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S.No.
Riboswitch Location and Strand
Riboswitch class
Downstream gene location and Strand
Downstream gene name/gene product description
Locus_tag of downstream gene
Single gene/within operon (According to DOOR database)
Operon details (List of genes within operon and their Locus_tag)
Predicted Structure
1
616380-616521
(-)
FMN
615648-616299 (-)
ribB
3;4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (2)
PP_0530
Single gene
DOOR ID:
1435391
PP_0530
(ribB)
View Structure
2
875978-876117
(-)
yybP-ykoY
875304-875889 (-)
PP_0760
PP_0760
Single gene
DOOR ID:
1435483
PP_0760
View Structure
3
1866934-1867155
(+)
cobalamin
1867274-1867886 (+)
cobO
Cob(I)yrinic acid a;c-diamide adenosyltransferase (7) (Cob(I)alamin adenosyltransferase) (Corrinoid adenosyltransferase)
PP_1672
Operon
DOOR ID:
32865
PP_1672
(cobO)
,
PP_1673
(cobB)
,
PP_1674,
PP_1675
(cobD)
,
PP_1676
(cobC)
,
PP_1677
(cobQ)
,
PP_1678
(cobU)
,
PP_1679
(cobT)
,
PP_1680,
PP_1681
(cobS)
,
PP_1682
View Structure
4
1897096-1897147
(-)
mini-ykkC
1896752-1897070 (-)
sugE
PP_1701
Operon
DOOR ID:
538425
SPP_1701,
SPP_1702
View Structure
5
2765025-2765223
(-)
cobalamin
2763903-2764998 (-)
PP_2418
Putative cobalamin ABC transporter; periplasmic
PP_2418
Operon
DOOR ID:
33015
PP_2416,
PP_2417,
PP_2418
View Structure
6
2768765-2768973
(-)
cobalamin
2766529-2768716 (-)
PP_2420
Outer membrane ferric siderophore receptor
PP_2420
Operon
DOOR ID:
33016
PP_2419,
PP_2420
View Structure
7
3613932-3614046
(+)
TPP
3614124-3614772 (+)
pet18
Aminopyrimidine aminohydrolase
PP_3185
Operon
DOOR ID:
33161
PP_3185
(pet18)
,
PP_3186
View Structure
8
3857543-3857766
(+)
cobalamin
3858739-3859129 (+)
PP_3409
Putative Cobalamin biosynthesis protein cobE
PP_3409
Operon
DOOR ID:
33210
PP_3409,
PP_3410
(cobM)
,
PP_3411
View Structure
9
3981798-3982004
(-)
cobalamin
3980630-3981698 (-)
cobW
Protein CobW
PP_3508
Operon
DOOR ID:
33229
PP_3506,
PP_3507
(cobN)
,
PP_3508
(cobW)
View Structure
10
5596228-5596334
(-)
TPP
5594192-5596073 (-)
thiC
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
PP_4922
Single gene
DOOR ID:
1437089
PP_4922
(thiC)
View Structure
11
5858006-5858075
(-)
SAH
5856064-5857456 (+)
PP_5133
PP_5133
Operon
DOOR ID:
33548
PP_5133,
PP_5134
View Structure
Genome:
Pseudomonas putida KT2440
(
NC_002947.3
);
Phylum:
Gammaproteobacteria
a:12:{i:0;a:18:{i:0;s:5:"S.No.";i:1;s:9:"Genome_ID";i:2;s:11:"Genome_Name";i:3;s:13:"Taxonomy_name";i:4;s:6:"Tax_ID";i:5;s:19:"Riboswitch_Location";i:6;s:17:"Riboswitch_strand";i:7;s:16:"Riboswitch_class";i:8;s:14:"Tandem_Aptamer";i:9;s:24:"Downstream_gene_location";i:10;s:11:"Gene_Strand";i:11;s:20:"Downstream_gene_name";i:12;s:24:"Gene_product_description";i:13;s:9:"Locus_tag";i:14;s:25:"Single_gene/within_operon";i:15;s:9:"Operon_ID";i:16;s:14:"Operon_details";i:17;s:22:"Biological_process[GO]";}i:1;a:19:{i:0;i:1;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:13:"616380-616521";i:6;s:1:"-";i:7;s:3:"FMN";i:8;s:0:"";i:9;s:13:"615648-616299";i:10;s:1:"-";i:11;s:4:"ribB";i:12;s:65:"3;4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (2)";i:13;s:7:"PP_0530";i:14;s:11:"Single gene";i:15;s:7:"1435391";i:16;s:13:"PP_0530(ribB)";i:17;s:44:"riboflavin biosynthetic process [GO:0009231]";i:18;s:15:"View Structure ";}i:2;a:19:{i:0;i:2;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:13:"875978-876117";i:6;s:1:"-";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:13:"875304-875889";i:10;s:1:"-";i:11;s:7:"PP_0760";i:12;s:0:"";i:13;s:7:"PP_0760";i:14;s:11:"Single gene";i:15;s:7:"1435483";i:16;s:7:"PP_0760";i:17;s:0:"";i:18;s:15:"View Structure ";}i:3;a:19:{i:0;i:3;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"1866934-1867155";i:6;s:1:"+";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"1867274-1867886";i:10;s:1:"+";i:11;s:4:"cobO";i:12;s:120:"Cob(I)yrinic acid a;c-diamide adenosyltransferase (7) (Cob(I)alamin adenosyltransferase) (Corrinoid adenosyltransferase)";i:13;s:7:"PP_1672";i:14;s:6:"Operon";i:15;s:5:"32865";i:16;s:135:"PP_1672(cobO);PP_1673(cobB);PP_1674;PP_1675(cobD);PP_1676(cobC);PP_1677(cobQ);PP_1678(cobU);PP_1679(cobT);PP_1680;PP_1681(cobS);PP_1682";i:17;s:108:"cobalamin biosynthetic process [GO:0009236]; porphyrin-containing compound biosynthetic process [GO:0006779]";i:18;s:15:"View Structure ";}i:4;a:19:{i:0;i:4;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"1897096-1897147";i:6;s:1:"-";i:7;s:9:"mini-ykkC";i:8;s:0:"";i:9;s:15:"1896752-1897070";i:10;s:1:"-";i:11;s:4:"sugE";i:12;s:0:"";i:13;s:7:"PP_1701";i:14;s:6:"Operon";i:15;s:6:"538425";i:16;s:17:"SPP_1701;SPP_1702";i:17;s:0:"";i:18;s:15:"View Structure ";}i:5;a:19:{i:0;i:5;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"2765025-2765223";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"2763903-2764998";i:10;s:1:"-";i:11;s:7:"PP_2418";i:12;s:47:"Putative cobalamin ABC transporter; periplasmic";i:13;s:7:"PP_2418";i:14;s:6:"Operon";i:15;s:5:"33015";i:16;s:23:"PP_2416;PP_2417;PP_2418";i:17;s:0:"";i:18;s:15:"View Structure ";}i:6;a:19:{i:0;i:6;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"2768765-2768973";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"2766529-2768716";i:10;s:1:"-";i:11;s:7:"PP_2420";i:12;s:42:"Outer membrane ferric siderophore receptor";i:13;s:7:"PP_2420";i:14;s:6:"Operon";i:15;s:5:"33016";i:16;s:15:"PP_2419;PP_2420";i:17;s:34:"siderophore transport [GO:0015891]";i:18;s:15:"View Structure ";}i:7;a:19:{i:0;i:7;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"3613932-3614046";i:6;s:1:"+";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"3614124-3614772";i:10;s:1:"+";i:11;s:5:"pet18";i:12;s:31:"Aminopyrimidine aminohydrolase ";i:13;s:7:"PP_3185";i:14;s:6:"Operon";i:15;s:5:"33161";i:16;s:22:"PP_3185(pet18);PP_3186";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:8;a:19:{i:0;i:8;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"3857543-3857766";i:6;s:1:"+";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"3858739-3859129";i:10;s:1:"+";i:11;s:7:"PP_3409";i:12;s:44:"Putative Cobalamin biosynthesis protein cobE";i:13;s:7:"PP_3409";i:14;s:6:"Operon";i:15;s:5:"33210";i:16;s:29:"PP_3409;PP_3410(cobM);PP_3411";i:17;s:43:"cobalamin biosynthetic process [GO:0009236]";i:18;s:15:"View Structure ";}i:9;a:19:{i:0;i:9;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"3981798-3982004";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"3980630-3981698";i:10;s:1:"-";i:11;s:4:"cobW";i:12;s:12:"Protein CobW";i:13;s:7:"PP_3508";i:14;s:6:"Operon";i:15;s:5:"33229";i:16;s:35:"PP_3506;PP_3507(cobN);PP_3508(cobW)";i:17;s:43:"cobalamin biosynthetic process [GO:0009236]";i:18;s:15:"View Structure ";}i:10;a:19:{i:0;i:10;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"5596228-5596334";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"5594192-5596073";i:10;s:1:"-";i:11;s:4:"thiC";i:12;s:176:"Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)";i:13;s:7:"PP_4922";i:14;s:11:"Single gene";i:15;s:7:"1437089";i:16;s:13:"PP_4922(thiC)";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:11;a:19:{i:0;i:11;i:1;s:11:"NC_002947.3";i:2;s:26:"Pseudomonas putida KT2440 ";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"5858006-5858075";i:6;s:1:"-";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:15:"5856064-5857456";i:10;s:1:"+";i:11;s:7:"PP_5133";i:12;s:0:"";i:13;s:7:"PP_5133";i:14;s:6:"Operon";i:15;s:5:"33548";i:16;s:15:"PP_5133;PP_5134";i:17;s:0:"";i:18;s:15:"View Structure ";}}
