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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
16458-16572
(+)
TPP
16662-18579 (+)
Pnap_0019
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
Pnap_0019
Single gene
DOOR ID:
1949655
Pnap_0019
View Structure
2
42765-42882
(-)
ykkC-yxkD
41692-42709 (-)
Pnap_0041
Aliphatic sulfonates family ABC transporter; periplasmic ligand-binding protein
Pnap_0041
Single gene
DOOR ID:
1949659
Pnap_0041
View Structure
3
125938-126030
(+)
SAH
126044-128864 (+)
Pnap_0117
Methionine synthase (3) (5-methyltetrahydrofolate--homocysteine methyltransferase)
Pnap_0117
Single gene
DOOR ID:
1949700
Pnap_0117
View Structure
4
516171-516245
(+)
SAH
516347-517784 (+)
Pnap_0489
Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)
Pnap_0489
Single gene
DOOR ID:
1949853
Pnap_0489
View Structure
5
2301570-2301808
(-)
cobalamin
2300550-2301375 (-)
Pnap_2163
Precorrin-4 C11-methyltransferase (33)
Pnap_2163
Operon
DOOR ID:
261623
Pnap_2156,
Pnap_2157,
Pnap_2158,
Pnap_2159,
Pnap_2160
(cbiD)
,
Pnap_2161,
Pnap_2162,
Pnap_2163
View Structure
6
2495155-2495439
(-)
cobalamin
2493212-2495066 (-)
Pnap_2368
TonB-dependent receptor; plug
Pnap_2368
Operon
DOOR ID:
261667
Pnap_2367,
Pnap_2368
View Structure
7
2825121-2825224
(+)
glycine
2825393-2826548 (+)
Pnap_2683
Glycine cleavage system T protein
Pnap_2683
Single gene
DOOR ID:
1950682
Pnap_2683
View Structure
8
2825246-2825347
(+)
glycine
2825393-2826548 (+)
Pnap_2683
Glycine cleavage system T protein
Pnap_2683
Single gene
DOOR ID:
1950682
Pnap_2683
View Structure
9
3062025-3062156
(+)
ZMP-ZTP
3062217-3063462 (+)
glyA
Serine hydroxymethyltransferase (SHMT) (Serine methylase)
Pnap_2907
Operon
DOOR ID:
261774
Pnap_2907
(glyA)
,
Pnap_2908
(nrdR)
View Structure
10
4389638-4389790
(-)
yybP-ykoY
4389010-4389577 (-)
Pnap_4103
Pnap_4103
Single gene
DOOR ID:
1951226
Pnap_4103
View Structure
Genome:
Polaromonas naphthalenivorans CJ2
(
NC_008781.1
);
Phylum:
Betaproteobacteria
a:11:{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_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:11:"16458-16572";i:6;s:1:"+";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:11:"16662-18579";i:10;s:1:"+";i:11;s:9:"Pnap_0019";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:"Pnap_0019";i:14;s:11:"Single gene";i:15;s:7:"1949655";i:16;s:9:"Pnap_0019";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:2;a:19:{i:0;i:2;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:11:"42765-42882";i:6;s:1:"-";i:7;s:9:"ykkC-yxkD";i:8;s:0:"";i:9;s:11:"41692-42709";i:10;s:1:"-";i:11;s:9:"Pnap_0041";i:12;s:79:"Aliphatic sulfonates family ABC transporter; periplasmic ligand-binding protein";i:13;s:9:"Pnap_0041";i:14;s:11:"Single gene";i:15;s:7:"1949659";i:16;s:9:"Pnap_0041";i:17;s:0:"";i:18;s:15:"View Structure ";}i:3;a:19:{i:0;i:3;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:13:"125938-126030";i:6;s:1:"+";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:13:"126044-128864";i:10;s:1:"+";i:11;s:9:"Pnap_0117";i:12;s:82:"Methionine synthase (3) (5-methyltetrahydrofolate--homocysteine methyltransferase)";i:13;s:9:"Pnap_0117";i:14;s:11:"Single gene";i:15;s:7:"1949700";i:16;s:9:"Pnap_0117";i:17;s:60:"pteridine-containing compound metabolic process [GO:0042558]";i:18;s:15:"View Structure ";}i:4;a:19:{i:0;i:4;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:13:"516171-516245";i:6;s:1:"+";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:13:"516347-517784";i:10;s:1:"+";i:11;s:9:"Pnap_0489";i:12;s:73:"Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)";i:13;s:9:"Pnap_0489";i:14;s:11:"Single gene";i:15;s:7:"1949853";i:16;s:9:"Pnap_0489";i:17;s:96:"one-carbon metabolic process [GO:0006730]; S-adenosylhomocysteine catabolic process [GO:0019510]";i:18;s:15:"View Structure ";}i:5;a:19:{i:0;i:5;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2301570-2301808";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"2300550-2301375";i:10;s:1:"-";i:11;s:9:"Pnap_2163";i:12;s:38:"Precorrin-4 C11-methyltransferase (33)";i:13;s:9:"Pnap_2163";i:14;s:6:"Operon";i:15;s:6:"261623";i:16;s:85:"Pnap_2156;Pnap_2157;Pnap_2158;Pnap_2159;Pnap_2160(cbiD);Pnap_2161;Pnap_2162;Pnap_2163";i:17;s:85:"cobalamin biosynthetic process [GO:0009236]; oxidation-reduction process [GO:0055114]";i:18;s:15:"View Structure ";}i:6;a:19:{i:0;i:6;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2495155-2495439";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"2493212-2495066";i:10;s:1:"-";i:11;s:9:"Pnap_2368";i:12;s:29:"TonB-dependent receptor; plug";i:13;s:9:"Pnap_2368";i:14;s:6:"Operon";i:15;s:6:"261667";i:16;s:19:"Pnap_2367;Pnap_2368";i:17;s:0:"";i:18;s:15:"View Structure ";}i:7;a:19:{i:0;i:7;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2825121-2825224";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"2825393-2826548";i:10;s:1:"+";i:11;s:9:"Pnap_2683";i:12;s:33:"Glycine cleavage system T protein";i:13;s:9:"Pnap_2683";i:14;s:11:"Single gene";i:15;s:7:"1950682";i:16;s:9:"Pnap_2683";i:17;s:38:"glycine catabolic process [GO:0006546]";i:18;s:15:"View Structure ";}i:8;a:19:{i:0;i:8;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2825246-2825347";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"2825393-2826548";i:10;s:1:"+";i:11;s:9:"Pnap_2683";i:12;s:33:"Glycine cleavage system T protein";i:13;s:9:"Pnap_2683";i:14;s:11:"Single gene";i:15;s:7:"1950682";i:16;s:9:"Pnap_2683";i:17;s:38:"glycine catabolic process [GO:0006546]";i:18;s:15:"View Structure ";}i:9;a:19:{i:0;i:9;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3062025-3062156";i:6;s:1:"+";i:7;s:7:"ZMP-ZTP";i:8;s:0:"";i:9;s:15:"3062217-3063462";i:10;s:1:"+";i:11;s:4:"glyA";i:12;s:58:"Serine hydroxymethyltransferase (SHMT) (Serine methylase) ";i:13;s:9:"Pnap_2907";i:14;s:6:"Operon";i:15;s:6:"261774";i:16;s:31:"Pnap_2907(glyA);Pnap_2908(nrdR)";i:17;s:100:"glycine biosynthetic process from serine [GO:0019264]; tetrahydrofolate interconversion [GO:0035999]";i:18;s:15:"View Structure ";}i:10;a:19:{i:0;i:10;i:1;s:11:"NC_008781.1";i:2;s:34:"Polaromonas naphthalenivorans CJ2 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4389638-4389790";i:6;s:1:"-";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:15:"4389010-4389577";i:10;s:1:"-";i:11;s:9:"Pnap_4103";i:12;s:0:"";i:13;s:9:"Pnap_4103";i:14;s:11:"Single gene";i:15;s:7:"1951226";i:16;s:9:"Pnap_4103";i:17;s:0:"";i:18;s:15:"View Structure ";}}
