format-version: 1.0
date: 12:07:2006 10:36
saved-by: julie
auto-generated-by: DAG-Edit 1.419 rev 3
default-namespace: mao.obo
remark: autogenerated-by:     DAG-Edit version 1.418
remark: saved-by:             julie
remark: date:                 Fri Jan 07 11:14:23 CET 2005
remark: version: $Revision: 1.30 $

[Term]
id: MAO:0000000
name: multiple_sequence_alignment
def: "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." [MAO:jt]
synonym: "msa" []

[Term]
id: MAO:0000001
name: structural_location
def: "The location of the residue in the 3D structure." [MAO:jt]
relationship: is_attribute MAO:0000120 ! amino_acid_residue

[Term]
id: MAO:0000002
name: residue_function
def: "Function of the residue\, such as catalysis\, binding or post-translational modification. A residue may exhibit zero, one or more activities." [MAO:jt]
relationship: is_attribute MAO:0000120 ! amino_acid_residue

[Term]
id: MAO:0000003
name: column_conservation_level
def: "The level of conservation associated with a given column. This may be specified by either a qualitative score or a quantitative score." [MAO:jt]
relationship: part_of MAO:0000077 ! column_conservation

[Term]
id: MAO:0000004
name: conserved_residue_list
def: "A user specified list of conserved residues." [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type
xref_unknown: MAO:jt

[Term]
id: MAO:0000005
name: biological_process
def: "GeneOntology interface" [GO:0008150]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000006
name: cellular_component
def: "GeneOntology interface" [GO:0005575]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000007
name: molecular_function
def: "GeneOntology interface" [GO:0003674]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000008
name: conserved_small_residue
def: "A conserved small residue e.g. PAGST" [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000009
name: conserved_negatively_charged_residue
def: "A conserved negatively charged residue e.g. DE" [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000010
name: conserved_hydrophobic_residue
def: "A conserved hydrophobic residue e.g. ACFGLIMVWY" [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000011
name: conserved_hydrophilic_residue
def: "A conserved hydrophilic residue e.g. DEHKNQRST" [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000012
name: quantitative_conservation_level
def: "A quantitative score for the conservation associated with a given column." [MAO:jt]
is_a: MAO:0000003 ! column_conservation_level

[Term]
id: MAO:0000013
name: qualitative_conservation_level
def: "A qualitative description of the level of conservation associated with a given column." [MAO:jt]
is_a: MAO:0000003 ! column_conservation_level

[Term]
id: MAO:0000014
name: low_conservation
def: "A low level of conservation associated with a given column." [MAO:jt]
is_a: MAO:0000013 ! qualitative_conservation_level

[Term]
id: MAO:0000015
name: medium_conservation
def: "A medium level of conservation associated with a given column." [MAO:jt]
is_a: MAO:0000013 ! qualitative_conservation_level

[Term]
id: MAO:0000016
name: high_conservation
def: "A high level of conservation associated with a given column." [MAO:jt]
is_a: MAO:0000013 ! qualitative_conservation_level

[Term]
id: MAO:0000017
name: catalytic_site
def: "A residue that is directly involved in some aspect of the reaction catalysed by the enzyme." [MAO:jt]
is_a: MAO:0000124 ! enzyme_active_site

[Term]
id: MAO:0000018
name: domain
def: "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. \[CHI Structural proteomics report\]  " [MAO:jt]
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000019
name: post translational modification
def: "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" [MAO:jt]
synonym: "ptm" []
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000020
name: psi_mutation
def: "PSI interface" [MI:0118]
is_a: MAO:0000126 ! mutation

[Term]
id: MAO:0000021
name: msa_construction_method
def: "The method used to construct the multiple sequence alignment." [MAO:jt]
relationship: is_annotation MAO:0000000 ! multiple_sequence_alignment

[Term]
id: MAO:0000022
name: surface_accessibility
def: "Surface area accessible to solvent" [MAO:jt]
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000023
name: N_terminal
def: "A residue in a protein chain that has a free amino group." [MAO:jt]
synonym: "amino_terminus" []
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000024
name: C_terminal
def: "A residue in a protein chain that has a free carboxyl group." [MAO:jt]
synonym: "carboxyl_terminus" []
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000025
name: in_domain
def: "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. \[NCBI Bioinformatics\] " [MAO:jt]
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000026
name: in_hinge_region
def: "A residue in a hinge region i.e. a flexible region of the protein between two globular domains." [MAO:jt]
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000027
name: in_transmembrane_region
def: "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.\[Folding@home glossary\, Stanford Univ\]." [MAO:jt]
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000028
name: in_helix
def: "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). \[The Biochemical Society Glossary\]." [MAO:jt]
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000029
name: in_strand
def: "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. \[The Biochemical Society Glossary\]." [MAO:jt]
synonym: "in_beta_strand" []
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000030
name: in_loop
def: "A residue in a loop i.e. a section of the protein chain connecting classical secondary structures like helix and sheet. \[The Biochemical Society Glossary\]." [MAO:jt]
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000031
name: sub_alignment
def: "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." [MAO:jt]
synonym: "cluster" []
synonym: "group" []
synonym: "sub_group" []
relationship: part_of MAO:0000000 ! multiple_sequence_alignment

[Term]
id: MAO:0000032
name: residue
def: "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." [MAO:jt]
relationship: part_of MAO:0000037 ! alignment_sequence
relationship: part_of MAO:0000084 ! alignment_column

[Term]
id: MAO:0000033
name: gap_character
def: "The character used to represent an insertion/deletion." [MAO:jt]
relationship: part_of MAO:0000037 ! alignment_sequence
relationship: part_of MAO:0000084 ! alignment_column

[Term]
id: MAO:0000034
name: unknown_residue_function
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000035
name: unknown_structural_location
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000036
name: kegg_id
def: "KEGG interface" [KEGG:xref]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000037
name: alignment_sequence
def: "The order of residues and insertions/deletions represented by gap characters in a single sequence. For proteins\, this is known as the primary structure." [MAO:jt]
relationship: part_of MAO:0000031 ! sub_alignment

[Term]
id: MAO:0000038
name: sequence_name
def: "The name given to the sequence." [MAO:jt]
relationship: is_name MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000039
name: column_score
def: "A score associated with a given column." [MAO:jt]
relationship: is_attribute MAO:0000084 ! alignment_column

[Term]
id: MAO:0000040
name: column_conservation_type
def: "The type of residue conserved in a given column." [MAO:jt]
relationship: part_of MAO:0000077 ! column_conservation

[Term]
id: MAO:0000041
name: organism
def: "The organism that was the source of the sequence." [MAO:jt]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000042
name: sequence_feature
def: "A region of the sequence\, defined by a start and stop residue\, that has a specific property." [MAO:jt]
synonym: "fitem" []
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000043
name: feature_start_residue
def: "The residue at the beginning of the feature." [MAO:jt]
relationship: part_of MAO:0000042 ! sequence_feature

[Term]
id: MAO:0000044
name: feature_stop_residue
def: "The residue at the end of the feature." [MAO:jt]
relationship: part_of MAO:0000042 ! sequence_feature

[Term]
id: MAO:0000045
name: consensus_sequence
def: "A pseudo-sequence that summarises the residue information contained in an aligned set of sequences." [MAO:jt]
relationship: part_of MAO:0000031 ! sub_alignment

[Term]
id: MAO:0000046
name: column_weight
def: "A weight associated with a given column." [MAO:jt]
relationship: is_attribute MAO:0000084 ! alignment_column

[Term]
id: MAO:0000047
name: sequence_weight
def: "A weight assigned to a sequence. " [MAO:jt]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000048
name: feature_description
def: "A general text description of the feature." [MAO:jt]
relationship: part_of MAO:0000042 ! sequence_feature

[Term]
id: MAO:0000049
name: protein:protein interactions
def: "PSI interface" [MI:0000]
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000050
name: msa_name
def: "The name given to the multiple sequence alignment." [MAO:jt]
relationship: is_name MAO:0000000 ! multiple_sequence_alignment
xref_unknown: MAO:jt

[Term]
id: MAO:0000051
name: ec_number
def: "Enzyme Commission interface" [EC:xref]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000052
name: hydrophobicity
def: "A measure of how insoluble a given molecule is when in water or other polar liquids." [MAO:jt]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000053
name: feature_name
def: "The name given to the feature." [MAO:jt]
relationship: is_name MAO:0000042 ! sequence_feature

[Term]
id: MAO:0000054
name: sequence_feature_type
def: "The type of the sequence feature." [MAO:jt]
is_a: MAO:0000042 ! sequence_feature

[Term]
id: MAO:0000055
name: interpro_domain
def: "Interpro interface" [IPR:xref]
is_a: MAO:0000018 ! domain

[Term]
id: MAO:0000056
name: transmembrane_helix
synonym: "tm" []
is_a: MAO:0000071 ! residue_hydrogen_bond

[Term]
id: MAO:0000057
name: coiled_coil
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000058
name: msa_core_block
def: "A conserved region in the sub_alignment." [MAO:jt]
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000059
name: helix
def: "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." [MAO:jt]
narrow_synonym: "alpha_helix" []
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000060
name: strand
def: "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." [MAO:jt]
synonym: "beta_strand" []
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000061
name: accession_number
def: "A unique identifier in the sequence databases.Accession numbers should remain static between database updates." [MAO:jt]
synonym: "accession" []
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000062
name: sequence_description
def: "A general description of the sequence." [MAO:jt]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000063
name: taxid
def: "NCBI taxonomy database interface" [taxid:xref]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000064
name: sequence_repeat
def: "A region which has multiple copies in the sequence. Repeats range from short stretches of adjacent\, similar residues to multiple copies of complete domains." [MAO:jt]
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000065
name: signal
def: "Extent of a signal sequence (prepeptide)." [MAO:jt]
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000066
name: sequence_variant
def: "A region where an alternative sequence has been observed." [MAO:jt]
synonym: "varsplic" []
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000067
name: low_complexity_region
def: "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)." [MAO:jt]
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000068
name: site
def: "A generic term for the extent of a user-specified site." [MAO:jt]
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000069
name: sequence_keyword_list
def: "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. " [MAO:jt]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000070
name: buried
def: "A residue in the core of the protein that has no surface area accessible to solvent." [MAO:jt]
synonym: "core_residue" []
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000071
name: residue_hydrogen_bond
def: "A type of attractive intermolecular force that exists between two partial electric charges of opposite polarity. " [MAO:jt]
is_a: MAO:0000152 ! residue_structural_bond

[Term]
id: MAO:0000072
name: conserved_aliphatic_residue
def: "A conserved aliphatic residue e.g. AGLIV" [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000073
name: conserved_aromatic_residue
def: "A conserved aromatic residue e.g. YWFH" [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000074
name: conserved_basic_residue
def: "A conserved basic residue e.g. HKR" [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000075
name: conserved_hydroxyl_residue
def: "A conserved hydroxyl residue e.g. STY" [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000076
name: dna_binding_site
def: "A residue that is directly involved in binding to dna." [MAO:jt]
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000077
name: column_conservation
def: "The conservation associated with a given column in the msa." [MAO:jt]
relationship: is_attribute MAO:0000084 ! alignment_column

[Term]
id: MAO:0000078
name: residue_function_detection_method
def: "The method used to detect the activity or function of the residue." [MAO:jt]
relationship: is_annotation MAO:0000002 ! residue_function

[Term]
id: MAO:0000079
name: column_conservation_construction_method
def: "The method used to construct the conservation score associated with a given column." [MAO:jt]
relationship: is_annotation MAO:0000077 ! column_conservation

[Term]
id: MAO:0000080
name: user_conservation_value
def: "A user defined conservation term e.g. mixed conservation from different methods" [MAO:jt]
is_a: MAO:0000013 ! qualitative_conservation_level

[Term]
id: MAO:0000081
name: strict_conservation
def: "A strictly conserved column." [MAO:jt]
is_a: MAO:0000013 ! qualitative_conservation_level

[Term]
id: MAO:0000082
name: no_conservation
def: "An unconserved column." [MAO:jt]
is_a: MAO:0000013 ! qualitative_conservation_level

[Term]
id: MAO:0000083
name: in_cavity
def: "The residue is touching a cavity." [MAO:pk]
synonym: "in_pocket" []
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000084
name: alignment_column
def: "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." [MAO:jt]
relationship: part_of MAO:0000031 ! sub_alignment

[Term]
id: MAO:0000085
name: sub_alignment_construction_method
def: "The method used to determine the sub_alignment or sub_families." [MAO:jt]
synonym: "cluster_construction_method" []
synonym: "group_construction_method" []
synonym: "sub_group_construction_method" []
relationship: is_annotation MAO:0000031 ! sub_alignment

[Term]
id: MAO:0000086
name: loop
def: "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." [MAO:jt]
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000087
name: interresidue_contact_list
def: "List of spatial contacts between two residues" [MAO:jt]
synonym: "residue_contact_list" []
relationship: is_attribute MAO:0000032 ! residue

[Term]
id: MAO:0000088
name: contact_residue1
def: "First residue involved in contact" [MAO:jt]
relationship: part_of MAO:0000087 ! interresidue_contact_list

[Term]
id: MAO:0000089
name: interresidue_contact
def: "Spatial contact between two residues" [MAO:jt]
synonym: "residue_contact" []
relationship:part_of MAO:0000087 ! interresidue_contact_list

[Term]
id: MAO:0000090
name: differential_conservation
def: "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." [MAO:jt]
is_a: MAO:0000013 ! qualitative_conservation_level

[Term]
id: MAO:0000091
name: conserved_gap_character
def: "A conserved insertion/deletion." [MAO:jt]
is_a: MAO:0000040 ! column_conservation_type

[Term]
id: MAO:0000092
name: structural_location_detection_method
def: "The method used to determine the location of the residue in the 3d structure." [MAO:jt]
relationship: is_annotation MAO:0000001 ! structural_location

[Term]
id: MAO:0000093
name: 3d_atomic_coordinates
def: "The coordinates of the atom in 3-dimensional space." [MAO:jt]
relationship: is_attribute MAO:0000094 ! atom

[Term]
id: MAO:0000094
name: atom
def: "The fundamental building blocks of chemistry\, which cannot be broken by any chemical means." [MAO:jt]
relationship: part_of MAO:0000120 ! amino_acid_residue
relationship: part_of MAO:0000121 ! nucleotide_residue

[Term]
id: MAO:0000095
name: other_residue_function
def: "A user specified activity or function associated with a residue." [MAO:jt]
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000096
name: pdb_name
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000097
name: msa_3d_superposition
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000098
name: msa_reference_structure_name
relationship: part_of MAO:0000097 ! msa_3d_superposition

[Term]
id: MAO:0000099
name: msa_superposed_regions
relationship: part_of MAO:0000097 ! msa_3d_superposition

[Term]
id: MAO:0000100
name: msa_symmetry_operator
relationship: part_of MAO:0000097 ! msa_3d_superposition

[Term]
id: MAO:0000101
name: msa_rmsd
relationship: part_of MAO:0000097 ! msa_3d_superposition

[Term]
id: MAO:0000102
name: tissue_type
def: "The tissue from which the sequence was extracted." [MAO:jt]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000103
name: developmental_stage
def: "The developmental stage of the organism's life cycle during which the sequence was extracted \nMGED Interface" [MAO:jt]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000104
name: exposed
def: "A residue on the surface of the protein that is accessible to solvent." [MAO:jt]
synonym: "surface_residue" []
is_a: MAO:0000001 ! structural_location

[Term]
id: MAO:0000105
name: residue_salt_bridge
def: "An interaction between positive and negative charges on side chains of a protein." [MAO:jt]
is_a: MAO:0000152 ! residue_structural_bond

[Term]
id: MAO:0000106
name: ramanchandran_plot
def: "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." [MAO:pk]
relationship: is_attribute MAO:0000120 ! amino_acid_residue

[Term]
id: MAO:0000107
name: phi_angle
def: "The phi  (N-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +180." [MAO:pk]
is_a: MAO:0000106 ! ramanchandran_plot

[Term]
id: MAO:0000108
name: 3d_coordinate_x
relationship: part_of MAO:0000093 ! 3d_atomic_coordinates

[Term]
id: MAO:0000109
name: psi_angle
def: "The psi  (C-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +180." [MAO:pk]
is_a: MAO:0000106 ! ramanchandran_plot

[Term]
id: MAO:0000110
name: 3d_coordinate_y
relationship: part_of MAO:0000093 ! 3d_atomic_coordinates

[Term]
id: MAO:0000111
name: 3d_coordinate_z
relationship: part_of MAO:0000093 ! 3d_atomic_coordinates

[Term]
id: MAO:0000112
name: bonded_residue
def: "The other residue bonded to the reference residue." [MAO:jt]
relationship: is_attribute MAO:0000152 ! residue_structural_bond

[Term]
id: MAO:0000113
name: msa_freetext_line
def: "A line of free text in the msa\, containing annotation associated with a sequence or group of sequences." [MAO:jt]
synonym: "aln_text" []
relationship: part_of MAO:0000031 ! sub_alignment

[Term]
id: MAO:0000114
name: msa_freetext_owner
def: "The alignment_sequence or sub_family that the msa_freetext is attached to." [MAO:jt]
synonym: "aln_text_owner" []
relationship: is_attribute MAO:0000113 ! msa_freetext_line

[Term]
id: MAO:0000115
name: msa_freetext_type
def: "The type of text supplied in the msa_freetext." [MAO:jt]
synonym: "aln_text_type" []
relationship: is_attribute MAO:0000113 ! msa_freetext_line

[Term]
id: MAO:0000116
name: consensus_sequence_construction_method
def: "The method used to determine the consensus sequence." [MAO:jt]
relationship: is_annotation MAO:0000045 ! consensus_sequence

[Term]
id: MAO:0000117
name: sequence_type
def: "The type of sequence e.g. protein or dna." [MAO:jt]
relationship: is_attribute MAO:0000037 ! alignment_sequence

[Term]
id: MAO:0000118
name: column_score_calculation_method
def: "The method used to calculate the score associated with a given column." [MAO:jt]
relationship: is_annotation MAO:0000039 ! column_score

[Term]
id: MAO:0000119
name: column_weight_calculation_method
def: "The method used to calculate the weight associated with a given column." [MAO:jt]
relationship: is_annotation MAO:0000084 ! alignment_column

[Term]
id: MAO:0000120
name: amino_acid_residue
def: "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. " [MAO:jt]
synonym: "aa" []
synonym: "aa_residue" []
synonym: "amino_acid" []
is_a: MAO:0000032 ! residue

[Term]
id: MAO:0000121
name: nucleotide_residue
def: "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. " [MAO:jt]
synonym: "base" []
synonym: "base_pair" []
synonym: "nucleotide" []
is_a: MAO:0000032 ! residue

[Term]
id: MAO:0000122
name: atom_name
relationship: is_name MAO:0000094 ! atom

[Term]
id: MAO:0000123
name: motif
def: " A pattern of conserved residues in a sequence that are located within a certain distance from each other in the sequence." [MAO:jt]
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000124
name: enzyme_active_site
def: "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)." [MAO:jt]
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000125
name: substrate_binding_site
def: "A residue that is directly involved in the binding of a specific substrate." [MAO:jt]
is_a: MAO:0000124 ! enzyme_active_site

[Term]
id: MAO:0000126
name: mutation
def: "A mutation is a permanent\, transmissible change to the genetic material (usually DNA or RNA) of a cell." [MAO:jt]
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000127
name: point_mutation
def: "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)." [MAO:jt]
is_a: MAO:0000126 ! mutation

[Term]
id: MAO:0000128
name: insertion_mutation
def: "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. " [MAO:jt]
is_a: MAO:0000126 ! mutation

[Term]
id: MAO:0000129
name: deletion_mutation
def: "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. " [MAO:jt]
is_a: MAO:0000126 ! mutation

[Term]
id: MAO:0000130
name: silent_mutation
def: "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." [MAO:jt]
synonym: "synonymous_mutation" []
is_a: MAO:0000127 ! point_mutation

[Term]
id: MAO:0000131
name: missense_mutation
def: "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." [MAO:jt]
synonym: "nonsynonymous_mutation" []
is_a: MAO:0000127 ! point_mutation

[Term]
id: MAO:0000132
name: nonsense_mutation
def: "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." [MAO:jt]
is_a: MAO:0000127 ! point_mutation

[Term]
id: MAO:0000133
name: mutation_type
def: "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. " [MAO:jt]
relationship: is_attribute MAO:0000126 ! mutation

[Term]
id: MAO:0000134
name: metal_binding_site
def: "A residue that is directly involved in the binding of a metal ion." [MAO:jt]
is_a: MAO:0000136 ! ligand_binding_site

[Term]
id: MAO:0000135
name: CSA_catalytic_site
def: "CSA Interface" [MAO:jt]
is_a: MAO:0000017 ! catalytic_site

[Term]
id: MAO:0000136
name: ligand_binding_site
def: "A residue that is directly involved in the binding of a specific ligand." [MAO:jt]
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000137
name: mutation_phenotypic_manifestation
def: "OBO_phenotype_ontology interface" [MAO:jt]
relationship: is_attribute MAO:0000126 ! mutation

[Term]
id: MAO:0000138
name: resid_ptm
def: "RESID database interface" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000139
name: acetylation
def: "N-terminal of some residues and side chain of lysine or cysteine" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000140
name: amidation
def: "Generally at the C-terminal of a mature active peptide after oxidative cleavage of last glycine" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000141
name: blocked
def: "Unidentified N- or C-terminal blocking group" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000142
name: formylation
def: "Of the N-terminal methionine" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000143
name: gamma_carboygluamic_acid
def: "Of glutamate" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000144
name: hydroxylation
def: "Generally of asparagine\, aspartate\, proline or lysine" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000145
name: methylation
def: "Generally of N-terminal phenylalanine\, side chain of lysine\, arginine\, histidine\, asparagine or glutamate\, and C-terminal cysteine" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000146
name: phosphorylation
def: "Of serine\, threonine\, tyrosine\, aspartate\, histidine or cysteine" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000147
name: pyrrolidone_carboxylic_acid
def: "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" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000148
name: sulfation
def: "Of tyrosine\, serine or threonine" [MAO:jt]
is_a: MAO:0000019 ! post translational modification

[Term]
id: MAO:0000149
name: carbohydrate_binding_site
is_a: MAO:0000136 ! ligand_binding_site

[Term]
id: MAO:0000150
name: lipid_binding_site
def: "A residue that is directly involved in the binding of a lipid." [MAO:jt]
is_a: MAO:0000136 ! ligand_binding_site

[Term]
id: MAO:0000151
name: residue_disulfide_bond
def: "A strong covalent bond between two sulfhydryl groups. This bond is very important to the folding\, structure\, and function of proteins." [MAO:jt]
synonym: "disulfide_bridge" []
is_a: MAO:0000152 ! residue_structural_bond

[Term]
id: MAO:0000152
name: residue_structural_bond
is_a: MAO:0000002 ! residue_function

[Term]
id: MAO:0000153
name: contact_residue2
def: "Second residue involved in spatial contact" [MAO:jt]
relationship:part_of MAO:0000089 ! interresidue_contact

[Term]
id: MAO:0000154
name: n_terminal_extension
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000155
name: c_terminal_extension
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000156
name: sequence_weight_calculation_method
relationship: is_annotation MAO:0000047 ! sequence_weight

[Term]
id: MAO:0000157
name: sequence_insertion
is_a: MAO:0000054 ! sequence_feature_type

[Term]
id: MAO:0000158
name: column_consensus
def: "A consensus character that summarises the residue information contained in an alignment_column." [MAO:jt]
relationship: is_attribute MAO:0000084 ! alignment_column

[Term]
id: MAO:0000159
name: feature_calculation_method
def: "The method used to determine the feature." [MAO:jt]
relationship: is_annotation MAO:0000042 ! sequence_feature

[Term]
id: MAO:0000160
name: column_consensus_calculation_method
def: "The method used to determine the consensus character associated with a column." [MAO:jt]
relationship: is_annotation MAO:0000158 ! column_consensus

[Term]
id: MAO:0000161
name: so_mutation
def: "SO interface" [MAO:jt]
is_a: MAO:0000126 ! mutation

[Term]
id: MAO:0000162
name: sequence_keyword
def: "A keyword provides information that can be used to generate indexes of the sequence entries based on functional\, structural\, or other categories. " [MAO:jt]
relationship: part_of MAO:0000069 ! sequence_keyword_list

[Term]
id: MAO:0000163
name: hydrophobicity_calculation_method
def: "The method used to calculate the hydrophobicity measure." [MAO:jt]
relationship:is_annotation MAO:0000052 ! hydrophobicity

[Term]
id: MAO:0000164
name: contact_distance
def: "Distance between two residues in spatial contact" [MAO:jt]
relationship:part_of MAO:0000089 ! interresidue_contact

[Term]
id: MAO:0000165
name: contact_description
def: "Textual comment describing spatial contact between two residues" [MAO:jt]
relation_ship:is_annotation MAO:0000089 ! interresidue_contact

[Typedef]
id: is_annotation
name: is_annotation

[Typedef]
id: is_attribute
name: is_attribute

[Typedef]
id: is_name
name: is_name

[Typedef]
id: part_of
name: part_of
is_transitive: true