SFLD Evidence Codes

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The definition of evidence codes varies depending on the context. The following table lists the evidence code and the respective definition for each context.

| BTC | CFM | FSM | ICR | ICS | IDA | IEA | IES | IGS | IME | IMP | ISS | MFR | NSA | SFA | TPR |

BTC - Below Trusted Cutoff

Annotation in other databases

Used when a sequence is labeled as misannotated because sequence similarity is too weak to assign the sequence to the funciton to which it was annotated (falls below family-defined cutoff). However, the sequence does exhibit detectable sequence similarity to other sequences that perform the function.

CFM - Canonical Family Member

Family Assignment

Indicates that a protein/domain is one of the canonical members of a family.

FSM - Founding Superfamily Member

Superfamily Assignment

Indicates that a protein/domain is one of the founding superfamily members used to create the definition of a superfamily.

ICR - Inferred from Catalytic Residues

Reaction Assignment

Used when reaction assignment is based on the presence of homologs to catalytic residues shown in similar enzymes to be required for the reaction (via a direct assay).

Partial Reaction Assignment

Used when partial reaction assignment is based on the presence of homologs to catalytic residues shown in similar enzymes to be required for the partial reaction (via a direct assay).

ICS - Inferred from Crystal Structure

Conserved Residue Assignment

Used when catalytic residue assignment is based on examination of a crystal structure (ex. Metal binding ligands).

Partial Reaction Assignment

Used when a theorized partial reaction is based on evidence from an X-ray crystal structure.

IDA - Inferred from Direct Assay

Reaction Assignment

Used when an enzyme is directly assayed for a reaction (for example, by monitoring the disappearance of reactant or appearance of product spectrophotometrically).

Partial Reaction Assignment

Used when there is experimental evidence to support a partial reaction (for example, the intermediate has been trapped).

Conserved Residue Assignment

Used when there is experimental evidence that suggests a particular amino acid is catalytically important (for example, site directed mutagenesis experiments).

IEA - Inferred from Electronic Annotation

Reaction Assignment

Used when a reaction is assigned based on electronic annotation (for example, an NCBI definition line), and has not been reviewed for accuracy by a human curator. Also used when reaction assignment is based on overall sequence or structural similarity to an enzyme/domain with reaction already assigned and has not been reviewed for accuracy by a human curator.

Partial Reaction Assignment

Used when partial reaction assignment is based on overall sequence or structural similarity to an enzyme/domain with partial reaction already assigned, and has not been reviewed for accuracy by a human curator.

Conserved Residue Assignment

Used when conserved residue assignment is based on an alignment to a family/superfamily member with conserved residues already assigned and has not been reviewed for accuracy by a human curator.

Superfamily Assignment

Used when superfamily assignment is based on overall sequence or structural similarity to existing superfamily members and has not been reviewed for accuracy by a human curator.

Family Assignment

Used when family assignment is based on overall sequence or structural similarity to existing family members and has not been reviewed for accuracy by a human curator.

IES - Inferred from Experiment and Sequence

Family Assignment

Used when family membership is assigned based on sequence/structural similarity to existing family members as well as a direct assay that shows that the enzyme/domain in question catalyzes the canonical family reaction.

IGS - Inferred from Genome Context and Sequence

Family Assignment

Used when family membership is assigned based on sequence/structural similarity to existing family members, as well as genome context information (the genomic region containing the gene for the putative family member also contains genes for other enzymes in the same biological pathway that the family enzymes are a part of).

Reaction Assignment

Used when reaction assignment is made based on sequence/structural similarity to other sequences known from experimental evidence to catalyze the reaction, as well as genome context information (the genomic region containing the gene for the enzyme to be assigned the reaction also contains genes for other enzymes in the same biological pathway that reaction is a part of).

IME - Inferred from Mutagenesis Experiment

Partial Reaction Assignment

Used when there is mutagenesis data that supports a particular partial reaction.

Conserved Residue Assignment

Used when there is mutagenesis data that supports the assignment of a particular functional role to a residue.

IMP - Inferred from Mutant Phenotype

Reaction Assignment

The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant.

ISS - Inferred from Sequence or Structural Similarity

Reaction Assignment

Used when reaction assignment is based on overall sequence or structural similarity to an enzyme/domain with reaction already assigned, and has been reviewed for accuracy by a human curator.

Partial Reaction Assignment

Used when partial reaction assignment is based on overall sequence or structural similarity to an enzyme/domain with partial reaction already assigned, and has been reviewed for accuracy by a human curator.

Conserved Residue Assignment

Used when conserved residue assignment is based on an alignment to a family/superfamily member with conserved residues already assigned, and has been reviewed for accuracy by a human curator.

Superfamily Assignment

Used when superfamily assignment is based on overall sequence or structural similarity to existing superfamily members that has been reviewed for accuracy by a human curator.

Family Assignment

Used when family assignment is based on overall sequence or structural similarity to existing family members that has been reviewed for accuracy by a human curator.

MFR - Missing Functionally Important Residues

Annotation in other databases

Used when a seqeuence is labeled as misannotated based upon the absence or mutation of residues known to be critical for the function to which the sequence was erroneously annotated.

NSA - No Superfamily Association

Annotation in other databases

Used when a sequence is labeled as misannotated because sequence similarity cannot assign the sequence to the superfamily of the function to which it was annotated.

SFA - Superfamily Associated Only

Annotation in other databases

Used when a sequence is a labeled as misannotated because sequence similarity can only assign the sequence to the superfamily of the function to which it was annotated (and not to the family).

TPR - Theorized Partial Reaction

Partial Reaction Assignment

Used when a partial reaction is assigned based on theory rather than experimental evidence.