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Network Biomass WormPaths
FBAFlux Balance Analysis PEAPathway Enrichment Analysis
Gene Overview
Name ..................................................... : tbh-1
Sequence ID ..................................................... : H13N06.6
Status (?) Can be one of the following two: Curated (manually annotated or based on a curated SACURE result), or Not curated (SACURE result reported without manual check). ..................................................... : Curated
KO (?) The KEGG orthology group (KO) that is associated with this gene. ..................................................... : K00503DBH; dopamine beta-monooxygenase [EC:1.14.17.1]
Enzymes in the model (?) Enzymes that are part of the current metabolic network model. ..................................................... : 1.14.17.-
Other enzymes (?) Enzymes that are associated with this gene in the WormFlux database, but not included in the current network model. ..................................................... : 1.14.17.1names: dopamine beta-monooxygenase;dopamine beta-hydroxylase;MDBH (membrane-associated dopamine beta-monooxygenase);SDBH (soluble dopamine beta-monooxygenase);dopamine-B-hydroxylase;3,4-dihydroxyphenethylamine beta-oxidase;4-(2-aminoethyl)pyrocatechol beta-oxidase;dopa beta-hydroxylase;dopamine beta-oxidase;dopamine hydroxylase;phenylamine beta-hydroxylase;(3,4-dihydroxyphenethylamine)beta-mono-oxygenase;DbetaM (gene name)
Model reactions (?) Reactions that are part of the current metabolic network model.

See the bottom of this page for a table of reactions. ..................................................... 		: RCC0156
Relevant model reactions (?) Model reactions that follow from the KEGG reactions associated with this gene, but that exclude this gene due to differences in reaction specificity or localization compared to the predictions for this gene. ..................................................... : ERROR
Other reactions (?) KEGG reactions that are associated with this gene in the WormFlux database, but not included in the current network model. ..................................................... : R02535

In WormPaths (?) Pathway maps where this gene is represented are listed here. ..................................................... : Tyrosine metabolism
► | Gene-KO-Enzyme-Reaction Associations (click to view)▼ | Gene-KO-Enzyme-Reaction Associations (click to hide)
SACURE (?) Associations established by SACURE (Systematic Annotation by CUration and REgression).

SACURE pipeline annotates genes based on a logistic function that converts evidence from multiple resources into a KEGG orthology decision, which is then associated with enzymes and reactions. False positives and false negatives of the logistic function are separated out during manual curation for making exceptional decisions.

See HELP in the upper menu for a description of the SACURE pipeline.

See below for a summary of association scores from SACURE.

Results (?) KO: Associated KEGG Orthology groups
Enzyme: Associated enzymes in EC numbering
Reactions: Associated reactions from KEGG reaction database.

Confidence level is indicated for each association as a function of overall SACURE score (a probability of true association; see below in the SACURE scores section). Score ranges for HIGH, MEDIUM, and LOW confidence levels are >0.99, 0.90-0.99, and 0.50-0.90, respectively. If an association is accepted with a probability less than 0.50 (due to an exceptional reason), then the confidence level is LOW.

Not determined indicates that annotation analysis resulted in no clear associations.

ID - Confidence
KO K00503 - High
Enzyme 1.14.17.1 - High
Reaction R02535 - High

Comments

  • Based on the logistic function.
  • See scores from predictors and the logistic function below (SACURE summary).

Reconstruction (?) Associations established during the reconstruction process by lenient annotation, literature search, or gap-filling.

Results (?) KO: Associated KEGG Orthology groups
Enzyme: Associated enzymes in EC numbering
Reactions: Associated reactions from KEGG reaction database or custom reactions developed during reconstruction.

ID - Confidence
KO Not determined
Enzyme 1.14.17.- - Medium
Reaction RCC0156 - High

Comments

► | SACURE Summary (click to view)▼ | SACURE scores (click to hide)

Score table (?) Association scores for KOs best matching to the query gene according to each annotation predictor, and for the accepted KO if there is any (rightmost columns).

The predictors are ordered in decreasing weight of contribution to the decision-making process in SACURE.

See above for the final decision on the annotation of this gene.

Predictor Best scoring KOs Best score K00503 ERROR
KEGG (?) Score represents the annotation in KEGG database by June 2014.

Takes a value of either 0 (KO is not associated with the query gene) or 1 (KO is associated with the query gene). 		Not applicable 0 0 ERROR
Cluster (?) Score represents the degree of relatedness of a KO to the query gene based on the clustering in the phylogenetic tree of protein sequences (see below for the tree).

Takes values from 0 to 1. 		K00503 0.67 0.67 ERROR
myKEGG (?) Score represents the degree of relatedness of a KO to the query gene based on the Smith-Waterman alignment of protein sequence with most similar sequences from all organisms in the KEGG database.

Takes values from 0 to 1.

KOunknown indicates the score for sequences without any KO association in KEGG database. 		K00503 0.86 0.86 ERROR
Tree (?) Score shows the degree of relatedness of a KO to the query gene based on the density of this KO in the phylogenetic tree of protein sequences (see below for the tree).

Takes values from 0 to 2 as the score is normalized to the second best KO.

KOunknown indicates the score for sequences without any KO association in KEGG database. 		K00503 1.95 1.95 ERROR
KOG (?) Score indicates the absence or presence of a KO in association with one of the orthologs of the query gene according to a eukaryotic orthology database independent of KEGG (see HELP in the upper menu for details).

Takes a value of either 0 (absent) or 1 (present). 		Not applicable 0 0 ERROR
WormBase (?) Score represents matching between the KEGG descriptions of a KO (KO name and all related enzyme names) and the descriptions of the query gene in WormBase (gene overview and protein domains).

Value is increased by 0.5 for every perfect word match and reduced by 0.1 for each character interruption. A non-matching word always creates a 0 score.

WormBase description used for this gene was:

"Copper type II ascorbate-dependent monooxygenase, C-terminal $ Copper type II ascorbate-dependent monooxygenase, N-terminal $ Copper type II, ascorbate-dependent monooxygenase, conserved site $ Copper type II, ascorbate-dependent monooxygenase, N-terminal $ Copper type II, ascorbate-dependent monooxygenase-like, C-terminal $ DOMON $ DOMON related $ Dopamine-beta-monooxygenase $$ tbh-1 encodes a tyramine beta-hydroxylase orthologous to human DBH (OMIM:609312, mutated in dopamine beta-hydroxylase deficiency); TBH-1 activity is required for biosynthesis of the octopamine neurotransmitter." 		K00503 1.5 1.5 ERROR
Overall (?) Overall score from SACURE that represents the logistic-regression-based probability of acceptance of a KO in association with the query gene. K00503 0.999 0.999 ERROR
► | Localization scores (click to view)▼ | Localization scores (click to hide)

Score table (?) Localization scores for proteins encoded by the query gene.

Each predictor is used to determine whether the protein is localized to mitochondria or other compartment.

Together with other genes and other predictors, these scores were used in the determination of the subcellular location of reactions associated with the query gene (see below for the reactions).

Predictor Mitochondrial Other
Mitoprot (?) Score represents the predicted probability that the protein is targeted to mitochondria (mitochondrial score) or not (other score) according to Mitoprot (click to reach).

If multiple isofoms of the same protein are available the highest scores are shown for each compartment. 		0.07 0.98
MitoMiner (?) Score evaluates the evidence for mitochondrial targeting based on the orthologs in 12 eukaryotic model organisms that are in the MitoMiner database (click to reach).

If clear orthologs for the query gene are available in MitoMiner organisms, the score takes a value between 0 and 1 as a function of the ratio of orthologs that have hits (contributes to the mitochondrial score) or no hits (determines the other score) in the database. Mitochondrial score is also a function of the strength of the evidence for the orthologs found in the database (experimental evidence is given a higher weight than theoretical evidence during scoring). 		0.00 1.00
UniProt (?) Score shows the subcellular localization of proteins encoded by this gene as reported in UniProt (click to reach) in October 2014.

If a report is available, the score takes a value of either 0 (not reported to be localized to the pertaining compartment) or 1 (reported to be localized to the pertaining compartment). 		0 1
Org. DB (?) Score shows the subcellular localization of proteins encoded by this gene as reported in Organelle Database (click to reach).

If a report is available, the score takes a value of either 0 (not reported to be localized to the pertaining compartment) or 1 (reported to be localized to the pertaining compartment). 		Not available Not available
► | Phylogenetic tree (click to view)▼ | Phylogenetic tree (click to hide)
K00504 CEL:cel pamn-1 (PB) K00504 CEL:cel pghm-1 (P) K00504 PLA:csl COCSUDRAFT_65252 (B) K00503 HSA:hsa DBH (R) K00503 MAM:shr DBH (R) K00503 VER:lcm DBH (R) K00503 INV:bfo BRAFLDRAFT_215529 (R) K00503 ART:aag AaeL_AAEL010856 (R) K00503 DME:dme Tbh (R) KO-TBD CEL:cel tbh-1 (SUBJECT) K00503 NEM:cbr Cbr-tbh-1 (R) 0.1
Sequence labels indicate KO, taxonomy or model organism, organism name (if taxonomic group), and gene name, respectively. CEL, C. elegans; HSA, H. sapiens; DME, D. melanogaster; ATH, A. thaliana; SCE, S. cerevisiae; BAC, bacteria; ARC, archaea; PRO, protists; FUN, fungi; PLA, plants; INV, invertebrates; NEM, nematodes; ART, arthropods; VER, vertebrates; MAM, mammals. Parenthetical information for organisms other than CEL indicates whether the genes are introduced as best matches (B) or reciprocal best hits (R) to the query gene. Parenthetical information for CEL indicates whether the genes are introduced as paralogues (P) of the query gene or as reciprocal best matches to one of the other organisms in the tree (B). Organism abbreviations are from KEGG.
Reactions
ID Enzyme Reactants Products Genes (?) Multiple genes are separated by OR (I) or AND (&).

I indicates that genes are redundant within the group (e.g. paralogs encoding the same enzyme).
& indicates that genes are non-redundant within the group (e.g. genes encoding different subunits of the same enzyme).

If there are multiple groups of genes, as in an enzyme complex with some enzymes associated with multiple genes, or in a case where the same enzyme is associated with different orthology groups with paralogs, each group with multiple genes is shown in parentheses. 		Pathway
RCC0156Name: tyramine beta-monooxygenase
Type: Regular
Location: Cytosol
KEGG ID: NA

click to see details on this item
1.14.17.-Name: tyramine beta-monooxygenase

click to see details on this item
[c] : tymName: Tyramine
Formula: C8H12NO
Charge: 1




click to see details on this item + ascb-LName: L-Ascorbate
Formula: C6H8O6
Charge: 0




click to see details on this item + o2Name: O2
Formula: O2
Charge: 0




click to see details on this item
octpmnName: Octopamine
Formula: C8H12NO2
Charge: 1




click to see details on this item + dhdascbName: Dehydroascorbate
Formula: C6H6O6
Charge: 0




click to see details on this item + h2oName: H2O
Formula: H2O
Charge: 0




click to see details on this item
tbh-1
Tyrosine metabolism
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