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
GCF_008370775.1_ASM837077v1	NZ_CP042980	Shigella flexneri Y strain PE577 chromosome, complete genome	1	64028-64143	1	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	Orphan	GATAAGACGCGCCAGCGTCGCATCAGGCGTT	31	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	NA,NA	NA|126aa|up_9|NZ_CP042980.1_50032_50410_-	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|274aa|up_8|NZ_CP042980.1_50412_51234_-	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|330aa|up_7|NZ_CP042980.1_51230_52220_-	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|429aa|up_6|NZ_CP042980.1_52219_53506_-	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|785aa|up_5|NZ_CP042980.1_53558_55913_-	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|272aa|up_4|NZ_CP042980.1_56167_56983_+	PRK09430, djlA, co-chaperone DjlA	NA|220aa|up_3|NZ_CP042980.1_57099_57759_-	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|969aa|up_2|NZ_CP042980.1_57770_60677_-	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|784aa|up_1|NZ_CP042980.1_60841_63193_-	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|232aa|up_0|NZ_CP042980.1_63267_63963_-	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|501aa|down_0|NZ_CP042980.1_64162_65665_-	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|567aa|down_1|NZ_CP042980.1_65675_67376_-	PRK04123, PRK04123, ribulokinase; Provisional	NA|293aa|down_2|NZ_CP042980.1_67714_68593_+	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|255aa|down_3|NZ_CP042980.1_68678_69443_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|233aa|down_4|NZ_CP042980.1_69556_70255_-	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|537aa|down_5|NZ_CP042980.1_70238_71849_-	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|328aa|down_6|NZ_CP042980.1_71824_72808_-	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|552aa|down_7|NZ_CP042980.1_72971_74627_-	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|44aa|down_8|NZ_CP042980.1_74715_74847_+	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT	NA|393aa|down_9|NZ_CP042980.1_74948_76127_+	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter
GCF_008370775.1_ASM837077v1	NZ_CP042980	Shigella flexneri Y strain PE577 chromosome, complete genome	2	845761-845909	2	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	Orphan	GTTCACTGCCGTACAGGCAGCTTAGAAAT	29	0	0	NA	NA	I-F	2	2	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	NA,NA	NA|300aa|up_9|NZ_CP042980.1_831893_832793_-	COG2431, COG2431, Predicted membrane protein [Function unknown]	NA|425aa|up_8|NZ_CP042980.1_832916_834190_-	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|232aa|up_7|NZ_CP042980.1_834585_835281_-	PRK05420, PRK05420, aquaporin Z; Provisional	NA|553aa|up_6|NZ_CP042980.1_836481_838140_+	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|319aa|up_5|NZ_CP042980.1_838136_839093_-	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|372aa|up_4|NZ_CP042980.1_839243_840359_+	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|649aa|up_3|NZ_CP042980.1_840355_842302_+	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|75aa|up_2|NZ_CP042980.1_842374_842599_-	PRK09937, PRK09937, cold shock-like protein CspD	NA|107aa|up_1|NZ_CP042980.1_842921_843242_+	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|759aa|up_0|NZ_CP042980.1_843272_845549_+	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|73aa|down_0|NZ_CP042980.1_846292_846511_-	PRK00276, infA, translation initiation factor IF-1; Validated	NA|235aa|down_1|NZ_CP042980.1_846795_847500_-	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|574aa|down_2|NZ_CP042980.1_847541_849263_-	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|589aa|down_3|NZ_CP042980.1_849263_851030_-	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|322aa|down_4|NZ_CP042980.1_851152_852118_-	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|165aa|down_5|NZ_CP042980.1_852661_853156_+	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|1343aa|down_6|NZ_CP042980.1_853290_857319_+	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|204aa|down_7|NZ_CP042980.1_857473_858085_+	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|448aa|down_8|NZ_CP042980.1_858095_859439_+	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|431aa|down_9|NZ_CP042980.1_859529_860822_+	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional
GCF_008370775.1_ASM837077v1	NZ_CP042980	Shigella flexneri Y strain PE577 chromosome, complete genome	3	1602564-1602672	3	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	Orphan	AGGAATTAAGGAAGTAAATATAAAGAG	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	NA|330aa|up_5|NZ_CP042980.1_1598740_1599730_-,NA|164aa|up_4|NZ_CP042980.1_1599814_1600306_-,NA|66aa|up_3|NZ_CP042980.1_1600416_1600614_-,NA|167aa|up_2|NZ_CP042980.1_1600626_1601127_-,NA|172aa|up_1|NZ_CP042980.1_1601116_1601632_-,NA|123aa|up_0|NZ_CP042980.1_1602062_1602431_-,NA	NA|114aa|up_9|NZ_CP042980.1_1594347_1594689_+	PRK13659, PRK13659, DUF1283 family protein	NA|237aa|up_8|NZ_CP042980.1_1595286_1595997_-	PRK02939, PRK02939, YnfC family lipoprotein	NA|102aa|up_7|NZ_CP042980.1_1596104_1596410_+	pfam06649, DUF1161, Protein of unknown function (DUF1161)	NA|107aa|up_6|NZ_CP042980.1_1596608_1596929_+	TIGR02166, Putative_dimethyl_sulfoxide_reductase_chain_YnfE, anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family	NA|330aa|up_5|NZ_CP042980.1_1598740_1599730_-	NA	NA|164aa|up_4|NZ_CP042980.1_1599814_1600306_-	NA	NA|66aa|up_3|NZ_CP042980.1_1600416_1600614_-	NA	NA|167aa|up_2|NZ_CP042980.1_1600626_1601127_-	NA	NA|172aa|up_1|NZ_CP042980.1_1601116_1601632_-	NA	NA|123aa|up_0|NZ_CP042980.1_1602062_1602431_-	NA	NA|390aa|down_0|NZ_CP042980.1_1603481_1604650_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|370aa|down_1|NZ_CP042980.1_1605739_1606849_+	TIGR02166, Putative_dimethyl_sulfoxide_reductase_chain_YnfE, anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family	NA|206aa|down_2|NZ_CP042980.1_1608958_1609576_+	TIGR02951, anaerobic_dimethyl_sulfoxide_reductase_subunit_B, DMSO reductase, iron-sulfur subunit	NA|285aa|down_3|NZ_CP042980.1_1609577_1610432_+	pfam04976, DmsC, DMSO reductase anchor subunit (DmsC)	NA|205aa|down_4|NZ_CP042980.1_1610474_1611089_+	PRK11621, PRK11621, Tat proofreading chaperone DmsD	NA|431aa|down_5|NZ_CP042980.1_1611247_1612540_+	PRK01610, PRK01610, putative voltage-gated ClC-type chloride channel ClcB; Provisional	NA|232aa|down_6|NZ_CP042980.1_1612492_1613188_-	PRK12374, PRK12374, ATP-dependent dethiobiotin synthetase BioD	NA|407aa|down_7|NZ_CP042980.1_1613312_1614533_-	COG1940, NagC, Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]	NA|304aa|down_8|NZ_CP042980.1_1614667_1615579_-	cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold	NA|270aa|down_9|NZ_CP042980.1_1615685_1616495_+	cd17324, MFS_NepI_like, Purine ribonucleoside efflux pump NepI and similar transporters of the Major Facilitator Superfamily
GCF_008370775.1_ASM837077v1	NZ_CP042980	Shigella flexneri Y strain PE577 chromosome, complete genome	4	2340474-2340600	4	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	Orphan	TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC	39	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	NA,NA	NA|550aa|up_9|NZ_CP042980.1_2318853_2320503_-	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|53aa|up_8|NZ_CP042980.1_2321066_2321225_-	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only]	NA|390aa|up_7|NZ_CP042980.1_2322777_2323946_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|208aa|up_6|NZ_CP042980.1_2326294_2326918_-	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|876aa|up_5|NZ_CP042980.1_2328751_2331379_-	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|241aa|up_4|NZ_CP042980.1_2331525_2332248_+	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|645aa|up_3|NZ_CP042980.1_2332375_2334310_-	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|552aa|up_2|NZ_CP042980.1_2334319_2335975_-	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|425aa|up_1|NZ_CP042980.1_2335993_2337267_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|762aa|up_0|NZ_CP042980.1_2338137_2340423_+	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|377aa|down_0|NZ_CP042980.1_2340656_2341787_+	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|85aa|down_1|NZ_CP042980.1_2341786_2342041_+	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|217aa|down_2|NZ_CP042980.1_2342094_2342745_-	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|359aa|down_3|NZ_CP042980.1_2343207_2344284_-	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|453aa|down_4|NZ_CP042980.1_2344288_2345647_-	PRK11273, glpT, glycerol-3-phosphate transporter	NA|543aa|down_5|NZ_CP042980.1_2345919_2347548_+	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|420aa|down_6|NZ_CP042980.1_2347537_2348797_+	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_7|NZ_CP042980.1_2348793_2349984_+	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|317aa|down_8|NZ_CP042980.1_2350176_2351127_+	PRK09956, PRK09956, ISNCY family transposase	NA|157aa|down_9|NZ_CP042980.1_2351167_2351638_-	PRK10128, PRK10128, 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional
GCF_008370775.1_ASM837077v1	NZ_CP042980	Shigella flexneri Y strain PE577 chromosome, complete genome	5	3236922-3237023	5	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	Orphan	TACAAAACACAACAACATCAACAA	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,RT	NA|55aa|up_0|NZ_CP042980.1_3236716_3236881_+,NA	NA|128aa|up_9|NZ_CP042980.1_3230662_3231046_+	PRK10629, PRK10629, EnvZ/OmpR regulon moderator MzrA	NA|102aa|up_8|NZ_CP042980.1_3231584_3231890_+	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]	NA|135aa|up_7|NZ_CP042980.1_3231892_3232297_+	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|100aa|up_6|NZ_CP042980.1_3232286_3232586_+	pfam13997, YqjK, YqjK-like protein	NA|129aa|up_5|NZ_CP042980.1_3232681_3233068_+	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|329aa|up_4|NZ_CP042980.1_3233137_3234124_+	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|123aa|up_3|NZ_CP042980.1_3234416_3234785_+	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|299aa|up_2|NZ_CP042980.1_3234991_3235888_-	cd08431, PBP2_HupR, The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold	NA|234aa|up_1|NZ_CP042980.1_3235992_3236694_+	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|55aa|up_0|NZ_CP042980.1_3236716_3236881_+	NA	NA|437aa|down_0|NZ_CP042980.1_3237092_3238403_-	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|444aa|down_1|NZ_CP042980.1_3238430_3239762_-	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|455aa|down_2|NZ_CP042980.1_3240036_3241401_-	PRK15040, PRK15040, L-serine ammonia-lyase	NA|130aa|down_3|NZ_CP042980.1_3241472_3241862_-	PRK11401, PRK11401, enamine/imine deaminase	NA|765aa|down_4|NZ_CP042980.1_3241875_3244170_-	cd01678, PFL1, Pyruvate formate lyase 1	NA|403aa|down_5|NZ_CP042980.1_3244203_3245412_-	PRK12379, PRK12379, propionate kinase	NA|444aa|down_6|NZ_CP042980.1_3245437_3246769_-	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|330aa|down_7|NZ_CP042980.1_3246790_3247780_-	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|313aa|down_8|NZ_CP042980.1_3247878_3248817_-	PRK10341, PRK10341, transcriptional regulator TdcA	NA|115aa|down_9|NZ_CP042980.1_3249006_3249351_+	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional
