HOME DOWNLOAD CITATION HELP
Umass Logo PSB Logo
(?) Enter a search word or phrase (left box), optionally select an appropriate field (middle), and hit the search button or press enter. This search engine is NOT case sensitive.

Use wild characters " ? " and " * " for efficient search:
  • ? : A single character. E.g., trehalose?phosphatase covers both trehalose phosphatase and trehalose-phosphatase, of which, only the latter fits the nomenclature used in this database.
  • * : Any number of characters. E.g.,tre-* brings all genes from trehalase family; coenzyme*A covers coenzyme A, coenzyme-A, and coenzymeA.
Network Biomass WormPaths
FBAFlux Balance Analysis PEAPathway Enrichment Analysis
WormClustClustering- and enrichment-based association of genes with the metabolic network
Gene Overview
Name ..................................................... : alh-11
Sequence ID ..................................................... : F42G9.5
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. ..................................................... : K00149ALDH9A1; aldehyde dehydrogenase family 9 member A1 [EC:1.2.1.47 1.2.1.3]
Enzymes in the model (?) Enzymes that are part of the current metabolic network model. ..................................................... : 1.2.1.3names: aldehyde dehydrogenase (NAD+);CoA-independent aldehyde dehydrogenase;m-methylbenzaldehyde dehydrogenase;NAD-aldehyde dehydrogenase;NAD-dependent 4-hydroxynonenal dehydrogenase;NAD-dependent aldehyde dehydrogenase;NAD-linked aldehyde dehydrogenase;propionaldehyde dehydrogenase;aldehyde dehydrogenase (NAD), 1.2.1.47names: 4-trimethylammoniobutyraldehyde dehydrogenase;4-trimethylaminobutyraldehyde dehydrogenase;4-N-trimethylaminobutyraldehyde dehydrogenase
Other enzymes (?) Enzymes that are associated with this gene in the WormFlux database, but not included in the current network model. ..................................................... : None
Model reactions (?) Reactions that are part of the current metabolic network model.

See the bottom of this page for a table of reactions. ..................................................... 		: RC00710, RC04903, RC02957, RC03283, RC01752, RC02678, RC05050, RC00631
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. ..................................................... : R00904, R03869, R02549, R02940, R04065, R04506, R01986

In WormPaths (?) Pathway maps where this gene is represented are listed here. ..................................................... :   Go to map
► | 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 Not determined
Enzyme Not determined
Reaction Not determined

Comments

  • Exception (False positive of logistic function):K00149 (dilemma: K00130 or K00149; dual comparison (score range from 0 to 1): K00130 (0.0) / K00149 (0.0); inconclusive).
  • 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 K00149 - High
Enzyme 1.2.1.47 - High
1.2.1.3 - High
Reaction R02678 - High
R02940 - High
R04903 - High
R01986 - High
R03869 - High
R02957 - High
R02549 - High
R00710 - High
R04065 - High
R03283 - High
R00904 - High
R05050 - High
R01752 - High
R00631 - High
R04506 - High

Comments

  • Based on new KEGG annotations.

► | 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 K00149 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. 		K00149 0.49 0.49 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. 		K00149 0.63 0.63 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. 		K00149 1.48 1.48 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). 		K00149 K00128
and 1 more...All best scoring KOs: K00149, K00128, K14085 		1 1 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:

"Aldehyde dehydrogenase $ Aldehyde dehydrogenase family $ Aldehyde dehydrogenase, conserved site $ Aldehyde dehydrogenase, C-terminal $ Aldehyde dehydrogenase, N-terminal $$ Aldehyde dehydrogenase" 		K00149 K11947
and 11 more...All best scoring KOs: K00149, K11947, K00132, K12907, K00138, K14085, K04072, K04021, K04073, K07469, K14519, K00128, K00129 		1.0 1.0 ERROR
Overall (?) Overall score from SACURE that represents the logistic-regression-based probability of acceptance of a KO in association with the query gene. K00149 0.998 0.998 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. 		0.48 0.94
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). 		0.97 0.00
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). 		Not available Not available
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)
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
RC00710Name: Acetaldehyde:NAD+ oxidoreductase
Type: Regular
Location: Cytosol
KEGG ID: R00710

click to see details on this item
1.2.1.3Name: aldehyde dehydrogenase (NAD+)
Other names: CoA-independent aldehyde dehydrogenase, m-methylbenzaldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, propionaldehyde dehydrogenase, aldehyde dehydrogenase (NAD)

click to see details on this item
[c] : acaldName: Acetaldehyde
Formula: C2H4O
Charge: 0




click to see details on this item + nadName: Nicotinamide adenine dinucleotide
Formula: C21H26N7O14P2
Charge: -1




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




click to see details on this item
acName: Acetate
Formula: C2H3O2
Charge: -1




click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced
Formula: C21H27N7O14P2
Charge: -2




click to see details on this item + (2) hName: H+
Formula: H
Charge: 1




click to see details on this item
(alh-2 | alh-4) | (alh-11 | alh-12)
Glycolysis / gluconeogenesis
RC04903Name: 5-Hydroxyindoleacetaldehyde:NAD+ oxidoreductase
Type: Regular
Location: Cytosol
KEGG ID: R04903

click to see details on this item
1.2.1.3Name: aldehyde dehydrogenase (NAD+)
Other names: CoA-independent aldehyde dehydrogenase, m-methylbenzaldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, propionaldehyde dehydrogenase, aldehyde dehydrogenase (NAD)

click to see details on this item
[c] : 5hoxindactName: 5-Hydroxyindoleacetaldehyde
Formula: C10H9NO2
Charge: 0




click to see details on this item + nadName: Nicotinamide adenine dinucleotide
Formula: C21H26N7O14P2
Charge: -1




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




click to see details on this item
5hoxindoaName: 5-Hydroxyindoleacetate
Formula: C10H8NO3
Charge: -1




click to see details on this item + (2) hName: H+
Formula: H
Charge: 1




click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced
Formula: C21H27N7O14P2
Charge: -2




click to see details on this item
(alh-2 | alh-4) | (alh-11 | alh-12)
Tryptophan degradation
RC02957Name: D-Glucuronolactone:NAD+ oxidoreductase
Type: Regular
Location: Cytosol
KEGG ID: R02957

click to see details on this item
1.2.1.3Name: aldehyde dehydrogenase (NAD+)
Other names: CoA-independent aldehyde dehydrogenase, m-methylbenzaldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, propionaldehyde dehydrogenase, aldehyde dehydrogenase (NAD)

click to see details on this item
[c] : glacName: "D-glucurono-6,3-lactone"
Formula: C6H8O6
Charge: 0




click to see details on this item + (2) h2oName: H2O
Formula: H2O
Charge: 0




click to see details on this item + nadName: Nicotinamide adenine dinucleotide
Formula: C21H26N7O14P2
Charge: -1




click to see details on this item
glcrName: D-Glucarate
Formula: C6H8O8
Charge: -2




click to see details on this item + (3) hName: H+
Formula: H
Charge: 1




click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced
Formula: C21H27N7O14P2
Charge: -2




click to see details on this item
(alh-2 | alh-4) | (alh-11 | alh-12)
Miscellaneous
RC03283Name: 4-Trimethylammoniobutanal:NAD+ 1-oxidoreductase
Type: Regular
Location: Cytosol
KEGG ID: R03283

click to see details on this item
1.2.1.3Name: aldehyde dehydrogenase (NAD+)
Other names: CoA-independent aldehyde dehydrogenase, m-methylbenzaldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, propionaldehyde dehydrogenase, aldehyde dehydrogenase (NAD)

click to see details on this item
1.2.1.47Name: 4-trimethylammoniobutyraldehyde dehydrogenase
Other names: 4-trimethylaminobutyraldehyde dehydrogenase, 4-N-trimethylaminobutyraldehyde dehydrogenase

click to see details on this item
[c] : 4tmeabutName: 4-Trimethylammoniobutanal
Formula: C7H16NO
Charge: 1




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




click to see details on this item + nadName: Nicotinamide adenine dinucleotide
Formula: C21H26N7O14P2
Charge: -1




click to see details on this item
4tmeabutnName: 4-Trimethylammoniobutanoate
Formula: C7H15NO2
Charge: 0




click to see details on this item + (2) hName: H+
Formula: H
Charge: 1




click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced
Formula: C21H27N7O14P2
Charge: -2




click to see details on this item
(alh-2 | alh-4) | (alh-11 | alh-12)
Carnitine biosynthesis
RC01752Name: D-Glyceraldehyde:NAD+ oxidoreductase
Type: Regular
Location: Cytosol
KEGG ID: R01752

click to see details on this item
1.2.1.3Name: aldehyde dehydrogenase (NAD+)
Other names: CoA-independent aldehyde dehydrogenase, m-methylbenzaldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, propionaldehyde dehydrogenase, aldehyde dehydrogenase (NAD)

click to see details on this item
[c] : glyaldName: D-Glyceraldehyde
Formula: C3H6O3
Charge: 0




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




click to see details on this item + nadName: Nicotinamide adenine dinucleotide
Formula: C21H26N7O14P2
Charge: -1




click to see details on this item
glyc-RName: (R)-Glycerate
Formula: C3H5O4
Charge: -1




click to see details on this item + (2) hName: H+
Formula: H
Charge: 1




click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced
Formula: C21H27N7O14P2
Charge: -2




click to see details on this item
(alh-2 | alh-4) | (alh-11 | alh-12)
Glycerolipid metabolism
RC02678Name: Indole-3-acetaldehyde:NAD+ oxidoreductase
Type: Regular
Location: Cytosol
KEGG ID: R02678

click to see details on this item
1.2.1.3Name: aldehyde dehydrogenase (NAD+)
Other names: CoA-independent aldehyde dehydrogenase, m-methylbenzaldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, propionaldehyde dehydrogenase, aldehyde dehydrogenase (NAD)

click to see details on this item
[c] : id3acaldName: Indole-3-acetaldehyde
Formula: C10H9NO
Charge: 0




click to see details on this item + nadName: Nicotinamide adenine dinucleotide
Formula: C21H26N7O14P2
Charge: -1




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




click to see details on this item
ind3acName: Indole-3-acetate
Formula: C10H8NO2
Charge: -1




click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced
Formula: C21H27N7O14P2
Charge: -2




click to see details on this item + (2) hName: H+
Formula: H
Charge: 1




click to see details on this item
(alh-2 | alh-4) | (alh-11 | alh-12)
Tryptophan degradation
RC05050Name: N4-Acetylaminobutanal:NAD+ oxidoreductase
Type: Regular
Location: Cytosol
KEGG ID: R05050

click to see details on this item
1.2.1.3Name: aldehyde dehydrogenase (NAD+)
Other names: CoA-independent aldehyde dehydrogenase, m-methylbenzaldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, propionaldehyde dehydrogenase, aldehyde dehydrogenase (NAD)

click to see details on this item
[c] : n4abutnName: N4-Acetylaminobutanal
Formula: C6H11NO2
Charge: 0




click to see details on this item + nadName: Nicotinamide adenine dinucleotide
Formula: C21H26N7O14P2
Charge: -1




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




click to see details on this item
4aabutnName: 4-Acetamidobutanoate
Formula: C6H10NO3
Charge: -1




click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced
Formula: C21H27N7O14P2
Charge: -2




click to see details on this item + (2) hName: H+
Formula: H
Charge: 1




click to see details on this item
(alh-2 | alh-4) | (alh-11 | alh-12)
Arginine metabolism
RC00631Name: aldehyde:NAD+ oxidoreductase
Type: Regular
Location: Cytosol
KEGG ID: R00631

click to see details on this item
1.2.1.3Name: aldehyde dehydrogenase (NAD+)
Other names: CoA-independent aldehyde dehydrogenase, m-methylbenzaldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, propionaldehyde dehydrogenase, aldehyde dehydrogenase (NAD)

click to see details on this item
[c] : fattyaldName: Fatty aldehyde
Formula: RC2H3O
Charge: 0




click to see details on this item + nadName: Nicotinamide adenine dinucleotide
Formula: C21H26N7O14P2
Charge: -1




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




click to see details on this item
Rtotal7Name: R total 7
Formula: C2H2O2R
Charge: -1




click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced
Formula: C21H27N7O14P2
Charge: -2




click to see details on this item + (2) hName: H+
Formula: H
Charge: 1




click to see details on this item
(alh-2 | alh-4) | (alh-11 | alh-12)
Miscellaneous
The information and tools provided in this website are to be used for academic purposes only.