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_009931475.1_ASM993147v1	NZ_CP045522	Shigella flexneri strain 5908.2 chromosome, complete genome	1	702851-702992	1	CRISPRCasFinder	no		cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	Orphan	AATGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACA	41	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	NA,NA	NA|79aa|up_9|NZ_CP045522.1_694422_694659_+	pfam07256, DUF1435, Protein of unknown function (DUF1435)	NA|344aa|up_8|NZ_CP045522.1_695218_696250_-	PRK09489, rsmC, 16S rRNA (guanine(1207)-N(2))-methyltransferase RsmC	NA|138aa|up_7|NZ_CP045522.1_696352_696766_+	COG3050, HolD, DNA polymerase III, psi subunit [DNA replication, recombination, and repair]	NA|149aa|up_6|NZ_CP045522.1_696734_697181_+	PRK09491, rimI, ribosomal-protein-alanine N-acetyltransferase; Provisional	NA|226aa|up_5|NZ_CP045522.1_697195_697873_+	PRK09449, PRK09449, dUMP phosphatase; Provisional	NA|530aa|up_4|NZ_CP045522.1_697963_699553_+	PRK00741, prfC, peptide chain release factor 3; Provisional	NA|202aa|up_3|NZ_CP045522.1_699945_700551_+	PRK10568, PRK10568, molecular chaperone OsmY	NA|54aa|up_2|NZ_CP045522.1_700677_700839_+	COG5487, COG5487, Small integral membrane protein [Function unknown]	NA|358aa|up_1|NZ_CP045522.1_700960_702034_+	COG4667, COG4667, Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]	NA|261aa|up_0|NZ_CP045522.1_702030_702813_+	PRK11449, PRK11449, metal-dependent hydrolase	NA|288aa|down_0|NZ_CP045522.1_703026_703890_-	TIGR04041, glycine_radical_enzyme_activase_YjjW_family, glycine radical enzyme activase, YjjW family	NA|514aa|down_1|NZ_CP045522.1_703861_705403_-	PRK10977, PRK10977, hypothetical protein; Provisional	NA|260aa|down_2|NZ_CP045522.1_705660_706440_+	PRK05283, PRK05283, deoxyribose-phosphate aldolase; Provisional	NA|441aa|down_3|NZ_CP045522.1_706566_707889_+	PRK05820, deoA, thymidine phosphorylase; Reviewed	NA|408aa|down_4|NZ_CP045522.1_707940_709164_+	PRK05362, PRK05362, phosphopentomutase; Provisional	NA|240aa|down_5|NZ_CP045522.1_709220_709940_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|88aa|down_6|NZ_CP045522.1_710100_710364_-	smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|215aa|down_7|NZ_CP045522.1_711439_712084_-	PRK11246, PRK11246, YtjB family periplasmic protein	NA|323aa|down_8|NZ_CP045522.1_712189_713158_+	PRK11133, serB, phosphoserine phosphatase; Provisional	NA|461aa|down_9|NZ_CP045522.1_713206_714589_+	TIGR00416, DNA_repair_protein_RadA_homolog, DNA repair protein RadA
GCF_009931475.1_ASM993147v1	NZ_CP045522	Shigella flexneri strain 5908.2 chromosome, complete genome	2	793103-793214	2	CRISPRCasFinder	no		cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	Orphan	GCTTATCCGGTCTACAAAATCGCAGCG	27	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	NA,NA	NA|126aa|up_9|NZ_CP045522.1_779143_779521_-	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|274aa|up_8|NZ_CP045522.1_779523_780345_-	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|330aa|up_7|NZ_CP045522.1_780341_781331_-	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|429aa|up_6|NZ_CP045522.1_781330_782617_-	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|785aa|up_5|NZ_CP045522.1_782669_785024_-	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|272aa|up_4|NZ_CP045522.1_785278_786094_+	PRK09430, djlA, co-chaperone DjlA	NA|220aa|up_3|NZ_CP045522.1_786210_786870_-	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|969aa|up_2|NZ_CP045522.1_786881_789788_-	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|784aa|up_1|NZ_CP045522.1_789952_792304_-	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|232aa|up_0|NZ_CP045522.1_792378_793074_-	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|501aa|down_0|NZ_CP045522.1_793273_794776_-	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|293aa|down_1|NZ_CP045522.1_796824_797703_+	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|255aa|down_2|NZ_CP045522.1_797788_798553_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|233aa|down_3|NZ_CP045522.1_798666_799365_-	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|537aa|down_4|NZ_CP045522.1_799348_800959_-	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|328aa|down_5|NZ_CP045522.1_800934_801918_-	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|552aa|down_6|NZ_CP045522.1_802081_803737_-	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|44aa|down_7|NZ_CP045522.1_803825_803957_+	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT	NA|393aa|down_8|NZ_CP045522.1_804058_805237_+	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter	NA|202aa|down_9|NZ_CP045522.1_805285_805891_-	PRK01641, leuD, 3-isopropylmalate dehydratase small subunit
GCF_009931475.1_ASM993147v1	NZ_CP045522	Shigella flexneri strain 5908.2 chromosome, complete genome	3	1570259-1570407	3	CRISPRCasFinder	no		cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	Orphan	GTTCACTGCCGTACAGGCAGCTTAGAAAT	29	0	0	NA	NA	I-F	2	2	Orphan	cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	NA,NA	NA|551aa|up_9|NZ_CP045522.1_1556707_1558360_-	PRK05290, PRK05290, hybrid cluster protein; Provisional	NA|300aa|up_8|NZ_CP045522.1_1558503_1559403_-	COG2431, COG2431, Predicted membrane protein [Function unknown]	NA|232aa|up_7|NZ_CP045522.1_1559859_1560555_-	PRK05420, PRK05420, aquaporin Z; Provisional	NA|553aa|up_6|NZ_CP045522.1_1560979_1562638_+	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|319aa|up_5|NZ_CP045522.1_1562634_1563591_-	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|372aa|up_4|NZ_CP045522.1_1563741_1564857_+	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|649aa|up_3|NZ_CP045522.1_1564853_1566800_+	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|75aa|up_2|NZ_CP045522.1_1566872_1567097_-	PRK09937, PRK09937, cold shock-like protein CspD	NA|107aa|up_1|NZ_CP045522.1_1567419_1567740_+	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|759aa|up_0|NZ_CP045522.1_1567770_1570047_+	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|73aa|down_0|NZ_CP045522.1_1570790_1571009_-	PRK00276, infA, translation initiation factor IF-1; Validated	NA|235aa|down_1|NZ_CP045522.1_1571293_1571998_-	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|574aa|down_2|NZ_CP045522.1_1572039_1573761_-	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|589aa|down_3|NZ_CP045522.1_1573761_1575528_-	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|322aa|down_4|NZ_CP045522.1_1575650_1576616_-	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|165aa|down_5|NZ_CP045522.1_1577160_1577655_+	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|1369aa|down_6|NZ_CP045522.1_1577789_1581896_+	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|204aa|down_7|NZ_CP045522.1_1582050_1582662_+	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|448aa|down_8|NZ_CP045522.1_1582672_1584016_+	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|431aa|down_9|NZ_CP045522.1_1584106_1585399_+	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional
GCF_009931475.1_ASM993147v1	NZ_CP045522	Shigella flexneri strain 5908.2 chromosome, complete genome	4	3058237-3058363	4	CRISPRCasFinder	no		cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	Orphan	TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC	39	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	NA,NA	NA|241aa|up_9|NZ_CP045522.1_3037465_3038188_-	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only]	NA|390aa|up_8|NZ_CP045522.1_3039740_3040909_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|208aa|up_7|NZ_CP045522.1_3043257_3043881_-	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|563aa|up_6|NZ_CP045522.1_3043877_3045566_-	COG4685, COG4685, Uncharacterized protein conserved in bacteria [Function unknown]	NA|876aa|up_5|NZ_CP045522.1_3045714_3048342_-	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|241aa|up_4|NZ_CP045522.1_3048488_3049211_+	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|644aa|up_3|NZ_CP045522.1_3049338_3051270_-	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|554aa|up_2|NZ_CP045522.1_3051282_3052944_-	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|410aa|up_1|NZ_CP045522.1_3053007_3054237_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|762aa|up_0|NZ_CP045522.1_3055900_3058186_+	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|377aa|down_0|NZ_CP045522.1_3058419_3059550_+	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|85aa|down_1|NZ_CP045522.1_3059549_3059804_+	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|217aa|down_2|NZ_CP045522.1_3059857_3060508_-	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|359aa|down_3|NZ_CP045522.1_3060955_3062032_-	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|453aa|down_4|NZ_CP045522.1_3062036_3063395_-	PRK11273, glpT, glycerol-3-phosphate transporter	NA|543aa|down_5|NZ_CP045522.1_3063667_3065296_+	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|420aa|down_6|NZ_CP045522.1_3065285_3066545_+	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_7|NZ_CP045522.1_3066541_3067732_+	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|300aa|down_8|NZ_CP045522.1_3067924_3068824_+	PRK09956, PRK09956, ISNCY family transposase	NA|74aa|down_9|NZ_CP045522.1_3068842_3069064_+	PRK09956, PRK09956, ISNCY family transposase
GCF_009931475.1_ASM993147v1	NZ_CP045522	Shigella flexneri strain 5908.2 chromosome, complete genome	5	3572945-3573028	5	CRISPRCasFinder	no		cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	Orphan	TTATCCCCGCTGACGCGGGGAAC	23	0	0	NA	NA	I-E	1	1	Orphan	cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	NA,NA|47aa|down_1|NZ_CP045522.1_3574956_3575097_+	NA|600aa|up_9|NZ_CP045522.1_3559619_3561419_-	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|121aa|up_8|NZ_CP045522.1_3561737_3562100_+	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|424aa|up_7|NZ_CP045522.1_3562177_3563449_+	PRK10015, PRK10015, oxidoreductase; Provisional	NA|87aa|up_6|NZ_CP045522.1_3563439_3563700_+	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]	NA|192aa|up_5|NZ_CP045522.1_3563716_3564292_+	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|287aa|up_4|NZ_CP045522.1_3564439_3565300_-	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|260aa|up_3|NZ_CP045522.1_3565296_3566076_-	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|470aa|up_2|NZ_CP045522.1_3566053_3567463_-	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|426aa|up_1|NZ_CP045522.1_3570112_3571390_+	cd06174, MFS, Major Facilitator Superfamily	NA|493aa|up_0|NZ_CP045522.1_3571416_3572895_+	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|224aa|down_0|NZ_CP045522.1_3574146_3574818_-	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|47aa|down_1|NZ_CP045522.1_3574956_3575097_+	NA	NA|291aa|down_2|NZ_CP045522.1_3575110_3575983_+	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|433aa|down_3|NZ_CP045522.1_3576042_3577341_-	PRK00077, eno, enolase; Provisional	NA|546aa|down_4|NZ_CP045522.1_3577428_3579066_-	PRK05380, pyrG, CTP synthetase; Validated	NA|264aa|down_5|NZ_CP045522.1_3579293_3580085_-	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|745aa|down_6|NZ_CP045522.1_3580180_3582415_-	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|434aa|down_7|NZ_CP045522.1_3582462_3583764_-	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|919aa|down_8|NZ_CP045522.1_3583820_3586577_+	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|447aa|down_9|NZ_CP045522.1_3586808_3588149_-	TIGR03247, glucar-dehydr, glucarate dehydratase
GCF_009931475.1_ASM993147v1	NZ_CP045522	Shigella flexneri strain 5908.2 chromosome, complete genome	6	3915535-3915636	6	CRISPRCasFinder	no		cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	Orphan	TACAAAACACAACAACATCAACAA	24	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,DinG,PrimPol,RT,c2c9_V-U4	NA|55aa|up_0|NZ_CP045522.1_3915329_3915494_+,NA|180aa|down_9|NZ_CP045522.1_3928145_3928685_+	NA|128aa|up_9|NZ_CP045522.1_3909179_3909563_+	PRK10629, PRK10629, EnvZ/OmpR regulon moderator MzrA	NA|102aa|up_8|NZ_CP045522.1_3910101_3910407_+	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]	NA|135aa|up_7|NZ_CP045522.1_3910409_3910814_+	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|100aa|up_6|NZ_CP045522.1_3910803_3911103_+	pfam13997, YqjK, YqjK-like protein	NA|161aa|up_5|NZ_CP045522.1_3911198_3911681_+	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|329aa|up_4|NZ_CP045522.1_3911750_3912737_+	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|123aa|up_3|NZ_CP045522.1_3913029_3913398_+	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|299aa|up_2|NZ_CP045522.1_3913604_3914501_-	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_CP045522.1_3914605_3915307_+	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|55aa|up_0|NZ_CP045522.1_3915329_3915494_+	NA	NA|431aa|down_0|NZ_CP045522.1_3915705_3916998_-	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|426aa|down_1|NZ_CP045522.1_3917025_3918303_-	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|455aa|down_2|NZ_CP045522.1_3918577_3919942_-	PRK15040, PRK15040, L-serine ammonia-lyase	NA|130aa|down_3|NZ_CP045522.1_3920013_3920403_-	PRK11401, PRK11401, enamine/imine deaminase	NA|403aa|down_4|NZ_CP045522.1_3922743_3923952_-	PRK12379, PRK12379, propionate kinase	NA|444aa|down_5|NZ_CP045522.1_3923977_3925309_-	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|330aa|down_6|NZ_CP045522.1_3925330_3926320_-	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|313aa|down_7|NZ_CP045522.1_3926418_3927357_-	PRK10341, PRK10341, transcriptional regulator TdcA	NA|115aa|down_8|NZ_CP045522.1_3927545_3927890_+	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional	NA|180aa|down_9|NZ_CP045522.1_3928145_3928685_+	NA
