bio 2.0.4 → 2.0.5

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.
@@ -530,22 +530,43 @@ class UniProtKB < EMBLDB
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  # http://br.expasy.org/sprot/userman.html#OH_line
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  def oh
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  unless @data['OH']
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- @data['OH'] = fetch('OH').split("\. ").map {|x|
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- if x =~ /NCBI_TaxID=(\d+);/
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- taxid = $1
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- else
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- raise ArgumentError, ["Error: Invalid OH line format (#{self.entry_id}):",
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- $!, "\n", get('OH'), "\n"].join
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-
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- end
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- if x =~ /NCBI_TaxID=\d+; (.+)/
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- host_name = $1
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- host_name.sub!(/\.$/, '')
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- else
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- host_name = nil
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+ oh = []
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+ a = fetch('OH').split(/(NCBI\_TaxID\=)(\d+)(\;)/)
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+ t = catch :error do
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+ taxid = nil
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+ host_name = nil
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+ while x = a.shift
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+ x = x.to_s.strip
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+ case x
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+ when ''
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+ next
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+ when 'NCBI_TaxID='
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+ if taxid then
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+ oh.push({'NCBI_TaxID' => taxid, 'HostName' => host_name})
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+ taxid = nil
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+ host_name = nil
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+ end
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+ taxid = a.shift
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+ throw :error, :missing_semicolon if a.shift != ';'
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+ else
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+ throw :error, :missing_taxid if host_name
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+ host_name = x
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+ host_name.sub!(/\.\z/, '')
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+ end
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+ end #while x...
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+ if taxid then
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+ oh.push({'NCBI_TaxID' => taxid, 'HostName' => host_name})
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+ elsif host_name then
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+ throw :error, :missing_taxid_last
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  end
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- {'NCBI_TaxID' => taxid, 'HostName' => host_name}
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- }
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+ nil
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+ end #t = catch...
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+ if t then
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+ raise ArgumentError,
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+ ["Error: Invalid OH line format (#{self.entry_id}):",
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+ $!, "\n", get('OH'), "\n"].join
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+ end
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+ @data['OH'] = oh
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  end
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  @data['OH']
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  end
@@ -922,6 +943,7 @@ class UniProtKB < EMBLDB
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  def cc_alternative_products(data)
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+ return nil unless data
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  ap = data.join('')
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  return ap unless ap
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@@ -960,6 +982,7 @@ class UniProtKB < EMBLDB
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  def cc_biophysiochemical_properties(data)
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+ return nil unless data
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  data = data[0]
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  hash = {'Absorption' => {},
@@ -995,6 +1018,7 @@ class UniProtKB < EMBLDB
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  def cc_caution(data)
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+ return nil unless data
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  data.join('')
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  end
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  private :cc_caution
@@ -1004,6 +1028,7 @@ class UniProtKB < EMBLDB
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  #
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  # CC P46527:CDKN1B; NbExp=1; IntAct=EBI-359815, EBI-519280;
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  def cc_interaction(data)
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+ return nil unless data
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  str = data.join('')
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  it = str.scan(/(.+?); NbExp=(.+?); IntAct=(.+?);/)
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  it.map {|ent|
@@ -1059,6 +1084,7 @@ class UniProtKB < EMBLDB
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  def cc_pathway(data)
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+ return nil unless data
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  data.map {|x| x.sub(/\.$/, '') }.map {|x|
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  x.split(/; | and |: /)
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  }[0]
@@ -1067,6 +1093,7 @@ class UniProtKB < EMBLDB
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  def cc_rna_editing(data)
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+ return nil unless data
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  data = data.join('')
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  entry = {'Modified_positions' => [], 'Note' => ""}
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  if data =~ /Modified_positions=(.+?)(\.|;)/
@@ -1083,6 +1110,7 @@ class UniProtKB < EMBLDB
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  def cc_subcellular_location(data)
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+ return nil unless data
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  data.map {|x|
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  x.split('. ').map {|y|
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  y.split('; ').map {|z|
@@ -1101,6 +1129,7 @@ class UniProtKB < EMBLDB
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  #++
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  def cc_web_resource(data)
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+ return nil unless data
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  data.map {|x|
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  entry = {'Name' => nil, 'Note' => nil, 'URL' => nil}
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  x.split(';').each do |y|
@@ -1235,10 +1264,14 @@ class UniProtKB < EMBLDB
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  begin
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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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- "#{$2}#{$4}", # From
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- $5.to_s, # To
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- [] # Qualifiers
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+ f_name = $1.to_s
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+ f_from = "#{$2}#{$4}"
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+ f_to = $5.to_s
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+ f_to = f_from if f_to.empty?
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+ cur_ft = [f_name, # Feature Name
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+ f_from, # From
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+ f_to, # To
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+ [] # Qualifiers
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  ]
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  table.push cur_ft
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  cont = false
data/lib/bio/version.rb CHANGED
@@ -10,7 +10,7 @@
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  module Bio
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  # BioRuby version (Array containing Integer)
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- BIORUBY_VERSION = [2, 0, 4].extend(Comparable).freeze
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+ BIORUBY_VERSION = [2, 0, 5].extend(Comparable).freeze
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  # Extra version specifier (String or nil).
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  # Existance of the value indicates development version.
@@ -0,0 +1,127 @@
1
+ ID 1A_AMVLE Reviewed; 1126 AA.
2
+ AC P03589;
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+ DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
4
+ DT 21-JUL-1986, sequence version 1.
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+ DT 22-FEB-2023, entry version 78.
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+ DE RecName: Full=Replication protein 1a;
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+ DE Includes:
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+ DE RecName: Full=ATP-dependent helicase;
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+ DE EC=3.6.4.-;
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+ DE Includes:
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+ DE RecName: Full=Methyltransferase;
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+ DE EC=2.1.1.-;
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+ GN ORFNames=ORF1a;
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+ OS Alfalfa mosaic virus (strain 425 / isolate Leiden).
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+ OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
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+ OC Martellivirales; Bromoviridae; Alfamovirus.
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+ OX NCBI_TaxID=12322;
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+ OH NCBI_TaxID=4045; Apium graveolens (Celery).
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+ OH NCBI_TaxID=83862; Astragalus glycyphyllos (Wild liquorice).
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+ OH NCBI_TaxID=4072; Capsicum annuum (Capsicum pepper).
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+ OH NCBI_TaxID=41386; Caryopteris incana.
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+ OH NCBI_TaxID=3827; Cicer arietinum (Chickpea) (Garbanzo).
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+ OH NCBI_TaxID=3847; Glycine max (Soybean) (Glycine hispida).
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+ OH NCBI_TaxID=35936; Lablab purpureus (Hyacinth bean) (Dolichos lablab).
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+ OH NCBI_TaxID=4236; Lactuca sativa (Garden lettuce).
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+ OH NCBI_TaxID=3864; Lens culinaris (Lentil) (Cicer lens).
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+ OH NCBI_TaxID=3869; Lupinus.
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+ OH NCBI_TaxID=145753; Malva parviflora (Little mallow) (Cheeseweed mallow).
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+ OH NCBI_TaxID=3879; Medicago sativa (Alfalfa).
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+ OH NCBI_TaxID=4097; Nicotiana tabacum (Common tobacco).
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+ OH NCBI_TaxID=3885; Phaseolus vulgaris (Kidney bean) (French bean).
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+ OH NCBI_TaxID=23113; Philadelphus.
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+ OH NCBI_TaxID=3888; Pisum sativum (Garden pea).
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+ OH NCBI_TaxID=4081; Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
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+ OH NCBI_TaxID=4113; Solanum tuberosum (Potato).
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+ OH NCBI_TaxID=157662; Teramnus repens.
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+ OH NCBI_TaxID=60916; Trifolium incarnatum (Crimson clover).
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+ OH NCBI_TaxID=85293; Viburnum opulus (High-bush cranberry).
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+ OH NCBI_TaxID=3916; Vigna radiata var. radiata (Mung bean) (Phaseolus aureus).
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+ OH NCBI_TaxID=3917; Vigna unguiculata (Cowpea).
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+ RN [1]
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+ RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
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+ RX PubMed=6298738; DOI=10.1093/nar/11.5.1253;
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+ RA Cornelissen B.J.C., Brederode F.T., Moormann R.J.M., Bol J.F.;
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+ RT "Complete nucleotide sequence of alfalfa mosaic virus RNA 1.";
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+ RL Nucleic Acids Res. 11:1253-1265(1983).
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+ CC -!- FUNCTION: Involved in the virus replication. Contains a helicase domain
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+ CC and a methyltransferase domain. The methyltransferase domain is
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+ CC probably involved in viral RNA capping. Involved in the formation of ER
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+ CC membrane spherular invaginations in which RNA replication complexes
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+ CC form (By similarity). {ECO:0000250}.
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+ CC -!- SUBUNIT: Interacts with RNA-directed RNA polymerase 2a. {ECO:0000250}.
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+ CC -!- SUBCELLULAR LOCATION: Host endoplasmic reticulum membrane
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+ CC {ECO:0000250}; Peripheral membrane protein {ECO:0000250}.
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+ CC -!- SIMILARITY: Belongs to the bromoviridae replication protein 1a family.
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+ CC {ECO:0000305}.
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+ CC ---------------------------------------------------------------------------
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+ CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
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+ CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
60
+ CC ---------------------------------------------------------------------------
61
+ DR EMBL; L00163; AAA46289.1; -; Genomic_RNA.
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+ DR PIR; A04197; WMFM12.
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+ DR RefSeq; NP_041192.1; NC_001495.1.
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+ DR SMR; P03589; -.
65
+ DR GeneID; 962667; -.
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+ DR KEGG; vg:962667; -.
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+ DR Proteomes; UP000000358; Genome.
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+ DR GO; GO:0044167; C:host cell endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
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+ DR GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
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+ DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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+ DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
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+ DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
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+ DR GO; GO:0008174; F:mRNA methyltransferase activity; IEA:InterPro.
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+ DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
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+ DR GO; GO:0006396; P:RNA processing; IEA:InterPro.
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+ DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
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+ DR InterPro; IPR027351; (+)RNA_virus_helicase_core_dom.
78
+ DR InterPro; IPR002588; Alphavirus-like_MT_dom.
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+ DR InterPro; IPR027417; P-loop_NTPase.
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+ DR Pfam; PF01443; Viral_helicase1; 1.
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+ DR Pfam; PF01660; Vmethyltransf; 1.
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+ DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
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+ DR PROSITE; PS51743; ALPHAVIRUS_MT; 1.
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+ DR PROSITE; PS51657; PSRV_HELICASE; 1.
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+ PE 3: Inferred from homology;
86
+ KW ATP-binding; Helicase; Host endoplasmic reticulum; Host membrane;
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+ KW Hydrolase; Membrane; Methyltransferase; Nucleotide-binding;
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+ KW Reference proteome; Transferase.
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+ FT CHAIN 1..1126
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+ FT /note="Replication protein 1a"
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+ FT /id="PRO_0000083254"
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+ FT DOMAIN 90..278
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+ FT /note="Alphavirus-like MT"
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+ FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01079"
95
+ FT DOMAIN 806..963
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+ FT /note="(+)RNA virus helicase ATP-binding"
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+ FT DOMAIN 964..1125
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+ FT /note="(+)RNA virus helicase C-terminal"
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+ FT REGION 69..406
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+ FT /note="Methyltransferase"
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+ FT REGION 834..1094
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+ FT /note="ATP-dependent helicase"
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+ FT BINDING 838..845
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+ FT /ligand="ATP"
105
+ FT /ligand_id="ChEBI:CHEBI:30616"
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+ FT /evidence="ECO:0000255"
107
+ SQ SEQUENCE 1126 AA; 125828 MW; BF5A8019B47D4CBF CRC64;
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+ MNADAQSTDA SLSMREPLSH ASIQEMLRRV VEKQAADDTT AIGKVFSEAG RAYAQDALPS
109
+ DKGEVLKISF SLDATQQNIL RANFPGRRTV FSNSSSSSHC FAAAHRLLET DFVYRCFGNT
110
+ VDSIIDLGGN FVSHMKVKRH NVHCCCPILD ARDGARLTER ILSLKSYVRK HPEIVGEADY
111
+ CMDTFQKCSR RADYAFAIHS TSDLDVGELA CSLDQKGVMK FICTMMVDAD MLIHNEGEIP
112
+ NFNVRWEIDR KKDLIHFDFI DEPNLGYSHR FSLLKHYLTY NAVDLGHAAY RIERKQDFGG
113
+ VMVIDLTYSL GFVPKMPHSN GRSCAWYNRV KGQMVVHTVN EGYYHHSYQT AVRRKVLVDK
114
+ KVLTRVTEVA FRQFRPNADA HSAIQSIATM LSSSTNHTII GGVTLISGKP LSPDDYIPVA
115
+ TTIYYRVKKL YNAIPEMLSL LDKGERLSTD AVLKGSEGPM WYSGPTFLSA LDKVNVPGDF
116
+ VAKALLSLPK RDLKSLFSRS ATSHSERTPV RDESPIRCTD GVFYPIRMLL KCLGSDKFES
117
+ VTITDPRSNT ETTVDLYQSF QKKIETVFSF ILGKIDGPSP LISDPVYFQS LEDVYYAEWH
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+ QGNAIDASNY ARTLLDDIRK QKEESLKAKA KEVEDAQKLN RAILQVHAYL EAHPDGGKIE
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+ GLGLSSQFIA KIPELAIPTP KPLPEFEKNA ETGEILRINP HSDAILEAID YLKSTSANSI
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+ ITLNKLGDHC QWTTKGLDVV WAGDDKRRAF IPKKNTWVGP TARSYPLAKY ERAMSKDGYV
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+ TLRWDGEVLD ANCVRSLSQY EIVFVDQSCV FASAEAIIPS LEKALGLEAH FSVTIVDGVA
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+ GCGKTTNIKQ IARSSGRDVD LILTSNRSSA DELKETIDCS PLTKLHYIRT CDSYLMSASA
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+ VKAQRLIFDE CFLQHAGLVY AAATLAGCSE VIGFGDTEQI PFVSRNPSFV FRHHKLTGKV
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+ ERKLITWRSP ADATYCLEKY FYKNKKPVKT NSRVLRSIEV VPINSPVSVE RNTNALYLCH
125
+ TQAEKAVLKA QTHLKGCDNI FTTHEAQGKT FDNVYFCRLT RTSTSLATGR DPINGPCNGL
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+ VALSRHKKTF KYFTIAHDSD DVIYNACRDA GNTDDSILAR SYNHNF
127
+ //
@@ -0,0 +1,232 @@
1
+ ID 5HT1B_RABIT Reviewed; 390 AA.
2
+ AC P49144;
3
+ DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
4
+ DT 01-FEB-1996, sequence version 1.
5
+ DT 22-FEB-2023, entry version 127.
6
+ DE RecName: Full=5-hydroxytryptamine receptor 1B;
7
+ DE Short=5-HT-1B;
8
+ DE Short=5-HT1B;
9
+ DE AltName: Full=Serotonin 1D beta receptor;
10
+ DE Short=5-HT-1D-beta;
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+ DE AltName: Full=Serotonin receptor 1B;
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+ GN Name=HTR1B;
13
+ OS Oryctolagus cuniculus (Rabbit).
14
+ OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
15
+ OC Eutheria; Euarchontoglires; Glires; Lagomorpha; Leporidae; Oryctolagus.
16
+ OX NCBI_TaxID=9986;
17
+ RN [1]
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+ RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
19
+ RC TISSUE=Liver;
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+ RX PubMed=8543023; DOI=10.1016/0014-5793(95)01308-3;
21
+ RA Harwood G.S., Lockyer M., Giles H., Fairweather N.;
22
+ RT "Cloning and characterisation of the rabbit 5-HT1D alpha and 5-HT1D beta
23
+ RT receptors.";
24
+ RL FEBS Lett. 377:73-76(1995).
25
+ RN [2]
26
+ RP NUCLEOTIDE SEQUENCE.
27
+ RC STRAIN=New Zealand white; TISSUE=Saphenous vein;
28
+ RA Wurch T., Cathala C., Palmer C., Valentin J.P., John G., Colpaert F.C.,
29
+ RA Pauwels P.J.;
30
+ RT "Molecular cloning and identification of a rabbit saphenous vein 5-HT 1DB
31
+ RT receptor gene.";
32
+ RL Neurosci. Res. Commun. 18:155-162(1996).
33
+ RN [3]
34
+ RP NUCLEOTIDE SEQUENCE.
35
+ RC STRAIN=New Zealand white;
36
+ RX PubMed=8878052; DOI=10.1007/bf00171053;
37
+ RA Bard J.A., Kucharewicz S.A., Zgombick J.M., Weinshank R.L., Branchek T.A.,
38
+ RA Cohen M.L.;
39
+ RT "Differences in ligand binding profiles between cloned rabbit and human 5-
40
+ RT HT1D alpha and 5-HT1D beta receptors: ketanserin and methiothepin
41
+ RT distinguish rabbit 5-HT1D receptor subtypes.";
42
+ RL Naunyn Schmiedebergs Arch. Pharmacol. 354:237-244(1996).
43
+ CC -!- FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine
44
+ CC (serotonin). Also functions as a receptor for various alkaloids and
45
+ CC psychoactive substances. Ligand binding causes a conformation change
46
+ CC that triggers signaling via guanine nucleotide-binding proteins (G
47
+ CC proteins) and modulates the activity of down-stream effectors, such as
48
+ CC adenylate cyclase. Signaling inhibits adenylate cyclase activity.
49
+ CC Arrestin family members inhibit signaling via G proteins and mediate
50
+ CC activation of alternative signaling pathways. Regulates the release of
51
+ CC 5-hydroxytryptamine, dopamine and acetylcholine in the brain, and
52
+ CC thereby affects neural activity, nociceptive processing, pain
53
+ CC perception, mood and behavior. Besides, plays a role in
54
+ CC vasoconstriction of cerebral arteries.
55
+ CC -!- SUBUNIT: Homodimer. Heterodimer with HTR1D (By similarity).
56
+ CC {ECO:0000250}.
57
+ CC -!- SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
58
+ CC -!- DOMAIN: Ligands are bound in a hydrophobic pocket formed by the
59
+ CC transmembrane helices. {ECO:0000250}.
60
+ CC -!- PTM: Phosphorylated. {ECO:0000250}.
61
+ CC -!- PTM: Palmitoylated. {ECO:0000250}.
62
+ CC -!- MISCELLANEOUS: A residue in the 7th transmembrane region ('Thr-355' in
63
+ CC human, 'Asn-351' in mouse and rat) is important for species-specific
64
+ CC sensitivity to various agonists. {ECO:0000250}.
65
+ CC -!- SIMILARITY: Belongs to the G-protein coupled receptor 1 family.
66
+ CC {ECO:0000255|PROSITE-ProRule:PRU00521}.
67
+ CC ---------------------------------------------------------------------------
68
+ CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
69
+ CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
70
+ CC ---------------------------------------------------------------------------
71
+ DR EMBL; Z50163; CAA90531.1; -; Genomic_DNA.
72
+ DR EMBL; X89731; CAA61883.1; -; mRNA.
73
+ DR EMBL; U60826; AAB58467.1; -; Genomic_DNA.
74
+ DR PIR; S58126; S58126.
75
+ DR PIR; S68422; S68422.
76
+ DR RefSeq; NP_001076259.1; NM_001082790.1.
77
+ DR AlphaFoldDB; P49144; -.
78
+ DR SMR; P49144; -.
79
+ DR STRING; 9986.ENSOCUP00000016295; -.
80
+ DR BindingDB; P49144; -.
81
+ DR ChEMBL; CHEMBL5717; -.
82
+ DR GlyCosmos; P49144; 2 sites, No reported glycans.
83
+ DR GeneID; 100009594; -.
84
+ DR KEGG; ocu:100009594; -.
85
+ DR CTD; 3351; -.
86
+ DR eggNOG; KOG3656; Eukaryota.
87
+ DR InParanoid; P49144; -.
88
+ DR OrthoDB; 2999405at2759; -.
89
+ DR TreeFam; TF316350; -.
90
+ DR PRO; PR:P49144; -.
91
+ DR Proteomes; UP000001811; Unplaced.
92
+ DR GO; GO:0005886; C:plasma membrane; ISS:UniProtKB.
93
+ DR GO; GO:0045202; C:synapse; IEA:GOC.
94
+ DR GO; GO:0004993; F:G protein-coupled serotonin receptor activity; ISS:UniProtKB.
95
+ DR GO; GO:0007198; P:adenylate cyclase-inhibiting serotonin receptor signaling pathway; ISS:UniProtKB.
96
+ DR GO; GO:0007610; P:behavior; IEA:UniProtKB-KW.
97
+ DR GO; GO:0046849; P:bone remodeling; IEA:InterPro.
98
+ DR GO; GO:0071312; P:cellular response to alkaloid; ISS:UniProtKB.
99
+ DR GO; GO:0071466; P:cellular response to xenobiotic stimulus; ISS:UniProtKB.
100
+ DR GO; GO:0007268; P:chemical synaptic transmission; IEA:InterPro.
101
+ DR GO; GO:0014063; P:negative regulation of serotonin secretion; ISS:UniProtKB.
102
+ DR GO; GO:0050795; P:regulation of behavior; IEA:InterPro.
103
+ DR GO; GO:0042310; P:vasoconstriction; IEA:InterPro.
104
+ DR CDD; cd15333; 7tmA_5-HT1B_1D; 1.
105
+ DR Gene3D; 1.20.1070.10; Rhodopsin 7-helix transmembrane proteins; 1.
106
+ DR InterPro; IPR002147; 5HT1B_rcpt.
107
+ DR InterPro; IPR002231; 5HT_rcpt.
108
+ DR InterPro; IPR000276; GPCR_Rhodpsn.
109
+ DR InterPro; IPR017452; GPCR_Rhodpsn_7TM.
110
+ DR PANTHER; PTHR24248; ADRENERGIC RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR; 1.
111
+ DR PANTHER; PTHR24248:SF66; OCTOPAMINE RECEPTOR BETA-3R; 1.
112
+ DR Pfam; PF00001; 7tm_1; 1.
113
+ DR PRINTS; PR00513; 5HT1BRECEPTR.
114
+ DR PRINTS; PR01101; 5HTRECEPTOR.
115
+ DR PRINTS; PR00237; GPCRRHODOPSN.
116
+ DR SMART; SM01381; 7TM_GPCR_Srsx; 1.
117
+ DR SUPFAM; SSF81321; Family A G protein-coupled receptor-like; 1.
118
+ DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1.
119
+ DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1.
120
+ PE 2: Evidence at transcript level;
121
+ KW Behavior; Cell membrane; Disulfide bond; G-protein coupled receptor;
122
+ KW Glycoprotein; Lipoprotein; Membrane; Palmitate; Phosphoprotein; Receptor;
123
+ KW Reference proteome; Transducer; Transmembrane; Transmembrane helix.
124
+ FT CHAIN 1..390
125
+ FT /note="5-hydroxytryptamine receptor 1B"
126
+ FT /id="PRO_0000068920"
127
+ FT TOPO_DOM 1..49
128
+ FT /note="Extracellular"
129
+ FT /evidence="ECO:0000250"
130
+ FT TRANSMEM 50..75
131
+ FT /note="Helical; Name=1"
132
+ FT /evidence="ECO:0000250"
133
+ FT TOPO_DOM 76..84
134
+ FT /note="Cytoplasmic"
135
+ FT /evidence="ECO:0000250"
136
+ FT TRANSMEM 85..110
137
+ FT /note="Helical; Name=2"
138
+ FT /evidence="ECO:0000250"
139
+ FT TOPO_DOM 111..123
140
+ FT /note="Extracellular"
141
+ FT /evidence="ECO:0000250"
142
+ FT TRANSMEM 124..145
143
+ FT /note="Helical; Name=3"
144
+ FT /evidence="ECO:0000250"
145
+ FT TOPO_DOM 146..165
146
+ FT /note="Cytoplasmic"
147
+ FT /evidence="ECO:0000250"
148
+ FT TRANSMEM 166..187
149
+ FT /note="Helical; Name=4"
150
+ FT /evidence="ECO:0000250"
151
+ FT TOPO_DOM 188..205
152
+ FT /note="Extracellular"
153
+ FT /evidence="ECO:0000250"
154
+ FT TRANSMEM 206..228
155
+ FT /note="Helical; Name=5"
156
+ FT /evidence="ECO:0000250"
157
+ FT TOPO_DOM 229..315
158
+ FT /note="Cytoplasmic"
159
+ FT /evidence="ECO:0000250"
160
+ FT TRANSMEM 316..336
161
+ FT /note="Helical; Name=6"
162
+ FT /evidence="ECO:0000250"
163
+ FT TOPO_DOM 337..349
164
+ FT /note="Extracellular"
165
+ FT /evidence="ECO:0000250"
166
+ FT TRANSMEM 350..371
167
+ FT /note="Helical; Name=7"
168
+ FT /evidence="ECO:0000250"
169
+ FT TOPO_DOM 372..390
170
+ FT /note="Cytoplasmic"
171
+ FT /evidence="ECO:0000250"
172
+ FT REGION 260..282
173
+ FT /note="Disordered"
174
+ FT /evidence="ECO:0000256|SAM:MobiDB-lite"
175
+ FT MOTIF 146..148
176
+ FT /note="DRY motif; important for ligand-induced conformation
177
+ FT changes and signaling"
178
+ FT /evidence="ECO:0000250"
179
+ FT MOTIF 365..369
180
+ FT /note="NPxxY motif; important for ligand-induced
181
+ FT conformation changes and signaling"
182
+ FT /evidence="ECO:0000250"
183
+ FT BINDING 129
184
+ FT /ligand="ergotamine"
185
+ FT /ligand_id="ChEBI:CHEBI:190463"
186
+ FT /ligand_note="agonist"
187
+ FT /evidence="ECO:0000250|UniProtKB:P28222"
188
+ FT BINDING 134
189
+ FT /ligand="ergotamine"
190
+ FT /ligand_id="ChEBI:CHEBI:190463"
191
+ FT /ligand_note="agonist"
192
+ FT /evidence="ECO:0000250|UniProtKB:P28222"
193
+ FT BINDING 201
194
+ FT /ligand="ergotamine"
195
+ FT /ligand_id="ChEBI:CHEBI:190463"
196
+ FT /ligand_note="agonist"
197
+ FT /evidence="ECO:0000250|UniProtKB:P28222"
198
+ FT SITE 355
199
+ FT /note="Important for species-specific agonist sensitivity"
200
+ FT /evidence="ECO:0000250"
201
+ FT LIPID 388
202
+ FT /note="S-palmitoyl cysteine"
203
+ FT /evidence="ECO:0000255"
204
+ FT CARBOHYD 24
205
+ FT /note="N-linked (GlcNAc...) asparagine"
206
+ FT /evidence="ECO:0000255"
207
+ FT CARBOHYD 32
208
+ FT /note="N-linked (GlcNAc...) asparagine"
209
+ FT /evidence="ECO:0000255"
210
+ FT DISULFID 122..199
211
+ FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00521"
212
+ FT CONFLICT 5
213
+ FT /note="G -> S (in Ref. 1 and 3)"
214
+ FT /evidence="ECO:0000305"
215
+ FT CONFLICT 7
216
+ FT /note="Q -> R (in Ref. 1 and 3)"
217
+ FT /evidence="ECO:0000305"
218
+ FT CONFLICT 14
219
+ FT /note="Missing (in Ref. 1 and 3)"
220
+ FT /evidence="ECO:0000305"
221
+ FT CONFLICT 171
222
+ FT /note="R -> A (in Ref. 1 and 3)"
223
+ FT /evidence="ECO:0000305"
224
+ SQ SEQUENCE 390 AA; 43496 MW; C22EBC077C6C897D CRC64;
225
+ MEEPGAQCAP PLAAGSQIAV PQANLSAAHS HNCSAEGYIY QDSIALPWKV LLVLLLALFT
226
+ LATTLSNAFV VATVYRTRKL HTPANYLIAS LAVTDLLVSI LVMPISTMYT VTGRWTLGQV
227
+ VCDLWLSSDI TCCTASIMHL CVIALDRYWA ITDAVEYSAK RTPKRAAIMI RLVWVFSICI
228
+ SLPPFFWRQA KAEEEVSECL VNTDHVLYTV YSTVGAFYLP TLLLIALYGR IYVEARSRIL
229
+ KQTPNRTGKR LTRAQLITDS PGSTTSVTSI NSRAPDVPSE SGSPVYVNQV KVRVSDALLE
230
+ KKKLMAARER KATKTLGIIL GVFIVCWLPF FIISLVMPIC KDACWFHQAI FDFFTWLGYV
231
+ NSLINPIIYT MSNEDFKQAF HKLIRFKCTS
232
+ //
@@ -187,8 +187,10 @@ module Bio
187
187
  return
188
188
  end
189
189
  assert_equal('', str.to_s.strip)
190
+ assert_equal('', err.to_s.strip)
190
191
  str, err = Bio::Command.query_command_open3(ary, @data)
191
192
  assert_equal(@sorted, str.to_s.strip.split(/\s+/))
193
+ assert_equal('', err.to_s.strip)
192
194
  end
193
195
  end #class FuncTestCommandQuery
194
196
 
@@ -38,7 +38,8 @@ module Bio
38
38
  "H01457 Diabetic retinopathy",
39
39
  "H01459 Diabetic neuropathy",
40
40
  "H01529 Avascular necrosis of femoral head",
41
- "H01709 Glucocorticoid-induced osteonecrosis"]
41
+ "H01709 Glucocorticoid-induced osteonecrosis",
42
+ "H02559 Microvascular complications of diabetes"]
42
43
 
43
44
  assert_equal(expected, @obj.diseases_as_strings)
44
45
  end
@@ -48,41 +49,54 @@ module Bio
48
49
  "H01457"=>"Diabetic retinopathy",
49
50
  "H01459"=>"Diabetic neuropathy",
50
51
  "H01529"=>"Avascular necrosis of femoral head",
51
- "H01709"=>"Glucocorticoid-induced osteonecrosis"}
52
+ "H01709"=>"Glucocorticoid-induced osteonecrosis",
53
+ "H02559"=>"Microvascular complications of diabetes"}
52
54
  assert_equal(expected, @obj.diseases_as_hash)
53
55
  end
54
56
 
55
57
  def test_drug_targets_as_strings
56
58
  expected = ["Abicipar pegol: D11517",
57
- "Aflibercept: D09574",
58
- "Aflibercept beta: D10819",
59
- "Bevacizumab: D06409",
59
+ "Aflibercept: D09574<JP/US>",
60
+ "Aflibercept beta: D10819<JP>",
61
+ "Bevacizumab: D06409<JP/US>",
60
62
  "Bevasiranib sodium: D08874",
61
- "Brolucizumab: D11083",
62
- "Faricimab: D11516",
63
+ "Brolucizumab: D11083<JP/US>",
64
+ "Dilpacimab: D11642",
65
+ "Emvododstat: D11890",
66
+ "Faricimab: D11516<JP/US>",
63
67
  "Navicixizumab: D11126",
64
68
  "Pegaptanib: D05386",
65
- "Ranibizumab: D05697",
69
+ "Ranibizumab: D05697<JP/US>",
70
+ "Tarcocimab: D12507",
71
+ "Tarcocimab tedromer: D12508",
66
72
  "Vanucizumab: D11244"]
67
73
  assert_equal(expected, @obj.drug_targets_as_strings)
68
74
  end
69
75
 
70
76
  def test_networks_as_strings
71
- expected = ["nt06114 PI3K signaling (virus)",
72
- "nt06124 Chemokine signaling (virus)",
77
+ expected = ["nt06124 Chemokine signaling (viruses)",
73
78
  "nt06164 Kaposi sarcoma-associated herpesvirus (KSHV)",
74
- "nt06214 PI3K signaling",
75
79
  "nt06219 JAK-STAT signaling",
76
80
  "nt06224 CXCR signaling",
77
81
  "nt06225 HIF-1 signaling",
82
+ "nt06227 Nuclear receptor signaling",
78
83
  "nt06262 Pancreatic cancer",
79
84
  "nt06264 Renal cell carcinoma",
85
+ "nt06360 Cushing syndrome",
86
+ "nt06526 MAPK signaling",
87
+ "nt06528 Calcium signaling",
88
+ "nt06530 PI3K signaling",
80
89
  "N00079 HIF-1 signaling pathway",
81
90
  "N00080 Loss of VHL to HIF-1 signaling pathway",
82
91
  "N00081 Mutation-inactivated VHL to HIF-1 signaling pathway",
83
92
  "N00095 ERBB2-overexpression to EGF-Jak-STAT signaling pathway",
84
93
  "N00157 KSHV vGPCR to GNB/G-ERK signaling pathway",
85
- "N00179 KSHV K1 to PI3K-NFKB signaling pathway"]
94
+ "N00317 AhR signaling pathway",
95
+ "N01412 Metals to HTF-1 signaling pathway",
96
+ "N01592 GF-RTK-RAS-ERK signaling pathway",
97
+ "N01641 RTK-PLCG-ITPR signaling pathway",
98
+ "N01656 GF-RTK-PI3K signaling pathway",
99
+ "N01658 GF-RTK-RAS-PI3K signaling pathway"]
86
100
  assert_equal(expected, @obj.networks_as_strings)
87
101
  end
88
102