Genome: Clostridium difficile R20291 (NC_013316.1); Taxonomy: Firmicutes
S.No.Riboswitch Location and StrandRiboswitch classDownstream gene location and StrandDownstream gene name/gene product descriptionLocus_tag of downstream geneSingle gene/within operon (According to DOOR database)Operon details (List of genes within operon and their Locus_tag)Predicted Structure
1 1510232-1510328 (-)c-di-GMP-I1510001-1510178 (-)CDR20291_1271

Uncharacterized protein		CDR20291_1271single gene

DOOR ID: 2697004		CDR20291_1271 View Structure
2 2224510-2224599 (+)c-di-GMP-I2224942-2225299 (-)CDR20291_1905

Putative transcriptional regulator		CDR20291_1905single gene

DOOR ID: 2697258		CDR20291_1905 View Structure
3 2236907-2237000 (-)c-di-GMP-I2236338-2236824 (-)CDR20291_1914

Uncharacterized protein		CDR20291_1914single gene

DOOR ID: 2697267		CDR20291_1914 View Structure
4 2237966-2238063 (+)c-di-GMP-I2238519-2238720 (+)cspC

Cold shock protein		CDR20291_1915single gene

DOOR ID: 2697268		CDR20291_1915 View Structure
5 2582672-2582761 (+)c-di-GMP-I2583215-2583416 (+)cspD

Cold shock protein		CDR20291_2199single gene

DOOR ID: 2697422		CDR20291_2199 View Structure
6 308010-308100 (+)c-di-GMP-I308506-308824 (+)flgB

Flagellar basal-body rod protein		CDR20291_0248operon

DOOR ID: 621900		CDR20291_0248,
CDR20291_0249,
CDR20291_0250,
CDR20291_0251,
CDR20291_0252,
CDR20291_0253,
CDR20291_0254,
CDR20291_0255,
CDR20291_0256,
CDR20291_0257,
CDR20291_0258,
CDR20291_0259,
CDR20291_0260,
CDR20291_0261,
CDR20291_0262,
CDR20291_0263,
CDR20291_0264,
CDR20291_0265,
CDR20291_0266,
CDR20291_0267,
CDR20291_0268,
CDR20291_0269,
CDR20291_0270,
CDR20291_0271		 View Structure
7 3176627-3176712 (-)c-di-GMP-I3170539-3176503 (-)CDR20291_2686

Putative exported protein		CDR20291_2686single gene

DOOR ID: 2697601		CDR20291_2686 View Structure
8 3217101-3217186 (-)c-di-GMP-I3216338-3217001 (-)CDR20291_2721

Putative exported protein		CDR20291_2721single gene

DOOR ID: 2697620		CDR20291_2721 View Structure
9 3831022-3831118 (+)c-di-GMP-I3831796-3832396 (+)CDR20291_3214

Uncharacterized protein		CDR20291_3214single gene

DOOR ID: 2697822		CDR20291_3214 View Structure
10 3220439-3220524 (-)c-di-GMP-II3217371-3220326 (-)CDR20291_2722

Putative collagen-binding protein		CDR20291_2722Single gene

DOOR ID: 2697621		CDR20291_2722 View Structure
11 3736548-3736631 (-)c-di-GMP-II3735290-3735968 (-)CDR20291_3128

Two-component response regulator		CDR20291_3128Operon

DOOR ID: 622475		CDR20291_3126,
CDR20291_3127,
CDR20291_3128		 View Structure
12 3986598-3986683 (-)c-di-GMP-II3985914-3986436 (-)CDR20291_3350

Pilin		CDR20291_3350Single gene

DOOR ID: 2697863		CDR20291_3350 View Structure
13 3356912-3357093 (-)cobalamin3355553-3356684 (-)CDR20291_2835

Putative iron ABC transporter; substrate-binding protein		CDR20291_2835Single gene

DOOR ID: 2697663		CDR20291_2835 View Structure
14 3892780-3892959 (-)cobalamin3891150-3892650 (-)cbiP

Cobyric acid synthase		CDR20291_3257Operon

DOOR ID: 622502		CDR20291_3241,
CDR20291_3242,
CDR20291_3243,
CDR20291_3244,
CDR20291_3245,
CDR20291_3246,
CDR20291_3247,
CDR20291_3248,
CDR20291_3249,
CDR20291_3250,
CDR20291_3251,
CDR20291_3252,
CDR20291_3253,
CDR20291_3254,
CDR20291_3255,
CDR20291_3256,
CDR20291_3257		 View Structure
15 392409-392601 (+)cobalamin392789-393542 (+)cbiM

Cobalt transport protein CbiM (Energy-coupling factor transporter probable substrate-capture protein CbiM) (ECF transporter S component CbiM)		CDR20291_0329Operon

DOOR ID: 621912		CDR20291_0329,
CDR20291_0330,
CDR20291_0331,
CDR20291_0332		 View Structure
16 702311-702387 (+)fluoride702651-703908 (+)CDR20291_0578

Putative chloride ion channel protein		CDR20291_0578Operon

DOOR ID: 621970		CDR20291_0578,
CDR20291_0579		 View Structure
17 1883259-1883380 (-)FMN1882023-1883127 (-)ribD

Riboflavin biosynthesis protein RibD [Includes: Diaminohydroxyphosphoribosylaminopyrimidine deaminase (DRAP deaminase) (93) (HTP reductase)]		CDR20291_1598Operon

DOOR ID: 622171		CDR20291_1597,
CDR20291_1598		 View Structure
18 192265-192382 (+)FMN192506-193112 (+)CDR20291_0146

Riboflavin transporter		CDR20291_0146Single gene

DOOR ID: 2696577		CDR20291_0146 View Structure
19 3771564-3771679 (+)FMN3771853-3773224 (+)CDR20291_3160

Probable transporter		CDR20291_3160Single gene

DOOR ID: 2697795		CDR20291_3160 View Structure
20 158660-158839 (+)glmS158892-160725 (+)glmS

Glutamine--fructose-6-phosphate aminotransferase [isomerizing] (6) (D-fructose-6-phosphate amidotransferase) (GFAT) (Glucosamine-6-phosphate synthase) (Hexosephosphate aminotransferase) (L-glutamine--D-fructose-6-phosphate amidotransferase)		CDR20291_0119Single gene

DOOR ID: 2696566		CDR20291_0119 View Structure
21 1834449-1834553 (+)glycine1834762-1837237 (+)CDR20291_1555

Multifunctional fusion protein [Includes: Aminomethyltransferase (Glycine cleavage system P-protein subunit 1) (Glycine decarboxylase subunit 1) (Glycine dehydrogenase (aminomethyl-transferring) subunit 1)]		CDR20291_1555Operon

DOOR ID: 622161		CDR20291_1555,
CDR20291_1556		 View Structure
22 2556943-2557031 (+)glycine2557220-2558588 (+)CDR20291_2174

Putative sodium:solute symporter		CDR20291_2174Single gene

DOOR ID: 2697410		CDR20291_2174 View Structure
23 2636526-2636636 (-)glycine2636050-2636422 (-)grdX

Putative glycine reductase complex component		CDR20291_2244Single gene

DOOR ID: 2697439		CDR20291_2244 View Structure
24 1831312-1831488 (+)lysine1831631-1833362 (+)CDR20291_1553

Putative Na+/H+ antiporter		CDR20291_1553Single gene

DOOR ID: 2697118		CDR20291_1553 View Structure
25 2289765-2289933 (-)lysine2288489-2289683 (-)lysC

Aspartokinase 		CDR20291_1961Operon

DOOR ID: 622240		CDR20291_1960,
CDR20291_1961		 View Structure
26 3488155-3488334 (-)lysine3486619-3488011 (-)CDR20291_2938

Putative C4-dicarboxylate anaerobic carrier		CDR20291_2938Operon

DOOR ID: 622432		CDR20291_2937,
CDR20291_2938		 View Structure
27 3682298-3682472 (+)lysine3682644-3683646 (+)asd

Aspartate-semialdehyde dehydrogenase (ASA dehydrogenase) (ASADH) (1) (Aspartate-beta-semialdehyde dehydrogenase)		CDR20291_3084Operon

DOOR ID: 622470		CDR20291_3084,
CDR20291_3085,
CDR20291_3086		 View Structure
28 1866436-1866479 (+)PreQ11866579-1867548 (+)iunH

Inosine-uridine preferring nucleoside hydrolase		CDR20291_1580Operon

DOOR ID: 622166		CDR20291_1580,
CDR20291_1581,
CDR20291_1582		 View Structure
29 2356890-2356992 (-)purine2355419-2356796 (-)CDR20291_2014

Putative xanthine/uracil permease		CDR20291_2014Single gene

DOOR ID: 2697323		CDR20291_2014 View Structure
30 251813-251914 (+)purine252134-253670 (+)guaA

GMP synthase [glutamine-hydrolyzing] (GMP synthetase) (Glutamine amidotransferase)		CDR20291_0198Single gene

DOOR ID: 2696603		CDR20291_0198 View Structure
31 2605562-2605663 (-)purine2604806-2605379 (-)xpt

Xanthine phosphoribosyltransferase (XPRTase) (2)		CDR20291_2219Operon

DOOR ID: 622287		CDR20291_2218,
CDR20291_2219		 View Structure
32 3039426-3039527 (+)purine3039599-3040943 (+)CDR20291_2592

Putative permease		CDR20291_2592Single gene

DOOR ID: 2697559		CDR20291_2592 View Structure
33 1219842-1219948 (+)SAM1220050-1221256 (+)hom1

Homoserine dehydrogenase (HDH) 		CDR20291_1003Single gene

DOOR ID: 2696898		CDR20291_1003 View Structure
34 1582788-1582894 (+)SAM1582984-1583965 (+)metN

Methionine import ATP-binding protein MetN 		CDR20291_1339Operon

DOOR ID: 622123		CDR20291_1339,
CDR20291_1340,
CDR20291_1341		 View Structure
35 169680-169783 (+)SAM169919-171113 (+)metE

S-adenosylmethionine synthase (AdoMet synthase) (MAT) (Methionine adenosyltransferase)		CDR20291_0129Single gene

DOOR ID: 2696571		CDR20291_0129 View Structure
36 1829965-1830070 (-)SAM1829054-1829852 (-)CDR20291_1551

Lipoprotein		CDR20291_1551Single gene

DOOR ID: 2697116		CDR20291_1551 View Structure
37 2013647-2013749 (+)SAM2013858-2015124 (+)cysD

Putative O-acetylhomoserine sulfhydrylase		CDR20291_1719Operon

DOOR ID: 622197		CDR20291_1719,
CDR20291_1720		 View Structure
38 1767068-1767160 (+)TPP1767259-1768054 (+)thiD

Putative phosphomethylpyrimidine kinase		CDR20291_1497Operon

DOOR ID: 622151		CDR20291_1497,
CDR20291_1498,
CDR20291_1499		 View Structure
39 1886140-1886251 (+)TPP1886278-1887694 (+)thiC

Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)		CDR20291_1600Single gene

DOOR ID: 2697134		CDR20291_1600 View Structure
40 2223791-2223890 (-)TPP2223369-2223660 (-)CDR20291_1904

CDR20291_1904Operon

DOOR ID: 622233		CDR20291_1901,
CDR20291_1902,
CDR20291_1903,
CDR20291_1904		 View Structure
41 2676833-2676927 (-)ykkC-yxkD2676064-2676769 (-)CDR20291_2282

CDR20291_2282Single gene

DOOR ID: 2697451		CDR20291_2282 View Structure
42 517180-517286 (+)ykkC-yxkD517355-517676 (+)sugE

Quaternary ammonium compound-resistance protein		CDR20291_0431Single gene

DOOR ID: 2696665		CDR20291_0431 View Structure