Regulog ydaO-yuaA - Clostridiaceae

Properties
Regulator type:	RNA regulatory element
Name:	ydaO-yuaA
RFAM:	RF00379
Regulation mode:
Biological process:	Cell wall metabolism; Osmotic stress response
Effector:
Phylum:	Firmicutes

Member of regulog collections

By taxonomy - Clostridiaceae
By RNA motif - ydaO-yuaA
By pathway - Cell wall metabolism
By pathway - Osmotic stress response

Statistics of regulated genes
Genome	Genes	Operons
Clostridium kluyveri DSM 555	2	2
Clostridium sp. SS2/1
Clostridium cellulolyticum H10	4	4
Clostridium phytofermentans ISDg	1	1
Clostridium tetani E88	2	2
Clostridium acetobutylicum ATCC 824	2	2
Clostridium botulinum A str. ATCC 3502	2	2
Clostridium novyi NT	1	1
Clostridium perfringens ATCC 13124
Clostridium difficile 630
Clostridium beijerincki NCIMB 8052	3	2
Clostridium sp. OhILAs	1	1
Clostridium sp. L2-50
Clostridium scindens ATCC 35704
Clostridium nexile DSM 1787
Clostridium leptum DSM 753
Clostridium hiranonis DSM 13275
Clostridium butyricum 5521
Clostridium bolteae ATCC BAA-613	1	1
Clostridium bartlettii DSM 16795

Clusters of co-Regulated Orthologous operoNs (CRONs)
Genes																					Function

CRON 1.
nhaP	Clostridium kluyveri DSM 555	Clostridium sp. SS2/1	Clostridium cellulolyticum H10	* Clostridium phytofermentans ISDg Site: position = -273 score = 75.1 sequence = ATGAAACAAATCCGA... Gene: null: NhaP-type Na+/H+ and K+/H+ antiporters	Clostridium tetani E88	Clostridium acetobutylicum ATCC 824	Clostridium botulinum A str. ATCC 3502	Clostridium novyi NT	Clostridium perfringens ATCC 13124	Clostridium difficile 630	Clostridium beijerincki NCIMB 8052	Clostridium sp. OhILAs Gene: Clos_2091: NhaP-type Na+/H+ and K+/H+ antiporters	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	Clostridium bolteae ATCC BAA-613	Clostridium bartlettii DSM 16795	NhaP-type Na+/H+ and K+/H+ antiporters

CRON 2.
SH3/COG0791	Clostridium kluyveri DSM 555	Clostridium sp. SS2/1	* Clostridium cellulolyticum H10 Site: position = -171 score = 77.09 sequence = CTTATAAAAGGCTGA... Gene: Ccel_2128: SH3 domain / Cell wall-associated hydrolase, COG0791	Clostridium phytofermentans ISDg	Clostridium tetani E88	Clostridium acetobutylicum ATCC 824	Clostridium botulinum A str. ATCC 3502	Clostridium novyi NT	Clostridium perfringens ATCC 13124	Clostridium difficile 630	Clostridium beijerincki NCIMB 8052	Clostridium sp. OhILAs	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	Clostridium bolteae ATCC BAA-613	Clostridium bartlettii DSM 16795	SH3 domain / Cell wall-associated hydrolase, COG0791

CRON 3.
COG0791	Clostridium kluyveri DSM 555	Clostridium sp. SS2/1	Clostridium cellulolyticum H10	Clostridium phytofermentans ISDg	* Clostridium tetani E88 Site: position = -131 score = 78.47 sequence = AATACGTACTATGCT... Gene: CTC02078: Cell wall-associated hydrolases (invasion-associated proteins)	Clostridium acetobutylicum ATCC 824	Clostridium botulinum A str. ATCC 3502	Clostridium novyi NT	Clostridium perfringens ATCC 13124	Clostridium difficile 630	Clostridium beijerincki NCIMB 8052	Clostridium sp. OhILAs	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	Clostridium bolteae ATCC BAA-613	Clostridium bartlettii DSM 16795	Cell wall-associated hydrolases (invasion-associated proteins)

CRON 4.
COG0591	Clostridium kluyveri DSM 555	Clostridium sp. SS2/1	Clostridium cellulolyticum H10	Clostridium phytofermentans ISDg	Clostridium tetani E88	Clostridium acetobutylicum ATCC 824	Clostridium botulinum A str. ATCC 3502	Clostridium novyi NT	Clostridium perfringens ATCC 13124	Clostridium difficile 630	Clostridium beijerincki NCIMB 8052	Clostridium sp. OhILAs	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	* Clostridium bolteae ATCC BAA-613 Site: position = -327 score = 79.77 sequence = TCACCAAGTCGCTTA... Gene: CLOBOL_01252: Na+/proline symporter	Clostridium bartlettii DSM 16795	Na+/proline symporter

CRON 5.
SH3/COG0791	Clostridium kluyveri DSM 555	Clostridium sp. SS2/1	* Clostridium cellulolyticum H10 Site: position = -148 score = 83.19 sequence = CGAAATTAAAAAGCT... Gene: Ccel_1956: SH3 domain / Cell wall-associated hydrolase, COG0791	Clostridium phytofermentans ISDg	Clostridium tetani E88	Clostridium acetobutylicum ATCC 824	Clostridium botulinum A str. ATCC 3502	Clostridium novyi NT	Clostridium perfringens ATCC 13124	Clostridium difficile 630	Clostridium beijerincki NCIMB 8052	Clostridium sp. OhILAs	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	Clostridium bolteae ATCC BAA-613	Clostridium bartlettii DSM 16795	SH3 domain / Cell wall-associated hydrolase, COG0791

CRON 6.
SH3/COG0791	Clostridium kluyveri DSM 555	Clostridium sp. SS2/1	* Clostridium cellulolyticum H10 Site: position = -140 score = 90.32 sequence = TACAAAATATGCTGA... Gene: Ccel_0747: SH3 domain / Cell wall-associated hydrolase, COG0791	Clostridium phytofermentans ISDg	Clostridium tetani E88	Clostridium acetobutylicum ATCC 824	Clostridium botulinum A str. ATCC 3502	Clostridium novyi NT	Clostridium perfringens ATCC 13124	Clostridium difficile 630	Clostridium beijerincki NCIMB 8052	Clostridium sp. OhILAs	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	Clostridium bolteae ATCC BAA-613	Clostridium bartlettii DSM 16795	SH3 domain / Cell wall-associated hydrolase, COG0791

CRON 7.
COG3773	* Clostridium kluyveri DSM 555 Site: position = -136 score = 85.22 sequence = ACAATATCATTAGCC... Gene: CKL_0312: Cell wall hydrolyses involved in spore germination	Clostridium sp. SS2/1	Clostridium cellulolyticum H10	Clostridium phytofermentans ISDg	* Clostridium tetani E88 Site: position = -103 score = 87.78 sequence = AATAACATAAGCCTA... Gene: CTC02551: Cell wall hydrolyses involved in spore germination	* Clostridium acetobutylicum ATCC 824 Site: position = -124 score = 76.9 sequence = ATCATTAGCCTAAAT... Gene: CAC3081: Cell wall hydrolyses involved in spore germination	* Clostridium botulinum A str. ATCC 3502 Site: position = -124 score = 94.71 sequence = ACTATTATTAGCCTA... Gene: CBO3432: Cell wall hydrolyses involved in spore germination	Clostridium novyi NT Gene: NT01CX_1160: Cell wall hydrolyses involved in spore germination	Clostridium perfringens ATCC 13124 Gene: CPF_2662: Cell wall hydrolyses involved in spore germination	Clostridium difficile 630 Gene: CD3563: Cell wall hydrolyses involved in spore germination	Clostridium beijerincki NCIMB 8052 Gene: Cbei_0199: Cell wall hydrolyses involved in spore germination	Clostridium sp. OhILAs	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521 Gene: CBY_2915: Cell wall hydrolyses involved in spore germination	Clostridium bolteae ATCC BAA-613	Clostridium bartlettii DSM 16795 Gene: CLOBAR_00229: Cell wall hydrolyses involved in spore germination	Cell wall hydrolyses involved in spore germination

CRON 8.
dapB	2 Clostridium kluyveri DSM 555 Gene: CKL_3205: Dihydrodipicolinate reductase (EC 1.3.1.26) Gene: CKL_2799: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium sp. SS2/1 Gene: CLOSS21_00346: Dihydrodipicolinate reductase (EC 1.3.1.26)	2 Clostridium cellulolyticum H10* Site: position = -281 score = 99.58 sequence = ATAATTTATCGCTGA... Gene: Ccel_0519: Dihydrodipicolinate reductase (EC 1.3.1.26) Gene: Ccel_0525: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium phytofermentans ISDg Gene: null: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium tetani E88 Gene: CTC02295: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium acetobutylicum ATCC 824 Gene: CAC2379: Dihydrodipicolinate reductase (EC 1.3.1.26)	2 Clostridium botulinum A str. ATCC 3502 Gene: CBO0791: Dihydrodipicolinate reductase (EC 1.3.1.26) Gene: CBO3153: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium novyi NT Gene: NT01CX_1745: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium perfringens ATCC 13124 Gene: CPF_2162: Dihydrodipicolinate reductase (EC 1.3.1.26)	2 Clostridium difficile 630 Gene: CD3226: Dihydrodipicolinate reductase (EC 1.3.1.26) Gene: CD3229: Dihydrodipicolinate reductase (EC 1.3.1.26)	2 Clostridium beijerincki NCIMB 8052* Site: position = -249 score = 98.79 sequence = TAATTATAACGCTGA... Gene: Cbei_2934: Dihydrodipicolinate reductase (EC 1.3.1.26) Gene: Cbei_1795: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium sp. OhILAs Gene: Clos_1164: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium sp. L2-50 Gene: CLOL250_00645: Dihydrodipicolinate reductase (EC 1.3.1.26)	2 Clostridium scindens ATCC 35704 Gene: CLOSCI_00327: Dihydrodipicolinate reductase (EC 1.3.1.26) Gene: CLOSCI_03685: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium nexile DSM 1787 Gene: CLONEX_02737: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium leptum DSM 753 Gene: CLOLEP_03141: Dihydrodipicolinate reductase (EC 1.3.1.26)	2 Clostridium hiranonis DSM 13275 Gene: CLOHIR_00816: Dihydrodipicolinate reductase (EC 1.3.1.26) Gene: CLOHIR_00814: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium butyricum 5521 Gene: CBY_0568: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium bolteae ATCC BAA-613 Gene: CLOBOL_04167: Dihydrodipicolinate reductase (EC 1.3.1.26)	Clostridium bartlettii DSM 16795 Gene: CLOBAR_00363: Dihydrodipicolinate reductase (EC 1.3.1.26)	Dihydrodipicolinate reductase (EC 1.3.1.26)
COG1246	Clostridium kluyveri DSM 555	Clostridium sp. SS2/1	Clostridium cellulolyticum H10	Clostridium phytofermentans ISDg	Clostridium tetani E88	Clostridium acetobutylicum ATCC 824	Clostridium botulinum A str. ATCC 3502	Clostridium novyi NT	Clostridium perfringens ATCC 13124	Clostridium difficile 630	2 Clostridium beijerincki NCIMB 8052* Site: position = -337 score = 97.02 sequence = GATATATGTAACGCT... Gene: Cbei_1453: N-acetylglutamate synthase and related acetyltransferases Gene: Cbei_2936: N-acetylglutamate synthase and related acetyltransferases	Clostridium sp. OhILAs	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	Clostridium bolteae ATCC BAA-613 Gene: CLOBOL_03581: N-acetylglutamate synthase and related acetyltransferases	Clostridium bartlettii DSM 16795	N-acetylglutamate synthase and related acetyltransferases

CRON 9.
Clos_0046	Clostridium kluyveri DSM 555	Clostridium sp. SS2/1	Clostridium cellulolyticum H10	Clostridium phytofermentans ISDg	Clostridium tetani E88	Clostridium acetobutylicum ATCC 824	Clostridium botulinum A str. ATCC 3502	Clostridium novyi NT	Clostridium perfringens ATCC 13124	Clostridium difficile 630	Clostridium beijerincki NCIMB 8052	* Clostridium sp. OhILAs Site: position = -286 score = 110.58 sequence = TATATACATAGCGCT... Gene: Clos_0046: hypothetical protein	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	Clostridium bolteae ATCC BAA-613	Clostridium bartlettii DSM 16795	hypothetical protein

CRON 10.
lysM/COG3773	* Clostridium kluyveri DSM 555 Site: position = -147 score = 88.26 sequence = ACTATAAAACAAGCC... Gene: CKL_0667: Peptidoglycan-binding lysin domain / Cell wall hydrolyses involved in spore germination	Clostridium sp. SS2/1	Clostridium cellulolyticum H10	Clostridium phytofermentans ISDg	Clostridium tetani E88	* Clostridium acetobutylicum ATCC 824 Site: position = -172 score = 83.59 sequence = CCTTAAGAGTGCCGA... Gene: CAC1232: Peptidoglycan-binding lysin domain / Cell wall hydrolyses involved in spore germination	* Clostridium botulinum A str. ATCC 3502 Site: position = -129 score = 79.38 sequence = TAAACAAATCATGCC... Gene: CBO1324: Peptidoglycan-binding lysin domain / Cell wall hydrolyses involved in spore germination	* Clostridium novyi NT Site: position = -135 score = 88.31 sequence = CATCTGAACAATGCC... Gene: NT01CX_1494: Peptidoglycan-binding lysin domain / Cell wall hydrolyses involved in spore germination	Clostridium perfringens ATCC 13124	Clostridium difficile 630	Clostridium beijerincki NCIMB 8052	Clostridium sp. OhILAs	Clostridium sp. L2-50	Clostridium scindens ATCC 35704	Clostridium nexile DSM 1787	Clostridium leptum DSM 753	Clostridium hiranonis DSM 13275	Clostridium butyricum 5521	Clostridium bolteae ATCC BAA-613	Clostridium bartlettii DSM 16795	Peptidoglycan-binding lysin domain / Cell wall hydrolyses involved in spore germination