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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
844994-845102
(+)
ZMP-ZTP
845268-846516 (+)
glyA
Serine hydroxymethyltransferase (SHMT) (Serine methylase)
Bphyt_0765
Operon
DOOR ID:
434398
Bphyt_0765
(glyA)
,
Bphyt_0766
(nrdR)
View Structure
2
1116245-1116503
(+)
cobalamin
1116593-1118483 (+)
Bphyt_0995
TonB-dependent receptor
Bphyt_0995
Operon
DOOR ID:
434450
Bphyt_0995,
Bphyt_0996,
Bphyt_0997,
Bphyt_0998
(cobT)
,
Bphyt_0999
(cobS)
View Structure
3
1472345-1472386
(+)
mini-ykkC
1472407-1472728 (+)
Bphyt_1313
Bphyt_1313
Single gene
DOOR ID:
2314372
Bphyt_1313
View Structure
4
1667858-1667937
(-)
c-di-GMP-I
1666930-1667803 (-)
Bphyt_1490
Conserved hypothetical signal peptide protein
Bphyt_1490
single gene
DOOR ID:
2314437
Bphyt_1490
View Structure
5
1800268-1800329
(-)
fluoride
1799808-1800189 (-)
Bphyt_1600
Putative fluoride ion transporter CrcB
Bphyt_1600
Single gene
DOOR ID:
2314485
Bphyt_1600
View Structure
6
2305005-2305191
(+)
yybP-ykoY
2305196-2305787 (+)
Bphyt_2039
Bphyt_2039
Single gene
DOOR ID:
2314719
Bphyt_2039
View Structure
7
3015583-3015701
(+)
TPP
3015794-3017726 (+)
Bphyt_2670
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
Bphyt_2670
Single gene
DOOR ID:
2315024
Bphyt_2670
View Structure
8
3743871-3744054
(-)
FMN
3743003-3743723 (-)
Bphyt_3324
3;4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (2)
Bphyt_3324
Single gene
DOOR ID:
2315337
Bphyt_3324
View Structure
9
4014318-4014441
(-)
TPP
4012970-4014101 (-)
Bphyt_3575
FAD dependent oxidoreductase
Bphyt_3575
Operon
DOOR ID:
434929
Bphyt_3572,
Bphyt_3573
(thiG)
,
Bphyt_3574,
Bphyt_3575
View Structure
10
4147580-4147651
(-)
fluoride
4146189-4147500 (-)
Bphyt_3703
Chloride channel core
Bphyt_3703
Operon
DOOR ID:
434953
Bphyt_3702,
Bphyt_3703
View Structure
11
4208320-4208453
(-)
SAH
4206865-4208287 (-)
Bphyt_3758
Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)
Bphyt_3758
Single gene
DOOR ID:
2315501
Bphyt_3758
View Structure
12
4299713-4299884
(-)
yybP-ykoY
4298601-4299612 (-)
Bphyt_3848
Sodium/calcium exchanger membrane region
Bphyt_3848
Single gene
DOOR ID:
2315525
Bphyt_3848
View Structure
13
4337937-4338038
(+)
glycine
4338306-4339425 (+)
gcvT
Aminomethyltransferase (0) (Glycine cleavage system T protein)
Bphyt_3880
Operon
DOOR ID:
434988
Bphyt_3880
(gcvT)
,
Bphyt_3881
View Structure
14
4338072-4338226
(+)
glycine
4338306-4339425 (+)
gcvT
Aminomethyltransferase (0) (Glycine cleavage system T protein)
Bphyt_3880
Operon
DOOR ID:
434988
Bphyt_3880
(gcvT)
,
Bphyt_3881
View Structure
Genome:
Burkholderia phytofirmans PsJN chromosome I
(
NC_010681.1
);
Phylum:
Betaproteobacteria
a:15:{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_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:13:"844994-845102";i:6;s:1:"+";i:7;s:7:"ZMP-ZTP";i:8;s:0:"";i:9;s:13:"845268-846516";i:10;s:1:"+";i:11;s:4:"glyA";i:12;s:58:"Serine hydroxymethyltransferase (SHMT) (Serine methylase) ";i:13;s:10:"Bphyt_0765";i:14;s:6:"Operon";i:15;s:6:"434398";i:16;s:33:"Bphyt_0765(glyA);Bphyt_0766(nrdR)";i:17;s:100:"glycine biosynthetic process from serine [GO:0019264]; tetrahydrofolate interconversion [GO:0035999]";i:18;s:15:"View Structure ";}i:2;a:19:{i:0;i:2;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1116245-1116503";i:6;s:1:"+";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"1116593-1118483";i:10;s:1:"+";i:11;s:10:"Bphyt_0995";i:12;s:23:"TonB-dependent receptor";i:13;s:10:"Bphyt_0995";i:14;s:6:"Operon";i:15;s:6:"434450";i:16;s:66:"Bphyt_0995;Bphyt_0996;Bphyt_0997;Bphyt_0998(cobT);Bphyt_0999(cobS)";i:17;s:0:"";i:18;s:15:"View Structure ";}i:3;a:19:{i:0;i:3;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1472345-1472386";i:6;s:1:"+";i:7;s:9:"mini-ykkC";i:8;s:0:"";i:9;s:15:"1472407-1472728";i:10;s:1:"+";i:11;s:10:"Bphyt_1313";i:12;s:0:"";i:13;s:10:"Bphyt_1313";i:14;s:11:"Single gene";i:15;s:7:"2314372";i:16;s:10:"Bphyt_1313";i:17;s:0:"";i:18;s:15:"View Structure ";}i:4;a:19:{i:0;i:4;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1667858-1667937";i:6;s:1:"-";i:7;s:10:"c-di-GMP-I";i:8;s:0:"";i:9;s:15:"1666930-1667803";i:10;s:1:"-";i:11;s:10:"Bphyt_1490";i:12;s:45:"Conserved hypothetical signal peptide protein";i:13;s:10:"Bphyt_1490";i:14;s:11:"single gene";i:15;s:7:"2314437";i:16;s:10:"Bphyt_1490";i:17;s:0:"";i:18;s:15:"View Structure ";}i:5;a:19:{i:0;i:5;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1800268-1800329";i:6;s:1:"-";i:7;s:8:"fluoride";i:8;s:0:"";i:9;s:15:"1799808-1800189";i:10;s:1:"-";i:11;s:10:"Bphyt_1600";i:12;s:38:"Putative fluoride ion transporter CrcB";i:13;s:10:"Bphyt_1600";i:14;s:11:"Single gene";i:15;s:7:"2314485";i:16;s:10:"Bphyt_1600";i:17;s:0:"";i:18;s:15:"View Structure ";}i:6;a:19:{i:0;i:6;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2305005-2305191";i:6;s:1:"+";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:15:"2305196-2305787";i:10;s:1:"+";i:11;s:10:"Bphyt_2039";i:12;s:0:"";i:13;s:10:"Bphyt_2039";i:14;s:11:"Single gene";i:15;s:7:"2314719";i:16;s:10:"Bphyt_2039";i:17;s:0:"";i:18;s:15:"View Structure ";}i:7;a:19:{i:0;i:7;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3015583-3015701";i:6;s:1:"+";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"3015794-3017726";i:10;s:1:"+";i:11;s:10:"Bphyt_2670";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:10:"Bphyt_2670";i:14;s:11:"Single gene";i:15;s:7:"2315024";i:16;s:10:"Bphyt_2670";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_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3743871-3744054";i:6;s:1:"-";i:7;s:3:"FMN";i:8;s:0:"";i:9;s:15:"3743003-3743723";i:10;s:1:"-";i:11;s:10:"Bphyt_3324";i:12;s:65:"3;4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (2)";i:13;s:10:"Bphyt_3324";i:14;s:11:"Single gene";i:15;s:7:"2315337";i:16;s:10:"Bphyt_3324";i:17;s:44:"riboflavin biosynthetic process [GO:0009231]";i:18;s:15:"View Structure ";}i:9;a:19:{i:0;i:9;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4014318-4014441";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"4012970-4014101";i:10;s:1:"-";i:11;s:10:"Bphyt_3575";i:12;s:28:"FAD dependent oxidoreductase";i:13;s:10:"Bphyt_3575";i:14;s:6:"Operon";i:15;s:6:"434929";i:16;s:49:"Bphyt_3572;Bphyt_3573(thiG);Bphyt_3574;Bphyt_3575";i:17;s:43:"D-amino acid metabolic process [GO:0046416]";i:18;s:15:"View Structure ";}i:10;a:19:{i:0;i:10;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4147580-4147651";i:6;s:1:"-";i:7;s:8:"fluoride";i:8;s:0:"";i:9;s:15:"4146189-4147500";i:10;s:1:"-";i:11;s:10:"Bphyt_3703";i:12;s:21:"Chloride channel core";i:13;s:10:"Bphyt_3703";i:14;s:6:"Operon";i:15;s:6:"434953";i:16;s:21:"Bphyt_3702;Bphyt_3703";i:17;s:0:"";i:18;s:15:"View Structure ";}i:11;a:19:{i:0;i:11;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4208320-4208453";i:6;s:1:"-";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:15:"4206865-4208287";i:10;s:1:"-";i:11;s:10:"Bphyt_3758";i:12;s:73:"Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)";i:13;s:10:"Bphyt_3758";i:14;s:11:"Single gene";i:15;s:7:"2315501";i:16;s:10:"Bphyt_3758";i:17;s:96:"one-carbon metabolic process [GO:0006730]; S-adenosylhomocysteine catabolic process [GO:0019510]";i:18;s:15:"View Structure ";}i:12;a:19:{i:0;i:12;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4299713-4299884";i:6;s:1:"-";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:15:"4298601-4299612";i:10;s:1:"-";i:11;s:10:"Bphyt_3848";i:12;s:40:"Sodium/calcium exchanger membrane region";i:13;s:10:"Bphyt_3848";i:14;s:11:"Single gene";i:15;s:7:"2315525";i:16;s:10:"Bphyt_3848";i:17;s:36:"transmembrane transport [GO:0055085]";i:18;s:15:"View Structure ";}i:13;a:19:{i:0;i:13;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4337937-4338038";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"4338306-4339425";i:10;s:1:"+";i:11;s:4:"gcvT";i:12;s:62:"Aminomethyltransferase (0) (Glycine cleavage system T protein)";i:13;s:10:"Bphyt_3880";i:14;s:6:"Operon";i:15;s:6:"434988";i:16;s:27:"Bphyt_3880(gcvT);Bphyt_3881";i:17;s:64:"glycine decarboxylation via glycine cleavage system [GO:0019464]";i:18;s:15:"View Structure ";}i:14;a:19:{i:0;i:14;i:1;s:11:"NC_010681.1";i:2;s:43:"Burkholderia phytofirmans PsJN chromosome I";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4338072-4338226";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"4338306-4339425";i:10;s:1:"+";i:11;s:4:"gcvT";i:12;s:62:"Aminomethyltransferase (0) (Glycine cleavage system T protein)";i:13;s:10:"Bphyt_3880";i:14;s:6:"Operon";i:15;s:6:"434988";i:16;s:27:"Bphyt_3880(gcvT);Bphyt_3881";i:17;s:64:"glycine decarboxylation via glycine cleavage system [GO:0019464]";i:18;s:15:"View Structure ";}}
