bio 2.0.3 → 2.0.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/ChangeLog +79 -0
- data/LEGAL +9 -0
- data/RELEASE_NOTES.rdoc +14 -0
- data/bioruby.gemspec +3 -1
- data/lib/bio/db/embl/uniprotkb.rb +136 -11
- data/lib/bio/version.rb +1 -1
- data/test/data/uniprot/P28907.uniprot +551 -0
- data/test/unit/bio/db/embl/test_uniprotkb_P28907.rb +325 -0
- metadata +4 -2
checksums.yaml
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 65cb8536e3646ee35c955bddcada6ecc10f0dda7540617f6bca71133894d25dd
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data.tar.gz: f7eacff38af5eec96bb377f4bc87d23fc03c3277cf843a156b5cb1b95c15afdf
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: ad51098d8e668c40b0457f9bdbc58c13e179f5a7929c2264928b3257152dc13f3b0632d3c73c2ac58e7c8e679dfa28188338a51b37a8bb31898fdb887b1e56e4
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data.tar.gz: 54f2c6da91324094ac87f0865e9e9b0c5333b8872abc9672cac73110b94ae13b7257f96ba1a75cf358f2fbb66440b4e2790c1ec50b15a381048cf5f04acd3bf8
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data/ChangeLog
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@@ -1,3 +1,82 @@
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commit 1bc877e557e165b42eea992d89f19a63996cb586
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:19:01 2022 +0900
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regenerate bioruby.gemspec with rake regemspec
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bioruby.gemspec | 4 +++-
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1 file changed, 3 insertions(+), 1 deletion(-)
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commit 190e4751b84cc45cbce636c4414482a8169b08df
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:18:06 2022 +0900
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prepare for BioRuby 2.0.4 release
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lib/bio/version.rb | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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commit a666639e0393e96b2de0bbcb447c13f8a14ad06d
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:17:11 2022 +0900
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update release notes for upcoming BioRuby 2.0.4
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RELEASE_NOTES.rdoc | 14 ++++++++++++++
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1 file changed, 14 insertions(+)
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commit c0d197343dd7fd8999d04083c9e8f24fa37a2f93
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:13:40 2022 +0900
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License of UniProt data is CC BY 4.0
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LEGAL | 9 +++++++++
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1 file changed, 9 insertions(+)
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commit e670102e6d4deb04c1fcae62459cc02861132d25
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:01:50 2022 +0900
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Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
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* Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
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after calling Bio::UniProtKB#de method.
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lib/bio/db/embl/uniprotkb.rb | 25 ++++++++++++++++++-------
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test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 11 +++++++++++
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2 files changed, 29 insertions(+), 7 deletions(-)
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commit 9c04e08e8d1316ffd7fc15ab311cea5dd6937d36
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 20:44:46 2022 +0900
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Supports format change of FT lines since UniProt release 2019_11
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* Bio::UniProtKB#ft: Supports text format change of FT lines since
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UniProt release 2019_11. (Details of the format changes:
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https://www.uniprot.org/release-notes/2019-12-18-release#text%5Fft )
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This closes https://github.com/bioruby/bioruby/issues/147 .
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* Tests are added with a new test data
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lib/bio/db/embl/uniprotkb.rb | 122 +++++-
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test/data/uniprot/P28907.uniprot | 551 +++++++++++++++++++++++++
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test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 314 ++++++++++++++
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3 files changed, 983 insertions(+), 4 deletions(-)
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create mode 100644 test/data/uniprot/P28907.uniprot
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create mode 100644 test/unit/bio/db/embl/test_uniprotkb_P28907.rb
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commit b18ee463d4328b5ef619733b46f568b18459be7a
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 23:49:18 2021 +0900
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BioRuby 2.0.3 is released
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ChangeLog | 136 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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1 file changed, 136 insertions(+)
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commit c16e230d15cf30478a3739563b4e4745dc57ef82
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 23:44:45 2021 +0900
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data/LEGAL
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@@ -114,6 +114,15 @@ test/data/uniprot/p53_human.uniprot:
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removed.
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test/data/uniprot/P28907.uniprot:
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Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
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Distributed under the Creative Commons Attribution (CC BY 4.0) License
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https://www.uniprot.org/help/license
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https://creativecommons.org/licenses/by/4.0/
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GPL:
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Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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data/RELEASE_NOTES.rdoc
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@@ -1,3 +1,17 @@
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= BioRuby 2.0.4 RELEASE NOTES
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Some fixes have been made in BioRuby 2.0.4 after the release of 2.0.3.
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== Fixes
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* Bio::UniProtKB#ft: Supports text format change of FT lines since
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UniProt release 2019_11.
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(https://github.com/bioruby/bioruby/issues/147 )
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* Bio::UniProtKB#protein_name and #synonyms methods may raise error
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after calling Bio::UniProtKB#de method.
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= BioRuby 2.0.3 RELEASE NOTES
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Some bug fixes have been made in BioRuby 2.0.3 after the release of 2.0.2.
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data/bioruby.gemspec
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#
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Gem::Specification.new do |s|
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s.name = 'bio'
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s.version = "2.0.
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s.version = "2.0.4"
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s.author = "BioRuby project"
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s.email = "staff@bioruby.org"
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"test/data/sim4/simple2-A4.sim4",
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"test/data/soft/GDS100_partial.soft",
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"test/data/soft/GSE3457_family_partial.soft",
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"test/data/uniprot/P28907.uniprot",
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"test/data/uniprot/p53_human.uniprot",
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"test/functional/bio/sequence/test_output_embl.rb",
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"test/functional/bio/test_command.rb",
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"test/unit/bio/db/embl/test_embl_to_bioseq.rb",
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"test/unit/bio/db/embl/test_uniprot.rb",
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"test/unit/bio/db/embl/test_uniprotkb.rb",
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"test/unit/bio/db/embl/test_uniprotkb_P28907.rb",
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"test/unit/bio/db/embl/test_uniprotkb_new_part.rb",
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"test/unit/bio/db/fasta/test_defline.rb",
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"test/unit/bio/db/fasta/test_defline_misc.rb",
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@@ -248,9 +248,8 @@ class UniProtKB < EMBLDB
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# SYNONYM >=0
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# CONTEINS >=0
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def protein_name
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-
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parsed_de_line
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if parsed_de_line then
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parsed_de_line = self.de
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if parsed_de_line.kind_of?(Array) then
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# since UniProtKB release 14.0 of 22-Jul-2008
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name = nil
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parsed_de_line.each do |a|
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return name
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end
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-
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# returns synonyms (unofficial and/or alternative names).
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# Returns an Array containing String objects.
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#
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# synonyms are each placed in () following the official name on the DE line.
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def synonyms
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ary = Array.new
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-
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parsed_de_line
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if parsed_de_line then
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parsed_de_line = self.de
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if parsed_de_line.kind_of?(Array) then
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# since UniProtKB release 14.0 of 22-Jul-2008
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parsed_de_line.each do |a|
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case a[0]
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return ary
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end
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# Returns an Array (for new format since rel 14)
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# or a String (for old format before rel 14) for the DE line.
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#
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def de
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return @data['DE'] if @data['DE']
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parsed_de_line = parse_DE_line_rel14(get('DE'))
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case parsed_de_line
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when Array # new format since rel14
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@data['DE'] ||= parsed_de_line
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else
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super
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end
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@data['DE']
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end
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# returns gene names in the GN line.
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#
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return ft[feature_key] if feature_key
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return @data['FT'] if @data['FT']
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1211
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ftstr = get('FT')
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ftlines = ftstr.split("\n")
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for i in 0..10 do
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if /^FT +([^\s]+) +(([^\s]+)\:)?([\<\?]?[0-9]+|\?)(?:\.\.([\>\?]?[0-9]+|\?))?\s*$/ =~ ftlines[i] &&
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/^FT +\/([^\s\=]+)(?:\=(\")?(.+)(\")?)?\s*$/ =~ ftlines[i+1] then
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fmt_2019_11 = true
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break #for i
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end
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end #for i
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hash = if fmt_2019_11 then
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ft_2019_11_parser(ftlines)
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else
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ft_legacy_parser(ftlines)
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end
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@data['FT'] = hash
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end
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# FT parser since UniProt release 2019_11
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# https://www.uniprot.org/release-notes/2019-12-18-release#text%5Fft
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def ft_2019_11_parser(ftlines)
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1232
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table = []
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1233
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cur_ft = nil
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cont = false
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begin
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1236
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ftlines.each do |line|
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if /^FT +([^\s]+) +(([^\s]+)\:)?([\<\?]?[0-9]+|\?)(?:\.\.([\>\?]?[0-9]+|\?))?\s*$/ =~ line
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cur_ft = [$1.to_s, # Feature Name
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1239
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"#{$2}#{$4}", # From
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$5.to_s, # To
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1241
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[] # Qualifiers
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1242
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]
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1243
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table.push cur_ft
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1244
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cont = false
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1245
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elsif cont && /^FT {19}/ =~ line
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1246
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str = $'
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1247
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str.rstrip!
|
1248
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orig = cur_ft[3][-1][1].to_s
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1249
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if orig.size > 0 && orig[-1] != ' ' &&
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1250
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str.length > 0 && str[0] != ' ' then
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orig.concat ' '
|
1252
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end
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1253
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orig.concat str
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cur_ft[3][-1][1] = orig
|
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if cont && orig[-1] == "\""
|
1256
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orig.chop!
|
1257
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cont = false
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end
|
1259
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elsif /^FT +\/([^\s\=]+)(?:\=(\")?(.+))?\s*$/ =~ line
|
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key = $1
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val = $3
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1262
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val.rstrip!
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1263
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cur_ft[3].push [ key, val ]
|
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cont = false
|
1265
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if $2 == "\""
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1266
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if val.to_s[-1] == "\""
|
1267
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val.chop!
|
1268
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else
|
1269
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cont = true
|
1270
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+
end
|
1271
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+
end
|
1272
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else
|
1273
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+
raise "FT parse error: #{line.inspect}"
|
1274
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+
end
|
1275
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+
end
|
1276
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+
|
1277
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hash = {}
|
1278
|
+
table.each do |feature|
|
1279
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+
cur_h = {
|
1280
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+
# Removing '<', '>' or '?' in FROM/TO endopoint.
|
1281
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'From' => feature[1].sub(/\D/, '').to_i,
|
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'To' => feature[2].sub(/\D/, '').to_i,
|
1283
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'diff' => [],
|
1284
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+
'original' => feature
|
1285
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}
|
1286
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hash[feature[0]] ||= []
|
1287
|
+
hash[feature[0]].push cur_h
|
1288
|
+
feature[3].each do |a|
|
1289
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+
case a[0]
|
1290
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+
when 'From', 'To', 'Description', 'FTId', 'diff', 'original'
|
1291
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+
; # do nothing
|
1292
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+
else
|
1293
|
+
cur_h[a[0]] = a[1]
|
1294
|
+
end
|
1295
|
+
end
|
1296
|
+
if cur_h["id"] then
|
1297
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+
cur_h['FTId'] = cur_h['id']
|
1298
|
+
end
|
1299
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+
|
1300
|
+
case feature[0]
|
1301
|
+
when 'VARSPLIC', 'VARIANT', 'VAR_SEQ', 'CONFLICT'
|
1302
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+
case cur_h['note'].to_s
|
1303
|
+
when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
|
1304
|
+
original_res = $1
|
1305
|
+
changed_res = $2
|
1306
|
+
original_res = original_res.gsub(/ /,'').strip
|
1307
|
+
chenged_res = changed_res.gsub(/ /,'').strip
|
1308
|
+
when /Missing/i
|
1309
|
+
original_res = seq.subseq(cur_h['From'],
|
1310
|
+
cur_h['To'])
|
1311
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+
changed_res = ''
|
1312
|
+
end
|
1313
|
+
cur_h['diff'] = [original_res, chenged_res]
|
1314
|
+
end
|
1315
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+
end
|
1316
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+
rescue
|
1317
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+
raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
|
1318
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+
end
|
1319
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+
|
1320
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+
hash
|
1321
|
+
end
|
1322
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+
private :ft_2019_11_parser
|
1323
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+
|
1324
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+
# FT parser for the format before Uniprot release 2019_11
|
1325
|
+
def ft_legacy_parser(ftlines)
|
1200
1326
|
table = []
|
1201
1327
|
begin
|
1202
|
-
|
1328
|
+
ftlines.each do |line|
|
1203
1329
|
if line =~ /^FT \w/
|
1204
1330
|
feature = line.chomp.ljust(74)
|
1205
1331
|
table << [feature[ 5..12].strip, # Feature Name
|
@@ -1256,10 +1382,9 @@ class UniProtKB < EMBLDB
|
|
1256
1382
|
raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
|
1257
1383
|
end
|
1258
1384
|
|
1259
|
-
|
1385
|
+
hash
|
1260
1386
|
end
|
1261
|
-
|
1262
|
-
|
1387
|
+
private :ft_legacy_parser
|
1263
1388
|
|
1264
1389
|
# returns a Hash of conteins in the SQ lines.
|
1265
1390
|
# * Bio::UniProtKBL#sq -> hsh
|
data/lib/bio/version.rb
CHANGED
@@ -10,7 +10,7 @@
|
|
10
10
|
module Bio
|
11
11
|
|
12
12
|
# BioRuby version (Array containing Integer)
|
13
|
-
BIORUBY_VERSION = [2, 0,
|
13
|
+
BIORUBY_VERSION = [2, 0, 4].extend(Comparable).freeze
|
14
14
|
|
15
15
|
# Extra version specifier (String or nil).
|
16
16
|
# Existance of the value indicates development version.
|
@@ -0,0 +1,551 @@
|
|
1
|
+
ID CD38_HUMAN Reviewed; 300 AA.
|
2
|
+
AC P28907; O00121; O00122; Q96HY4;
|
3
|
+
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
|
4
|
+
DT 23-NOV-2004, sequence version 2.
|
5
|
+
DT 03-AUG-2022, entry version 213.
|
6
|
+
DE RecName: Full=ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1;
|
7
|
+
DE EC=3.2.2.6;
|
8
|
+
DE AltName: Full=2'-phospho-ADP-ribosyl cyclase;
|
9
|
+
DE AltName: Full=2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase;
|
10
|
+
DE EC=2.4.99.20;
|
11
|
+
DE AltName: Full=2'-phospho-cyclic-ADP-ribose transferase;
|
12
|
+
DE AltName: Full=ADP-ribosyl cyclase 1;
|
13
|
+
DE Short=ADPRC 1;
|
14
|
+
DE AltName: Full=Cyclic ADP-ribose hydrolase 1;
|
15
|
+
DE Short=cADPr hydrolase 1;
|
16
|
+
DE AltName: Full=T10;
|
17
|
+
DE AltName: CD_antigen=CD38;
|
18
|
+
GN Name=CD38;
|
19
|
+
OS Homo sapiens (Human).
|
20
|
+
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
|
21
|
+
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
|
22
|
+
OC Homo.
|
23
|
+
OX NCBI_TaxID=9606;
|
24
|
+
RN [1]
|
25
|
+
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
|
26
|
+
RX PubMed=2319135;
|
27
|
+
RA Jackson D.G., Bell J.I.;
|
28
|
+
RT "Isolation of a cDNA encoding the human CD38 (T10) molecule, a cell surface
|
29
|
+
RT glycoprotein with an unusual discontinuous pattern of expression during
|
30
|
+
RT lymphocyte differentiation.";
|
31
|
+
RL J. Immunol. 144:2811-2815(1990).
|
32
|
+
RN [2]
|
33
|
+
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1
|
34
|
+
RP AND 2), AND TISSUE SPECIFICITY.
|
35
|
+
RC TISSUE=Esophageal carcinoma, and Pancreas;
|
36
|
+
RX PubMed=9074508; DOI=10.1016/s0378-1119(96)00723-8;
|
37
|
+
RA Nata K., Takamura T., Karasawa T., Kumagai T., Hashioka W., Tohgo A.,
|
38
|
+
RA Yonekura H., Takasawa S., Nakamura S., Okamoto H.;
|
39
|
+
RT "Human gene encoding CD38 (ADP-ribosyl cyclase/cyclic ADP-ribose
|
40
|
+
RT hydrolase): organization, nucleotide sequence and alternative splicing.";
|
41
|
+
RL Gene 186:285-292(1997).
|
42
|
+
RN [3]
|
43
|
+
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
|
44
|
+
RC TISSUE=B-cell;
|
45
|
+
RX PubMed=15489334; DOI=10.1101/gr.2596504;
|
46
|
+
RG The MGC Project Team;
|
47
|
+
RT "The status, quality, and expansion of the NIH full-length cDNA project:
|
48
|
+
RT the Mammalian Gene Collection (MGC).";
|
49
|
+
RL Genome Res. 14:2121-2127(2004).
|
50
|
+
RN [4]
|
51
|
+
RP SIMILARITY TO NADASE.
|
52
|
+
RX PubMed=1471258; DOI=10.1016/0968-0004(92)90337-9;
|
53
|
+
RA States D.J., Walseth T.F., Lee H.C.;
|
54
|
+
RT "Similarities in amino acid sequences of Aplysia ADP-ribosyl cyclase and
|
55
|
+
RT human lymphocyte antigen CD38.";
|
56
|
+
RL Trends Biochem. Sci. 17:495-495(1992).
|
57
|
+
RN [5]
|
58
|
+
RP CHARACTERIZATION.
|
59
|
+
RX PubMed=8253715; DOI=10.1016/s0021-9258(19)74275-6;
|
60
|
+
RA Takasawa S., Tohgo A., Noguchi N., Koguma T., Nata K., Sugimoto T.,
|
61
|
+
RA Yonekura H., Okamoto H.;
|
62
|
+
RT "Synthesis and hydrolysis of cyclic ADP-ribose by human leukocyte antigen
|
63
|
+
RT CD38 and inhibition of the hydrolysis by ATP.";
|
64
|
+
RL J. Biol. Chem. 268:26052-26054(1993).
|
65
|
+
RN [6]
|
66
|
+
RP ACTIVE SITE, AND MUTAGENESIS OF CYS-119; CYS-160; CYS-173 AND CYS-201.
|
67
|
+
RX PubMed=7961800; DOI=10.1016/s0021-9258(19)61940-x;
|
68
|
+
RA Tohgo A., Takasawa S., Noguchi N., Koguma T., Nata K., Sugimoto T.,
|
69
|
+
RA Furuya Y., Yonekura H., Okamoto H.;
|
70
|
+
RT "Essential cysteine residues for cyclic ADP-ribose synthesis and hydrolysis
|
71
|
+
RT by CD38.";
|
72
|
+
RL J. Biol. Chem. 269:28555-28557(1994).
|
73
|
+
RN [7]
|
74
|
+
RP SPLICE ISOFORM(S) THAT ARE POTENTIAL NMD TARGET(S).
|
75
|
+
RX PubMed=14759258; DOI=10.1186/gb-2004-5-2-r8;
|
76
|
+
RA Hillman R.T., Green R.E., Brenner S.E.;
|
77
|
+
RT "An unappreciated role for RNA surveillance.";
|
78
|
+
RL Genome Biol. 5:R8.1-R8.16(2004).
|
79
|
+
RN [8]
|
80
|
+
RP CATALYTIC ACTIVITY.
|
81
|
+
RX PubMed=16690024; DOI=10.1016/j.bbrc.2006.04.096;
|
82
|
+
RA Moreschi I., Bruzzone S., Melone L., De Flora A., Zocchi E.;
|
83
|
+
RT "NAADP+ synthesis from cADPRP and nicotinic acid by ADP-ribosyl cyclases.";
|
84
|
+
RL Biochem. Biophys. Res. Commun. 345:573-580(2006).
|
85
|
+
RN [9]
|
86
|
+
RP GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-100; ASN-209 AND ASN-219.
|
87
|
+
RC TISSUE=Liver;
|
88
|
+
RX PubMed=19159218; DOI=10.1021/pr8008012;
|
89
|
+
RA Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.;
|
90
|
+
RT "Glycoproteomics analysis of human liver tissue by combination of multiple
|
91
|
+
RT enzyme digestion and hydrazide chemistry.";
|
92
|
+
RL J. Proteome Res. 8:651-661(2009).
|
93
|
+
RN [10]
|
94
|
+
RP GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-219.
|
95
|
+
RC TISSUE=Leukemic T-cell;
|
96
|
+
RX PubMed=19349973; DOI=10.1038/nbt.1532;
|
97
|
+
RA Wollscheid B., Bausch-Fluck D., Henderson C., O'Brien R., Bibel M.,
|
98
|
+
RA Schiess R., Aebersold R., Watts J.D.;
|
99
|
+
RT "Mass-spectrometric identification and relative quantification of N-linked
|
100
|
+
RT cell surface glycoproteins.";
|
101
|
+
RL Nat. Biotechnol. 27:378-386(2009).
|
102
|
+
RN [11]
|
103
|
+
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
|
104
|
+
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
|
105
|
+
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
|
106
|
+
RA Bennett K.L., Superti-Furga G., Colinge J.;
|
107
|
+
RT "Initial characterization of the human central proteome.";
|
108
|
+
RL BMC Syst. Biol. 5:17-17(2011).
|
109
|
+
RN [12]
|
110
|
+
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
|
111
|
+
RX PubMed=25944712; DOI=10.1002/pmic.201400617;
|
112
|
+
RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
|
113
|
+
RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
|
114
|
+
RT "N-terminome analysis of the human mitochondrial proteome.";
|
115
|
+
RL Proteomics 15:2519-2524(2015).
|
116
|
+
RN [13]
|
117
|
+
RP X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS) OF 45-300, AND DISULFIDE BONDS.
|
118
|
+
RX PubMed=16154090; DOI=10.1016/j.str.2005.05.012;
|
119
|
+
RA Liu Q., Kriksunov I.A., Graeff R., Munshi C., Lee H.C., Hao Q.;
|
120
|
+
RT "Crystal structure of human CD38 extracellular domain.";
|
121
|
+
RL Structure 13:1331-1339(2005).
|
122
|
+
RN [14]
|
123
|
+
RP VARIANT TRP-140.
|
124
|
+
RX PubMed=9754820; DOI=10.1007/s001250051026;
|
125
|
+
RA Yagui K., Shimada F., Mimura M., Hashimoto N., Suzuki Y., Tokuyama Y.,
|
126
|
+
RA Nata K., Tohgo A., Ikehata F., Takasawa S., Okamoto H., Makino H.,
|
127
|
+
RA Saito Y., Kanatsuka A.;
|
128
|
+
RT "A missense mutation in the CD38 gene, a novel factor for insulin
|
129
|
+
RT secretion: association with Type II diabetes mellitus in Japanese subjects
|
130
|
+
RT and evidence of abnormal function when expressed in vitro.";
|
131
|
+
RL Diabetologia 41:1024-1028(1998).
|
132
|
+
CC -!- FUNCTION: Synthesizes the second messengers cyclic ADP-ribose and
|
133
|
+
CC nicotinate-adenine dinucleotide phosphate, the former a second
|
134
|
+
CC messenger for glucose-induced insulin secretion. Also has cADPr
|
135
|
+
CC hydrolase activity. Also moonlights as a receptor in cells of the
|
136
|
+
CC immune system.
|
137
|
+
CC -!- CATALYTIC ACTIVITY:
|
138
|
+
CC Reaction=H2O + NAD(+) = ADP-D-ribose + H(+) + nicotinamide;
|
139
|
+
CC Xref=Rhea:RHEA:16301, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
|
140
|
+
CC ChEBI:CHEBI:17154, ChEBI:CHEBI:57540, ChEBI:CHEBI:57967; EC=3.2.2.6;
|
141
|
+
CC Evidence={ECO:0000269|PubMed:16690024};
|
142
|
+
CC -!- CATALYTIC ACTIVITY:
|
143
|
+
CC Reaction=NADP(+) + nicotinate = nicotinamide + nicotinate-adenine
|
144
|
+
CC dinucleotide phosphate; Xref=Rhea:RHEA:38599, ChEBI:CHEBI:17154,
|
145
|
+
CC ChEBI:CHEBI:32544, ChEBI:CHEBI:58349, ChEBI:CHEBI:75967;
|
146
|
+
CC EC=2.4.99.20; Evidence={ECO:0000269|PubMed:16690024};
|
147
|
+
CC -!- ACTIVITY REGULATION: ATP inhibits the hydrolyzing activity.
|
148
|
+
CC -!- SUBCELLULAR LOCATION: Membrane; Single-pass type II membrane protein.
|
149
|
+
CC -!- ALTERNATIVE PRODUCTS:
|
150
|
+
CC Event=Alternative splicing; Named isoforms=2;
|
151
|
+
CC Name=1;
|
152
|
+
CC IsoId=P28907-1; Sequence=Displayed;
|
153
|
+
CC Name=2;
|
154
|
+
CC IsoId=P28907-2; Sequence=VSP_000707, VSP_000708;
|
155
|
+
CC -!- TISSUE SPECIFICITY: Expressed at high levels in pancreas, liver,
|
156
|
+
CC kidney, brain, testis, ovary, placenta, malignant lymphoma and
|
157
|
+
CC neuroblastoma. {ECO:0000269|PubMed:9074508}.
|
158
|
+
CC -!- DEVELOPMENTAL STAGE: Preferentially expressed at both early and late
|
159
|
+
CC stages of the B and T-cell maturation. It is also detected on erythroid
|
160
|
+
CC and myeloid progenitors in bone marrow, where the level of surface
|
161
|
+
CC expression was shown to decrease during differentiation of blast-
|
162
|
+
CC forming unit E to colony-forming unit E.
|
163
|
+
CC -!- MISCELLANEOUS: [Isoform 2]: May be produced at very low levels due to a
|
164
|
+
CC premature stop codon in the mRNA, leading to nonsense-mediated mRNA
|
165
|
+
CC decay. {ECO:0000305}.
|
166
|
+
CC -!- SIMILARITY: Belongs to the ADP-ribosyl cyclase family. {ECO:0000305}.
|
167
|
+
CC -!- WEB RESOURCE: Name=Wikipedia; Note=CD38 entry;
|
168
|
+
CC URL="https://en.wikipedia.org/wiki/CD38";
|
169
|
+
CC -!- WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and
|
170
|
+
CC Haematology;
|
171
|
+
CC URL="http://atlasgeneticsoncology.org/Genes/CD38ID978ch4p15.html";
|
172
|
+
CC ---------------------------------------------------------------------------
|
173
|
+
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
|
174
|
+
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
|
175
|
+
CC ---------------------------------------------------------------------------
|
176
|
+
DR EMBL; M34461; AAA68482.1; -; mRNA.
|
177
|
+
DR EMBL; D84276; BAA18964.1; -; mRNA.
|
178
|
+
DR EMBL; D84277; BAA18965.1; -; mRNA.
|
179
|
+
DR EMBL; D84284; BAA18966.1; -; Genomic_DNA.
|
180
|
+
DR EMBL; BC007964; AAH07964.1; -; mRNA.
|
181
|
+
DR CCDS; CCDS3417.1; -. [P28907-1]
|
182
|
+
DR PIR; A43521; A43521.
|
183
|
+
DR RefSeq; NP_001766.2; NM_001775.3. [P28907-1]
|
184
|
+
DR PDB; 1YH3; X-ray; 1.91 A; A/B=45-300.
|
185
|
+
DR PDB; 1ZVM; X-ray; 2.20 A; A/B/C/D=45-300.
|
186
|
+
DR PDB; 2EF1; X-ray; 2.40 A; A/B=45-300.
|
187
|
+
DR PDB; 2HCT; X-ray; 1.95 A; A/B=45-300.
|
188
|
+
DR PDB; 2I65; X-ray; 1.90 A; A/B=45-300.
|
189
|
+
DR PDB; 2I66; X-ray; 1.70 A; A/B=45-300.
|
190
|
+
DR PDB; 2I67; X-ray; 1.71 A; A/B=45-300.
|
191
|
+
DR PDB; 2O3Q; X-ray; 1.98 A; A/B=45-300.
|
192
|
+
DR PDB; 2O3R; X-ray; 1.75 A; A/B=45-300.
|
193
|
+
DR PDB; 2O3S; X-ray; 1.50 A; A/B=45-300.
|
194
|
+
DR PDB; 2O3T; X-ray; 1.68 A; A/B=45-300.
|
195
|
+
DR PDB; 2O3U; X-ray; 2.11 A; A/B=45-300.
|
196
|
+
DR PDB; 2PGJ; X-ray; 1.71 A; A/B=45-300.
|
197
|
+
DR PDB; 2PGL; X-ray; 1.76 A; A/B=45-300.
|
198
|
+
DR PDB; 3DZF; X-ray; 2.01 A; A/B/C/D/E/F=45-300.
|
199
|
+
DR PDB; 3DZG; X-ray; 1.65 A; A/B=45-300.
|
200
|
+
DR PDB; 3DZH; X-ray; 1.60 A; A/B=45-300.
|
201
|
+
DR PDB; 3DZI; X-ray; 1.73 A; A/B=45-300.
|
202
|
+
DR PDB; 3DZJ; X-ray; 1.90 A; A/B=45-300.
|
203
|
+
DR PDB; 3DZK; X-ray; 1.81 A; A/B=45-300.
|
204
|
+
DR PDB; 3F6Y; X-ray; 1.45 A; A=45-300.
|
205
|
+
DR PDB; 3I9M; X-ray; 1.75 A; A/B=45-300.
|
206
|
+
DR PDB; 3I9N; X-ray; 2.01 A; A/B=45-300.
|
207
|
+
DR PDB; 3OFS; X-ray; 2.20 A; A/B/C/D/E/F=46-300.
|
208
|
+
DR PDB; 3RAJ; X-ray; 3.04 A; A=46-300.
|
209
|
+
DR PDB; 3ROK; X-ray; 1.65 A; A/B=45-296.
|
210
|
+
DR PDB; 3ROM; X-ray; 2.04 A; A/B=45-296.
|
211
|
+
DR PDB; 3ROP; X-ray; 1.94 A; A/B=45-296.
|
212
|
+
DR PDB; 3ROQ; X-ray; 2.10 A; A/B=45-296.
|
213
|
+
DR PDB; 3U4H; X-ray; 1.88 A; A/B=45-300.
|
214
|
+
DR PDB; 3U4I; X-ray; 2.12 A; A/B=45-300.
|
215
|
+
DR PDB; 4CMH; X-ray; 1.53 A; A=45-300.
|
216
|
+
DR PDB; 4F45; X-ray; 2.10 A; A/B=46-300.
|
217
|
+
DR PDB; 4F46; X-ray; 1.69 A; A/B=46-300.
|
218
|
+
DR PDB; 4OGW; X-ray; 2.05 A; A=46-300.
|
219
|
+
DR PDB; 4TMF; X-ray; 2.05 A; A/B=50-300.
|
220
|
+
DR PDB; 4XJS; X-ray; 2.80 A; A=46-300.
|
221
|
+
DR PDB; 4XJT; X-ray; 2.60 A; A=46-300.
|
222
|
+
DR PDB; 5F1K; X-ray; 2.30 A; A/B=45-300.
|
223
|
+
DR PDB; 5F1O; X-ray; 2.20 A; A=46-300.
|
224
|
+
DR PDB; 5F21; X-ray; 1.90 A; A=46-300.
|
225
|
+
DR PDB; 6EDR; X-ray; 2.40 A; A/B=45-300.
|
226
|
+
DR PDB; 6VUA; X-ray; 1.50 A; A/B=45-300.
|
227
|
+
DR PDB; 7DHA; X-ray; 2.55 A; A=45-300.
|
228
|
+
DR PDB; 7DUO; X-ray; 2.81 A; B=57-285.
|
229
|
+
DR PDBsum; 1YH3; -.
|
230
|
+
DR PDBsum; 1ZVM; -.
|
231
|
+
DR PDBsum; 2EF1; -.
|
232
|
+
DR PDBsum; 2HCT; -.
|
233
|
+
DR PDBsum; 2I65; -.
|
234
|
+
DR PDBsum; 2I66; -.
|
235
|
+
DR PDBsum; 2I67; -.
|
236
|
+
DR PDBsum; 2O3Q; -.
|
237
|
+
DR PDBsum; 2O3R; -.
|
238
|
+
DR PDBsum; 2O3S; -.
|
239
|
+
DR PDBsum; 2O3T; -.
|
240
|
+
DR PDBsum; 2O3U; -.
|
241
|
+
DR PDBsum; 2PGJ; -.
|
242
|
+
DR PDBsum; 2PGL; -.
|
243
|
+
DR PDBsum; 3DZF; -.
|
244
|
+
DR PDBsum; 3DZG; -.
|
245
|
+
DR PDBsum; 3DZH; -.
|
246
|
+
DR PDBsum; 3DZI; -.
|
247
|
+
DR PDBsum; 3DZJ; -.
|
248
|
+
DR PDBsum; 3DZK; -.
|
249
|
+
DR PDBsum; 3F6Y; -.
|
250
|
+
DR PDBsum; 3I9M; -.
|
251
|
+
DR PDBsum; 3I9N; -.
|
252
|
+
DR PDBsum; 3OFS; -.
|
253
|
+
DR PDBsum; 3RAJ; -.
|
254
|
+
DR PDBsum; 3ROK; -.
|
255
|
+
DR PDBsum; 3ROM; -.
|
256
|
+
DR PDBsum; 3ROP; -.
|
257
|
+
DR PDBsum; 3ROQ; -.
|
258
|
+
DR PDBsum; 3U4H; -.
|
259
|
+
DR PDBsum; 3U4I; -.
|
260
|
+
DR PDBsum; 4CMH; -.
|
261
|
+
DR PDBsum; 4F45; -.
|
262
|
+
DR PDBsum; 4F46; -.
|
263
|
+
DR PDBsum; 4OGW; -.
|
264
|
+
DR PDBsum; 4TMF; -.
|
265
|
+
DR PDBsum; 4XJS; -.
|
266
|
+
DR PDBsum; 4XJT; -.
|
267
|
+
DR PDBsum; 5F1K; -.
|
268
|
+
DR PDBsum; 5F1O; -.
|
269
|
+
DR PDBsum; 5F21; -.
|
270
|
+
DR PDBsum; 6EDR; -.
|
271
|
+
DR PDBsum; 6VUA; -.
|
272
|
+
DR PDBsum; 7DHA; -.
|
273
|
+
DR PDBsum; 7DUO; -.
|
274
|
+
DR AlphaFoldDB; P28907; -.
|
275
|
+
DR SMR; P28907; -.
|
276
|
+
DR BioGRID; 107390; 10.
|
277
|
+
DR IntAct; P28907; 5.
|
278
|
+
DR STRING; 9606.ENSP00000226279; -.
|
279
|
+
DR BindingDB; P28907; -.
|
280
|
+
DR ChEMBL; CHEMBL4660; -.
|
281
|
+
DR DrugBank; DB09331; Daratumumab.
|
282
|
+
DR DrugBank; DB14811; Isatuximab.
|
283
|
+
DR DrugBank; DB16370; Mezagitamab.
|
284
|
+
DR DrugCentral; P28907; -.
|
285
|
+
DR GuidetoPHARMACOLOGY; 2766; -.
|
286
|
+
DR GlyConnect; 997; 1 N-Linked glycan (1 site).
|
287
|
+
DR GlyGen; P28907; 5 sites, 1 N-linked glycan (1 site).
|
288
|
+
DR iPTMnet; P28907; -.
|
289
|
+
DR PhosphoSitePlus; P28907; -.
|
290
|
+
DR SwissPalm; P28907; -.
|
291
|
+
DR BioMuta; CD38; -.
|
292
|
+
DR DMDM; 55977782; -.
|
293
|
+
DR EPD; P28907; -.
|
294
|
+
DR jPOST; P28907; -.
|
295
|
+
DR MassIVE; P28907; -.
|
296
|
+
DR MaxQB; P28907; -.
|
297
|
+
DR PaxDb; P28907; -.
|
298
|
+
DR PeptideAtlas; P28907; -.
|
299
|
+
DR PRIDE; P28907; -.
|
300
|
+
DR ProteomicsDB; 54507; -. [P28907-1]
|
301
|
+
DR ProteomicsDB; 54508; -. [P28907-2]
|
302
|
+
DR ABCD; P28907; 65 sequenced antibodies.
|
303
|
+
DR Antibodypedia; 9844; 2499 antibodies from 55 providers.
|
304
|
+
DR CPTC; P28907; 1 antibody.
|
305
|
+
DR DNASU; 952; -.
|
306
|
+
DR Ensembl; ENST00000226279.8; ENSP00000226279.2; ENSG00000004468.13. [P28907-1]
|
307
|
+
DR Ensembl; ENST00000502843.5; ENSP00000427277.1; ENSG00000004468.13. [P28907-2]
|
308
|
+
DR GeneID; 952; -.
|
309
|
+
DR KEGG; hsa:952; -.
|
310
|
+
DR MANE-Select; ENST00000226279.8; ENSP00000226279.2; NM_001775.4; NP_001766.2.
|
311
|
+
DR UCSC; uc003gol.2; human. [P28907-1]
|
312
|
+
DR CTD; 952; -.
|
313
|
+
DR DisGeNET; 952; -.
|
314
|
+
DR GeneCards; CD38; -.
|
315
|
+
DR HGNC; HGNC:1667; CD38.
|
316
|
+
DR HPA; ENSG00000004468; Tissue enhanced (lymphoid).
|
317
|
+
DR MIM; 107270; gene.
|
318
|
+
DR neXtProt; NX_P28907; -.
|
319
|
+
DR OpenTargets; ENSG00000004468; -.
|
320
|
+
DR PharmGKB; PA26214; -.
|
321
|
+
DR VEuPathDB; HostDB:ENSG00000004468; -.
|
322
|
+
DR eggNOG; ENOG502S1HV; Eukaryota.
|
323
|
+
DR GeneTree; ENSGT00390000017291; -.
|
324
|
+
DR HOGENOM; CLU_2025937_0_0_1; -.
|
325
|
+
DR InParanoid; P28907; -.
|
326
|
+
DR OMA; MNYDSCP; -.
|
327
|
+
DR PhylomeDB; P28907; -.
|
328
|
+
DR TreeFam; TF332530; -.
|
329
|
+
DR BioCyc; MetaCyc:HS00103-MON; -.
|
330
|
+
DR BRENDA; 2.4.99.20; 2681.
|
331
|
+
DR BRENDA; 3.2.2.5; 2681.
|
332
|
+
DR BRENDA; 3.2.2.6; 2681.
|
333
|
+
DR PathwayCommons; P28907; -.
|
334
|
+
DR Reactome; R-HSA-196807; Nicotinate metabolism.
|
335
|
+
DR SABIO-RK; P28907; -.
|
336
|
+
DR SignaLink; P28907; -.
|
337
|
+
DR SIGNOR; P28907; -.
|
338
|
+
DR BioGRID-ORCS; 952; 8 hits in 1077 CRISPR screens.
|
339
|
+
DR ChiTaRS; CD38; human.
|
340
|
+
DR EvolutionaryTrace; P28907; -.
|
341
|
+
DR GeneWiki; CD38; -.
|
342
|
+
DR GenomeRNAi; 952; -.
|
343
|
+
DR Pharos; P28907; Tclin.
|
344
|
+
DR PRO; PR:P28907; -.
|
345
|
+
DR Proteomes; UP000005640; Chromosome 4.
|
346
|
+
DR RNAct; P28907; protein.
|
347
|
+
DR Bgee; ENSG00000004468; Expressed in seminal vesicle and 129 other tissues.
|
348
|
+
DR ExpressionAtlas; P28907; baseline and differential.
|
349
|
+
DR Genevisible; P28907; HS.
|
350
|
+
DR GO; GO:0016323; C:basolateral plasma membrane; IEA:Ensembl.
|
351
|
+
DR GO; GO:0009986; C:cell surface; IEA:Ensembl.
|
352
|
+
DR GO; GO:0070062; C:extracellular exosome; HDA:UniProtKB.
|
353
|
+
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
|
354
|
+
DR GO; GO:0016020; C:membrane; TAS:ProtInc.
|
355
|
+
DR GO; GO:0005634; C:nucleus; IEA:Ensembl.
|
356
|
+
DR GO; GO:0005886; C:plasma membrane; IDA:HPA.
|
357
|
+
DR GO; GO:0030667; C:secretory granule membrane; IEA:Ensembl.
|
358
|
+
DR GO; GO:0042802; F:identical protein binding; IEA:Ensembl.
|
359
|
+
DR GO; GO:0050135; F:NAD(P)+ nucleosidase activity; IEA:UniProtKB-EC.
|
360
|
+
DR GO; GO:0003953; F:NAD+ nucleosidase activity; IBA:GO_Central.
|
361
|
+
DR GO; GO:0061809; F:NAD+ nucleotidase, cyclic ADP-ribose generating; IEA:UniProtKB-EC.
|
362
|
+
DR GO; GO:0016849; F:phosphorus-oxygen lyase activity; IBA:GO_Central.
|
363
|
+
DR GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
|
364
|
+
DR GO; GO:0097190; P:apoptotic signaling pathway; TAS:ProtInc.
|
365
|
+
DR GO; GO:0014824; P:artery smooth muscle contraction; IEA:Ensembl.
|
366
|
+
DR GO; GO:0042100; P:B cell proliferation; IEA:Ensembl.
|
367
|
+
DR GO; GO:0050853; P:B cell receptor signaling pathway; IMP:UniProtKB.
|
368
|
+
DR GO; GO:0007565; P:female pregnancy; IEA:Ensembl.
|
369
|
+
DR GO; GO:0060292; P:long-term synaptic depression; IEA:Ensembl.
|
370
|
+
DR GO; GO:0019674; P:NAD metabolic process; TAS:Reactome.
|
371
|
+
DR GO; GO:0043066; P:negative regulation of apoptotic process; IMP:UniProtKB.
|
372
|
+
DR GO; GO:0045779; P:negative regulation of bone resorption; IEA:Ensembl.
|
373
|
+
DR GO; GO:0010977; P:negative regulation of neuron projection development; IEA:Ensembl.
|
374
|
+
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IMP:UniProtKB.
|
375
|
+
DR GO; GO:0030890; P:positive regulation of B cell proliferation; IMP:UniProtKB.
|
376
|
+
DR GO; GO:0030307; P:positive regulation of cell growth; IEA:Ensembl.
|
377
|
+
DR GO; GO:0007204; P:positive regulation of cytosolic calcium ion concentration; IEA:Ensembl.
|
378
|
+
DR GO; GO:0032024; P:positive regulation of insulin secretion; IEA:Ensembl.
|
379
|
+
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:UniProtKB.
|
380
|
+
DR GO; GO:0045907; P:positive regulation of vasoconstriction; IEA:Ensembl.
|
381
|
+
DR GO; GO:0032355; P:response to estradiol; IEA:Ensembl.
|
382
|
+
DR GO; GO:0033194; P:response to hydroperoxide; IEA:Ensembl.
|
383
|
+
DR GO; GO:0001666; P:response to hypoxia; IEA:Ensembl.
|
384
|
+
DR GO; GO:0070555; P:response to interleukin-1; IEA:Ensembl.
|
385
|
+
DR GO; GO:0032570; P:response to progesterone; IEA:Ensembl.
|
386
|
+
DR GO; GO:0032526; P:response to retinoic acid; IEA:Ensembl.
|
387
|
+
DR GO; GO:0009410; P:response to xenobiotic stimulus; IMP:UniProtKB.
|
388
|
+
DR GO; GO:0007165; P:signal transduction; NAS:ProtInc.
|
389
|
+
DR CDD; cd04759; Rib_hydrolase; 1.
|
390
|
+
DR InterPro; IPR003193; ADP-ribosyl_cyclase.
|
391
|
+
DR InterPro; IPR033567; CD38.
|
392
|
+
DR PANTHER; PTHR10912; PTHR10912; 1.
|
393
|
+
DR PANTHER; PTHR10912:SF5; PTHR10912:SF5; 1.
|
394
|
+
DR Pfam; PF02267; Rib_hydrolayse; 1.
|
395
|
+
PE 1: Evidence at protein level;
|
396
|
+
KW 3D-structure; Alternative splicing; Diabetes mellitus; Disulfide bond;
|
397
|
+
KW Glycoprotein; Hydrolase; Membrane; NAD; NADP; Receptor; Reference proteome;
|
398
|
+
KW Signal-anchor; Transferase; Transmembrane; Transmembrane helix.
|
399
|
+
FT CHAIN 1..300
|
400
|
+
FT /note="ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1"
|
401
|
+
FT /id="PRO_0000144066"
|
402
|
+
FT TOPO_DOM 1..21
|
403
|
+
FT /note="Cytoplasmic"
|
404
|
+
FT /evidence="ECO:0000255"
|
405
|
+
FT TRANSMEM 22..42
|
406
|
+
FT /note="Helical; Signal-anchor for type II membrane protein"
|
407
|
+
FT /evidence="ECO:0000255"
|
408
|
+
FT TOPO_DOM 43..300
|
409
|
+
FT /note="Extracellular"
|
410
|
+
FT /evidence="ECO:0000255"
|
411
|
+
FT ACT_SITE 119
|
412
|
+
FT /evidence="ECO:0000269|PubMed:7961800"
|
413
|
+
FT ACT_SITE 201
|
414
|
+
FT /evidence="ECO:0000269|PubMed:7961800"
|
415
|
+
FT CARBOHYD 100
|
416
|
+
FT /note="N-linked (GlcNAc...) asparagine"
|
417
|
+
FT /evidence="ECO:0000269|PubMed:19159218"
|
418
|
+
FT CARBOHYD 164
|
419
|
+
FT /note="N-linked (GlcNAc...) asparagine"
|
420
|
+
FT /evidence="ECO:0000255"
|
421
|
+
FT CARBOHYD 209
|
422
|
+
FT /note="N-linked (GlcNAc...) asparagine"
|
423
|
+
FT /evidence="ECO:0000269|PubMed:19159218"
|
424
|
+
FT CARBOHYD 219
|
425
|
+
FT /note="N-linked (GlcNAc...) asparagine"
|
426
|
+
FT /evidence="ECO:0000269|PubMed:19159218,
|
427
|
+
FT ECO:0000269|PubMed:19349973"
|
428
|
+
FT DISULFID 67..82
|
429
|
+
FT /evidence="ECO:0000269|PubMed:16154090"
|
430
|
+
FT DISULFID 99..180
|
431
|
+
FT /evidence="ECO:0000269|PubMed:16154090"
|
432
|
+
FT DISULFID 160..173
|
433
|
+
FT /evidence="ECO:0000269|PubMed:16154090"
|
434
|
+
FT DISULFID 254..275
|
435
|
+
FT /evidence="ECO:0000269|PubMed:16154090"
|
436
|
+
FT DISULFID 287..296
|
437
|
+
FT /evidence="ECO:0000269|PubMed:16154090"
|
438
|
+
FT VAR_SEQ 122
|
439
|
+
FT /note="I -> K (in isoform 2)"
|
440
|
+
FT /evidence="ECO:0000303|PubMed:9074508"
|
441
|
+
FT /id="VSP_000707"
|
442
|
+
FT VAR_SEQ 123..300
|
443
|
+
FT /note="Missing (in isoform 2)"
|
444
|
+
FT /evidence="ECO:0000303|PubMed:9074508"
|
445
|
+
FT /id="VSP_000708"
|
446
|
+
FT VARIANT 140
|
447
|
+
FT /note="R -> W (seems to contribute to the development of
|
448
|
+
FT type II diabetes; 50% reduction in activity;
|
449
|
+
FT dbSNP:rs1800561)"
|
450
|
+
FT /evidence="ECO:0000269|PubMed:9754820"
|
451
|
+
FT /id="VAR_001323"
|
452
|
+
FT MUTAGEN 119
|
453
|
+
FT /note="C->K: Loss of cADPr hydrolase activity."
|
454
|
+
FT /evidence="ECO:0000269|PubMed:7961800"
|
455
|
+
FT MUTAGEN 119
|
456
|
+
FT /note="C->R,E,A: Loss of cADPr hydrolase and ADP-ribosyl
|
457
|
+
FT cyclase activity."
|
458
|
+
FT /evidence="ECO:0000269|PubMed:7961800"
|
459
|
+
FT MUTAGEN 160
|
460
|
+
FT /note="C->A: Loss of cADPr hydrolase and ADP-ribosyl
|
461
|
+
FT cyclase activity."
|
462
|
+
FT /evidence="ECO:0000269|PubMed:7961800"
|
463
|
+
FT MUTAGEN 173
|
464
|
+
FT /note="C->A: Loss of cADPr hydrolase and ADP-ribosyl
|
465
|
+
FT cyclase activity."
|
466
|
+
FT /evidence="ECO:0000269|PubMed:7961800"
|
467
|
+
FT MUTAGEN 201
|
468
|
+
FT /note="C->D,K,A: Loss of cADPr hydrolase and ADP-ribosyl
|
469
|
+
FT cyclase activity."
|
470
|
+
FT /evidence="ECO:0000269|PubMed:7961800"
|
471
|
+
FT MUTAGEN 201
|
472
|
+
FT /note="C->E: Loss of cADPr hydrolase activity."
|
473
|
+
FT /evidence="ECO:0000269|PubMed:7961800"
|
474
|
+
FT CONFLICT 49
|
475
|
+
FT /note="Q -> T (in Ref. 1; AAA68482)"
|
476
|
+
FT /evidence="ECO:0000305"
|
477
|
+
FT STRAND 51..53
|
478
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
479
|
+
FT HELIX 59..73
|
480
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
481
|
+
FT HELIX 75..77
|
482
|
+
FT /evidence="ECO:0007829|PDB:2O3S"
|
483
|
+
FT HELIX 82..93
|
484
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
485
|
+
FT STRAND 94..96
|
486
|
+
FT /evidence="ECO:0007829|PDB:3RAJ"
|
487
|
+
FT HELIX 98..100
|
488
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
489
|
+
FT HELIX 103..106
|
490
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
491
|
+
FT HELIX 107..112
|
492
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
493
|
+
FT HELIX 119..121
|
494
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
495
|
+
FT STRAND 122..127
|
496
|
+
FT /evidence="ECO:0007829|PDB:2O3S"
|
497
|
+
FT STRAND 132..134
|
498
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
499
|
+
FT HELIX 136..141
|
500
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
501
|
+
FT STRAND 142..144
|
502
|
+
FT /evidence="ECO:0007829|PDB:3RAJ"
|
503
|
+
FT HELIX 145..147
|
504
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
505
|
+
FT HELIX 149..154
|
506
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
507
|
+
FT STRAND 165..167
|
508
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
509
|
+
FT STRAND 171..173
|
510
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
511
|
+
FT TURN 176..179
|
512
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
513
|
+
FT STRAND 181..183
|
514
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
515
|
+
FT HELIX 184..199
|
516
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
517
|
+
FT STRAND 202..209
|
518
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
519
|
+
FT STRAND 212..216
|
520
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
521
|
+
FT STRAND 218..220
|
522
|
+
FT /evidence="ECO:0007829|PDB:2EF1"
|
523
|
+
FT HELIX 221..224
|
524
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
525
|
+
FT HELIX 227..229
|
526
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
527
|
+
FT TURN 232..234
|
528
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
529
|
+
FT STRAND 235..243
|
530
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
531
|
+
FT STRAND 246..249
|
532
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
533
|
+
FT HELIX 253..255
|
534
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
535
|
+
FT HELIX 257..268
|
536
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
537
|
+
FT STRAND 272..278
|
538
|
+
FT /evidence="ECO:0007829|PDB:3F6Y"
|
539
|
+
FT HELIX 281..289
|
540
|
+
FT /evidence="ECO:0007829|PDB:2O3S"
|
541
|
+
FT TURN 291..293
|
542
|
+
FT /evidence="ECO:0007829|PDB:3DZG"
|
543
|
+
FT HELIX 294..296
|
544
|
+
FT /evidence="ECO:0007829|PDB:5F21"
|
545
|
+
SQ SEQUENCE 300 AA; 34328 MW; 47BBE38C3DE3E6AA CRC64;
|
546
|
+
MANCEFSPVS GDKPCCRLSR RAQLCLGVSI LVLILVVVLA VVVPRWRQQW SGPGTTKRFP
|
547
|
+
ETVLARCVKY TEIHPEMRHV DCQSVWDAFK GAFISKHPCN ITEEDYQPLM KLGTQTVPCN
|
548
|
+
KILLWSRIKD LAHQFTQVQR DMFTLEDTLL GYLADDLTWC GEFNTSKINY QSCPDWRKDC
|
549
|
+
SNNPVSVFWK TVSRRFAEAA CDVVHVMLNG SRSKIFDKNS TFGSVEVHNL QPEKVQTLEA
|
550
|
+
WVIHGGREDS RDLCQDPTIK ELESIISKRN IQFSCKNIYR PDKFLQCVKN PEDSSCTSEI
|
551
|
+
//
|
@@ -0,0 +1,325 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
#
|
3
|
+
# test/unit/bio/db/embl/test_uniprotkb_P28907.rb - Unit tests for Bio::UniProtKB
|
4
|
+
#
|
5
|
+
# Copyright::: Copyright (C) 2022 BioRuby Project <staff@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
# Contributor:: 2005 Mitsuteru Nakao <n@bioruby.org>
|
8
|
+
# 2022 Naohisa Goto <ng@bioruby.org>
|
9
|
+
#
|
10
|
+
|
11
|
+
# loading helper routine for testing bioruby
|
12
|
+
require 'pathname'
|
13
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
|
14
|
+
'bioruby_test_helper.rb')).cleanpath.to_s
|
15
|
+
|
16
|
+
# libraries needed for the tests
|
17
|
+
require 'test/unit'
|
18
|
+
require 'bio/db/embl/uniprotkb'
|
19
|
+
|
20
|
+
module Bio
|
21
|
+
class TestUniProtKB_P28907 < Test::Unit::TestCase
|
22
|
+
|
23
|
+
def setup
|
24
|
+
data = File.read(File.join(BioRubyTestDataPath,
|
25
|
+
'uniprot', 'P28907.uniprot'))
|
26
|
+
@obj = Bio::UniProtKB.new(data)
|
27
|
+
end
|
28
|
+
|
29
|
+
def test_id_line
|
30
|
+
assert(@obj.id_line)
|
31
|
+
end
|
32
|
+
|
33
|
+
def test_id_line_entry_name
|
34
|
+
assert_equal('CD38_HUMAN', @obj.id_line('ENTRY_NAME'))
|
35
|
+
end
|
36
|
+
|
37
|
+
def test_id_line_data_class
|
38
|
+
assert_equal('Reviewed', @obj.id_line('DATA_CLASS'))
|
39
|
+
end
|
40
|
+
|
41
|
+
#def test_id_line_molecule_type
|
42
|
+
# assert_equal('PRT', @obj.id_line('MOLECULE_TYPE'))
|
43
|
+
#end
|
44
|
+
|
45
|
+
def test_id_line_sequence_length
|
46
|
+
assert_equal(300, @obj.id_line('SEQUENCE_LENGTH'))
|
47
|
+
end
|
48
|
+
|
49
|
+
def test_entry
|
50
|
+
entry = 'CD38_HUMAN'
|
51
|
+
assert_equal(entry, @obj.entry)
|
52
|
+
assert_equal(entry, @obj.entry_name)
|
53
|
+
assert_equal(entry, @obj.entry_id)
|
54
|
+
end
|
55
|
+
|
56
|
+
#def test_molecule
|
57
|
+
# assert_equal('PRT', @obj.molecule)
|
58
|
+
# assert_equal('PRT', @obj.molecule_type)
|
59
|
+
#end
|
60
|
+
|
61
|
+
def test_sequence_length
|
62
|
+
seqlen = 300
|
63
|
+
assert_equal(seqlen, @obj.sequence_length)
|
64
|
+
assert_equal(seqlen, @obj.aalen)
|
65
|
+
end
|
66
|
+
|
67
|
+
def test_ac
|
68
|
+
acs = ["P28907", "O00121", "O00122", "Q96HY4"].freeze
|
69
|
+
assert_equal(acs, @obj.ac)
|
70
|
+
assert_equal(acs, @obj.accessions)
|
71
|
+
end
|
72
|
+
|
73
|
+
def test_accession
|
74
|
+
assert_equal('P28907', @obj.accession)
|
75
|
+
end
|
76
|
+
|
77
|
+
def test_dr
|
78
|
+
assert_equal(81, @obj.dr.size)
|
79
|
+
assert_equal(39, @obj.dr['GO'].size)
|
80
|
+
assert_equal([["IPR003193", "ADP-ribosyl_cyclase"],
|
81
|
+
["IPR033567", "CD38"]],
|
82
|
+
@obj.dr['InterPro'])
|
83
|
+
end
|
84
|
+
|
85
|
+
def test_dr_with_key
|
86
|
+
pfam = [{" " => "1",
|
87
|
+
"Version" => "Rib_hydrolayse",
|
88
|
+
"Accession" => "PF02267",
|
89
|
+
"Molecular Type" => nil
|
90
|
+
}].freeze
|
91
|
+
assert_equal(pfam, @obj.dr('Pfam'))
|
92
|
+
embl = [{"Accession" => "M34461",
|
93
|
+
"Version" => "AAA68482.1",
|
94
|
+
" " => "-",
|
95
|
+
"Molecular Type" => "mRNA"},
|
96
|
+
{"Accession" => "D84276",
|
97
|
+
"Version" => "BAA18964.1",
|
98
|
+
" " => "-",
|
99
|
+
"Molecular Type" => "mRNA"},
|
100
|
+
{"Accession" => "D84277",
|
101
|
+
"Version" => "BAA18965.1",
|
102
|
+
" " => "-",
|
103
|
+
"Molecular Type" => "mRNA"},
|
104
|
+
{"Accession" => "D84284",
|
105
|
+
"Version" => "BAA18966.1",
|
106
|
+
" " => "-",
|
107
|
+
"Molecular Type" => "Genomic_DNA"},
|
108
|
+
{"Accession" => "BC007964",
|
109
|
+
"Version" => "AAH07964.1",
|
110
|
+
" " => "-",
|
111
|
+
"Molecular Type" => "mRNA"}].freeze
|
112
|
+
assert_equal(embl, @obj.dr('EMBL'))
|
113
|
+
end
|
114
|
+
|
115
|
+
def test_dr_with_key_empty
|
116
|
+
assert_equal([], @obj.dr('NOT_A_DATABASE'))
|
117
|
+
end
|
118
|
+
|
119
|
+
def test_dt
|
120
|
+
assert(@obj.dt)
|
121
|
+
end
|
122
|
+
|
123
|
+
def test_dt_created
|
124
|
+
assert_equal('01-DEC-1992, integrated into UniProtKB/Swiss-Prot.',
|
125
|
+
@obj.dt('created'))
|
126
|
+
end
|
127
|
+
|
128
|
+
def test_dt_sequence
|
129
|
+
assert_equal('23-NOV-2004, sequence version 2.',
|
130
|
+
@obj.dt('sequence'))
|
131
|
+
end
|
132
|
+
|
133
|
+
def test_dt_annotation
|
134
|
+
assert_equal('03-AUG-2022, entry version 213.',
|
135
|
+
@obj.dt('annotation'))
|
136
|
+
end
|
137
|
+
|
138
|
+
def test_de
|
139
|
+
assert(@obj.de)
|
140
|
+
end
|
141
|
+
|
142
|
+
def test_protein_name
|
143
|
+
assert_equal("ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1",
|
144
|
+
@obj.protein_name)
|
145
|
+
end
|
146
|
+
|
147
|
+
def test_synonyms
|
148
|
+
ary = [
|
149
|
+
"EC 3.2.2.6",
|
150
|
+
"2'-phospho-ADP-ribosyl cyclase",
|
151
|
+
"2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase",
|
152
|
+
"EC 2.4.99.20",
|
153
|
+
"2'-phospho-cyclic-ADP-ribose transferase",
|
154
|
+
"ADP-ribosyl cyclase 1",
|
155
|
+
"ADPRC 1",
|
156
|
+
"Cyclic ADP-ribose hydrolase 1",
|
157
|
+
"cADPr hydrolase 1",
|
158
|
+
"T10",
|
159
|
+
"CD_antigen=CD38"
|
160
|
+
].freeze
|
161
|
+
assert_equal(ary, @obj.synonyms)
|
162
|
+
end
|
163
|
+
|
164
|
+
def test_protein_name_after_calling_de
|
165
|
+
assert(@obj.de)
|
166
|
+
assert_equal("ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1",
|
167
|
+
@obj.protein_name)
|
168
|
+
end
|
169
|
+
|
170
|
+
def test_synonyms_after_calling_de
|
171
|
+
assert(@obj.de)
|
172
|
+
assert_equal(11, @obj.synonyms.size)
|
173
|
+
end
|
174
|
+
|
175
|
+
def test_gn
|
176
|
+
assert_equal([{:orfs=>[], :synonyms=>[], :name=>"CD38", :loci=>[]}],
|
177
|
+
@obj.gn)
|
178
|
+
end
|
179
|
+
|
180
|
+
def test_gn_uniprot_parser
|
181
|
+
assert_equal([{:orfs=>[], :loci=>[], :name=>"CD38", :synonyms=>[]}],
|
182
|
+
@obj.instance_eval("gn_uniprot_parser"))
|
183
|
+
end
|
184
|
+
|
185
|
+
def test_gn_old_parser
|
186
|
+
assert_equal([["Name=CD38;"]],
|
187
|
+
@obj.instance_eval("gn_old_parser"))
|
188
|
+
end
|
189
|
+
|
190
|
+
def test_gene_names
|
191
|
+
assert_equal(["CD38"], @obj.gene_names)
|
192
|
+
end
|
193
|
+
|
194
|
+
def test_gene_name
|
195
|
+
assert_equal('CD38', @obj.gene_name)
|
196
|
+
end
|
197
|
+
|
198
|
+
def test_os
|
199
|
+
assert(@obj.os)
|
200
|
+
end
|
201
|
+
|
202
|
+
def test_os_access
|
203
|
+
assert_equal("Homo sapiens (Human)", @obj.os(0))
|
204
|
+
end
|
205
|
+
|
206
|
+
def test_os_access2
|
207
|
+
assert_equal({"name"=>"(Human)", "os"=>"Homo sapiens"}, @obj.os[0])
|
208
|
+
end
|
209
|
+
|
210
|
+
def test_oc
|
211
|
+
assert_equal(["Eukaryota", "Metazoa", "Chordata", "Craniata",
|
212
|
+
"Vertebrata", "Euteleostomi", "Mammalia", "Eutheria",
|
213
|
+
"Euarchontoglires", "Primates",
|
214
|
+
"Haplorrhini", "Catarrhini", "Hominidae", "Homo"],
|
215
|
+
@obj.oc)
|
216
|
+
end
|
217
|
+
|
218
|
+
def test_ox
|
219
|
+
assert_equal({"NCBI_TaxID"=>["9606"]}, @obj.ox)
|
220
|
+
end
|
221
|
+
|
222
|
+
def test_ref # Bio::UniProtKB#ref
|
223
|
+
assert_equal(Array, @obj.ref.class)
|
224
|
+
end
|
225
|
+
|
226
|
+
def test_cc
|
227
|
+
assert_equal(Hash, @obj.cc.class)
|
228
|
+
end
|
229
|
+
|
230
|
+
def test_cc_database
|
231
|
+
assert_equal(nil, @obj.cc('DATABASE'))
|
232
|
+
end
|
233
|
+
|
234
|
+
def test_cc_alternative_products
|
235
|
+
ap = { "Event"=>["Alternative splicing"],
|
236
|
+
"Named isoforms"=>"2",
|
237
|
+
"Comment"=>"",
|
238
|
+
"Variants"=>
|
239
|
+
[{"Name"=>"1",
|
240
|
+
"Synonyms"=>[],
|
241
|
+
"IsoId"=>["P28907-1"],
|
242
|
+
"Sequence"=>["Displayed"]},
|
243
|
+
{"Name"=>"2",
|
244
|
+
"Synonyms"=>[],
|
245
|
+
"IsoId"=>["P28907-2"],
|
246
|
+
"Sequence"=>["VSP_000707", "VSP_000708"]}]}
|
247
|
+
assert_equal(ap, @obj.cc('ALTERNATIVE PRODUCTS'))
|
248
|
+
end
|
249
|
+
|
250
|
+
def test_cc_mass_spectrometry
|
251
|
+
assert_equal(nil, @obj.cc('MASS SPECTROMETRY'))
|
252
|
+
end
|
253
|
+
|
254
|
+
|
255
|
+
def test_kw
|
256
|
+
keywords = ["3D-structure", "Alternative splicing",
|
257
|
+
"Diabetes mellitus", "Disulfide bond",
|
258
|
+
"Glycoprotein", "Hydrolase", "Membrane",
|
259
|
+
"NAD", "NADP", "Receptor", "Reference proteome",
|
260
|
+
"Signal-anchor", "Transferase", "Transmembrane",
|
261
|
+
"Transmembrane helix"]
|
262
|
+
assert_equal(keywords, @obj.kw)
|
263
|
+
end
|
264
|
+
|
265
|
+
def test_ft
|
266
|
+
assert(@obj.ft)
|
267
|
+
name = 'TOPO_DOM'
|
268
|
+
data = [{"From"=>1,
|
269
|
+
"To"=>21,
|
270
|
+
"diff"=>[],
|
271
|
+
"original"=>
|
272
|
+
["TOPO_DOM",
|
273
|
+
"1",
|
274
|
+
"21",
|
275
|
+
[["note", "Cytoplasmic"],
|
276
|
+
["evidence", "ECO:0000255"]]],
|
277
|
+
"note"=>"Cytoplasmic",
|
278
|
+
"evidence"=>"ECO:0000255"},
|
279
|
+
{"From"=>43,
|
280
|
+
"To"=>300,
|
281
|
+
"diff"=>[],
|
282
|
+
"original"=>
|
283
|
+
["TOPO_DOM",
|
284
|
+
"43",
|
285
|
+
"300",
|
286
|
+
[["note", "Extracellular"],
|
287
|
+
["evidence", "ECO:0000255"]]],
|
288
|
+
"note"=>"Extracellular",
|
289
|
+
"evidence"=>"ECO:0000255"}].freeze
|
290
|
+
|
291
|
+
assert_equal(data, @obj.ft[name])
|
292
|
+
end
|
293
|
+
|
294
|
+
def test_sq
|
295
|
+
assert_equal({"CRC64"=>"47BBE38C3DE3E6AA", "aalen"=>300, "MW"=>34328},
|
296
|
+
@obj.sq)
|
297
|
+
end
|
298
|
+
|
299
|
+
def test_sq_crc64
|
300
|
+
assert_equal("47BBE38C3DE3E6AA", @obj.sq('CRC64'))
|
301
|
+
end
|
302
|
+
|
303
|
+
def test_sq_mw
|
304
|
+
mw = 34328
|
305
|
+
assert_equal(mw, @obj.sq('mw'))
|
306
|
+
assert_equal(mw, @obj.sq('molecular'))
|
307
|
+
assert_equal(mw, @obj.sq('weight'))
|
308
|
+
end
|
309
|
+
|
310
|
+
def test_sq_len
|
311
|
+
length = 300
|
312
|
+
assert_equal(length, @obj.sq('len'))
|
313
|
+
assert_equal(length, @obj.sq('length'))
|
314
|
+
assert_equal(length, @obj.sq('AA'))
|
315
|
+
end
|
316
|
+
|
317
|
+
def test_seq
|
318
|
+
seq = "MANCEFSPVSGDKPCCRLSRRAQLCLGVSILVLILVVVLAVVVPRWRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCNITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFNTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLNGSRSKIFDKNSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI"
|
319
|
+
assert_equal(seq, @obj.seq)
|
320
|
+
assert_equal(seq, @obj.aaseq)
|
321
|
+
end
|
322
|
+
|
323
|
+
end # class TestUniProtKB
|
324
|
+
end # module Bio
|
325
|
+
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 2.0.
|
4
|
+
version: 2.0.4
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- BioRuby project
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2022-09-13 00:00:00.000000000 Z
|
12
12
|
dependencies: []
|
13
13
|
description: BioRuby is a library for bioinformatics (biology + information science).
|
14
14
|
email: staff@bioruby.org
|
@@ -465,6 +465,7 @@ files:
|
|
465
465
|
- test/data/sim4/simple2-A4.sim4
|
466
466
|
- test/data/soft/GDS100_partial.soft
|
467
467
|
- test/data/soft/GSE3457_family_partial.soft
|
468
|
+
- test/data/uniprot/P28907.uniprot
|
468
469
|
- test/data/uniprot/p53_human.uniprot
|
469
470
|
- test/functional/bio/sequence/test_output_embl.rb
|
470
471
|
- test/functional/bio/test_command.rb
|
@@ -509,6 +510,7 @@ files:
|
|
509
510
|
- test/unit/bio/db/embl/test_embl_to_bioseq.rb
|
510
511
|
- test/unit/bio/db/embl/test_uniprot.rb
|
511
512
|
- test/unit/bio/db/embl/test_uniprotkb.rb
|
513
|
+
- test/unit/bio/db/embl/test_uniprotkb_P28907.rb
|
512
514
|
- test/unit/bio/db/embl/test_uniprotkb_new_part.rb
|
513
515
|
- test/unit/bio/db/fasta/test_defline.rb
|
514
516
|
- test/unit/bio/db/fasta/test_defline_misc.rb
|