assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	1	32087-32179	1	CRISPRCasFinder	no		csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Orphan	GTTGGCGCTGTGCGTTAGCACTTTAAGCAAC	31	1	2	32118-32148|32118-32148	CP029154.1_17782-17812|CP029154.1_1171645-1171675	NA	1	1	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA|74aa|up_1|CP029154.1_28502_28724_+,NA|138aa|down_0|CP029154.1_39447_39861_+	NA|258aa|up_9|CP029154.1_9856_10630_+	TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G subfamily	NA|170aa|up_8|CP029154.1_21323_21833_+	COG1827, COG1827, Predicted small molecule binding protein (contains 3H domain) [General function prediction only]	NA|294aa|up_7|CP029154.1_21844_22726_+	PRK10334, PRK10334, small-conductance mechanosensitive channel MscS	NA|424aa|up_6|CP029154.1_23184_24456_+	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional	NA|152aa|up_5|CP029154.1_24776_25232_+	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|546aa|up_4|CP029154.1_25702_27340_+	PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated	NA|117aa|up_3|CP029154.1_27398_27749_+	PRK00153, PRK00153, YbaB/EbfC family nucleoid-associated protein	NA|200aa|up_2|CP029154.1_27761_28361_+	PRK00076, recR, recombination protein RecR; Reviewed	NA|74aa|up_1|CP029154.1_28502_28724_+	NA	NA|402aa|up_0|CP029154.1_28794_30000_-	cd17507, GT28_Beta-DGS-like, beta-diglucosyldiacylglycerol synthase and similar proteins	NA|138aa|down_0|CP029154.1_39447_39861_+	NA	NA|1144aa|down_1|CP029154.1_40169_43601_+	PRK12999, PRK12999, pyruvate carboxylase; Reviewed	NA|643aa|down_2|CP029154.1_43842_45771_+	PRK12740, PRK12740, elongation factor G-like protein EF-G2	NA|155aa|down_3|CP029154.1_46227_46692_+	COG4463, CtsR, Transcriptional repressor of class III stress genes [Transcription]	NA|165aa|down_4|CP029154.1_46698_47193_+	COG3880, COG3880, Modulator of heat shock repressor CtsR, McsA [Signal transduction    mechanisms]	NA|342aa|down_5|CP029154.1_47208_48234_+	PRK01059, PRK01059, ATP:guanido phosphotransferase; Provisional	NA|816aa|down_6|CP029154.1_48220_50668_+	COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]	NA|458aa|down_7|CP029154.1_50847_52221_+	PRK11823, PRK11823, DNA repair protein RadA; Provisional	NA|357aa|down_8|CP029154.1_52223_53294_+	PRK13482, PRK13482, DNA integrity scanning protein DisA; Provisional	NA|365aa|down_9|CP029154.1_53382_54477_+	COG4956, COG4956, Integral membrane protein (PIN domain superfamily) [General function prediction only]
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	2	641941-642065	2	CRISPRCasFinder	no	WYL	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Unclear	TGATGGTTGATAAGAATAGTAAGAAAAAAATAGATAATTAAAG	43	0	0	NA	NA	NA	1	1	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA|204aa|up_4|CP029154.1_636643_637255_+,NA|219aa|down_0|CP029154.1_642276_642933_+,NA|116aa|down_8|CP029154.1_651043_651391_-	NA|147aa|up_9|CP029154.1_632612_633053_+	cd00732, CheW, CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea	NA|268aa|up_8|CP029154.1_633088_633892_+	COG1352, CheR, Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]	NA|199aa|up_7|CP029154.1_633931_634528_+	cd16432, CheB_Rec, Chemotaxis response regulator protein-glutamate methylesterase, CheB, with N-terminal REC domain	NA|288aa|up_6|CP029154.1_634633_635497_+	pfam13739, DUF4163, Domain of unknown function (DUF4163)	NA|330aa|up_5|CP029154.1_635563_636553_+	PRK08618, PRK08618, ornithine cyclodeaminase family protein	NA|204aa|up_4|CP029154.1_636643_637255_+	NA	NA|260aa|up_3|CP029154.1_637701_638481_+	pfam06161, DUF975, Protein of unknown function (DUF975)	NA|120aa|up_2|CP029154.1_638685_639045_+	pfam03965, Penicillinase_R, Penicillinase repressor	NA|461aa|up_1|CP029154.1_639055_640438_+	cd07341, M56_BlaR1_MecR1_like, Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase	NA|137aa|up_0|CP029154.1_640653_641064_+	pfam02181, FH2, Formin Homology 2 Domain	NA|219aa|down_0|CP029154.1_642276_642933_+	NA	NA|424aa|down_1|CP029154.1_643403_644675_-	pfam01471, PG_binding_1, Putative peptidoglycan binding domain	NA|239aa|down_2|CP029154.1_644919_645636_+	pfam13367, PrsW-protease, Protease prsW family	NA|437aa|down_3|CP029154.1_645714_647025_+	PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed	NA|179aa|down_4|CP029154.1_647124_647661_+	TIGR02227, Inactive_signal_peptidase_IA	NA|179aa|down_5|CP029154.1_647826_648363_+	TIGR02227, Inactive_signal_peptidase_IA	NA|252aa|down_6|CP029154.1_648372_649128_+	pfam01261, AP_endonuc_2, Xylose isomerase-like TIM barrel	NA|556aa|down_7|CP029154.1_649201_650869_+	cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2	NA|116aa|down_8|CP029154.1_651043_651391_-	NA	NA|310aa|down_9|CP029154.1_651840_652770_+	TIGR03814, Glutaminase_1, glutaminase A
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	6	1578987-1579214	1,6,1	PILER-CR,CRISPRCasFinder,CRT	no	DinG	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Type IV-A	TGTTTTATATTAACTAAGTGGTATGTAAATAAAATAAAATT,GTTTTATATTAACTAAGTGGTATGTAAATA,GTTTTATATTAACTAAGTGGTATGTAAATA	41,30,30	0	0	NA	NA	I-A:I-A:I-A	2,3,3	3	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA|183aa|up_5|CP029154.1_1573673_1574222_-,NA|80aa|down_4|CP029154.1_1586363_1586603_+,NA|59aa|down_5|CP029154.1_1586789_1586966_-,NA|45aa|down_9|CP029154.1_1589579_1589714_+	NA|195aa|up_9|CP029154.1_1568861_1569446_-	pfam00882, Zn_dep_PLPC, Zinc dependent phospholipase C	NA|477aa|up_8|CP029154.1_1569645_1571076_-	COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	NA|315aa|up_7|CP029154.1_1571403_1572348_+	TIGR00950, Uncharacterized_inner_membrane_transporter_YicL, Carboxylate/Amino Acid/Amine Transporter	NA|312aa|up_6|CP029154.1_1572618_1573554_-	COG1242, COG1242, Predicted Fe-S oxidoreductase [General function prediction only]	NA|183aa|up_5|CP029154.1_1573673_1574222_-	NA	NA|143aa|up_4|CP029154.1_1574373_1574802_+	pfam04657, DMT_YdcZ, Putative inner membrane exporter, YdcZ	NA|223aa|up_3|CP029154.1_1574868_1575537_+	cd01994, Alpha_ANH_like_IV, This is a subfamily of Adenine nucleotide alpha hydrolases superfamily	NA|452aa|up_2|CP029154.1_1575654_1577010_-	cd13143, MATE_MepA_like, Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA	NA|165aa|up_1|CP029154.1_1577513_1578008_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|131aa|up_0|CP029154.1_1578067_1578460_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|578aa|down_0|CP029154.1_1579538_1581272_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|282aa|down_1|CP029154.1_1581508_1582354_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|745aa|down_2|CP029154.1_1582384_1584619_-	cd01948, EAL, EAL domain	NA|270aa|down_3|CP029154.1_1585401_1586211_+	cd00592, HTH_MerR-like, Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators	NA|80aa|down_4|CP029154.1_1586363_1586603_+	NA	NA|59aa|down_5|CP029154.1_1586789_1586966_-	NA	NA|225aa|down_6|CP029154.1_1587457_1588132_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|185aa|down_7|CP029154.1_1588351_1588906_-	cd01014, nicotinamidase_related, Nicotinamidase_ related amidohydrolases	NA|122aa|down_8|CP029154.1_1588983_1589349_-	COG1733, COG1733, Predicted transcriptional regulators [Transcription]	NA|45aa|down_9|CP029154.1_1589579_1589714_+	NA
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	7	1688407-1689093	7,2	CRISPRCasFinder,CRT	no		csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Orphan	GTTTTATATTAACTATATGGAATGTAAAT,GTTTTATATTAACTATATGGAATGTAAAT	29,29	1	1	1688962-1688997	CP029154.1_3030658-3030623	I-A:I-A	10,10	10	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA|50aa|up_9|CP029154.1_1677497_1677647_+,NA|190aa|up_7|CP029154.1_1678561_1679131_+,NA|61aa|up_4|CP029154.1_1681814_1681997_-,NA|323aa|down_4|CP029154.1_1694005_1694974_+	NA|50aa|up_9|CP029154.1_1677497_1677647_+	NA	NA|300aa|up_8|CP029154.1_1677657_1678557_+	TIGR02163, Ferredoxin-type_protein_NapH_homolog, ferredoxin-type protein, NapH/MauN family	NA|190aa|up_7|CP029154.1_1678561_1679131_+	NA	NA|216aa|up_6|CP029154.1_1679297_1679945_-	pfam02589, LUD_dom, LUD domain	NA|305aa|up_5|CP029154.1_1680334_1681249_-	pfam11155, DUF2935, Domain of unknown function (DUF2935)	NA|61aa|up_4|CP029154.1_1681814_1681997_-	NA	NA|283aa|up_3|CP029154.1_1682407_1683256_-	PRK00380, panC, pantoate--beta-alanine ligase; Reviewed	NA|276aa|up_2|CP029154.1_1683274_1684102_-	PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed	NA|308aa|up_1|CP029154.1_1684076_1685000_-	pfam10728, DUF2520, Domain of unknown function (DUF2520)	NA|698aa|up_0|CP029154.1_1685652_1687746_+	cd01948, EAL, EAL domain	NA|273aa|down_0|CP029154.1_1689741_1690560_+	cd04782, HTH_BltR, Helix-Turn-Helix DNA binding domain of the BltR transcription regulator	NA|707aa|down_1|CP029154.1_1690692_1692813_-	COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]	NA|76aa|down_2|CP029154.1_1692838_1693066_-	pfam04023, FeoA, FeoA domain	NA|147aa|down_3|CP029154.1_1693392_1693833_-	COG2153, ElaA, Predicted acyltransferase [General function prediction only]	NA|323aa|down_4|CP029154.1_1694005_1694974_+	NA	NA|403aa|down_5|CP029154.1_1695450_1696659_+	PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional	NA|294aa|down_6|CP029154.1_1696719_1697601_-	cd10944, CE4_SmPgdA_like, Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins	NA|305aa|down_7|CP029154.1_1698016_1698931_+	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]	NA|182aa|down_8|CP029154.1_1699153_1699699_+	cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding domain	NA|383aa|down_9|CP029154.1_1699789_1700938_+	COG2006, COG2006, Uncharacterized conserved protein [Function unknown]
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	8	1779875-1780169	2,8,3	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Orphan	GTTTTAGATTAACTATATGGAATGTAAAT,GTTTTAGATTAACTATATGGAATGTAAA,GTTTTAGATTAACTATATGGAATGTAAAT	29,28,29	0	0	NA	NA	I-A:NA:I-A	3,4,4	4	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA|134aa|up_9|CP029154.1_1774560_1774962_+,NA|116aa|up_8|CP029154.1_1774955_1775303_+,NA|146aa|up_6|CP029154.1_1775720_1776158_+,NA|59aa|up_5|CP029154.1_1776150_1776327_+,NA|54aa|up_0|CP029154.1_1778977_1779139_+,NA|58aa|down_1|CP029154.1_1781342_1781516_+,NA|132aa|down_2|CP029154.1_1782071_1782467_+	NA|134aa|up_9|CP029154.1_1774560_1774962_+	NA	NA|116aa|up_8|CP029154.1_1774955_1775303_+	NA	NA|142aa|up_7|CP029154.1_1775302_1775728_+	pfam04883, HK97-gp10_like, Bacteriophage HK97-gp10, putative tail-component	NA|146aa|up_6|CP029154.1_1775720_1776158_+	NA	NA|59aa|up_5|CP029154.1_1776150_1776327_+	NA	NA|437aa|up_4|CP029154.1_1776327_1777638_+	pfam04984, Phage_sheath_1, Phage tail sheath protein subtilisin-like domain	NA|157aa|up_3|CP029154.1_1777654_1778125_+	pfam09393, DUF2001, Phage tail tube protein	NA|147aa|up_2|CP029154.1_1778196_1778637_+	pfam08890, Phage_TAC_5, Phage XkdN-like tail assembly chaperone protein, TAC	NA|65aa|up_1|CP029154.1_1778636_1778831_+	TIGR02247, Hypothetical_protein_K09H11	NA|54aa|up_0|CP029154.1_1778977_1779139_+	NA	NA|251aa|down_0|CP029154.1_1780286_1781039_+	pfam09851, SHOCT, Short C-terminal domain	NA|58aa|down_1|CP029154.1_1781342_1781516_+	NA	NA|132aa|down_2|CP029154.1_1782071_1782467_+	NA	NA|193aa|down_3|CP029154.1_1783104_1783683_+	pfam00542, Ribosomal_L12, Ribosomal protein L7/L12 C-terminal domain	NA|789aa|down_4|CP029154.1_1783758_1786125_+	TIGR02675, Mu-like_prophage_FluMu_protein_gp42, tape measure domain	NA|234aa|down_5|CP029154.1_1786140_1786842_+	PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional	NA|655aa|down_6|CP029154.1_1786834_1788799_+	pfam00877, NLPC_P60, NlpC/P60 family	NA|87aa|down_7|CP029154.1_1788812_1789073_+	pfam10844, DUF2577, Protein of unknown function (DUF2577)	NA|140aa|down_8|CP029154.1_1789077_1789497_+	pfam10934, DUF2634, Protein of unknown function (DUF2634)	NA|349aa|down_9|CP029154.1_1789497_1790544_+	pfam04865, Baseplate_J, Baseplate J-like protein
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	9	1782769-1782994	4,9,3	CRT,CRISPRCasFinder,PILER-CR	no		csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Orphan	GTTTTATATTAACTATGTGGTATGTAAAT,TTTTATATTAACTATGTGGTATGTAAAT,TTTTATATTAACTATGTGGTATGTAAAT	29,28,28	0	0	NA	NA	I-A:I-A:I-A	3,3,2	3	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA|146aa|up_9|CP029154.1_1775720_1776158_+,NA|59aa|up_8|CP029154.1_1776150_1776327_+,NA|54aa|up_3|CP029154.1_1778977_1779139_+,NA|58aa|up_1|CP029154.1_1781342_1781516_+,NA|132aa|up_0|CP029154.1_1782071_1782467_+,NA|116aa|down_9|CP029154.1_1793907_1794255_+	NA|146aa|up_9|CP029154.1_1775720_1776158_+	NA	NA|59aa|up_8|CP029154.1_1776150_1776327_+	NA	NA|437aa|up_7|CP029154.1_1776327_1777638_+	pfam04984, Phage_sheath_1, Phage tail sheath protein subtilisin-like domain	NA|157aa|up_6|CP029154.1_1777654_1778125_+	pfam09393, DUF2001, Phage tail tube protein	NA|147aa|up_5|CP029154.1_1778196_1778637_+	pfam08890, Phage_TAC_5, Phage XkdN-like tail assembly chaperone protein, TAC	NA|65aa|up_4|CP029154.1_1778636_1778831_+	TIGR02247, Hypothetical_protein_K09H11	NA|54aa|up_3|CP029154.1_1778977_1779139_+	NA	NA|251aa|up_2|CP029154.1_1780286_1781039_+	pfam09851, SHOCT, Short C-terminal domain	NA|58aa|up_1|CP029154.1_1781342_1781516_+	NA	NA|132aa|up_0|CP029154.1_1782071_1782467_+	NA	NA|193aa|down_0|CP029154.1_1783104_1783683_+	pfam00542, Ribosomal_L12, Ribosomal protein L7/L12 C-terminal domain	NA|789aa|down_1|CP029154.1_1783758_1786125_+	TIGR02675, Mu-like_prophage_FluMu_protein_gp42, tape measure domain	NA|234aa|down_2|CP029154.1_1786140_1786842_+	PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional	NA|655aa|down_3|CP029154.1_1786834_1788799_+	pfam00877, NLPC_P60, NlpC/P60 family	NA|87aa|down_4|CP029154.1_1788812_1789073_+	pfam10844, DUF2577, Protein of unknown function (DUF2577)	NA|140aa|down_5|CP029154.1_1789077_1789497_+	pfam10934, DUF2634, Protein of unknown function (DUF2634)	NA|349aa|down_6|CP029154.1_1789497_1790544_+	pfam04865, Baseplate_J, Baseplate J-like protein	NA|206aa|down_7|CP029154.1_1790536_1791154_+	pfam10076, DUF2313, Uncharacterized protein conserved in bacteria (DUF2313)	NA|331aa|down_8|CP029154.1_1791165_1792158_+	pfam12571, DUF3751, Phage tail-collar fibre protein	NA|116aa|down_9|CP029154.1_1793907_1794255_+	NA
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	10	1924167-1924586	4,10,5	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Orphan	GTTTTATATTAACTATGTGGTATGTAAAT,GTTTTATATTAACTATGTGGTATGTAAAT,GTTTTATATTAACTATGTGGTATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	6,6,6	6	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA,NA|96aa|down_0|CP029154.1_1924992_1925280_+,NA|59aa|down_5|CP029154.1_1931665_1931842_-,NA|341aa|down_6|CP029154.1_1932409_1933432_+,NA|258aa|down_8|CP029154.1_1934338_1935112_+	NA|266aa|up_9|CP029154.1_1908109_1908907_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|329aa|up_8|CP029154.1_1909216_1910203_-	TIGR00545, Probable_lipoate-protein_ligase_A, lipoyltransferase and lipoate-protein ligase	NA|577aa|up_7|CP029154.1_1910685_1912416_+	COG1757, NhaC, Na+/H+ antiporter [Energy production and conversion]	NA|172aa|up_6|CP029154.1_1912940_1913456_+	pfam13787, HXXEE, Protein of unknown function with HXXEE motif	NA|825aa|up_5|CP029154.1_1914245_1916720_+	PRK00451, PRK00451, aminomethyl-transferring glycine dehydrogenase subunit GcvPA	NA|486aa|up_4|CP029154.1_1916719_1918177_+	PRK04366, PRK04366, aminomethyl-transferring glycine dehydrogenase subunit GcvPB	NA|786aa|up_3|CP029154.1_1918599_1920957_+	cd02609, P-type_ATPase, uncharacterized subfamily of P-type ATPase transporter, similar to uncharacterized Streptococcus pneumoniae exported protein 7, Exp7	NA|106aa|up_2|CP029154.1_1921042_1921360_-	pfam06865, DUF1255, Protein of unknown function (DUF1255)	NA|424aa|up_1|CP029154.1_1922250_1923522_-	cd01303, GDEase, Guanine deaminase (GDEase)	NA|59aa|up_0|CP029154.1_1923739_1923916_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|96aa|down_0|CP029154.1_1924992_1925280_+	NA	NA|184aa|down_1|CP029154.1_1925818_1926370_-	cd02209, cupin_XRE_C, XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain	NA|321aa|down_2|CP029154.1_1926560_1927523_+	cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase	NA|615aa|down_3|CP029154.1_1927814_1929659_+	cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases	NA|195aa|down_4|CP029154.1_1929979_1930564_+	cd03357, LbH_MAT_GAT, Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates	NA|59aa|down_5|CP029154.1_1931665_1931842_-	NA	NA|341aa|down_6|CP029154.1_1932409_1933432_+	NA	NA|296aa|down_7|CP029154.1_1933445_1934333_+	cd03264, ABC_drug_resistance_like, ABC-type multidrug transport system, ATPase component	NA|258aa|down_8|CP029154.1_1934338_1935112_+	NA	NA|242aa|down_9|CP029154.1_1935223_1935949_+	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	11	2724328-2724488	11,5	CRISPRCasFinder,PILER-CR	no	cas3,cas5,cas7,cas6,c2c9_V-U4	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Unclear	TGAAATCCACTTAGTTAATCTTAAAC,TAGGTTTAAGATTAACTAAGTGGATTTCA	26,29	0	0	NA	NA	NA:NA	2,2	2	Unclear	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA,NA|489aa|down_3|CP029154.1_2728909_2730376_-	NA|448aa|up_9|CP029154.1_2716784_2718128_-	pfam06898, YqfD, Putative stage IV sporulation protein YqfD	NA|81aa|up_8|CP029154.1_2718140_2718383_-	pfam07873, YabP, YabP family	NA|188aa|up_7|CP029154.1_2718591_2719155_-	cd00552, RaiA, RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY,  is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site	NA|166aa|up_6|CP029154.1_2719347_2719845_-	cd15904, TSPO_MBR, Translocator protein (TSPO)/peripheral-type benzodiazepine receptor (MBR) family	NA|148aa|up_5|CP029154.1_2719955_2720399_-	pfam09424, YqeY, Yqey-like protein	NA|60aa|up_4|CP029154.1_2720428_2720608_-	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed	NA|117aa|up_3|CP029154.1_2720770_2721121_-	cd01276, PKCI_related, Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides	NA|433aa|up_2|CP029154.1_2721163_2722462_-	COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	NA|253aa|up_1|CP029154.1_2722463_2723222_-	PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE; Provisional	NA|316aa|up_0|CP029154.1_2723240_2724188_-	pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA)	cas3|803aa|down_0|CP029154.1_2724628_2727037_-	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas5|266aa|down_1|CP029154.1_2727063_2727861_-	cd09658, Cas5_I-B, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas7|338aa|down_2|CP029154.1_2727876_2728890_-	cd09687, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas7	NA|489aa|down_3|CP029154.1_2728909_2730376_-	NA	cas6|246aa|down_4|CP029154.1_2730380_2731118_-	cd09652, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily protein Cas6	c2c9_V-U4|388aa|down_5|CP029154.1_2731926_2733090_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|370aa|down_6|CP029154.1_2733242_2734352_+	PRK11650, ugpC, sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC	NA|256aa|down_7|CP029154.1_2734381_2735149_+	COG2508, COG2508, Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]	NA|458aa|down_8|CP029154.1_2735336_2736710_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|312aa|down_9|CP029154.1_2736745_2737681_-	COG1940, NagC, Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	12	2814077-2814365	6,6	CRT,PILER-CR	no		csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Orphan	ANTCCATATAGTNTAATATAAAAC,GGTTTTATATTAACTATATGGAATGTAAATT	24,31	0	0	NA	NA	NA:I-A	4,3	4	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA|59aa|up_6|CP029154.1_2809530_2809707_+,NA|53aa|down_0|CP029154.1_2814649_2814808_-	NA|543aa|up_9|CP029154.1_2805838_2807467_+	TIGR03801, For_A_Pyridoxal-5-_Phosphate, aspartate 4-decarboxylase	NA|332aa|up_8|CP029154.1_2807587_2808583_+	cd08964, L-asparaginase_II, Type II (periplasmic) bacterial L-asparaginase	NA|128aa|up_7|CP029154.1_2808767_2809151_-	pfam03965, Penicillinase_R, Penicillinase repressor	NA|59aa|up_6|CP029154.1_2809530_2809707_+	NA	NA|67aa|up_5|CP029154.1_2809932_2810133_+	COG1278, CspC, Cold shock proteins [Transcription]	NA|446aa|up_4|CP029154.1_2810563_2811901_+	cd16935, HATPase_AgrC-ComD-like, Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Staphylococcus aureus AgrC and Streptococcus pneumoniae ComD which are involved in quorum sensing	NA|194aa|up_3|CP029154.1_2811943_2812525_+	pfam04647, AgrB, Accessory gene regulator B	NA|54aa|up_2|CP029154.1_2812542_2812704_+	TIGR04223, quorum_AgrD, cyclic lactone autoinducer peptide	NA|266aa|up_1|CP029154.1_2812725_2813523_-	cd02696, MurNAc-LAA, N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3	NA|87aa|up_0|CP029154.1_2813519_2813780_-	pfam16079, Phage_holin_5_2, Phage holin family Hol44, in holin superfamily V	NA|53aa|down_0|CP029154.1_2814649_2814808_-	NA	NA|457aa|down_1|CP029154.1_2815165_2816536_-	NF033435, S-layer_Clost, S-layer protein SlpA	NA|141aa|down_2|CP029154.1_2816934_2817357_+	pfam14659, Phage_int_SAM_3, Phage integrase, N-terminal SAM-like domain	NA|223aa|down_3|CP029154.1_2818342_2819011_-	pfam04892, VanZ, VanZ like family	NA|128aa|down_4|CP029154.1_2819109_2819493_-	smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|807aa|down_5|CP029154.1_2819892_2822313_-	PRK00390, leuS, leucyl-tRNA synthetase; Validated	NA|117aa|down_6|CP029154.1_2822666_2823017_-	pfam02410, RsfS, Ribosomal silencing factor during starvation	NA|191aa|down_7|CP029154.1_2823133_2823706_-	COG1713, COG1713, Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]	NA|230aa|down_8|CP029154.1_2823706_2824396_-	PRK00071, nadD, nicotinate-nucleotide adenylyltransferase	NA|213aa|down_9|CP029154.1_2824671_2825310_+	PRK00117, recX, recombination regulator RecX; Reviewed
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	18	3760096-3760299	17	CRISPRCasFinder	no		csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Orphan	TCATCATATAAACCTATTAAATATTATCTTATTTATTGGTATATGGAAT	49	0	0	NA	NA	NA	1	1	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA,NA|50aa|down_3|CP029154.1_3764647_3764797_+	NA|85aa|up_9|CP029154.1_3749083_3749338_-	pfam00269, SASP, Small, acid-soluble spore proteins, alpha/beta type	NA|373aa|up_8|CP029154.1_3749459_3750578_-	cd05670, M20_Acy1_YkuR-like, M20 Peptidase aminoacyclase-1 YkuR-like proteins, including YkuR and Ama/HipO/HyuC proteins	NA|398aa|up_7|CP029154.1_3750783_3751977_-	TIGR00720, hypothetical_protein_NEICINOT_00681, L-serine dehydratase, iron-sulfur-dependent, single chain form	NA|294aa|up_6|CP029154.1_3752299_3753181_+	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional	NA|334aa|up_5|CP029154.1_3753610_3754612_+	PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase; Provisional	NA|296aa|up_4|CP029154.1_3754728_3755616_+	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional	NA|250aa|up_3|CP029154.1_3755682_3756432_+	PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional	NA|239aa|up_2|CP029154.1_3756650_3757367_+	TIGR03532, DapD_Ac, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase	NA|330aa|up_1|CP029154.1_3757797_3758787_-	cd03402, SPFH_like_u2, Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily	NA|252aa|up_0|CP029154.1_3759226_3759982_+	PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional	NA|556aa|down_0|CP029154.1_3760414_3762082_-	PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional	NA|180aa|down_1|CP029154.1_3762260_3762800_-	COG0634, Hpt, Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]	NA|428aa|down_2|CP029154.1_3763127_3764411_-	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|50aa|down_3|CP029154.1_3764647_3764797_+	NA	NA|592aa|down_4|CP029154.1_3764846_3766622_-	COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	NA|190aa|down_5|CP029154.1_3766833_3767403_-	COG2226, UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]	NA|212aa|down_6|CP029154.1_3767586_3768222_-	PRK05813, PRK05813, single-stranded DNA-binding protein; Provisional	NA|294aa|down_7|CP029154.1_3768889_3769771_-	pfam01925, TauE, Sulfite exporter TauE/SafE	NA|336aa|down_8|CP029154.1_3769890_3770898_-	PRK13969, PRK13969, proline racemase; Provisional	NA|161aa|down_9|CP029154.1_3770917_3771400_-	TIGR04480, D-proline_reductase_PrdA_proprotein, D-proline reductase (dithiol), PrdA proprotein
GCA_003095675.1_ASM309567v1	CP029154	Clostridioides difficile strain CD161 chromosome, complete genome	20	4147950-4148084	18	CRISPRCasFinder	no		csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	Orphan	GTTGCTTAAAGTGCTAACGCACAGCGCCAAC	31	1	2	4147981-4148053|4147981-4148053	CP029154.1_32190-32118|CP029154.1_1171717-1171645	NA	1	1	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA,NA|94aa|down_0|CP029154.1_4149966_4150248_-	NA|477aa|up_9|CP029154.1_4135722_4137153_+	PRK09243, PRK09243, nicotinate phosphoribosyltransferase; Validated	NA|143aa|up_8|CP029154.1_4137189_4137618_+	COG1522, Lrp, Transcriptional regulators [Transcription]	NA|235aa|up_7|CP029154.1_4137805_4138510_-	TIGR02692, putative_tRNA_nucleotidyltransferase, tRNA adenylyltransferase	NA|278aa|up_6|CP029154.1_4138532_4139366_-	cd11648, RsmI, Ribosomal RNA small subunit methyltransferase I (RsmI), also known as rRNA (cytidine-2'-O-)-methyltransferase	NA|249aa|up_5|CP029154.1_4139366_4140113_-	COG4123, COG4123, Predicted O-methyltransferase [General function prediction only]	NA|298aa|up_4|CP029154.1_4140190_4141084_-	COG1774, COG1774, Uncharacterized homolog of PSP1 [Function unknown]	NA|312aa|up_3|CP029154.1_4141080_4142016_-	PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated	NA|230aa|up_2|CP029154.1_4142018_4142708_-	COG0125, Tmk, Thymidylate kinase [Nucleotide transport and metabolism]	NA|470aa|up_1|CP029154.1_4142828_4144238_-	COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]	NA|64aa|up_0|CP029154.1_4144392_4144584_-	pfam04070, DUF378, Domain of unknown function (DUF378)	NA|94aa|down_0|CP029154.1_4149966_4150248_-	NA	NA|510aa|down_1|CP029154.1_4150469_4151999_-	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|160aa|down_2|CP029154.1_4152013_4152493_-	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|323aa|down_3|CP029154.1_4152601_4153570_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|257aa|down_4|CP029154.1_4153706_4154477_-	PRK13318, PRK13318, type III pantothenate kinase	NA|197aa|down_5|CP029154.1_4154495_4155086_-	COG4684, COG4684, Predicted membrane protein [Function unknown]	NA|323aa|down_6|CP029154.1_4155268_4156237_-	cd02252, nylC_like, nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC	NA|326aa|down_7|CP029154.1_4156229_4157207_-	PRK11886, PRK11886, bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA	NA|665aa|down_8|CP029154.1_4157528_4159523_-	TIGR01241, ATP-dependent_zinc_metalloprotease_FtsH, ATP-dependent metalloprotease FtsH	NA|463aa|down_9|CP029154.1_4159532_4160921_-	TIGR02432, tRNAIle-lysidine_synthase, tRNA(Ile)-lysidine synthetase, N-terminal domain
GCA_003095675.1_ASM309567v1	CP029156	Clostridioides difficile strain CD161 plasmid unnamed2, complete sequence	1	3830-3928	1	CRISPRCasFinder	no			Orphan	GTCACAAATCGGACATTTTTTAG	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas14j,PD-DExK,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,c2c9_V-U4,RT	NA|182aa|up_0|CP029156.1_3235_3781_-,NA|86aa|down_0|CP029156.1_4476_4734_-,NA|162aa|down_1|CP029156.1_4753_5239_-,NA|87aa|down_2|CP029156.1_5262_5523_-,NA|269aa|down_3|CP029156.1_5547_6354_-,NA|109aa|down_5|CP029156.1_6901_7228_-,NA|61aa|down_8|CP029156.1_8353_8536_-,NA|235aa|down_9|CP029156.1_8592_9297_-	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|153aa|up_2|CP029156.1_1914_2373_-	pfam13518, HTH_28, Helix-turn-helix domain	NA|215aa|up_1|CP029156.1_2587_3232_-	cd01192, INT_C_like_3, Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain	NA|182aa|up_0|CP029156.1_3235_3781_-	NA	NA|86aa|down_0|CP029156.1_4476_4734_-	NA	NA|162aa|down_1|CP029156.1_4753_5239_-	NA	NA|87aa|down_2|CP029156.1_5262_5523_-	NA	NA|269aa|down_3|CP029156.1_5547_6354_-	NA	NA|179aa|down_4|CP029156.1_6365_6902_-	COG1704, LemA, Uncharacterized conserved protein [Function unknown]	NA|109aa|down_5|CP029156.1_6901_7228_-	NA	NA|195aa|down_6|CP029156.1_7417_8002_-	TIGR02937, RNA_polymerase_sigma_factor, RNA polymerase sigma factor, sigma-70 family	NA|126aa|down_7|CP029156.1_7979_8357_-	cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB)	NA|61aa|down_8|CP029156.1_8353_8536_-	NA	NA|235aa|down_9|CP029156.1_8592_9297_-	NA
