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Seekerandreasprlic
Seeker
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andreasprlic
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/* I've noticed some misprints in BioJavaX Documentation and in the source code. */
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‎wiki/User_talk:Seeker.md‎

Lines changed: 27 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -33,29 +33,29 @@ the following text fragment:
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/mol_type="genomic DNA"
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/strain="168"
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/db_xref="taxon:224308"
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gene 110477..110953
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/gene="ispF"
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/locus_tag="BSU00910"
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/db_xref="GeneID:936634"
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CDS 110477..110953
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/gene="ispF"
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/locus_tag="BSU00910"
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/function="unknown"
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/note="yacN; catalyzes the conversion of
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4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate
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into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate"
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gene 4866..6782
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/gene="gyrB"
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/locus_tag="BSU00060"
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/note="synonym: novA"
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/db_xref="GeneID:939456"
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CDS 4866..6782
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/gene="gyrB"
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/locus_tag="BSU00060"
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/EC_number="5.99.1.3"
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/function="initation of replication cycle and DNA
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elongation"
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/note="decatenates newly replicated chromosomal DNA and
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relaxes positive and negative DNA supercoiling"
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/codon_start=1
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/transl_table=11
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/product="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
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synthase"
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/protein_id="NP_387972.1"
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/db_xref="GI:16077159"
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/db_xref="GOA:Q06756"
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/db_xref="UniProtKB/Swiss-Prot:Q06756"
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/db_xref="GeneID:936634"
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/translation="MFRIGQGFDVHQLVEGRPLIIGGIEIPYEKGLLGHSDADVLLHT
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VADACLGAVGEGDIGKHFPDTDPEFKDADSFKLLQHVWGIVKQKGYVLGNIDCTIIAQ
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KPKMLPYIEDMRKRIAEGLEADVSQVNVKATTTEKLGFTGRAEGIAAQATVLIQKG"
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/product="DNA topoisomerase IV subunit B"
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/protein_id="NP_387887.1"
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/db_xref="GI:16077074"
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/db_xref="GOA:P05652"
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/db_xref="UniProtKB/Swiss-Prot:P05652"
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/db_xref="GeneID:939456"
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/translation="MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWE
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IVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMT"
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...
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`
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@@ -100,12 +100,12 @@ The output was as follows:
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<code>
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`Function:`
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`4-diphosphocytidyl-2-C-methyl-D-erythritol`
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`kinase`
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`initation of replication cycle and DNA`
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`elongation`
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`Note:`
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`catalyzes the phosphorylation of`
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`4-diphosphocytidyl-2-C-methyl-D-erythritol in the`
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`nonmevalonate pathway of isoprenoid biosynthesis`
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`Translation:   MRILEKAPAKINLSLDVTRKRPDGYHEVEMIMTTIDLADRIELTELAEDEVRVSSHNRFVPDDQRNLAYQAAKLIKDRYNVKKGVSIMITKVIPVAAGLAGGSSDAAATLRGLNRLWNLNLSAETLAELGAEIGSDVSFCVYGGTALATGRGEKIKHISTPPHCWVILAKPTIGVSTAEVYRALKLDGIEHPDVQGMIEAIEEKSFQKMCSRLGNVLESVTLDMHPEVAMIKNQMKRFGADAVLMSGSGPTVFGLVQYESKVQRIYNGLRGFCDQVYAVRMIGEQNALD`
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`decatenates newly replicated chromosomal DNA and`
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`relaxes positive and negative DNA supercoiling`
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`Translation:`
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`MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMT               `
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\<\\code\>

‎wiki/User_talk:Seeker.mediawiki‎

Lines changed: 27 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -17,29 +17,29 @@ Iwas working with sequence file in GenBank format. This file contained the follo
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/mol_type="genomic DNA"
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/strain="168"
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/db_xref="taxon:224308"
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gene 110477..110953
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/gene="ispF"
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/locus_tag="BSU00910"
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/db_xref="GeneID:936634"
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CDS 110477..110953
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/gene="ispF"
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/locus_tag="BSU00910"
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/function="unknown"
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/note="yacN; catalyzes the conversion of
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4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate
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into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate"
20+
gene 4866..6782
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/gene="gyrB"
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/locus_tag="BSU00060"
23+
/note="synonym: novA"
24+
/db_xref="GeneID:939456"
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CDS 4866..6782
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/gene="gyrB"
27+
/locus_tag="BSU00060"
28+
/EC_number="5.99.1.3"
29+
/function="initation of replication cycle and DNA
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elongation"
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/note="decatenates newly replicated chromosomal DNA and
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relaxes positive and negative DNA supercoiling"
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/codon_start=1
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/transl_table=11
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/product="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
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synthase"
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/protein_id="NP_387972.1"
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/db_xref="GI:16077159"
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/db_xref="GOA:Q06756"
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/db_xref="UniProtKB/Swiss-Prot:Q06756"
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/db_xref="GeneID:936634"
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/translation="MFRIGQGFDVHQLVEGRPLIIGGIEIPYEKGLLGHSDADVLLHT
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VADACLGAVGEGDIGKHFPDTDPEFKDADSFKLLQHVWGIVKQKGYVLGNIDCTIIAQ
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KPKMLPYIEDMRKRIAEGLEADVSQVNVKATTTEKLGFTGRAEGIAAQATVLIQKG"
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/product="DNA topoisomerase IV subunit B"
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/protein_id="NP_387887.1"
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/db_xref="GI:16077074"
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/db_xref="GOA:P05652"
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/db_xref="UniProtKB/Swiss-Prot:P05652"
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/db_xref="GeneID:939456"
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/translation="MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWE
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IVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMT"
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...
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</code>
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@@ -83,11 +83,11 @@ The output was as follows:
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<code>
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Function:
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4-diphosphocytidyl-2-C-methyl-D-erythritol
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kinase
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initation of replication cycle and DNA
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elongation
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Note:
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catalyzes the phosphorylation of
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4-diphosphocytidyl-2-C-methyl-D-erythritol in the
91-
nonmevalonate pathway of isoprenoid biosynthesis
92-
Translation: MRILEKAPAKINLSLDVTRKRPDGYHEVEMIMTTIDLADRIELTELAEDEVRVSSHNRFVPDDQRNLAYQAAKLIKDRYNVKKGVSIMITKVIPVAAGLAGGSSDAAATLRGLNRLWNLNLSAETLAELGAEIGSDVSFCVYGGTALATGRGEKIKHISTPPHCWVILAKPTIGVSTAEVYRALKLDGIEHPDVQGMIEAIEEKSFQKMCSRLGNVLESVTLDMHPEVAMIKNQMKRFGADAVLMSGSGPTVFGLVQYESKVQRIYNGLRGFCDQVYAVRMIGEQNALD
89+
decatenates newly replicated chromosomal DNA and
90+
relaxes positive and negative DNA supercoiling
91+
Translation:
92+
MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMT
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<\code>

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