part_of
is_annotation
is_attribute
is_name
multiple_sequence_alignment
msa
A representation of a set of sequences, in which structurally or functionally equivalent residues are aligned together. The rows of the multiple alignment represent the different sequences, while the columns represent equivalent residues. Insertions/deletions in the sequences are represented by one or more gap characters.
structural_location
The location of the residue in the 3D structure.
residue_function
Function of the residue, such as catalysis, binding or post-translational modification. A residue may exhibit zero, one or more activities.
column_conservation_level
The level of conservation associated with a given column. This may be specified by either a qualitative score or a quantitative score.
conserved_residue_list
A user specified list of conserved residues.
biological_process
GeneOntology interface
cellular_component
molecular_function
conserved_small_residue
A conserved small residue e.g. PAGST
conserved_negatively_charged_residue
A conserved negatively charged residue e.g. DE
conserved_hydrophobic_residue
A conserved hydrophobic residue e.g. ACFGLIMVWY
conserved_hydrophilic_residue
A conserved hydrophilic residue e.g. DEHKNQRST
quantitative_conservation_level
A quantitative score for the conservation associated with a given column.
qualitative_conservation_level
A qualitative description of the level of conservation associated with a given column.
low_conservation
A low level of conservation associated with a given column.
medium_conservation
A medium level of conservation associated with a given column.
high_conservation
A high level of conservation associated with a given column.
catalytic_site
A residue that is directly involved in some aspect of the reaction catalysed by the enzyme.
domain
A discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function. [NCBI Bioinformatics] A region of a proteins amino acid sequence that has evolutionary, structural, or functional significance. The amino acid sequence of a domain determines a proteins 3D structure. [CHI Structural proteomics report]
post translational modification
A sequence modification that occurs after synthesis of the protein on the ribosome. e.g. cleavage (thus eliminating signal sequences, transit or pro- peptides and initiator methionines) or addition of simple chemical groups or more complex molecules, such as sugars and lipids. (Human Proteomics Initiative) http://www.expasy.ch/sprot/hpi/ n
ptm
psi_mutation
PSI interface
msa_construction_method
The method used to construct the multiple sequence alignment.
surface_accessibility
Surface area accessible to solvent
N_terminal
A residue in a protein chain that has a free amino group.
amino_terminus
C_terminal
A residue in a protein chain that has a free carboxyl group.
carboxyl_terminus
in_domain
A residue in a domain i.e. in a discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function. [NCBI Bioinformatics]
in_hinge_region
A residue in a hinge region i.e. a flexible region of the protein between two globular domains.
in_transmembrane_region
A residue in a transmembrane region i.e. in a domain in a amphipathic membrane protein where the hydrophobic regions traverse the lipid bilayers of the membranes, while the hydrophilic regions extend on either side of the membrane and interact with water.[Folding@home glossary, Stanford Univ].
in_helix
A residue in a helical portion of a protein structure i.e. in a frequently highly stable protein chain conformation stabilised by hydrogen bonding between peptide groups and having side chains projecting outwards in a spiral (3.6 residues per turn). [The Biochemical Society Glossary].
in_strand
in_beta_strand
A residue in a beta_strand i.e. a stable "zig-zag" conformation of protein chain which can align with sections of chain in same conformation and cross-link efficiently via hydrogen bonds between the peptide linkages. [The Biochemical Society Glossary].
in_loop
A residue in a loop i.e. a section of the protein chain connecting classical secondary structures like helix and sheet. [The Biochemical Society Glossary].
sub_alignment
cluster
group
sub_group
A subset of sequences in the msa. e.g. a phylogenetic subgroup such as 'mammals', or a sequence cluster calculated by an automatic method such as secator/dpc or any other subset.
residue
The part of a single sugar that appears in a polysaccharide; of a single amino acid in a protein; of a single nucleotide in a nucleic acid, etc.; usually the monomer minus the elements of water.Glossary of Biochemistry and Molecular Biology, David M. Glick.
gap_character
The character used to represent an insertion/deletion.
unknown_residue_function
unknown_structural_location
kegg_id
KEGG interface
alignment_sequence
The order of residues and insertions/deletions represented by gap characters in a single sequence. For proteins, this is known as the primary structure.
sequence_name
The name given to the sequence.
column_score
A score associated with a given column.
column_conservation_type
The type of residue conserved in a given column.
organism
The organism that was the source of the sequence.
sequence_feature
A region of the sequence, defined by a start and stop residue, that has a specific property.
fitem
feature_start_residue
The residue at the beginning of the feature.
feature_stop_residue
The residue at the end of the feature.
consensus_sequence
A pseudo-sequence that summarises the residue information contained in an aligned set of sequences.
column_weight
A weight associated with a given column.
sequence_weight
A weight assigned to a sequence.
feature_description
A general text description of the feature.
protein:protein interactions
msa_name
The name given to the multiple sequence alignment.
ec_number
Enzyme Commission interface
hydrophobicity
A measure of how insoluble a given molecule is when in water or other polar liquids.
feature_name
The name given to the feature.
sequence_feature_type
The type of the sequence feature.
interpro_domain
Interpro interface
transmembrane_helix
coiled_coil
msa_core_block
A conserved region in the sub_alignment.
helix
A frequently highly stable protein chain conformation stabilised by hydrogen bonding between peptide groups and having side chains projecting outwards in a spiral (3.6 residues per turn). The Biochemical Society Glossary.
alpha_helix
strand
Stable "zig-zag" conformation of protein chain which can align with sections of chain in same conformation and cross-link efficiently via hydrogen bonds between the peptide linkages. The Biochemical Society Glossary.
beta_strand
accession_number
accession
A unique identifier in the sequence databases.Accession numbers should remain static between database updates.
sequence_description
A general description of the sequence.
taxid
NCBI taxonomy database interface
sequence_repeat
A region which has multiple copies in the sequence. Repeats range from short stretches of adjacent, similar residues to multiple copies of complete domains.
signal
Extent of a signal sequence (prepeptide).
sequence_variant
varsplic
A region where an alternative sequence has been observed.
low_complexity_region
A region of biased residue composition, e.g. homopolymeric runs, short repeats, and more subtle overrepresentations of one or a few residues. Low-complexity regions in amino acid sequences typically assume non-globular structure in proteins. [NCBI sef.glossary).
site
A generic term for the extent of a user-specified site.
sequence_keyword_list
A list of keywords that provide information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
buried
A residue in the core of the protein that has no surface area accessible to solvent.
core_residue
residue_hydrogen_bond
A type of attractive intermolecular force that exists between two partial electric charges of opposite polarity.
conserved_aliphatic_residue
A conserved aliphatic residue e.g. AGLIV
conserved_aromatic_residue
A conserved aromatic residue e.g. YWFH
conserved_basic_residue
A conserved basic residue e.g. HKR
conserved_hydroxyl_residue
A conserved hydroxyl residue e.g. STY
dna_binding_site
A residue that is directly involved in binding to dna.
column_conservation
The conservation associated with a given column in the msa.
residue_function_detection_method
The method used to detect the activity or function of the residue.
column_conservation_construction_method
The method used to construct the conservation score associated with a given column.
user_conservation_value
A user defined conservation term e.g. mixed conservation from different methods
strict_conservation
A strictly conserved column.
no_conservation
An unconserved column.
in_cavity
in_pocket
The residue is touching a cavity.
alignment_column
The alignment_column contains one residue (or a gap character) from each sequence. The residues in the column are considered to be equivalent. If no equivalent residue exists for a given sequence, a gap character is inserted.
sub_alignment_construction_method
sub_group_construction_method
The method used to determine the sub_alignment or sub_families.
cluster_construction_method
group_construction_method
loop
A section of the protein chain connecting classical secondary structures like helix and sheet. Often of irregular structure, surface exposed and containing hydrophilic residues. The Biochemical Society Glossary.
interresidue_contact_list
residue_contact_list
List of spatial contacts between two residues
contact_residue1
First residue involved in contact
interresidue_contact
residue_contact
Spatial contact between two residues
differential_conservation
A column that is conserved differently in the different sub_families. e.g. a residue that is conserved in mammals, but is divergent in the other organisms.
conserved_gap_character
A conserved insertion/deletion.
structural_location_detection_method
The method used to determine the location of the residue in the 3d structure.
3d_atomic_coordinates
The coordinates of the atom in 3-dimensional space.
atom
The fundamental building blocks of chemistry, which cannot be broken by any chemical means.
other_residue_function
A user specified activity or function associated with a residue.
pdb_name
msa_3d_superposition
msa_reference_structure_name
msa_superposed_regions
msa_symmetry_operator
msa_rmsd
tissue_type
The tissue from which the sequence was extracted.
developmental_stage
The developmental stage of the organism's life cycle during which the sequence was extracted nMGED Interface
exposed
surface_residue
A residue on the surface of the protein that is accessible to solvent.
residue_salt_bridge
An interaction between positive and negative charges on side chains of a protein.
ramanchandran_plot
The Ramachandran plot is a graph of the protein backbone torsional angles psi (Calpha-C bond) versus phi (N-Calpha bond). The psi and phi angles cover the ranges from -180 to +180.
phi_angle
The phi (N-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +180.
3d_coordinate_x
psi_angle
The psi (C-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +180.
3d_coordinate_y
3d_coordinate_z
bonded_residue
The other residue bonded to the reference residue.
msa_freetext_line
aln_text
A line of free text in the msa, containing annotation associated with a sequence or group of sequences.
msa_freetext_owner
The alignment_sequence or sub_family that the msa_freetext is attached to.
aln_text_owner
msa_freetext_type
The type of text supplied in the msa_freetext.
aln_text_type
consensus_sequence_construction_method
The method used to determine the consensus sequence.
sequence_type
The type of sequence e.g. protein or dna.
column_score_calculation_method
The method used to calculate the score associated with a given column.
column_weight_calculation_method
The method used to calculate the weight associated with a given column.
amino_acid_residue
An organic compound that generally contains an amino (-NH2) and a carboxyl (-COOH) group. There are 20 different kinds of amino acids. A protein consists of a specific sequence of amino acids.
amino_acid
aa_residue
nucleotide_residue
base
A DNA sequence consists of a specific sequence of nucleotides. A nucleotide is made of a molecule of sugar, a molecule of phosphoric acid, and a molecule called a base. The bases are the "letters" that spell out the genetic code. In DNA, the code letters are A, T, G, and C, which stand for the chemicals adenine, thymine, guanine, and cytosine, respectively. In base pairing, adenine always pairs with thymine, and guanine always pairs with cytosine. [NHGRI] A DNA sequence consists of a specific sequence of nucleotides.
base_pair
nucleotide
atom_name
motif
A pattern of conserved residues in a sequence that are located within a certain distance from each other in the sequence.
enzyme_active_site
The active site of an enzyme is the binding site where catalysis occurs. The structure and chemical properties of the active site allow the recognition and binding of the substrate. The active site consists of the catalytic amino acids and one or more binding sites that bind the substrate(s).
substrate_binding_site
A residue that is directly involved in the binding of a specific substrate.
mutation
A mutation is a permanent, transmissible change to the genetic material (usually DNA or RNA) of a cell.
point_mutation
A point mutation is usually caused by chemicals or malfunction of DNA replication and exchanges a single nucleotide for another. Most common is the transition that exchanges a purine for a purine or a pyrimidine for a pyrimidine (A ? G, C ? T). Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ? A/G).
insertion_mutation
The addition of one or more extra nucleotides into the DNA. They are usually caused by transposable elements, or errors during replication of repeating elements (e.g. AT repeats). Insertions in a gene can cause a shift in the reading frame (frameshift) or alter splicing of the mRNA, both of which can significantly alter the gene product.
deletion_mutation
Deletions remove one or more nucleotides from the DNA. Like insertions, these mutations can alter the reading frame of the gene. Deletions in a gene can cause a shift in the reading frame (frameshift) or alter splicing of the mRNA, both of which can significantly alter the gene product.
silent_mutation
A silent mutation is a DNA mutation that does not alter the final amino acid, and hence does not affect the final protein. Anaylsis of mutations in genes causing genetic disorders has shown that silent mutations can affect gene transcription, leading to the formation of truncated protein with reduced or no function.
synonymous_mutation
missense_mutation
A missense mutations is a type of point mutation where a nucleotide is changed which results in a different amino acid. This in turn can render the resulting protein nonfunctional.
nonsynonymous_mutation
nonsense_mutation
A nonsense mutation is a point mutation that results in a premature stop codon in the transcribed mRNA, and possibly a truncated (and often nonfunctional) protein product.
mutation_type
The type fo mutation. e.g. germline mutation, which can be passed on to progeny or somatic mutation, which often leads to the malfunction or death of a cell and can cause cancer.
metal_binding_site
A residue that is directly involved in the binding of a metal ion.
CSA_catalytic_site
CSA Interface
ligand_binding_site
A residue that is directly involved in the binding of a specific ligand.
mutation_phenotypic_manifestation
OBO_phenotype_ontology interface
resid_ptm
RESID database interface
acetylation
N-terminal of some residues and side chain of lysine or cysteine
amidation
Generally at the C-terminal of a mature active peptide after oxidative cleavage of last glycine
blocked
Unidentified N- or C-terminal blocking group
formylation
Of the N-terminal methionine
gamma_carboygluamic_acid
Of glutamate
hydroxylation
Generally of asparagine, aspartate, proline or lysine
methylation
Generally of N-terminal phenylalanine, side chain of lysine, arginine, histidine, asparagine or glutamate, and C-terminal cysteine
phosphorylation
Of serine, threonine, tyrosine, aspartate, histidine or cysteine
pyrrolidone_carboxylic_acid
N-terminal glutamine which has formed an internal cyclic lactam. This is also called 'pyro-Glu'. Very rarely, pyro-Glu can be produced by modification of a N-terminal glutamate
sulfation
Of tyrosine, serine or threonine
carbohydrate_binding_site
lipid_binding_site
A residue that is directly involved in the binding of a lipid.
residue_disulfide_bond
A strong covalent bond between two sulfhydryl groups. This bond is very important to the folding, structure, and function of proteins.
disulfide_bridge
residue_structural_bond
contact_residue2
Second residue involved in spatial contact
n_terminal_extension
c_terminal_extension
sequence_weight_calculation_method
sequence_insertion
column_consensus
A consensus character that summarises the residue information contained in an alignment_column.
feature_calculation_method
The method used to determine the feature.
column_consensus_calculation_method
The method used to determine the consensus character associated with a column.
so_mutation
SO interface
sequence_keyword
A keyword provides information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
hydrophobicity_calculation_method
The method used to calculate the hydrophobicity measure.
contact_distance
Distance between two residues in spatial contact
contact_description
Textual comment describing spatial contact between two residues