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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
58126-58228
(+)
yybP-ykoY
58321-58879 (+)
PBPRA0058
Conserved hypothetical membrane protein
PBPRA0058
Single gene
DOOR ID:
1634804
PBPRA0058
View Structure
2
106620-106717
(+)
TPP
106854-108777 (+)
PBPRA0106
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
PBPRA0106
Operon
DOOR ID:
114046
PBPRA0106,
PBPRA0107
(thiE)
,
PBPRA0108
View Structure
3
420393-420522
(-)
TPP
419247-420234 (-)
tbpA
Putative ABC-type thiamine transport system;periplasmic component
PBPRA0413
Operon
DOOR ID:
114106
PBPRA0411,
PBPRA0412
(thiP)
,
PBPRA0413
(tbpA)
View Structure
4
1201127-1201310
(+)
lysine
1201504-1203004 (+)
PBPRA1083
Putative Na+/H+ antiporter
PBPRA1083
Single gene
DOOR ID:
1635218
PBPRA1083
View Structure
5
1247584-1247737
(+)
MOCO
1248864-1249362 (+)
moaC
Cyclic pyranopterin monophosphate synthase (7) (Molybdenum cofactor biosynthesis protein C)
PBPRA1125
Operon
DOOR ID:
114243
PBPRA1125
(moaC)
,
PBPRA1126
(moaD)
,
PBPRA1127
View Structure
6
1717696-1717779
(-)
fluoride
1716785-1717478 (-)
PBPRA1515
PBPRA1515
Operon
DOOR ID:
114314
PBPRA1514,
PBPRA1515
View Structure
7
2427572-2427677
(+)
c-di-GMP-I
2427797-2428388 (+)
PBPRA2110
Uncharacterized protein
PBPRA2110
single gene
DOOR ID:
1635815
PBPRA2110
View Structure
8
2453318-2453475
(+)
glycine
2453693-2455085 (+)
PBPRA2132
Putative sodium/alanine symporter
PBPRA2132
Single gene
DOOR ID:
1635829
PBPRA2132
View Structure
9
2453496-2453611
(+)
glycine
2453693-2455085 (+)
PBPRA2132
Putative sodium/alanine symporter
PBPRA2132
Single gene
DOOR ID:
1635829
PBPRA2132
View Structure
10
2634481-2634568
(+)
c-di-GMP-I
2634668-2637323 (+)
PBPRA2288
Hypothetical ToxR-regulated lipoprotein
PBPRA2288
single gene
DOOR ID:
1635909
PBPRA2288
View Structure
11
3172735-3172907
(+)
lysine
3172989-3174573 (+)
PBPRA2736
Putative Na+/H+ antiporter
PBPRA2736
Single gene
DOOR ID:
1636145
PBPRA2736
View Structure
12
3733830-3734021
(+)
lysine
3734129-3735509 (+)
PBPRA3293
Aspartokinase
PBPRA3293
Single gene
DOOR ID:
1636338
PBPRA3293
View Structure
13
3919359-3919583
(-)
cobalamin
3917500-3919321 (-)
PBPRA3464
Vitamin B12 transporter BtuB (Cobalamin receptor) (Outer membrane cobalamin translocator)
PBPRA3464
Single gene
DOOR ID:
1636393
PBPRA3464
View Structure
Genome:
Photobacterium profundum SS9 chromosome I
(
NC_006370.1
);
Phylum:
Gammaproteobacteria
a:14:{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_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:11:"58126-58228";i:6;s:1:"+";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:11:"58321-58879";i:10;s:1:"+";i:11;s:9:"PBPRA0058";i:12;s:39:"Conserved hypothetical membrane protein";i:13;s:9:"PBPRA0058";i:14;s:11:"Single gene";i:15;s:7:"1634804";i:16;s:9:"PBPRA0058";i:17;s:0:"";i:18;s:15:"View Structure ";}i:2;a:19:{i:0;i:2;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:13:"106620-106717";i:6;s:1:"+";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:13:"106854-108777";i:10;s:1:"+";i:11;s:9:"PBPRA0106";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:9:"PBPRA0106";i:14;s:6:"Operon";i:15;s:6:"114046";i:16;s:35:"PBPRA0106;PBPRA0107(thiE);PBPRA0108";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:3;a:19:{i:0;i:3;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:13:"420393-420522";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:13:"419247-420234";i:10;s:1:"-";i:11;s:4:"tbpA";i:12;s:65:"Putative ABC-type thiamine transport system;periplasmic component";i:13;s:9:"PBPRA0413";i:14;s:6:"Operon";i:15;s:6:"114106";i:16;s:41:"PBPRA0411;PBPRA0412(thiP);PBPRA0413(tbpA)";i:17;s:31:"thiamine transport [GO:0015888]";i:18;s:15:"View Structure ";}i:4;a:19:{i:0;i:4;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"1201127-1201310";i:6;s:1:"+";i:7;s:6:"lysine";i:8;s:0:"";i:9;s:15:"1201504-1203004";i:10;s:1:"+";i:11;s:9:"PBPRA1083";i:12;s:26:"Putative Na+/H+ antiporter";i:13;s:9:"PBPRA1083";i:14;s:11:"Single gene";i:15;s:7:"1635218";i:16;s:9:"PBPRA1083";i:17;s:0:"";i:18;s:15:"View Structure ";}i:5;a:19:{i:0;i:5;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"1247584-1247737";i:6;s:1:"+";i:7;s:4:"MOCO";i:8;s:0:"";i:9;s:15:"1248864-1249362";i:10;s:1:"+";i:11;s:4:"moaC";i:12;s:91:"Cyclic pyranopterin monophosphate synthase (7) (Molybdenum cofactor biosynthesis protein C)";i:13;s:9:"PBPRA1125";i:14;s:6:"Operon";i:15;s:6:"114243";i:16;s:41:"PBPRA1125(moaC);PBPRA1126(moaD);PBPRA1127";i:17;s:59:"Mo-molybdopterin cofactor biosynthetic process [GO:0006777]";i:18;s:15:"View Structure ";}i:6;a:19:{i:0;i:6;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"1717696-1717779";i:6;s:1:"-";i:7;s:8:"fluoride";i:8;s:0:"";i:9;s:15:"1716785-1717478";i:10;s:1:"-";i:11;s:9:"PBPRA1515";i:12;s:0:"";i:13;s:9:"PBPRA1515";i:14;s:6:"Operon";i:15;s:6:"114314";i:16;s:19:"PBPRA1514;PBPRA1515";i:17;s:0:"";i:18;s:15:"View Structure ";}i:7;a:19:{i:0;i:7;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"2427572-2427677";i:6;s:1:"+";i:7;s:10:"c-di-GMP-I";i:8;s:0:"";i:9;s:15:"2427797-2428388";i:10;s:1:"+";i:11;s:9:"PBPRA2110";i:12;s:23:"Uncharacterized protein";i:13;s:9:"PBPRA2110";i:14;s:11:"single gene";i:15;s:7:"1635815";i:16;s:9:"PBPRA2110";i:17;s:0:"";i:18;s:15:"View Structure ";}i:8;a:19:{i:0;i:8;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"2453318-2453475";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"2453693-2455085";i:10;s:1:"+";i:11;s:9:"PBPRA2132";i:12;s:33:"Putative sodium/alanine symporter";i:13;s:9:"PBPRA2132";i:14;s:11:"Single gene";i:15;s:7:"1635829";i:16;s:9:"PBPRA2132";i:17;s:0:"";i:18;s:15:"View Structure ";}i:9;a:19:{i:0;i:9;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"2453496-2453611";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"2453693-2455085";i:10;s:1:"+";i:11;s:9:"PBPRA2132";i:12;s:33:"Putative sodium/alanine symporter";i:13;s:9:"PBPRA2132";i:14;s:11:"Single gene";i:15;s:7:"1635829";i:16;s:9:"PBPRA2132";i:17;s:0:"";i:18;s:15:"View Structure ";}i:10;a:19:{i:0;i:10;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"2634481-2634568";i:6;s:1:"+";i:7;s:10:"c-di-GMP-I";i:8;s:0:"";i:9;s:15:"2634668-2637323";i:10;s:1:"+";i:11;s:9:"PBPRA2288";i:12;s:39:"Hypothetical ToxR-regulated lipoprotein";i:13;s:9:"PBPRA2288";i:14;s:11:"single gene";i:15;s:7:"1635909";i:16;s:9:"PBPRA2288";i:17;s:0:"";i:18;s:15:"View Structure ";}i:11;a:19:{i:0;i:11;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"3172735-3172907";i:6;s:1:"+";i:7;s:6:"lysine";i:8;s:0:"";i:9;s:15:"3172989-3174573";i:10;s:1:"+";i:11;s:9:"PBPRA2736";i:12;s:26:"Putative Na+/H+ antiporter";i:13;s:9:"PBPRA2736";i:14;s:11:"Single gene";i:15;s:7:"1636145";i:16;s:9:"PBPRA2736";i:17;s:0:"";i:18;s:15:"View Structure ";}i:12;a:19:{i:0;i:12;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"3733830-3734021";i:6;s:1:"+";i:7;s:6:"lysine";i:8;s:0:"";i:9;s:15:"3734129-3735509";i:10;s:1:"+";i:11;s:9:"PBPRA3293";i:12;s:14:"Aspartokinase ";i:13;s:9:"PBPRA3293";i:14;s:11:"Single gene";i:15;s:7:"1636338";i:16;s:9:"PBPRA3293";i:17;s:105:"lysine biosynthetic process via diaminopimelate [GO:0009089]; threonine biosynthetic process [GO:0009088]";i:18;s:15:"View Structure ";}i:13;a:19:{i:0;i:13;i:1;s:11:"NC_006370.1";i:2;s:41:"Photobacterium profundum SS9 chromosome I";i:3;s:19:"Gammaproteobacteria";i:4;s:4:"1236";i:5;s:15:"3919359-3919583";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"3917500-3919321";i:10;s:1:"-";i:11;s:9:"PBPRA3464";i:12;s:89:"Vitamin B12 transporter BtuB (Cobalamin receptor) (Outer membrane cobalamin translocator)";i:13;s:9:"PBPRA3464";i:14;s:11:"Single gene";i:15;s:7:"1636393";i:16;s:9:"PBPRA3464";i:17;s:26:"ion transport [GO:0006811]";i:18;s:15:"View Structure ";}}
