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_000006925.2_ASM692v2	NC_004337	Shigella flexneri 2a str. 301 chromosome, complete genome	1	64543-64658	1	CRISPRCasFinder	no		DEDDh,DinG,cas3,csa3,RT	Orphan	GATAAGACGCGCCAGCGTCGCATCAGGCGTT	31	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,csa3,RT	NA,NA	NA|126aa|up_9|NC_004337.2_50546_50924_-	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|274aa|up_8|NC_004337.2_50926_51748_-	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|330aa|up_7|NC_004337.2_51744_52734_-	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|429aa|up_6|NC_004337.2_52733_54020_-	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|785aa|up_5|NC_004337.2_54072_56427_-	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|272aa|up_4|NC_004337.2_56681_57497_+	PRK09430, djlA, co-chaperone DjlA	NA|229aa|up_3|NC_004337.2_57644_58331_-	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|969aa|up_2|NC_004337.2_58285_61192_-	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|784aa|up_1|NC_004337.2_61356_63708_-	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|232aa|up_0|NC_004337.2_63782_64478_-	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|567aa|down_0|NC_004337.2_66189_67890_-	PRK04123, PRK04123, ribulokinase; Provisional	NA|293aa|down_1|NC_004337.2_68228_69107_+	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|255aa|down_2|NC_004337.2_69192_69957_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|233aa|down_3|NC_004337.2_70070_70769_-	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|537aa|down_4|NC_004337.2_70752_72363_-	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|328aa|down_5|NC_004337.2_72338_73322_-	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|552aa|down_6|NC_004337.2_73485_75141_-	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|393aa|down_7|NC_004337.2_75462_76641_+	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter	NA|202aa|down_8|NC_004337.2_76689_77295_-	PRK01641, leuD, 3-isopropylmalate dehydratase small subunit	NA|467aa|down_9|NC_004337.2_77305_78706_-	PRK05478, PRK05478, 3-isopropylmalate dehydratase large subunit
GCF_000006925.2_ASM692v2	NC_004337	Shigella flexneri 2a str. 301 chromosome, complete genome	2	877065-877213	2	CRISPRCasFinder	no		DEDDh,DinG,cas3,csa3,RT	Orphan	GTTCACTGCCGTACAGGCAGCTTAGAAAT	29	0	0	NA	NA	I-F	2	2	Orphan	DEDDh,DinG,cas3,csa3,RT	NA|45aa|up_5|NC_004337.2_870501_870636_+,NA	NA|168aa|up_9|NC_004337.2_866636_867140_-	pfam03400, DDE_Tnp_IS1, IS1 transposase	NA|92aa|up_8|NC_004337.2_867058_867334_-	COG3677, COG3677, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|553aa|up_7|NC_004337.2_867785_869444_+	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|331aa|up_6|NC_004337.2_869440_870433_-	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|45aa|up_5|NC_004337.2_870501_870636_+	NA	NA|372aa|up_4|NC_004337.2_870547_871663_+	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|649aa|up_3|NC_004337.2_871659_873606_+	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|75aa|up_2|NC_004337.2_873678_873903_-	PRK09937, PRK09937, cold shock-like protein CspD	NA|107aa|up_1|NC_004337.2_874225_874546_+	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|759aa|up_0|NC_004337.2_874576_876853_+	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|73aa|down_0|NC_004337.2_877596_877815_-	PRK00276, infA, translation initiation factor IF-1; Validated	NA|235aa|down_1|NC_004337.2_878099_878804_-	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|574aa|down_2|NC_004337.2_878845_880567_-	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|589aa|down_3|NC_004337.2_880567_882334_-	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|322aa|down_4|NC_004337.2_882456_883422_-	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|165aa|down_5|NC_004337.2_883965_884460_+	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|1343aa|down_6|NC_004337.2_884594_888623_+	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|205aa|down_7|NC_004337.2_888774_889389_+	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|448aa|down_8|NC_004337.2_889399_890743_+	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|431aa|down_9|NC_004337.2_890833_892126_+	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional
GCF_000006925.2_ASM692v2	NC_004337	Shigella flexneri 2a str. 301 chromosome, complete genome	3	2363954-2364080	3	CRISPRCasFinder	no		DEDDh,DinG,cas3,csa3,RT	Orphan	TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC	39	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,csa3,RT	NA,NA	NA|950aa|up_9|NC_004337.2_2338428_2341278_-	PRK10841, PRK10841, two-component system sensor histidine kinase RcsC	NA|259aa|up_8|NC_004337.2_2341552_2342329_-	COG4676, COG4676, Uncharacterized protein conserved in bacteria [Function unknown]	NA|550aa|up_7|NC_004337.2_2342333_2343983_-	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|280aa|up_6|NC_004337.2_2346257_2347097_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|113aa|up_5|NC_004337.2_2347123_2347462_-	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|208aa|up_4|NC_004337.2_2349774_2350398_-	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|876aa|up_3|NC_004337.2_2352231_2354859_-	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|241aa|up_2|NC_004337.2_2355005_2355728_+	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|280aa|up_1|NC_004337.2_2359907_2360747_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|762aa|up_0|NC_004337.2_2361617_2363903_+	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|390aa|down_0|NC_004337.2_2364097_2365267_+	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|85aa|down_1|NC_004337.2_2365266_2365521_+	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|217aa|down_2|NC_004337.2_2365574_2366225_-	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|69aa|down_3|NC_004337.2_2366439_2366646_+	PRK09729, PRK09729, hypothetical protein; Provisional	NA|359aa|down_4|NC_004337.2_2366687_2367764_-	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|453aa|down_5|NC_004337.2_2367768_2369127_-	PRK11273, glpT, glycerol-3-phosphate transporter	NA|543aa|down_6|NC_004337.2_2369399_2371028_+	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|420aa|down_7|NC_004337.2_2371017_2372277_+	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_8|NC_004337.2_2372273_2373464_+	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|317aa|down_9|NC_004337.2_2373656_2374607_+	PRK09956, PRK09956, ISNCY family transposase
GCF_000006925.2_ASM692v2	NC_004337	Shigella flexneri 2a str. 301 chromosome, complete genome	4	2832890-2833036	4	CRISPRCasFinder	no	cas3	DEDDh,DinG,cas3,csa3,RT	Unclear	CTGCTTAAAAAAAGAACAAATGGTAGTGTCCGCTATTGCCAGTACACCTCAAA	53	1	40	2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983|2832943-2832983	NC_004337.2_263500-263460|NC_004337.2_311830-311790|NC_004337.2_317155-317195|NC_004337.2_325622-325582|NC_004337.2_330452-330412|NC_004337.2_700355-700395|NC_004337.2_712998-712958|NC_004337.2_725781-725821|NC_004337.2_827014-827054|NC_004337.2_1081767-1081807|NC_004337.2_1390393-1390353|NC_004337.2_1402281-1402321|NC_004337.2_1414941-1414981|NC_004337.2_1426917-1426957|NC_004337.2_1467499-1467539|NC_004337.2_1475913-1475953|NC_004337.2_1575749-1575789|NC_004337.2_1592695-1592735|NC_004337.2_1828378-1828338|NC_004337.2_1843681-1843721|NC_004337.2_1939732-1939772|NC_004337.2_1964469-1964509|NC_004337.2_2050261-2050221|NC_004337.2_2057289-2057249|NC_004337.2_2072012-2072052|NC_004337.2_2083128-2083088|NC_004337.2_2204900-2204940|NC_004337.2_3058230-3058270|NC_004337.2_3354627-3354667|NC_004337.2_3912577-3912617|NC_004337.2_4463794-4463834|NC_004337.2_4532537-4532497|NC_004337.2_1306795-1306835|NC_004337.2_1582600-1582560|NC_004337.2_2695475-2695515|NC_004851.1_6155-6115|NC_004851.1_88401-88361|NC_004851.1_98103-98143|NC_004851.1_196776-196736|NC_004851.1_206376-206336	NA	1	1	Unclear	DEDDh,DinG,cas3,csa3,RT	NA|65aa|up_3|NC_004337.2_2825947_2826142_-,NA	NA|91aa|up_9|NC_004337.2_2820211_2820484_+	PRK10409, PRK10409, HypC/HybG/HupF family hydrogenase formation chaperone	NA|374aa|up_8|NC_004337.2_2820483_2821605_+	PRK15062, PRK15062, hydrogenase isoenzymes formation protein HypD; Provisional	NA|323aa|up_7|NC_004337.2_2821643_2822612_+	TIGR02124, Hydrogenase_expression/formation_protein_HypE, hydrogenase expression/formation protein HypE	NA|693aa|up_6|NC_004337.2_2822685_2824764_+	PRK15429, PRK15429, formate hydrogenlyase transcriptional activator FlhA	NA|118aa|up_5|NC_004337.2_2824800_2825154_-	pfam11756, YgbA_NO, Nitrous oxide-stimulated promoter	NA|168aa|up_4|NC_004337.2_2825216_2825720_-	pfam03400, DDE_Tnp_IS1, IS1 transposase	NA|65aa|up_3|NC_004337.2_2825947_2826142_-	NA	NA|854aa|up_2|NC_004337.2_2826217_2828779_+	PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional	NA|266aa|up_1|NC_004337.2_2829587_2830385_-	COG1349, GlpR, Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]	NA|101aa|up_0|NC_004337.2_2831740_2832043_+	pfam01527, HTH_Tnp_1, Transposase	NA|699aa|down_0|NC_004337.2_2833130_2835227_-	pfam09299, Mu-transpos_C, Mu transposase, C-terminal	NA|84aa|down_1|NC_004337.2_2835228_2835480_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|188aa|down_2|NC_004337.2_2835644_2836208_+	pfam07022, Phage_CI_repr, Bacteriophage CI repressor helix-turn-helix domain	NA|198aa|down_3|NC_004337.2_2837427_2838021_-	COG0163, UbiX family flavin prenyltransferase [Coenzyme transport and metabolism]	NA|136aa|down_4|NC_004337.2_2838167_2838575_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|343aa|down_5|NC_004337.2_2838694_2839723_-	PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated	NA|380aa|down_6|NC_004337.2_2839749_2840889_-	PRK10871, nlpD, murein hydrolase activator NlpD	NA|209aa|down_7|NC_004337.2_2841028_2841655_-	PRK00312, pcm, protein-L-isoaspartate(D-aspartate) O-methyltransferase	NA|254aa|down_8|NC_004337.2_2841648_2842410_-	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional	NA|350aa|down_9|NC_004337.2_2842390_2843440_-	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed
GCF_000006925.2_ASM692v2	NC_004337	Shigella flexneri 2a str. 301 chromosome, complete genome	5	3246675-3246776	5	CRISPRCasFinder	no		DEDDh,DinG,cas3,csa3,RT	Orphan	TACAAAACACAACAACATCAACAA	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,csa3,RT	NA|55aa|up_0|NC_004337.2_3246469_3246634_+,NA	NA|123aa|up_9|NC_004337.2_3240430_3240799_+	PRK10629, PRK10629, EnvZ/OmpR regulon moderator MzrA	NA|102aa|up_8|NC_004337.2_3241337_3241643_+	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]	NA|135aa|up_7|NC_004337.2_3241645_3242050_+	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|100aa|up_6|NC_004337.2_3242039_3242339_+	pfam13997, YqjK, YqjK-like protein	NA|129aa|up_5|NC_004337.2_3242434_3242821_+	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|329aa|up_4|NC_004337.2_3242890_3243877_+	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|123aa|up_3|NC_004337.2_3244169_3244538_+	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|299aa|up_2|NC_004337.2_3244744_3245641_-	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|NC_004337.2_3245745_3246447_+	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|55aa|up_0|NC_004337.2_3246469_3246634_+	NA	NA|437aa|down_0|NC_004337.2_3246845_3248156_-	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|444aa|down_1|NC_004337.2_3248183_3249515_-	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|455aa|down_2|NC_004337.2_3249789_3251154_-	PRK15040, PRK15040, L-serine ammonia-lyase	NA|130aa|down_3|NC_004337.2_3251225_3251615_-	PRK11401, PRK11401, enamine/imine deaminase	NA|765aa|down_4|NC_004337.2_3251628_3253923_-	cd01678, PFL1, Pyruvate formate lyase 1	NA|403aa|down_5|NC_004337.2_3253956_3255165_-	PRK12379, PRK12379, propionate kinase	NA|444aa|down_6|NC_004337.2_3255190_3256522_-	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|330aa|down_7|NC_004337.2_3256543_3257533_-	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|313aa|down_8|NC_004337.2_3257631_3258570_-	PRK10341, PRK10341, transcriptional regulator TdcA	NA|115aa|down_9|NC_004337.2_3258759_3259104_+	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional
