are responsible for gonadal development and
growth in vertebrates.
In addition to the hypothalamic GnRH (also called GnRH1 or GnRH-I), many vertebrate species have been found to express other GnRH forms. These include a midbrain GnRH (called GnRH-II or GnRH2) and a telencephalic GnRH (called GnRH-III or GnRH3). The function of these non-hypothalamic forms remains unclear.
Histone, Histone Sequence Database
Database of aligned histone protein sequences.
Also contains sequences of proteins identified as
containing the histone fold motif.
Structures of all known histone and histone fold
proteins.
Information included regarding discrepancies between similar sequence entries in different source databases. Multiple sequence alignments for each histone.
Homeobox
Information relevant to homeobox genes (in particular about
classification/evolution).
HOX DataBase
Contains description of homeotic Hox genes and features of
encoding HD-proteins that are sequence-specific transcription
factors, part of a developmental regulatory system
HOX Pro database
The HOX-Pro is aimed at
HSP100 Alignments
Information on the HSP100 proteins.
The Integrin Page
Integrins are receptor proteins which are of crucial importance. They
are the main way that cells both bind to and respond to the
extracellular matrix.
InBase, The New England Biolabs Intein Database
Protein splicing is defined as the excision of an intervening protein sequence (the INTEIN)
from a protein precursor and the concomitant ligation of the flanking protein fragments
(the EXTEINS) to form a mature extein protein and the free intein (Perler 1994). Protein
splicing results in a native peptide bond between the ligated exteins (Cooper 1993). Extein
ligation differentiates protein splicing from other forms of autoproteolysis. Inteins are
named with a 3 letter genus/species designation followed by the extein gene name. If more
than 1 intein is present in an extein gene, the inteins are given a numerical suffix.
Ion Channel Network
The Ion Channel Network (ICN) is a pilot WWW site aimed at making distributed
information about ion channel molecules more 'accessible' and 'systematic' in
coverage.
Ion Channel Resources
Resources for ion channel research
Insulin gene family
The insulin gene family is an ancient and highly diverse group that
includes insulin, insulin-like growth factor I (IGF I ), ( IGF II ), and
relaxin , from a wide variety of vertebrate species, and a number of
related peptides in the invertebrates, such as insect
prothoracicotrophic hormone ( PTTH ) and molluscan insulin-related
peptides ( MIP I and MIP II ).
Inteins - protein introns
Inteins are proteins inserted in-frame and translated together with their host proteins. The
precursor protein then undergoes protein splicing resulting in two products: the host protein
and the intein. This reaction is autoproteolytic.
This site mainly focuses on intein sequence motifs and evolution.
The Kinesin Home Page
Kinesin is a mechanochemical protein capable of utilizing chemical energy from ATP
hydrolysis to generate mechanical force. In the presence of ATP, kinesin can bind to and
move on microtubules. The ability to translocate along the microtubule
lattice has led to the classification of kinesin as a microtubule motor protein. Kinesin is
unrelated in sequence to the other known class of microtubule motor proteins, the dyneins,
and is thought to perform functions in the cell distinct from the dyneins.
Kinesins
Information on the kinesin protein family.
Labial Homeobox
The homeodomain sequences and references of over 40 putative labial
genes among metazoan organisms, as well as several hexapeptide
sequences, are presented in alignments.
MADS-box Gene
The MADS box is a highly conserved sequence motif found in a family of
transcription factors. The conserved domain was recognized after the
first four members of the family, which were MCM1, AGAMOUS, DEFICIENS
and SRF (serum response factor). The name MADS was constructed form the
"initials" of these four "founders".
MEROPS - The Peptidase Database
This database employs a structure-based classification of peptidases by
clan, and family. Each peptidase is given a unique MEROPS identifier.
Links give access to database entries for the enzymology, protein and
nucleic acid sequences, tertiary structures, genetics and more.
Metallothionein
Metallothioneins (MTs) are ubiquitous low molecular weight proteins and polypeptides of
extremely high metal and sulfur content. They are thought to play roles both in the
intracellular fixation of the essential trace elements zinc and copper, in controlling the
concentrations of the free ions of these elements, in regulating their flow to their cellular
destinations, in neutralising the harmful influences of exposure to toxic elements such as
cadmium and mercury and in the protection from of a variety of stress conditions.
MutS Protein Family
The ability of many species to repair mismatches in double-stranded DNA
has been well documented. The first critical step in this process is
the recognition of the mismatched DNA. In the major mismatch repair
pathway in Escherichia coli, this is accomplished by the MutS protein.
The Nuclear Receptor Resource
The Nuclear Receptor Resource (NRR) Project is a collection of individual databases on members of the
steroid and thyroid hormone receptor superfamily. Although the databases are located on different
servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the
separate databases and allows an interactive forum for the dissemination of information about the
superfamily.
Olfactory Receptor DataBase
ORDB is a database of sequences of olfactory receptor proteins. It contains
public and private sections which provide tools for investigators to analyze
the functions of this very large gene family of G protein-coupled receptors.
It also provides links to a local cluster of databases of related information,
and to other relevant databases worldwide.
PAX family
Members of the mammalian PAX (paired box) family of genes were initially identified due to
sequence homology to the Drosophila segmentation genes paired and gooseberry (Burri et
al, 1989). Currently, nine members of this family have been identified in the human
(designated PAX1 through PAX9). PAX genes have also been identified in mouse and zebrafish,
where they are expressed in a tissue specific manner and appear to play a role in embryonic
development. The PAX family is characterized by the presence of paired box domains. Some
members of the family (PAX3, PAX4, PAX6, PAX7) also contain a functional homeobox
domain.
Pentapeptide repeat
The pentapeptide repeat is found in several bacterial proteins of
uncertain function [1]. Pentapeptide repeat proteins contain a striking
repeat of five residues which can be clearly seen in self dot-plots.
The repeat can be approximately described as A(D/N)LXX, where X can be
any amino acid. This family is found to have many members in the
bacterial genome of the cyanobacterium Synechocystis sp.
PHD-finger
PHD-finger, a zinc finger-like motif , occurs in a set of proteins that
includes members of the Drosophila Polycomb and trithorax group genes.
These genes regulate the expression of the homeotic genes through a
mechanism thought to involve some aspect of chromatin structure.
PROMISE - The Prosthetic groups and Metal Ions in Protein Active Sites Database
The PROMISE (Prosthetic centres and metal ions in protein active sites) database aims to
gather together comprehensive sequence, structural, functional and bibliographic
information on proteins which possess prosthetic centres, with an emphasis on active site
structure and function.
Protein Kinase Database Project
The Protein Kinase Database Project at SDSC aims to create a system that
is narrowly focused on kinases, phosphatases, and related molecules. It
will integrate structural, genetic, and molecular biological data.
The RecA Protein Family Web Site
The RecA protein is involved in at least three distinct biological processes in E.
coli:
The Ribonuclease P Database
The RNase P Database is a compilation of RNase P sequences, sequence alignments,
secondary structures, three-dimensional models, and accessory information. The database
primarily contains information on the bacterial and archaeal enzymes, focusing on the RNA
subunit. Some information is also included on the eucaryal and organellar RNase P RNAs.
SAND domain
The SAND domain adds to the burgeoning set of domains present in modular
chromatin-associated proteins. The functions of most of these domains
are not at all well understood, and gaining a better understanding will
be one key to understanding how chromatin is assembled and regulated.
The SAND domain appears in various nuclear contexts. Sp100/Sp140 are
found in recently described nuclear bodies or dots, discrete structures
within the nucleus that do not yet have known functions.
SANT domain
SANT domains are a epeated motif in N-CoR, the nuclear receptor
co-repressor.
SNF2 family of proteins
The SNF2 family of proteins is defined by the presence of a conserved set of
amino-acid motifs which together are called the SNF2 domain.
The Thyroid Hormone Receptor Resource
The TRR provides a variety of information on TRs as well as
more general information shared with other NHRR sites.
Topoisomerases
Topoisomerase enzymes (topo) are critical to normal function of any living
cell. They adjust DNA winding (topology) by making temporary cuts in the DNA for
transcription and replication.
Transposases
The Mutator transposable element system of maize is one of the most
active transposable element systems known in plants. The autonomous
element of this system, MUDRA, encodes two proteins MUDRB.
Wnt and Frizzled gene Homepage
Wnt proteins are now recognized as one of the major families of
developmentally important signaling molecules, with mutations in Wnt
genes displaying remarkable phenotypes in the mouse, Caenorhabditis
elegans, and Drosophila. Among functions provided by Wnt proteins are such intriguing
processes as embryonic induction, the generation of cell polarity, and the specification of
cell fate.
Any Comments, Questions? Support@hgmp.mrc.ac.uk
