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goname |
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Optionally the search can be restricted to specified GO namespaces.
% goname glycoprotein Find GO ontology terms by name Obo output file [goname.obo]: |
Go to the output files for this example
Find GO ontology terms by name
Version: EMBOSS:6.5.6.0
Standard (Mandatory) qualifiers:
[-query] string Name(s) to search for in ontology (Any
string)
[-outfile] outobo [*.goname] Output ontology term file name
Additional (Optional) qualifiers:
-namespace menu [*] By default all terms are returned.
Searches can be limited to one or a few
namespaces. (Values: biological_process
(Biological process); cellular_component
(Cellular component); molecular_function
(Molecular function))
Advanced (Unprompted) qualifiers:
-subclasses boolean [N] Extend the query matches to include all
terms which are specialisations (GO
sub-classes) of the matched type.
-obsolete boolean [N] The default behaviour is to not use or
return obsolete terms. This option if set
will include all terms.
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory2 string Output directory
-oformat2 string Ontology term output format
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
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| Qualifier | Type | Description | Allowed values | Default | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||
| [-query] (Parameter 1) |
string | Name(s) to search for in ontology | Any string | |||||||
| [-outfile] (Parameter 2) |
outobo | Output ontology term file name | OBO ontology term(s) | <*>.goname | ||||||
| Additional (Optional) qualifiers | ||||||||||
| -namespace | list | By default all terms are returned. Searches can be limited to one or a few namespaces. |
|
* | ||||||
| Advanced (Unprompted) qualifiers | ||||||||||
| -subclasses | boolean | Extend the query matches to include all terms which are specialisations (GO sub-classes) of the matched type. | Boolean value Yes/No | No | ||||||
| -obsolete | boolean | The default behaviour is to not use or return obsolete terms. This option if set will include all terms. | Boolean value Yes/No | No | ||||||
| Associated qualifiers | ||||||||||
| "-outfile" associated outobo qualifiers | ||||||||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |||||||
| -oformat2 -oformat_outfile |
string | Ontology term output format | Any string | |||||||
| General qualifiers | ||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||
The output is a standard EMBOSS ontology term file.
The results can be output in one of several styles by using the command-line qualifier -oformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: obo, brief, list, html, xml, json, excel.
See: http://emboss.sf.net/docs/themes/OntologyFormats.html for further information on ontology formats.
[Term]
id: GO:0036071
name: N-glycan fucosylation
namespace: biological_process
def: The process of transferring a fucosyl group to an N-glycan. An N-glycan is the carbohydrate portion of an N-glycoprotein when attached to a nitrogen from asparagine or arginine side-chains.
synonym: "glycoprotein fucosylation" RELATED [GOC:bf]
is_a: GO:0036065 ! fucosylation
[Term]
id: GO:0035977
name: protein deglycosylation involved in glycoprotein catabolic process
namespace: biological_process
def: The removal of sugar residues from a glycosylated protein that contributes to the breakdown of a glycoprotein.
is_a: GO:0006517 ! protein deglycosylation
relationship: part_of GO:0006516 ! glycoprotein catabolic process
[Term]
id: GO:0034436
name: glycoprotein transport
namespace: biological_process
def: The directed movement of a glycoprotein, any protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
is_a: GO:0015031 ! protein transport
[Term]
id: GO:0008424
name: glycoprotein 6-alpha-L-fucosyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + GDP-L-fucose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-[alpha-L-fucosyl-(1->6)]-N-acetyl-beta-D-glucosaminyl}asparagine + GDP + H(+).
synonym: "FucT" RELATED [EC:2.4.1.68]
synonym: "GDP-fucose--glycoprotein fucosyltransferase activity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha(1,6)fucosyltransferase activity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha(1->6)fucosyltransferase activity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha-(1,6)fucosyltransferase activity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha-(1->6)fucosyltransferase activity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-fucose--glycoprotein fucosyltransferase activity" EXACT [EC:2.4.1.68]
synonym: "GDPfucose-glycoprotein fucosyltransferase activity" EXACT [EC:2.4.1.68]
synonym: "glycoprotein fucosyltransferase activity" BROAD [EC:2.4.1.68]
synonym: "guanosine diphosphofucose--glycoprotein fucosyltransferase activity" EXACT [EC:2.4.1.68]
xref: EC:2.4.1.68
xref: KEGG:R05988
xref: MetaCyc:2.4.1.68-RXN
xref: Reactome:REACT_25399 "Addition of alpha 1,6 fucose to the first GlcNAc of the N-glycan, Homo sapiens"
xref: RHEA:12988
is_a: GO:0046921 ! alpha-(1->6)-fucosyltransferase activity
[Term]
id: GO:0018010
name: glycoprotein N-palmitoyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: palmitoyl-CoA + glycoprotein = CoA + N-palmitoylglycoprotein.
[Part of this file has been deleted for brevity]
synonym: "cell wall hydroxyproline-rich glycoprotein metabolism" EXACT []
is_a: GO:0010384 ! cell wall proteoglycan metabolic process
[Term]
id: GO:0004653
name: polypeptide N-acetylgalactosaminyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: UDP-N-acetyl-D-galactosamine + polypeptide = UDP + N-acetyl-D-galactosaminyl-polypeptide. This reaction is the modification of serine or threonine residues in polypeptide chains by the transfer of a N-acetylgalactose from UDP-N-acetylgalactose to the hydroxyl group of the amino acid; it is the first step in O-glycan biosynthesis.
synonym: "glycoprotein acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "polypeptide-N-acetylgalactosamine transferase activity" EXACT [EC:2.4.1.41]
synonym: "protein-UDP acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-acetylgalactosamine-glycoprotein acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-acetylgalactosamine:peptide-N-galactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-GalNAc:polypeptide N-acetylgalactosaminyl transferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyl-transferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine-glycoprotein N-acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine-protein N-acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine:kappa-casein polypeptide N-acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine:protein N-acetylgalactosaminyl transferase activity" EXACT [EC:2.4.1.41]
synonym: "uridine diphosphoacetylgalactosamine-glycoprotein acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.41]
xref: EC:2.4.1.41
xref: MetaCyc:2.4.1.41-RXN
xref: Reactome:REACT_115586 "Addition of GalNAc to mucins to form the Tn antigen, Homo sapiens"
is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
[Term]
id: GO:0003827
name: alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R + UDP-N-acetyl-alpha-D-glucosamine = 3-(2-[N-acetyl-beta-D-glucosaminyl]-alpha-D-mannosyl)-beta-D-mannosyl-R + H(+) + UDP.
synonym: "alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.101]
synonym: "alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.101]
synonym: "alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferase activity" EXACT []
synonym: "GnTI" RELATED [EC:2.4.1.101]
synonym: "GNTI activity" EXACT [EC:2.4.1.101]
synonym: "N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetyl-D-glucosamine:3-(alpha-D-mannosyl)-beta-D-mannosyl-glycoprotein 2-beta-N-acetyl-D-glucosaminyltransferase activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetylglucosaminyl:alpha-1,3-D-mannoside-beta-1,2-N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetylglucosaminyl:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "uridine diphosphoacetylglucosamine-alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.101]
xref: EC:2.4.1.101
xref: KEGG:R05983
xref: MetaCyc:2.4.1.101-RXN
xref: Reactome:REACT_25236 "Addition of GlcNAc to the glycan on the A arm, Homo sapiens"
xref: RHEA:11459
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
|
| Program name | Description |
|---|---|
| edamdef | Find EDAM ontology terms by definition |
| edamhasinput | Find EDAM ontology terms by has_input relation |
| edamhasoutput | Find EDAM ontology terms by has_output relation |
| edamisformat | Find EDAM ontology terms by is_format_of relation |
| edamisid | Find EDAM ontology terms by is_identifier_of relation |
| edamname | Find EDAM ontology terms by name |
| godef | Find GO ontology terms by definition |
| ontoget | Get ontology term(s) |
| ontogetcommon | Get common ancestor for terms |
| ontogetdown | Get ontology term(s) by parent id |
| ontogetobsolete | Get ontology ontology terms |
| ontogetroot | Get ontology root terms by child identifier |
| ontogetsibs | Get ontology term(s) by id with common parent |
| ontogetup | Get ontology term(s) by id of child |
| ontoisobsolete | Report whether an ontology term id is obsolete |
| ontotext | Get ontology term(s) original full text |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.