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changeset 5:69e0806b63a4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
author devteam
date Tue, 01 Oct 2019 12:20:13 -0400
parents 0232f19d300f
children 6ea09f60dee9
files cuff_macros.xml gffread.xml test-data/ecoli-k12.gff3 test-data/ecoli-k12.processed.gff3
diffstat 4 files changed, 86 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/cuff_macros.xml	Sun Feb 19 12:09:52 2017 -0500
+++ b/cuff_macros.xml	Tue Oct 01 12:20:13 2019 -0400
@@ -66,7 +66,7 @@
   </token>
   <xml name="cufflinks_gtf_inputs">
     <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
-    <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)">
+    <repeat name="additional_inputs" title="Additional GTF Inputs (type Dataset Collection Lists)">
       <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
     </repeat>
   </xml>
--- a/gffread.xml	Sun Feb 19 12:09:52 2017 -0500
+++ b/gffread.xml	Tue Oct 01 12:20:13 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="gffread" name="gffread" version="@VERSION@.1">
+<tool id="gffread" name="gffread" version="@VERSION@.2">
     <description>Filters and/or converts GFF3/GTF2 records</description>
     <macros>
         <import>cuff_macros.xml</import>
@@ -84,6 +84,11 @@
     #if $chr_replace:
         -m '$chr_replace'
     #end if
+
+    $full_gff_attribute_preservation
+    $decode_url
+    $expose
+
     ##
     ## Although documented, does not appear to be used in the gffread code
     ## #if $seq_info:
@@ -262,6 +267,13 @@
         </test>
 
         <test>
+            <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
+            <param name="gff_fmt" value="gff"/>
+            <param name="full_gff_attribute_preservation" value="-F"/>
+            <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
+        </test>
+
+        <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="filtering" value="--no-pseudo"/>
             <param name="gff_fmt" value="gtf"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ecoli-k12.gff3	Tue Oct 01 12:20:13 2019 -0400
@@ -0,0 +1,40 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM584v2
+#!genome-build-accession NCBI_Assembly:GCF_000005845.2
+##sequence-region NC_000913.3 1 4641652
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145
+NC_000913.3	RefSeq	region	1	4641652	.	+	.	ID=NC_000913.3:1..4641652;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655
+NC_000913.3	RefSeq	gene	190	255	.	+	.	ID=gene-b0001;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001
+NC_000913.3	RefSeq	CDS	190	255	.	+	0	ID=cds-NP_414542.1;Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;gene=thrL;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
+NC_000913.3	RefSeq	gene	337	2799	.	+	.	ID=gene-b0002;Dbxref=ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,thrA1,thrA2,thrD;locus_tag=b0002
+NC_000913.3	RefSeq	CDS	337	2799	.	+	0	ID=cds-NP_414543.1;Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;gene=thrA;locus_tag=b0002;orig_transcript_id=gnl|b0002|mrna.b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
+NC_000913.3	RefSeq	gene	2801	3733	.	+	.	ID=gene-b0003;Dbxref=ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003;locus_tag=b0003
+NC_000913.3	RefSeq	CDS	2801	3733	.	+	0	ID=cds-NP_414544.1;Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;gene=thrB;locus_tag=b0003;orig_transcript_id=gnl|b0003|mrna.b0003;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
+NC_000913.3	RefSeq	gene	3734	5020	.	+	.	ID=gene-b0004;Dbxref=ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004;locus_tag=b0004
+NC_000913.3	RefSeq	CDS	3734	5020	.	+	0	ID=cds-NP_414545.1;Parent=gene-b0004;Dbxref=UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;gbkey=CDS;gene=thrC;locus_tag=b0004;orig_transcript_id=gnl|b0004|mrna.b0004;product=threonine synthase;protein_id=NP_414545.1;transl_table=11
+NC_000913.3	RefSeq	gene	5234	5530	.	+	.	ID=gene-b0005;Dbxref=ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005;locus_tag=b0005
+NC_000913.3	RefSeq	CDS	5234	5530	.	+	0	ID=cds-NP_414546.1;Parent=gene-b0005;Dbxref=UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;locus_tag=b0005;orig_transcript_id=gnl|b0005|mrna.b0005;product=DUF2502 domain-containing protein YaaX;protein_id=NP_414546.1;transl_table=11
+NC_000913.3	RefSeq	repeat_region	5566	5601	.	+	.	ID=id-12;Note=REP1a;gbkey=repeat_region;rpt_type=other
+NC_000913.3	RefSeq	repeat_region	5637	5670	.	-	.	ID=id-13;Note=REP1b;gbkey=repeat_region;rpt_type=other
+NC_000913.3	RefSeq	gene	5683	6459	.	-	.	ID=gene-b0006;Dbxref=ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006;locus_tag=b0006
+NC_000913.3	RefSeq	CDS	5683	6459	.	-	0	ID=cds-NP_414547.1;Parent=gene-b0006;Dbxref=UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;locus_tag=b0006;orig_transcript_id=gnl|b0006|mrna.b0006;product=peroxide stress resistance protein YaaA;protein_id=NP_414547.1;transl_table=11
+NC_000913.3	RefSeq	gene	6529	7959	.	-	.	ID=gene-b0007;Dbxref=ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=yaaJ;gbkey=Gene;gene=yaaJ;gene_biotype=protein_coding;gene_synonym=ECK0007;locus_tag=b0007
+NC_000913.3	RefSeq	CDS	6529	7959	.	-	0	ID=cds-NP_414548.1;Parent=gene-b0007;Dbxref=UniProtKB/Swiss-Prot:P30143,Genbank:NP_414548.1,ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=NP_414548.1;gbkey=CDS;gene=yaaJ;locus_tag=b0007;orig_transcript_id=gnl|b0007|mrna.b0007;product=putative transporter YaaJ;protein_id=NP_414548.1;transl_table=11
+NC_000913.3	RefSeq	gene	8238	9191	.	+	.	ID=gene-b0008;Dbxref=ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=talB;gbkey=Gene;gene=talB;gene_biotype=protein_coding;gene_synonym=ECK0008,yaaK;locus_tag=b0008
+NC_000913.3	RefSeq	CDS	8238	9191	.	+	0	ID=cds-NP_414549.1;Parent=gene-b0008;Dbxref=UniProtKB/Swiss-Prot:P0A870,Genbank:NP_414549.1,ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=NP_414549.1;gbkey=CDS;gene=talB;locus_tag=b0008;orig_transcript_id=gnl|b0008|mrna.b0008;product=transaldolase B;protein_id=NP_414549.1;transl_table=11
+NC_000913.3	RefSeq	gene	9306	9893	.	+	.	ID=gene-b0009;Dbxref=ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=mog;gbkey=Gene;gene=mog;gene_biotype=protein_coding;gene_synonym=bisD,chlG,ECK0009,mogA,yaaG;locus_tag=b0009
+NC_000913.3	RefSeq	CDS	9306	9893	.	+	0	ID=cds-NP_414550.1;Parent=gene-b0009;Dbxref=UniProtKB/Swiss-Prot:P0AF03,Genbank:NP_414550.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=NP_414550.1;gbkey=CDS;gene=mog;locus_tag=b0009;orig_transcript_id=gnl|b0009|mrna.b0009;product=molybdopterin adenylyltransferase;protein_id=NP_414550.1;transl_table=11
+NC_000913.3	RefSeq	gene	9928	10494	.	-	.	ID=gene-b0010;Dbxref=ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=satP;gbkey=Gene;gene=satP;gene_biotype=protein_coding;gene_synonym=ECK0010,yaaH;locus_tag=b0010
+NC_000913.3	RefSeq	CDS	9928	10494	.	-	0	ID=cds-NP_414551.1;Parent=gene-b0010;Dbxref=UniProtKB/Swiss-Prot:P0AC98,Genbank:NP_414551.1,ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=NP_414551.1;gbkey=CDS;gene=satP;locus_tag=b0010;orig_transcript_id=gnl|b0010|mrna.b0010;product=acetate/succinate:H(+) symporter;protein_id=NP_414551.1;transl_table=11
+NC_000913.3	RefSeq	gene	10643	11356	.	-	.	ID=gene-b0011;Dbxref=ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=yaaW;gbkey=Gene;gene=yaaW;gene_biotype=protein_coding;gene_synonym=ECK0011;locus_tag=b0011
+NC_000913.3	RefSeq	CDS	10643	11356	.	-	0	ID=cds-NP_414552.1;Parent=gene-b0011;Dbxref=UniProtKB/Swiss-Prot:P75617,Genbank:NP_414552.1,ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=NP_414552.1;gbkey=CDS;gene=yaaW;locus_tag=b0011;orig_transcript_id=gnl|b0011|mrna.b0011;product=putative enzyme-specific chaperone YaaW;protein_id=NP_414552.1;transl_table=11
+NC_000913.3	RefSeq	gene	10830	11315	.	+	.	ID=gene-b0012;Dbxref=ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=mbiA;gbkey=Gene;gene=mbiA;gene_biotype=protein_coding;gene_synonym=ECK0012,htgA,htpY;locus_tag=b0012
+NC_000913.3	RefSeq	CDS	10830	11315	.	+	0	ID=cds-YP_009518733.1;Parent=gene-b0012;Dbxref=UniProtKB/Swiss-Prot:P28697,Genbank:YP_009518733.1,ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=YP_009518733.1;gbkey=CDS;gene=mbiA;locus_tag=b0012;orig_transcript_id=gnl|b0012|mrna.CDS13;product=uncharacterized protein MbiA;protein_id=YP_009518733.1;transl_table=11
+NC_000913.3	RefSeq	gene	11382	11786	.	-	.	ID=gene-b0013;Dbxref=ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=yaaI;gbkey=Gene;gene=yaaI;gene_biotype=protein_coding;gene_synonym=ECK0013;locus_tag=b0013
+NC_000913.3	RefSeq	CDS	11382	11786	.	-	0	ID=cds-NP_414554.1;Parent=gene-b0013;Dbxref=UniProtKB/Swiss-Prot:P28696,Genbank:NP_414554.1,ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=NP_414554.1;gbkey=CDS;gene=yaaI;locus_tag=b0013;orig_transcript_id=gnl|b0013|mrna.b0013;product=DUF2541 domain-containing protein YaaI;protein_id=NP_414554.1;transl_table=11
+NC_000913.3	RefSeq	gene	12163	14079	.	+	.	ID=gene-b0014;Dbxref=ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=dnaK;gbkey=Gene;gene=dnaK;gene_biotype=protein_coding;gene_synonym=ECK0014,groPAB,groPC,groPF,grpC,grpF,seg;locus_tag=b0014
+NC_000913.3	RefSeq	CDS	12163	14079	.	+	0	ID=cds-NP_414555.1;Parent=gene-b0014;Dbxref=UniProtKB/Swiss-Prot:P0A6Y8,Genbank:NP_414555.1,ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=NP_414555.1;gbkey=CDS;gene=dnaK;locus_tag=b0014;orig_transcript_id=gnl|b0014|mrna.b0014;product=chaperone protein DnaK;protein_id=NP_414555.1;transl_table=11
+NC_000913.3	RefSeq	gene	14168	15298	.	+	.	ID=gene-b0015;Dbxref=ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=dnaJ;gbkey=Gene;gene=dnaJ;gene_biotype=protein_coding;gene_synonym=ECK0015,groP,grpC;locus_tag=b0015
+NC_000913.3	RefSeq	CDS	14168	15298	.	+	0	ID=cds-NP_414556.1;Parent=gene-b0015;Dbxref=UniProtKB/Swiss-Prot:P08622,Genbank:NP_414556.1,ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=NP_414556.1;gbkey=CDS;gene=dnaJ;locus_tag=b0015;orig_transcript_id=gnl|b0015|mrna.b0015;product=chaperone protein DnaJ;protein_id=NP_414556.1;transl_table=11
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ecoli-k12.processed.gff3	Tue Oct 01 12:20:13 2019 -0400
@@ -0,0 +1,32 @@
+# gffread /home/hxr/arbeit/galaxy/database/files/000/dataset_791.dat -F -D -E -o output.gff3
+##gff-version 3
+NC_000913.3	RefSeq	gene	190	255	.	+	.	ID=gene-b0001;geneID=gene-b0001;gene_name=thrL;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001;protein_id=NP_414542.1
+NC_000913.3	RefSeq	CDS	190	255	.	+	0	Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;transl_table=11
+NC_000913.3	RefSeq	gene	337	2799	.	+	.	ID=gene-b0002;geneID=gene-b0002;gene_name=thrA;Dbxref=ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,thrA1,thrA2,thrD;locus_tag=b0002;protein_id=NP_414543.1
+NC_000913.3	RefSeq	CDS	337	2799	.	+	0	Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;locus_tag=b0002;orig_transcript_id=gnl|b0002|mrna.b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;transl_table=11
+NC_000913.3	RefSeq	gene	2801	3733	.	+	.	ID=gene-b0003;geneID=gene-b0003;gene_name=thrB;Dbxref=ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0003;locus_tag=b0003;protein_id=NP_414544.1
+NC_000913.3	RefSeq	CDS	2801	3733	.	+	0	Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;locus_tag=b0003;orig_transcript_id=gnl|b0003|mrna.b0003;product=homoserine kinase;transl_table=11
+NC_000913.3	RefSeq	gene	3734	5020	.	+	.	ID=gene-b0004;geneID=gene-b0004;gene_name=thrC;Dbxref=ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0004;locus_tag=b0004;protein_id=NP_414545.1
+NC_000913.3	RefSeq	CDS	3734	5020	.	+	0	Parent=gene-b0004;Dbxref=UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;gbkey=CDS;locus_tag=b0004;orig_transcript_id=gnl|b0004|mrna.b0004;product=threonine synthase;transl_table=11
+NC_000913.3	RefSeq	gene	5234	5530	.	+	.	ID=gene-b0005;geneID=gene-b0005;gene_name=yaaX;Dbxref=ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0005;locus_tag=b0005;protein_id=NP_414546.1
+NC_000913.3	RefSeq	CDS	5234	5530	.	+	0	Parent=gene-b0005;Dbxref=UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;locus_tag=b0005;orig_transcript_id=gnl|b0005|mrna.b0005;product=DUF2502 domain-containing protein YaaX;transl_table=11
+NC_000913.3	RefSeq	gene	5683	6459	.	-	.	ID=gene-b0006;geneID=gene-b0006;gene_name=yaaA;Dbxref=ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0006;locus_tag=b0006;protein_id=NP_414547.1
+NC_000913.3	RefSeq	CDS	5683	6459	.	-	0	Parent=gene-b0006;Dbxref=UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;locus_tag=b0006;orig_transcript_id=gnl|b0006|mrna.b0006;product=peroxide stress resistance protein YaaA;transl_table=11
+NC_000913.3	RefSeq	gene	6529	7959	.	-	.	ID=gene-b0007;geneID=gene-b0007;gene_name=yaaJ;Dbxref=ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=yaaJ;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0007;locus_tag=b0007;protein_id=NP_414548.1
+NC_000913.3	RefSeq	CDS	6529	7959	.	-	0	Parent=gene-b0007;Dbxref=UniProtKB/Swiss-Prot:P30143,Genbank:NP_414548.1,ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=NP_414548.1;gbkey=CDS;locus_tag=b0007;orig_transcript_id=gnl|b0007|mrna.b0007;product=putative transporter YaaJ;transl_table=11
+NC_000913.3	RefSeq	gene	8238	9191	.	+	.	ID=gene-b0008;geneID=gene-b0008;gene_name=talB;Dbxref=ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=talB;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0008,yaaK;locus_tag=b0008;protein_id=NP_414549.1
+NC_000913.3	RefSeq	CDS	8238	9191	.	+	0	Parent=gene-b0008;Dbxref=UniProtKB/Swiss-Prot:P0A870,Genbank:NP_414549.1,ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=NP_414549.1;gbkey=CDS;locus_tag=b0008;orig_transcript_id=gnl|b0008|mrna.b0008;product=transaldolase B;transl_table=11
+NC_000913.3	RefSeq	gene	9306	9893	.	+	.	ID=gene-b0009;geneID=gene-b0009;gene_name=mog;Dbxref=ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=mog;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=bisD,chlG,ECK0009,mogA,yaaG;locus_tag=b0009;protein_id=NP_414550.1
+NC_000913.3	RefSeq	CDS	9306	9893	.	+	0	Parent=gene-b0009;Dbxref=UniProtKB/Swiss-Prot:P0AF03,Genbank:NP_414550.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=NP_414550.1;gbkey=CDS;locus_tag=b0009;orig_transcript_id=gnl|b0009|mrna.b0009;product=molybdopterin adenylyltransferase;transl_table=11
+NC_000913.3	RefSeq	gene	9928	10494	.	-	.	ID=gene-b0010;geneID=gene-b0010;gene_name=satP;Dbxref=ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=satP;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0010,yaaH;locus_tag=b0010;protein_id=NP_414551.1
+NC_000913.3	RefSeq	CDS	9928	10494	.	-	0	Parent=gene-b0010;Dbxref=UniProtKB/Swiss-Prot:P0AC98,Genbank:NP_414551.1,ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=NP_414551.1;gbkey=CDS;locus_tag=b0010;orig_transcript_id=gnl|b0010|mrna.b0010;product=acetate/succinate:H(+) symporter;transl_table=11
+NC_000913.3	RefSeq	gene	10643	11356	.	-	.	ID=gene-b0011;geneID=gene-b0011;gene_name=yaaW;Dbxref=ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=yaaW;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0011;locus_tag=b0011;protein_id=NP_414552.1
+NC_000913.3	RefSeq	CDS	10643	11356	.	-	0	Parent=gene-b0011;Dbxref=UniProtKB/Swiss-Prot:P75617,Genbank:NP_414552.1,ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=NP_414552.1;gbkey=CDS;locus_tag=b0011;orig_transcript_id=gnl|b0011|mrna.b0011;product=putative enzyme-specific chaperone YaaW;transl_table=11
+NC_000913.3	RefSeq	gene	10830	11315	.	+	.	ID=gene-b0012;geneID=gene-b0012;gene_name=mbiA;Dbxref=ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=mbiA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0012,htgA,htpY;locus_tag=b0012;protein_id=YP_009518733.1
+NC_000913.3	RefSeq	CDS	10830	11315	.	+	0	Parent=gene-b0012;Dbxref=UniProtKB/Swiss-Prot:P28697,Genbank:YP_009518733.1,ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=YP_009518733.1;gbkey=CDS;locus_tag=b0012;orig_transcript_id=gnl|b0012|mrna.CDS13;product=uncharacterized protein MbiA;transl_table=11
+NC_000913.3	RefSeq	gene	11382	11786	.	-	.	ID=gene-b0013;geneID=gene-b0013;gene_name=yaaI;Dbxref=ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=yaaI;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0013;locus_tag=b0013;protein_id=NP_414554.1
+NC_000913.3	RefSeq	CDS	11382	11786	.	-	0	Parent=gene-b0013;Dbxref=UniProtKB/Swiss-Prot:P28696,Genbank:NP_414554.1,ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=NP_414554.1;gbkey=CDS;locus_tag=b0013;orig_transcript_id=gnl|b0013|mrna.b0013;product=DUF2541 domain-containing protein YaaI;transl_table=11
+NC_000913.3	RefSeq	gene	12163	14079	.	+	.	ID=gene-b0014;geneID=gene-b0014;gene_name=dnaK;Dbxref=ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=dnaK;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0014,groPAB,groPC,groPF,grpC,grpF,seg;locus_tag=b0014;protein_id=NP_414555.1
+NC_000913.3	RefSeq	CDS	12163	14079	.	+	0	Parent=gene-b0014;Dbxref=UniProtKB/Swiss-Prot:P0A6Y8,Genbank:NP_414555.1,ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=NP_414555.1;gbkey=CDS;locus_tag=b0014;orig_transcript_id=gnl|b0014|mrna.b0014;product=chaperone protein DnaK;transl_table=11
+NC_000913.3	RefSeq	gene	14168	15298	.	+	.	ID=gene-b0015;geneID=gene-b0015;gene_name=dnaJ;Dbxref=ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=dnaJ;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0015,groP,grpC;locus_tag=b0015;protein_id=NP_414556.1
+NC_000913.3	RefSeq	CDS	14168	15298	.	+	0	Parent=gene-b0015;Dbxref=UniProtKB/Swiss-Prot:P08622,Genbank:NP_414556.1,ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=NP_414556.1;gbkey=CDS;locus_tag=b0015;orig_transcript_id=gnl|b0015|mrna.b0015;product=chaperone protein DnaJ;transl_table=11