CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
NC_013739	Conexibacter woesei DSM 14684, complete sequence	5 crisprs	csa3,WYL,DEDDh,DinG,cas3,cas4	2	6	2	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_013739_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_013739_1

466299-466442

Orphan

Consensus_repeat	Method
GGCTCGACGCCGTCGCCGCGCGCG	CRISPRCasFinder

2 spacers

The CRISPR arrays of NC_013739_1

>merge|NC_013739|1|466299-466442|CRISPRCasFinder
GGCTCGACGCCGTCGCCGCGCGCGCGGCGATCGAGCGTCGCGTCGGCGCGCCGCTCGGGCTCGACGCCGTCGCCGCCGCGGAGGCGGTCCTCGAACTCGCCACCGAGCAGATGGCGGCAGCGCTCGACGAGCTGGTCGCGCACG

>NC_013739|1|1|466299-466442|CRISPRCasFinder
GGCTCGACGCCGTCGCCGCGCGCG	CGGCGATCGAGCGTCGCGTCGGCGCGCCGCTCG
GGCTCGACGCCGTCGCCGCCGCGG	AGGCGGTCCTCGAACTCGCCACCGAGCAGATGGCGGCAG
CGCTCGACGAGCTGGTCGCGCACG

Protein	Signature genes	Signature genes Name	Protein_function
NC_013739.1\|WP_012931931.1\|451462_453103_+\|long-chain-fatty-acid--CoA-ligase	unknown	unknown	gnl\|CDD\|341284
NC_013739.1\|WP_012931932.1\|453099_454293_+\|FAD-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|369639
NC_013739.1\|WP_012931940.1\|463847_465125_+\|aspartate-aminotransferase-family-protein	unknown	unknown	gnl\|CDD\|223154
NC_013739.1\|WP_012931945.1\|471716_473312_+\|family-5-extracellular-solute-binding-protein	unknown	unknown	gnl\|CDD\|173877
NC_013739.1\|WP_012931938.1\|462097_462736_+\|DUF1211-domain-containing-protein	unknown	unknown	gnl\|CDD\|377696
NC_013739.1\|WP_041730025.1\|477262_477658_-\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_012931943.1\|469033_470845_+\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|223521
NC_013739.1\|WP_012931946.1\|473311_474316_+\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|223674
NC_013739.1\|WP_012931944.1\|470841_471720_+\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224094
NC_013739.1\|WP_012931936.1\|459170_460583_+\|MFS-transporter	unknown	unknown	gnl\|CDD\|129794
NC_013739.1\|WP_012931934.1\|455337_455967_-\|TetR/AcrR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|380061
NC_013739.1\|WP_160165464.1\|462743_463781_-\|TetR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|379409
NC_013739.1\|WP_012931950.1\|475613_477266_+\|CocE/NonD-family-hydrolase	unknown	unknown	gnl\|CDD\|225487
NC_013739.1\|WP_012931942.1\|467202_468942_+\|hydantoinase-B/oxoprolinase-family-protein	unknown	unknown	gnl\|CDD\|376810
NC_013739.1\|WP_012931947.1\|474347_474932_+\|isochorismatase-family-protein	unknown	unknown	gnl\|CDD\|238494
NC_013739.1\|WP_012931935.1\|456067_458959_+\|LuxR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|226415
NC_013739.1\|WP_041731325.1\|460570_462019_-\|type-I-glutamate--ammonia-ligase	unknown	unknown	gnl\|CDD\|273198
NC_013739.1\|WP_012931933.1\|454327_455290_+\|2,3-dihydroxybiphenyl-1,2-dioxygenase	unknown	unknown	gnl\|CDD\|274480
NC_013739.1\|WP_012931949.1\|475322_475580_-\|type-II-toxin-antitoxin-system-Phd/YefM-family-antitoxin	unknown	unknown	gnl\|CDD\|376852
NC_013739.1\|WP_012931948.1\|474921_475335_-\|PIN-domain-containing-protein	unknown	unknown	gnl\|CDD\|350300

Protein	Function_ID	Function_description	E-value
NC_013739.1\|WP_012931931.1\|451462_453103_+\|long-chain-fatty-acid--CoA-ligase	gnl\|CDD\|341284	cd12119, ttLC_FACS_AlkK_like, Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles. This family includes fatty acyl-CoA synthetases that can activate medium-chain to long-chain fatty acids. They catalyze the ATP-dependent acylation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. The fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of fatty acyl-CoA esters. The fatty acyl-CoA synthetase from Thermus thermophiles in this family catalyzes the long-chain fatty acid, myristoyl acid, while another member in this family, the AlkK protein identified from Pseudomonas oleovorans, targets medium chain fatty acids. This family also includes uncharacterized FACS proteins.	0
NC_013739.1\|WP_012931932.1\|453099_454293_+\|FAD-dependent-oxidoreductase	gnl\|CDD\|369639	pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	1.24855e-45
NC_013739.1\|WP_012931940.1\|463847_465125_+\|aspartate-aminotransferase-family-protein	gnl\|CDD\|223154	COG0076, GadB, Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism].	2.93856e-68
NC_013739.1\|WP_012931945.1\|471716_473312_+\|family-5-extracellular-solute-binding-protein	gnl\|CDD\|173877	cd08512, PBP2_NikA_DppA_OppA_like_7, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.	8.15763e-82
NC_013739.1\|WP_012931938.1\|462097_462736_+\|DUF1211-domain-containing-protein	gnl\|CDD\|377696	pfam06736, DUF1211, Protein of unknown function (DUF1211). This family represents a conserved region within a number of hypothetical proteins of unknown function found in eukaryotes, bacteria and archaea. These may possibly be integral membrane proteins.	1.06794e-31
NC_013739.1\|WP_012931943.1\|469033_470845_+\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|223521	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism].	1.87479e-111
NC_013739.1\|WP_012931946.1\|473311_474316_+\|ABC-transporter-permease	gnl\|CDD\|223674	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].	7.17626e-97
NC_013739.1\|WP_012931944.1\|470841_471720_+\|ABC-transporter-permease	gnl\|CDD\|224094	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].	3.41714e-78
NC_013739.1\|WP_012931936.1\|459170_460583_+\|MFS-transporter	gnl\|CDD\|129794	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Other].	3.10438e-56
NC_013739.1\|WP_012931934.1\|455337_455967_-\|TetR/AcrR-family-transcriptional-regulator	gnl\|CDD\|380061	pfam17932, TetR_C_24, Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in family members such as HTH-type transcriptional repressor KstR2 as well as fatty acid metabolism regulator proteins. In Mycobacterium smegmatis, KstR2 is involved in involved in cholesterol catabolism, while YsiA in Bacillus subtilis is involved in fatty acid degradation.	8.80458e-29
NC_013739.1\|WP_160165464.1\|462743_463781_-\|TetR-family-transcriptional-regulator	gnl\|CDD\|379409	pfam13977, TetR_C_6, BetI-type transcriptional repressor, C-terminal. This family comprises the C-terminal portion of proteins that belong to the TetR family of transcriptional regulators. The C-terminus represents the regulatory region, and does not include the DNA binding helix-turn-helix domain. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. One of the target proteins is BetI, an osmoprotectant which controls the choline-glycine betaine pathway in E.coli.	5.53885e-15
NC_013739.1\|WP_012931950.1\|475613_477266_+\|CocE/NonD-family-hydrolase	gnl\|CDD\|225487	COG2936, COG2936, Predicted acyl esterases [General function prediction only].	4.47534e-146
NC_013739.1\|WP_012931942.1\|467202_468942_+\|hydantoinase-B/oxoprolinase-family-protein	gnl\|CDD\|376810	pfam02538, Hydantoinase_B, Hydantoinase B/oxoprolinase. This family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase EC:3.5.2.9 which catalyzes the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to pfam01968.	1.60814e-128
NC_013739.1\|WP_012931947.1\|474347_474932_+\|isochorismatase-family-protein	gnl\|CDD\|238494	cd01012, YcaC_related, YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them. Multimerisation interface seems not to be conserved in all members.	1.09268e-35
NC_013739.1\|WP_012931935.1\|456067_458959_+\|LuxR-family-transcriptional-regulator	gnl\|CDD\|226415	COG3899, COG3899, Predicted ATPase [General function prediction only].	2.17493e-31
NC_013739.1\|WP_041731325.1\|460570_462019_-\|type-I-glutamate--ammonia-ligase	gnl\|CDD\|273198	TIGR00653, Glutamine_synthetase, glutamine synthetase, type I. Alternate name: glutamate--ammonia ligase. This model represents the dodecameric form, which can be subdivided into 1-alpha and 1-beta forms. The phylogeny of the 1-alpha and 1-beta forms appears polyphyletic. E. coli, Synechocystis PCC6803, Aquifex aeolicus, and the crenarcheon Sulfolobus acidocaldarius have form 1-beta, while Bacillus subtilis, Thermotoga maritima, and various euryarchaea has form 1-alpha. The 1-beta dodecamer from the crenarcheon Sulfolobus acidocaldarius differs from that in E. coli in that it is not regulated by adenylylation. [Amino acid biosynthesis, Glutamate family].	0
NC_013739.1\|WP_012931933.1\|454327_455290_+\|2,3-dihydroxybiphenyl-1,2-dioxygenase	gnl\|CDD\|274480	TIGR03211, catechol_2_3, catechol 2,3 dioxygenase. Members of this family all are enzymes active as catechol 2,3 dioxygenase (1.13.11.2), although some members have highly significant activity on catechol derivatives such as 3-methylcatechol, 3-chlorocatechol, and 4-chlorocatechol (see Mars, et al.). This enzyme is also called metapyrocatechase, as it performs a meta-cleavage (an extradiol ring cleavage), in contrast to the ortho-cleavage (intradiol ring cleavage)performed by catechol 1,2-dioxygenase (EC 1.13.11.1), also called pyrocatechase. [Energy metabolism, Other].	6.11826e-100
NC_013739.1\|WP_012931949.1\|475322_475580_-\|type-II-toxin-antitoxin-system-Phd/YefM-family-antitoxin	gnl\|CDD\|376852	pfam02604, PhdYeFM_antitox, Antitoxin Phd_YefM, type II toxin-antitoxin system. Members of this family act as antitoxins in type II toxin-antitoxin systems. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin. This domain complexes with Txe toxins containing pfam06769, Fic/DOC toxins containing pfam02661 and YafO toxins containing pfam13957.	6.57687e-06
NC_013739.1\|WP_012931948.1\|474921_475335_-\|PIN-domain-containing-protein	gnl\|CDD\|350300	cd18733, PIN_RfVapC1-like, VapC-like PIN domain of Rickettsia felis VapC1 and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Rickettsia felis VapC1, a ribonuclease toxin of the VapBC toxin/antitoxin (TA) system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC TA systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.	3.25745e-37

>NC_013739.1|WP_012931940.1|463847_465125_+|aspartate-aminotransferase-family-protein
MSEQTRLETLPQGGRGWNDIERDLGSLQAHDPPLIDGTFDLWWPVLPADLQGVARLAHSAFMHANAFFTTAVPSLERIDAELRAMVADVLRVPASGTVTLTGGGTESNFLAVKGARDWARAHRPGIERPRLVLPLTAHPSFDKAADVMDLAVTRVGVRPDWRADPAQIAAALDDDVILVAGSVPQYAHGVVDPIGELASVAAERGIWMHVDACVGGFLHRWVDEVGSGLPPFDFAAVPGVWSVSADLHKFGFCPHGISTLSLREAELAEYHTYHAGTVWPTGGYSRRGFTGSRPASPVVAAWAVMQFLGADGYRGIAREIVALQELFVRRLAAIPALEPVVEPELGVLAVASRDADVGIPDVAEALSRRGWHPARIAEPEGLHLLFGPVPVSMLDRYLADLEDAVADARSGRVRSLQREATYVSE
>NC_013739.1|WP_160165464.1|462743_463781_-|TetR-family-transcriptional-regulator
MPRRPSEQTCAAWLWRRLSDDGRHAYCPRCGADRPFRLRRGDIRYACRVCEMALDPRAGTAFEGSRTPLGTWFVATAMLREDPQLTPTALAAEAGVSYATSWRMLRRLRELPAGAFELRAGLGDEPGREPSTRVSLPSDDLIADPKLTSILRGAATAIVARGFAETRISDIADEAGVSAATVLHHFRTREAVLLAALRWAGAVATMQLSEELDPDASARDWLRKSVGSILPADEEQRAEAVLQLECWNVALHEPELVVHTEDIARRWRATLAELVQHGIDRGEFSTAAPAADVADLIAAALNGLWPKVLLGFEDYPRERCIELAETLLDTLLPAGAARAAPPVAR
>NC_013739.1|WP_012931938.1|462097_462736_+|DUF1211-domain-containing-protein
MTAGEREHEHEVEDEGSVGYERAVAFSDGVFAIAITLLVLGLGVPEVADGELPDALRDLGPQVMSYFIGFAVIGAFWLGHHRFFGVLRRFDSTLLVLNLAFLSFISLMPFTTGLLGRYGGVEAAVVAYAANVIAASAADTAMLWVALRRRLLAPGHGRDPRARLFASFFPGLVFLCSIPVALAAPRAAPYTWLALFLGGPRVARLWARARGR
>NC_013739.1|WP_041731325.1|460570_462019_-|type-I-glutamate--ammonia-ligase
MHSQGAGPDDVAAFAREHDARLVDLKFTDLPGTWQHFAVAARELEEDLLTAGAGFDGSSIRGFQSIDESDMLLVPDPSTAVIDPFHEQPTLSLVCDVRDPATGAPYSRDPRHVARKAERHLAASGVADTAFFGPEAEFYVFDHVAYAQQANRAFYEVDSGEGFWNAGAGFSSNGERLTPNLASRNRSQQGYFPAPPLDTLADLRGRMALTLERMGVVVEVHHHEVGGPGQAEIDLRFLPLLQMADAVQLYKYVVRNVARRAGKTATFMPKPIFAENGSGMHTHQSLWRAGETLMFDADGYGLLSELARHYVGGLLAHAPALLAFSAPTTNSYKRLVPGYEAPVSLLYSQRNRSAAVRVPVYFSSPKSKRVEFRSPDPTANPYLAFAAMLMAGLDGIRHRTEPPDPVDANLYELPPERQQSIRQAPTSLDAVLDALEADRDFLLDGDVFTRDLLDAYVAHKRAEIDEVRLRPHPWEFALYYDS
>NC_013739.1|WP_012931936.1|459170_460583_+|MFS-transporter
MQQQTQQEQDGAAEARRRGRRWWALLVIALAQLMIVLDGTIVNIALPSMQADLGMSDADRQWAITAYALAFGGLLLLGGRISGIFGHRRTFLVSLIGFAGASALGGAATGAPMLVGARVLQGAFAAGMAPAALSLLILTFTDPHDRGRAFGVYGAMGAAGSGVGLLAGGVLTEFLDWRWCLWANVPIAAVALLGLPFVHRDEPAGGAGRLDVPGALLSVSGLAALVYGFGEAGPRGWDDPLVVAMLAASVLLLALFVVAESRAKDPLLPLRVIVDRVRGGAVLTTTLMMAALFGCFLFLSYYAQTVLGYTPVEAGLTVMVLVAGSLTGSLLIAARLLSRVSARTLIVPGLLAMAAGLLLLSRLEADSEHVLALYLVPAQLVIGVGLGVVLTAATSLATAGVQVADTGSASATFNAAQQVGGALGTALFNTVAVVSGFGPALLVSAGIMLAAALVAALLLGARAADPPQLS
>NC_013739.1|WP_012931935.1|456067_458959_+|LuxR-family-transcriptional-regulator
MTRVELFGRAREVAVLAELVAAASAGEGALAWLQGEGGIGKSALVASAADVAREHGMAVLSAGADELERHRPFGVLVDCLGVGGRSDDARHTAVARLLAADATPAPEPDEPNLRGGGELTFGIGEALLALVEELCCEAPALLVLEDLQWADVQSLELLGRLARRAAELPLAVLCTARVAPRRAAVERAVARSLERGARQLVLAPLDAAAADALAARLAGGPPGTNLRARVAACGGNPLFVSVLVDALEAGGAIERSAGGEAEIASAADPVPASLALAVLGRLRALPAETVELLGLASVLGSEFALAELAALTGRPVAALSAPVREALAAGALVERGERLGFGHDVVREALYDDLPRSVRAGLHLEVGRALAAAGADAAAVAEHLVRGAAPGDAEAVAWLERAAREAASRSAGVAAELLEAALELAAPGDPARGRLEAELALSLVAAGRRQDGEALARCVLDDRAYSPGEGALRLALARSLLERGRLFDALAEAGRAAESPGVGAVDRAEALAYATIGSLLAHDLDAAAAEARHAQAVAEEAGATHVVAVSLTRRAHVAGFRGEFAEQERLAARAVAVAVQDGGREVQHASHAHLNHALALADCDRPHDGVAAVAAGRRVYERLGMEETLRNSHHYAGYPLMLAGRWDDALAELETASALSEESDIGWTVDVLATRAVLLARRNELEAARALVDAATQALAAGAPEFRLGWPAWAQALVQEAEGDRDGALETLWSAWTRVGAAGAVGEQRTFAPDLARMLAAAGDAARGAEVAAAVEALARGNPELETIEALALRCRALAGGSGRDGDAAGGGAGDGADALARAAERYPDGPRPHERALAYEDAAVAFVAAGRLDRARAFADEALEAYARLGARRDAARAEGRLRAGGLRRGRRGSRTRATDGWEALTPSERRVAELAAEGLSNPQIAERLVISRHTVATHVSHALAKLGLRSRFELAAARRAE
>NC_013739.1|WP_012931934.1|455337_455967_-|TetR/AcrR-family-transcriptional-regulator
MVTSPRTPPPADDSDWDRKRRDILNGAAEVFFEHGFERGTTKEIAERVGLSQPSIYHYVGAKKELIAEIARQVDRDFTEALERGLRDAADPAEQLRNVIVAFTEALAVNRLTWAVYWQEQRAIPADVAEAVYDSQLQYVRRVDDVVRRCQEAGVLPAEHPTHVLTEAILGMLSWTYRWYKPEGRYGPEELAGAFSDLLGLRAGAAAPQG
>NC_013739.1|WP_012931933.1|454327_455290_+|2,3-dihydroxybiphenyl-1,2-dioxygenase
MTPRLVKLGHIALSTPDLERSLWFFRDVVGLDEVERADGVVHLRAWGEREHHSLSLRAGETGVDHIAWRASAPGDVEAFAARLEAGGVAVERVPAGTEAGQGDAIRFSSPGGHPYEIYFDVDRPPAAEEIRSRLGSSVSRMWRRGMSPRRIDHVNVAARDVDAGTEWLSQQLGMQLREFIRPTGRGIVSSWMAVTSQVHDVALTRELAGRDGRLHHLAYWFDTRDDVMRAADIAVDQGLAIDLGPGMHGVSRGFFCYLRDPGSGHRLELFTGGYQIYDPDWEPVEWTERDIREGLVWWGPEYTPGRGHVFDETTPCGAAA
>NC_013739.1|WP_012931932.1|453099_454293_+|FAD-dependent-oxidoreductase
MTALHAPGARVAIAGGSLAGLSAARTLRAEGFDGELTIVGAEPHLPYERPALSKAALGGAVAPAELAVSLALDLGDLDATWRLGTRAAALDLGARELRLDGGERLAYDGLVVATGAAPRALPGCEVPVHRLRTLEDAAALNAALATGGRLAIVGGGFIGCEVAAGARARGLDVTVIEGAAAPLAAPLGAAVAHALAARLRALGVELRCGRGVSAVSEAGVTLDDGTLLEADHVLVAIGASPATGWLAGSGLVCRDGVVCDSECATAGSRVVAAGDVARWWHPGCGRRVRVEHWEHAELHGAAAARRLLHGPRGVPFAPVPFVASELGPHVLHLAGWPRGGLELLDGALDDGPFAAAWVDGPHVSGVVALDSPRAFRRLRRRLDGGLAAADLHAAAAA
>NC_013739.1|WP_012931931.1|451462_453103_+|long-chain-fatty-acid--CoA-ligase
MTPYQLSIAALLRHGAAIHADSVVRCYDGERVERCTYADVVADAARLAAGLESLGLGPGDRIGVGLWNTREHLAAFLAIPAMGATIHTVNPRLSAEQLTFVLADAEDRLLVLDATMLPAFAGVDLGPVEHVVVVGGVDDAAHAALAALDRPWTPHGALVDGRPETYEWRDGDELDVATLCYTTGTTGEPKGAAYTQRHVVLHSLGECSANTLAISRDDVVMPISPMFHVNAWGLPYTAWLAGADLVLTGRHVQGEHLIRLIEQERPTVAAGVPTILADVLRCGEGRALDLSSLRLLMSGGSPVPRAVVEQFDRRWGVPVTQALGMTENGLLALARPPAGADREEAIGWRSRTGRVIAGVEVRAVAEDGTPLPADGESAGELEVRGWWVVGSYWNGRGADRFRDGWLRTGDVGTVDRSGWIEISDRLKDVIKSGGEWISSVAVEAAAMEHPAVAEAAVIAVPDERWFERPLVCVALRDGARLSPGELRAFLAERLQSWWLPERVAFVAAVPKTSVGKFDKKALRRQLQDGELEIELTRSASDAPARP
>NC_013739.1|WP_012931942.1|467202_468942_+|hydantoinase-B/oxoprolinase-family-protein
MSLDGARLAILASRLDAITRRMTVTLLRSARSTIINAARDFSCCLLTADGRLLAVGESLPIHVLAGTDEVARGLLELDEPVARGDAFLHNSPYHGNSHAADHCILVPVFDDAGSHQFTVLVKAHQADCGNSQPTTYFAGARDVYEEGALIFPWVRVQHEYRMREDVLRMCAMRIRVPEQWHGDFTAALGTARIGERLVAELAADVGWDELSKLADGIVAHGRRSMRAAIAALPAGSASIRTRHDAIPELPEGIELNVGVELLPQEGRVVVDLRDNPDCVPCGLNLTAATARAAATLGVFNGLGAEVAPNAGSLACVEVLLRRGCVVGIPEHPTSCSVATSNLTQRVASAVSCAMADLADGIGLAEAGTGLPPAVAVASGTSPEGTPFVNQLSLALTGGPAAPHADGWLTLAGVETAGMCRLDSVEVDELRYPLRVDQQRLIPDSGGAGRTRGAAAARVELGPVGCDVELAWTSDGTDAPARGARGGAPGSRARQVVVDATGAERPAGISGVFAIRDGERVLADSCGGGGYGDPGERAREEVRRDVAEGLVSAAAAVEAYGLEAVSAPAGLAVAARPFGP
>NC_013739.1|WP_012931943.1|469033_470845_+|ABC-transporter-ATP-binding-protein
MEPSQQREATAVGALDGDPAAGAVVEVRGLSVAFESGARPLRGVDLTLQAGRVTGLVGESGSGKSMLGAATLGMLPGGARADGEARLAGTDMLRSGAEERRLVRLRQAGAVFQDPMTSLDPTMRVGRQVAEVAGSEDAAIEALDLCGIPDARRRAAQYPHELSGGLRQRALIALAVARRPRYVLLDEPTTALDVLVQRGILRLFRSICDELDAAMLFITHDLLVAAEVADRLVVLYGGQVAEEGPVDAVLRDPAHPYTAGLLATRLSARRDVARPVPALPGEPPDVRRRGGACSFAPRCAFAQEPCGEREPASVRRSPQRADACLRFDELQPLSERAAVAHRRAAVAELDELAPVDAPQAAGPTAAALEVTGLRKAFGRGAAKRTVLDGIDLRLDHGSSMAIVGASGCGKTTLLRCVMGLERADAGEVRHAGVPPQLVPQDSGASLTPWMTIGDLLGERLGVGKVPRAERPAAIERALAQVGLPAEVAGRRPRQLSGGQRQRVAIARAIVLPPSVLVCDEPTSALDVSLTATVVNLLHQLRDDLGLAVLFVTHDLGVARSVADEIAVLQDGRVVERGAAPQVLDAPAHAATRELLDAMPEELR
>NC_013739.1|WP_012931944.1|470841_471720_+|ABC-transporter-permease
MSATTAVAPRTAEPAGRGRRIVRRLRRLGLPERFGLAMLAAATLLALLGPLLAPHDPRRPVGEALISPGSEFLLGTDELGRDIFSRVLYGIQITWLSALVVVAAGLLVGGAIGLVAGVRGGRVDNVLMRIVDTGLALPGAVLAIAITVALGASLTTTVISIAAFWWPFYARLVRGEARAIAVLPHVEAARASGIGSVRLALKHVLPGALPPVIVAASLDLGIVVLVLAGLTFIGLGAQPPTPELGAMAALGLDFLFTHAWVPLAPAFAVFLLALSANLGGDGLRDLLEDEDV
>NC_013739.1|WP_012931945.1|471716_473312_+|family-5-extracellular-solute-binding-protein
MTMKLARGVATLLAAALVVAGCGGTSSNNDSTGSTGSGGGTSASFDAEATIRTAQFGDGVGGMDPEIWYDLNGGSLHTAVYEGLLRYKTGTTEIEPALAESYEVSRDGRTYTFKLRQGVRFHDGTPLTPEAVAGSFARRAALRGPSAYLTAGVADVRPRGSDTVVIKLRSPEIGFLDALASIYGPRVISPAALRAHGAGEDGKRWFASNAVGTGPLRLLSFRLGDGATLERFDGYWGEQAKAKRYEVDTLPSSGEQQLQLRSGQLDYLSGGSLQPAQLKAFDGNPRYEVTRLDQAFRPMLVLNTNKPPFDDVEKRKAFVAALDVDAAIRQVWGDELMEAPTSYISPFLLDPALNRIEPLTSDAALDEPVTFEYVGAIQSHRQFSEVIQQQLRDEDVELRLSATTGGEVFSWPQDVQKAPNAAIVTVYGDSAYVQSLVDPFFRTGSAVNFLGYSNRTVDATLDEAAIQTDRDKALQLFADANRIVAVDDASIIPLGDLKQPIVARRGVSGFQGTPTSIDVVQLAAIGKSADA
>NC_013739.1|WP_012931946.1|473311_474316_+|ABC-transporter-permease
MIGLVVSRVAGMLLVVWLLATLVFMLGTVVPGDPARAYAGPGATAEVLADKRAELGLDRPFPERYVDYLGKLATLDLSESVTTRNPVRDDLADRTPATLELALVAALLAIAMGGIVGAATARAKRGSAAIRVLLSAGASVPSFTLGLLLLLVFYGQLDVLPAGGRLSPEHGEFDGATGFLLLDGVLAGRPEITLDAAWHLILPAFCLALTPALLIARVFRSSIHSTLRADHVRTVRASGMPEGRIFRRHVVRNSLNAPLTVTGLTFGVMLGSTAVVELIFGWPGLGLYVSQAIPQSDIPAIAGVTLVVGLAFVLGNALVDIAQTVADPRLRTVR
>NC_013739.1|WP_012931947.1|474347_474932_+|isochorismatase-family-protein
MPLLDRNDSLLAVIDTQPGFYRGRADVDAGAFDAFVGCVAWLAGAARALDVPIVVLEEEPERYGATADAVRANLPAGTVGLPKAQFGLMGNPELRAAVERTGRRTAVLVGMETDVCVAHSAIGLRDAGYRVAVATDALFSPPGAHEHGLSRLRDCGTELLSAKGVLYDWLRTVQASIDFVKDNPDLADPPGFSL
>NC_013739.1|WP_012931948.1|474921_475335_-|PIN-domain-containing-protein
MERLIVDTGVLVALERGRLSPDALPDDADIAIAAITASELLVGVQLADGQRRETRAATVDAILGTFEILAFDLDIAREHAVLLAHARRTGRPRGAHDLQIAATASATGRLVVTTDQRAFDDLPGVRFRLGTAPSIRG
>NC_013739.1|WP_012931949.1|475322_475580_-|type-II-toxin-antitoxin-system-Phd/YefM-family-antitoxin
MTEISATEASKRFADVLDAVEHRGEMFTVLRRGRVVATIAPARRGNGADLRRIMTEHPPDDRWAEDLQDLRRFSGAAPTVDPWND
>NC_013739.1|WP_012931950.1|475613_477266_+|CocE/NonD-family-hydrolase
MRIEVETDVETPARDGTLLRADIYRPAGGGALPTLVRRTPYDKSLAVRTDVDVLRLVRAGYAVVVQDVRGRYASEGRFEPFRTEASDGADAVAWAAAQPWSSGAVGMVGASYEGMTQWLAASAAPPALRAIAPLVTSVDPYDGWAYQGGAFELGFGLLWNAGNLASEPLAQDPRDDFEAAARRRPLRELAPDAGLAGFHRDWLGHPGRDGWWEQLVPPERVGAVAVPALSVGGWYDLFLRGTLAGHSRMRAHANGSRLVVGPWSHMVSGGVFPQRSYGWRAAADAVDLTGLHLRWFDRHLRGVENGVEREPAVRLFVMGADRWRDADDWPLPGTAWTRFHLGGGGALSAEAPGAGGEDAYRYDPRDPVPTAGGATFLPGQDVGACAGPLDQRAVQRRADVLVYRTPPLERDVEVIGPVELVLYVSSSAVDTDFTGKLVDVHPDGRAELLTDGILRARWRESQSTPVPLVPGRVYELRVDLGATANVFRVGHRIGLEISSSNFPRFDRNTNTGGTIADEREEDVAVAVNRVHHGRAHPSHLMLPAIPAAQA
>NC_013739.1|WP_041730025.1|477262_477658_-|hypothetical-protein
MRILVALLAVGTLIALAGCGGDDKPAYCSDRSSLESSVKELANITRNTGLSGLRAQLGEVESDATALVDSAKSDFPEQTSAIRSSVDTLAGAVRSLQANPSAQQAATVATDAAAVVGYVSDFTSASSSECD

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Crispr_ID: NC_013739_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_013739_2

1272898-1272992

Orphan

Consensus_repeat	Method
CGATGCGGCTCGCTCCGGCGAAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_013739_2

>merge|NC_013739|2|1272898-1272992|CRISPRCasFinder
CGATGCGGCTCGCTCCGGCGAAGTCGTCATCGCTGACGATGCGGCTCGCTCCGGCGAAGTCGTCATCGCTGACGATGCGGCTCGCTCCGGCGAAG

>NC_013739|2|2|1272898-1272992|CRISPRCasFinder
CGATGCGGCTCGCTCCGGCGAAG	TCGTCATCGCTGACGATGCGGCTCGCTCCGGCGAAGTCGTCATCGCTGA
CGATGCGGCTCGCTCCGGCGAAG

Protein	Signature genes	Signature genes Name	Protein_function
NC_013739.1\|WP_012932697.1\|1273923_1275324_+\|PLP-dependent-aminotransferase-family-protein	unknown	unknown	gnl\|CDD\|224089
NC_013739.1\|WP_012932692.1\|1269520_1269835_-\|multidrug-efflux-SMR-transporter	unknown	unknown	gnl\|CDD\|224987
NC_013739.1\|WP_012932689.1\|1266345_1266702_+\|GntR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224639
NC_013739.1\|WP_012932687.1\|1265641_1265911_+\|pH-regulation-protein-F	unknown	unknown	gnl\|CDD\|225122
NC_013739.1\|WP_012932703.1\|1282619_1283228_-\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_012932704.1\|1283519_1284389_+\|AraC-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|378964
NC_013739.1\|WP_012932699.1\|1276391_1277441_+\|LLM-class-flavin-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|274646
NC_013739.1\|WP_012932693.1\|1269831_1270449_-\|flavodoxin-family-protein	unknown	unknown	gnl\|CDD\|223728
NC_013739.1\|WP_012932690.1\|1266695_1267661_+\|DUF1648-domain-containing-protein	unknown	unknown	gnl\|CDD\|377929
NC_013739.1\|WP_041731715.1\|1284491_1284896_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|319943
NC_013739.1\|WP_012932698.1\|1275375_1276290_-\|branched-chain-amino-acid-transaminase	unknown	unknown	gnl\|CDD\|235841
NC_013739.1\|WP_012932702.1\|1279807_1282465_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|367875
NC_013739.1\|WP_012932696.1\|1273223_1273898_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|366102
NC_013739.1\|WP_012932700.1\|1277437_1278904_+\|glucose-6-phosphate-dehydrogenase	unknown	unknown	gnl\|CDD\|237234
NC_013739.1\|WP_012932701.1\|1279112_1279793_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|367875
NC_013739.1\|WP_012932691.1\|1267657_1269421_-\|EAL-domain-containing-protein	unknown	unknown	gnl\|CDD\|182070
NC_013739.1\|WP_012932686.1\|1265120_1265642_+\|Na+/H+-antiporter-subunit-E	unknown	unknown	gnl\|CDD\|376653
NC_013739.1\|WP_012932685.1\|1263708_1265124_+\|oxidoreductase	unknown	unknown	gnl\|CDD\|237163
NC_013739.1\|WP_012932688.1\|1265907_1266267_+\|monovalent-cation/proton-antiporter-subunit-MnhG/PhaG	unknown	unknown	gnl\|CDD\|237169
NC_013739.1\|WP_012932694.1\|1270662_1271151_+\|MarR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224759

Protein	Function_ID	Function_description	E-value
NC_013739.1\|WP_012932697.1\|1273923_1275324_+\|PLP-dependent-aminotransferase-family-protein	gnl\|CDD\|224089	COG1167, ARO8, Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism].	3.98631e-81
NC_013739.1\|WP_012932692.1\|1269520_1269835_-\|multidrug-efflux-SMR-transporter	gnl\|CDD\|224987	COG2076, EmrE, Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism].	5.90804e-24
NC_013739.1\|WP_012932689.1\|1266345_1266702_+\|GntR-family-transcriptional-regulator	gnl\|CDD\|224639	COG1725, COG1725, Predicted transcriptional regulators [Transcription].	1.70718e-23
NC_013739.1\|WP_012932687.1\|1265641_1265911_+\|pH-regulation-protein-F	gnl\|CDD\|225122	COG2212, MnhF, Multisubunit Na+/H+ antiporter, MnhF subunit [Inorganic ion transport and metabolism].	6.39745e-06
NC_013739.1\|WP_012932704.1\|1283519_1284389_+\|AraC-family-transcriptional-regulator	gnl\|CDD\|378964	pfam12833, HTH_18, Helix-turn-helix domain.	1.04978e-17
NC_013739.1\|WP_012932699.1\|1276391_1277441_+\|LLM-class-flavin-dependent-oxidoreductase	gnl\|CDD\|274646	TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1. The Pfam domain family pfam00296 is named for luciferase-like monooxygenases, but the family also contains several coenzyme F420-dependent enzymes. This protein family represents a well-resolved clade within family pfam00296 and shows no restriction to coenzyme F420-positive species, unlike some other clades within pfam00296. [Unknown function, Enzymes of unknown specificity].	6.34345e-146
NC_013739.1\|WP_012932693.1\|1269831_1270449_-\|flavodoxin-family-protein	gnl\|CDD\|223728	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only].	1.60618e-30
NC_013739.1\|WP_012932690.1\|1266695_1267661_+\|DUF1648-domain-containing-protein	gnl\|CDD\|377929	pfam07853, DUF1648, Protein of unknown function (DUF1648). Members of this family are hypothetical proteins expressed by either bacterial or archaeal species. Some of these are annotated as being transmembrane proteins, and in fact many of these sequences contain a high proportion of hydrophobic residues.	0.000359743
NC_013739.1\|WP_041731715.1\|1284491_1284896_+\|hypothetical-protein	gnl\|CDD\|319943	cd08355, TioX_like, Micromonospora sp. TioX and similar proteins. Micromonospora sp. TioX is encoded by a gene of the thiocoraline biosynthetic gene cluster. Thiocoraline is a thiodepsipeptide with potent antitumor activity. TioX may be involved in thiocoraline resistance or secretion. TioX belongs to vicinal oxygen chelate (VOC) superfamily that is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.	4.32376e-53
NC_013739.1\|WP_012932698.1\|1275375_1276290_-\|branched-chain-amino-acid-transaminase	gnl\|CDD\|235841	PRK06606, PRK06606, branched-chain amino acid transaminase.	6.75113e-170
NC_013739.1\|WP_012932702.1\|1279807_1282465_+\|hypothetical-protein	gnl\|CDD\|367875	pfam04213, HtaA, Htaa. This domain is found in HtaA, a secreted protein implicated in iron acquisition and transport.	3.63084e-11
NC_013739.1\|WP_012932696.1\|1273223_1273898_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|366102	pfam00440, TetR_N, Bacterial regulatory proteins, tetR family.	5.13394e-12
NC_013739.1\|WP_012932700.1\|1277437_1278904_+\|glucose-6-phosphate-dehydrogenase	gnl\|CDD\|237234	PRK12854, PRK12854, glucose-6-phosphate 1-dehydrogenase; Provisional.	0
NC_013739.1\|WP_012932701.1\|1279112_1279793_+\|hypothetical-protein	gnl\|CDD\|367875	pfam04213, HtaA, Htaa. This domain is found in HtaA, a secreted protein implicated in iron acquisition and transport.	5.16259e-12
NC_013739.1\|WP_012932691.1\|1267657_1269421_-\|EAL-domain-containing-protein	gnl\|CDD\|182070	PRK09776, PRK09776, putative diguanylate cyclase; Provisional.	4.54421e-86
NC_013739.1\|WP_012932686.1\|1265120_1265642_+\|Na+/H+-antiporter-subunit-E	gnl\|CDD\|376653	pfam01899, MNHE, Na+/H+ ion antiporter subunit. Subunit of a Na+/H+ Prokaryotic antiporter complex.	2.21676e-28
NC_013739.1\|WP_012932685.1\|1263708_1265124_+\|oxidoreductase	gnl\|CDD\|237163	PRK12663, PRK12663, Na+/H+ antiporter subunit D.	2.57829e-83
NC_013739.1\|WP_012932688.1\|1265907_1266267_+\|monovalent-cation/proton-antiporter-subunit-MnhG/PhaG	gnl\|CDD\|237169	PRK12674, PRK12674, putative monovalent cation/H+ antiporter subunit G; Reviewed.	2.23522e-16
NC_013739.1\|WP_012932694.1\|1270662_1271151_+\|MarR-family-transcriptional-regulator	gnl\|CDD\|224759	COG1846, MarR, Transcriptional regulators [Transcription].	1.00658e-12

>NC_013739.1|WP_012932694.1|1270662_1271151_+|MarR-family-transcriptional-regulator
MAEGGVAGPFSSNLCWLLARGYYTLTTEIAAELQAVDLTPRMHEVLAAAAGGDRTQTELVRMIGLDKTTMVVTLDELEAAGLAERRPSRTDRRARVIGVTRAGRRKLVQADEIIHRVHADVLSVLPARDRRVFMASLKTLIGGRLAEPVASAPTVRRRAVRA
>NC_013739.1|WP_012932693.1|1269831_1270449_-|flavodoxin-family-protein
MPAPHSQISVAIAFHSATGHTARQAAAVAAGAAAVADASAALVRLDMLADDDWTTLDEADAIVFGSPTHMGAPSAPFTAFAAATQGRWLEDRWRDKVAAGFTNSGTIAGDKLNTLQTFSILAAQHGMIWVGLDLKAGWATSDGSPDELNRLGSWLGAMSHSPLDLDAAAAPRDSDLRTAEHLGRRVARLALELRRGRTPAAEVVA
>NC_013739.1|WP_012932692.1|1269520_1269835_-|multidrug-efflux-SMR-transporter
MSWVYLLLAGAVEVVWSQSLKPTDGFTRLGPSIVALVLGGTAVYLLTLALRDLPTGTGYAVFTGIGTIGAVSLGIALHDDPVTAGRLGAIALIVAGVLTARVTA
>NC_013739.1|WP_012932691.1|1267657_1269421_-|EAL-domain-containing-protein
MILLLPVIALLAGTALLGARRLHRRSIRRAESNLRTIFDTAPIGNAVLDDGDRVVVANPALARIVGFTPEELRGRTLAELVHPEDLPRLSGAIAALRAGERRGLETEIRCLHATGQPVPAAVHAAALRDTDGGRSRVLVQVLDITERKRVEAHLQHMADHDPLTGLLNRRRFEQELERHVAHVRRYGPEGAVLVVDVDRFKQVNDAYGHTAGDRVIASVARVLHRRLRSTDTVARIGGDEFAVLLPKADRAEAEIVARRLVEAVRAQADPGDGERTHVTISVGATVLDERSELSAEAAVVDADLAMYDAKDSGGDGFAFFEADVHARSRSRARTTWRDRIVDALAHDRFALVAQPVVDATSGVVVQHELLLRLTGSHGDLIPPAAFLSIAERDGLIVAIDSWVARRAIGLLAELERSGTATPLEVNVSGRSLADTDLLAAIAGELRRTGVDPRNLVFEIPETAAVADIQLARAFAQQVRALGCRFAIDDFGAGLGSLYYLKHLPFDMLKLDGELVEQCSRTVADRLVIESAVNVAHGLGAVAIAEQVGDAETHALLTGLGVDLIQGHHIAMPQPLAVAFGELSPEAV
>NC_013739.1|WP_012932690.1|1266695_1267661_+|DUF1648-domain-containing-protein
MLKRFVLLLGGPLAALTAVAAAIATAGGLPNPIATHWDAGGTPDGHTPPVAFAGGLLLLCLLAWGVLLLQARRRGPAGLRLTAAPSVWATIAFLCGIAVVTFGANAGAASWREAGDMTLGTLLAVVGASAAAGLVAWALERGRPVAPERTVHAVAPIALAAGEQVVWSRSLASRPAAIGCVAIGGGMAVAGLFVGGAAGWGLVAGGIATAVLLSALSEIVATVDASGLTIAYGPLGWPRQTVPLADVASAERTEIDPWSVGGWGYRKAGSGKTAVVLRGGEGLRVVRQDGRELLVTVPDAATAAGLLTALRGRAGVPGRAA
>NC_013739.1|WP_012932689.1|1266345_1266702_+|GntR-family-transcriptional-regulator
MLIRIDPARAVPLHEQIDAGVRAAIAAGDVADGERLPAARELARSLDVNVHTVLRAYATLRDDGLIELRRGRGAVVRADDVARRRLAVVALAQDLVAHARRHGVSDADVVRMVQEAQC
>NC_013739.1|WP_012932688.1|1265907_1266267_+|monovalent-cation/proton-antiporter-subunit-MnhG/PhaG
MTLVLAALPGAIDLALEVLGVALIALGIVVTGVTVYGVVRMRGLYPRLQAASKASMLGAVAILAASVGTRDGATIGRALVVSLFLLLTTPIAAHAIAQAAYRRDREREGEAGEAEPEEE
>NC_013739.1|WP_012932687.1|1265641_1265911_+|pH-regulation-protein-F
MPEIVIVVALVCVTGMLAIGAAVLLRARDVLERIVALDLLTVICVALLALLTYLRDVSYYLDAALALAALSFVATLAAVRSERGGGPFR
>NC_013739.1|WP_012932686.1|1265120_1265642_+|Na+/H+-antiporter-subunit-E
MSGFAKRVLAVAVLLAIYLLTLGSLALGDVAVGLVLAVLMELGWRRRVLRGGTVADPATPPGVPLRRALLALPRLVLAVVAEITRGTWEVAKYSLGIREPVHEGTVEIELEGISEEGVAAWAFISTISPGELVLDVDEERGVLVIHALDASDPEAIRRRHHDFYERYQRKVIP
>NC_013739.1|WP_012932685.1|1263708_1265124_+|oxidoreductase
MTIAIALLIPWVAGVLLLLADGRRRSWGWFAVAAMAGNLAALVVLAVKVLPDGSERVVTGGWEGGVGIVLEADPLGVAFALVSSLVVLAALVHEVLDGVRSRTFPALVVLLATGLTGLFLTGDVFNFYVFFELAMIAAYVLTAYGDDRHQLGAALIFAVVNLVGSFLFLIAVAATYHVTGTLEMAGIATRMSDVEPNAAILIAVTFFVAFGTKLGLFPFHFWLPAVYAGTRPAVAAILSGALANIGAYGLLRFGAGLLPEELELGSTVLIVIGSASVIYGALLAVSRRDPAEMLAYSAIGQAGYVLVALGVGGPVGLAAAVLYAILNALSKALLFLSAGLRGALVAGAFAVGALSLAGMPPAAGFVGKLALFRTGVDAGSVALVVLLFVGGALSFVYAFQLYQHEFWRGSRVRPGGADAEATGAPVPASNPVGVRLVSVALALLVLALGLWPEPLLSLSSDAAAVLHGGAP
>NC_013739.1|WP_012932696.1|1273223_1273898_+|helix-turn-helix-transcriptional-regulator
MDRGSLDHSPAAAAPSQPRRGGGVSAVELPVVGAAPPERADAARNRRRIVAAAEALFAERGVGDVTVAEVAARAGVGKATVFRRFGDKAALLDALLGERERELQEAVLRGPAPLGPGAPPRERLLAFFAALTDFCERHRHVLLASETARAGARYTTGAYVAWHQHVAVLLAELRPELDAVLLADLLLAPFSAELLAHLRDGRGIPRERLERTLAALAQSVVAGA
>NC_013739.1|WP_012932697.1|1273923_1275324_+|PLP-dependent-aminotransferase-family-protein
MSDVTRLTAQLGAWRERHGSLAERLAAALAAVIERGGLDGRRLPAERRLAEALDVSRATVVHAYAELRERRLVASRERSGTVVRSVGRHGRAPGTQLPQLSRLLAPDAQRIDLAVAAPQLDDLVAGIRVELGHAAGLMQPHGYDPQGIGALREAIAQRLTHDGLAATADEVLITSGAHEALALIAALFVGRGQPVAVDAPTYPGALELFERAGGRPVTVAGDAAGMRPDALQALLARTVVALLYLMPGCHSPTGASIALGRRPALLRVAADHELLVVEDAALDKLRFDGPLPSLPSLVPERVLRVGSLDKLAWAGLRIGWICGPRAAIGRLTRLKAARDLGTGVLGQLAALHLLRDVDTLRRARVAQAQARMRHLHGELSRRLPDWRIAQPEGGWSLWAELPPRVGADGDALVAAAARHGVDVAAGRAHVAGGPRVDAVRIAYAAPESLLTLGAARLQAAWGELTT
>NC_013739.1|WP_012932698.1|1275375_1276290_-|branched-chain-amino-acid-transaminase
MQPTEQIWMSGRFVPWAEANVHVLTHGLHYGTGVFDSLRVYATPSGPALVHHRSHHERLRDSAKLYGMELPFSVDELVDATRTLVRTCGLSESYVRTIAFRGSGAMGVSPRSSPVEVAIATWGWGAYLGEDAMTRGIRAKVSSWRRIGHGTHLPGAKATAHYLNSVLARVEAEELGFDEAILLDDDGLLAEGSGENLFLVRDGTLLTPSLASGALGGITRLAVLELAAALSIPVAERPLTRGELYLADELFMTGTAAEITPVREVDGRPIGSGARGPVTQAVQQAYDDAVHGRDSRFAHWLDVL
>NC_013739.1|WP_012932699.1|1276391_1277441_+|LLM-class-flavin-dependent-oxidoreductase
MRISVLDQSPISEGSNGTEALHNTLDLARTADRLGFHRYWVAEHHGGPMLAGPSPEVLIGPIASATERIRVGSGGVMLPHYSPLKVAENFSMLAGLFPNRIDLGIGRAPGTDGHTMLALQRDRRQAAPDDFPQQLAELLGYFEDALPHGHPFARYAKWLPGRPGRPEPWLLGSSAQSALWAAELGLPYSFADFINPQGAEIARDYHARFQPSRRRESPEVSVGVWAIAAETDEEAQLLATSARMSMTLLRQGRLIEIPPVEKAVRFLESQGSPIEGRPAGRRTIVGTPERVREQIEQVGAEYDADEAIVVTITHDHDARRRSYELIAEAFELDAGDTVADVPDRASALR
>NC_013739.1|WP_012932700.1|1277437_1278904_+|glucose-6-phosphate-dehydrogenase
MSTTVAPSPITRRLPAPDDHVIVLFGATGDLAKRKLFPGLFHLFAAGLMPEEFRIIGSGRHSPGSDDDFREQVRAALAEFGRREVRDEIWEAFSRRLSFTVSSADDGAELADAVREAEEEVGCGTRRLLYLSVPPGAMQPMVRMLGTSGLAAGARLILEKPFGTDLASARELNAVLAEVVEEDQIFRIDHFLGKEAAQNILAFRFANGLFEPAWNRNHIAYVQIDVPEALTVEGRAGFYEQTGAFRDMVVTHLFQLLGFVALEPPVRLTAKALHDEKAKVFEAMRPLRAEHAVFGQYEGYRDEAGIDGASRVETFAALAVRLDTWRWEGVPFLLRTGKALAEGRRSITIGFKEPPLRMFADDGDFAHCQRPNELIFELSDTPQITVDVRAKVPGPTMELGAAALRLDFDDTFPRGSGLEAYERLVLDVMRGDHTLFTRSDEIERLWEVSDPLLRDPPPPQLYPRGSWGPEAANALAAPRGWRLQQRPC
>NC_013739.1|WP_012932701.1|1279112_1279793_+|hypothetical-protein
MQRGIGGRTRGLLAMVVALMALVALPAVASAGTATSGSGVQFQRESFMRYMYGLGFGGTVTGTGTGTFARNTAAYDDDTLTYTFDGTNTTYNITRGGGSGTLALSGGISYQMPAHYIDVSVSDPRVAITSTTASAAVISAVVSYDPLESGTQIRNPTTPTRIDVFRVNLGSAGVFSGGGTRTHTWTRAPAVLTADGARAFNGGGNGSYSDGSAFGFWTLSGTTPAF
>NC_013739.1|WP_012932702.1|1279807_1282465_+|hypothetical-protein
MLRRLLLARARRGTALLTTSTALALLVSAGAADASIPFDLGAYDGAALRFGAPFGESAGARVAGDCELSGDGRPDVAIAAADATTGAGANAGRVYVVPGSASRTPGSYALSGSGTPAGAIVIEGAAAADFAGAELACAGDVNADGSDDLVIAAPGAGDFGAAYVVFGGAQLAGAGTVDLAALGAHGFAITGPADTLLGRSVAGVGDLDGDGYDEIAVGDEWGDEHSNTWPGTVYVVAGRRTTTAVDLTQPGSTLLRIHGAADNDRLNFVARAGDVNRDGTPDLVVGAAEHDGPHGVDSGAAYVIDGRARGNVEVGGWATPGSGVLFPIWSPAAARLDGTRTLFGSDLAPAGDVNGDGRADLALGLTGASASGPVRGRVAIVYGKSGDDAVDLDDPGASAALIRGLPASSDDGFGTSGLASAGDVNGDGRGDLVVGAPGVAAPSGENAGAAYLLYGTASTATREVANLTCEGGARLHGGALGDALGVSAGAAGNGFTSANAPTLLVGAGRGFVRAIPLTDLPNACGRDRGRDPDPEPTALDVDWGFRENFRRYVSDGFNPAAPAVPISAANGATCDANPDPVRGGCDPLLRASRGDPLRQRALRWTSVGASATDGTDATVGAIGRVTFRFPGHFFTLNLEDPWFVVSGGQVTVRARVDLDVADGFAGARSVDVRVNLGTFPLGGAPVVRPQYVVWRTQPGTLTDEAAVALGGFLGRGAELDPITIAIPRSLGPLPAEPGVPDPPRPPYDPPRTPDQPRTPVKTGPPKTGPRTPATVTAGRRRATVRRAGRVTVATIRCAAAAGADCRVSVPASVRLRAGRARVALRVTAPKRIARGKRAAVRLTLTRAALRALAGRRATVRLPIAVRAGSRRMTKTVTVVLKVPRG
>NC_013739.1|WP_012932703.1|1282619_1283228_-|hypothetical-protein
MATQTTLIPTADPSDARLHMPEQTPSPEPHDDAVVNDPGTTPVIPVAGLAQHLLATILCFVQNGYAIEDDISGETIAGIEHYADLLDLDNPRPLSSVEQHALAQVSVELSTGAVAGLGGRSFDGIDAFGLLGVFEAFTPPRHHDLEAATRTLVERKRDDTAVSGGTGRATERAIKATGLIAQHVYDVHGRFPATVPAAYAGT
>NC_013739.1|WP_012932704.1|1283519_1284389_+|AraC-family-transcriptional-regulator
MTAPAIQVERHASLLGRWEMAFRAPWPELAPIVQHYVGWDETTPGPLRRRELPIGAIPVIISFGPSFELLDPHDEEHGPRRRRVSFVAGLHDAFSVVEHQGVSRGVEIYFTPLGARRFFGLPLGEVAQQVVELEDVLGTRIAAELVERLATAPGWAERFALLDATIVGRLAEAAEPPASVAWAWRRLTETDGRLPIAALAQEIGCSRRHLVAQMREQVGLPPKTIARVLRFNRAVELLQRDDGARFAEIAVDCGYYDQAHLNRDFRAFAGDAPTAFLARRLPGSAGYAG
>NC_013739.1|WP_041731715.1|1284491_1284896_+|hypothetical-protein
MATPAIVPVLNFRGGAATIDWLCDAFGFERAMVVQGDDDYVHHAELTLGGAMVMGGSERGEQRSEYAKIAHPAGTAMLYVALEEDLRVHCERARRAGAEIVMELADKEHGSDYTARDPEGNLWTFGRYVPEVPA

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Crispr_ID: NC_013739_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_013739_3

1472591-1472811

Orphan

Consensus_repeat	Method
CCGCTGGCGGGGCTGACGAACCT	CRISPRCasFinder

3 spacers

The CRISPR arrays of NC_013739_3

>merge|NC_013739|3|1472591-1472811|CRISPRCasFinder
CCGCTGGCGGGGCTGACGAACCTCACGTCGCTGCACCTGCAGAGCGGCAAGGCGCGCAACCTGAGACCGCTGGCGGGTCTGACGAACCTGGCGGCCCTCACGGTGCAGGGCCAGGGCGTGACCAATCCGACGCCGCTGGCGTCGCTGACGAACCTGACGTCGCTGAACCTGACCAACAACGCGATCAGCGATGCCAGCCGGCTGCCGCAGCTGCTGAACCT

>NC_013739|3|3|1472591-1472811|CRISPRCasFinder
CCGCTGGCGGGGCTGACGAACCT	CACGTCGCTGCACCTGCAGAGCGGCAAGGCGCGCAACCTGAGA
CCGCTGGCGGGTCTGACGAACCT	GGCGGCCCTCACGGTGCAGGGCCAGGGCGTGACCAATCCGACG
CCGCTGGCGTCGCTGACGAACCT	GACGTCGCTGAACCTGACCAACAACGCGATCAGCGATGCCAGC
CGGCTGCCGCAGCTGCTGAACCT

Protein	Signature genes	Signature genes Name	Protein_function
NC_013739.1\|WP_049793197.1\|1480138_1481290_-\|HAMP-domain-containing-histidine-kinase	unknown	unknown	gnl\|CDD\|223715
NC_013739.1\|WP_148260920.1\|1466971_1468108_-\|acyl-CoA-desaturase	unknown	unknown	gnl\|CDD\|239583
NC_013739.1\|WP_012932892.1\|1482064_1483105_+\|alpha-keto-acid-dehydrogenase	unknown	unknown	gnl\|CDD\|240661
NC_013739.1\|WP_012932885.1\|1476738_1477101_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226318
NC_013739.1\|WP_049793196.1\|1478501_1479398_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|223656
NC_013739.1\|WP_041730208.1\|1481282_1481978_-\|response-regulator-transcription-factor	unknown	unknown	gnl\|CDD\|223816
NC_013739.1\|WP_012932878.1\|1464746_1466756_+\|PKD-domain-containing-protein	unknown	unknown	gnl\|CDD\|238084
NC_013739.1\|WP_041730204.1\|1464134_1464338_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|227721
NC_013739.1\|WP_049793194.1\|1470256_1472005_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|376421
NC_013739.1\|WP_012932880.1\|1468065_1469157_-\|ferredoxin-reductase	unknown	unknown	gnl\|CDD\|99812
NC_013739.1\|WP_012932877.1\|1464491_1464668_+\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_012932889.1\|1479428_1480142_-\|FadR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|225097
NC_013739.1\|WP_012932873.1\|1460916_1461189_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|376540
NC_013739.1\|WP_148261263.1\|1477114_1477660_-\|dihydrofolate-reductase	unknown	unknown	gnl\|CDD\|223340
NC_013739.1\|WP_012932876.1\|1462133_1464062_+\|endopygalactorunase	unknown	unknown	gnl\|CDD\|227721
NC_013739.1\|WP_012932874.1\|1461185_1461530_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|227054
NC_013739.1\|WP_012932893.1\|1483097_1484138_+\|D-alanine--(R)-lactate-ligase	unknown	unknown	gnl\|CDD\|184750
NC_013739.1\|WP_012932887.1\|1477800_1478550_+\|glucose-1-dehydrogenase	unknown	unknown	gnl\|CDD\|235816
NC_013739.1\|WP_012932884.1\|1475998_1476721_+\|dihydrofolate-reductase	unknown	unknown	gnl\|CDD\|223340
NC_013739.1\|WP_012932881.1\|1469392_1469965_+\|collagen-like-protein	unknown	unknown	gnl\|CDD\|189968

Protein	Function_ID	Function_description	E-value
NC_013739.1\|WP_148260920.1\|1466971_1468108_-\|acyl-CoA-desaturase	gnl\|CDD\|239583	cd03506, Delta6-FADS-like, The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases are required for the synthesis of highly unsaturated fatty acids (HUFAs), which are mainly esterified into phospholipids and contribute to maintaining membrane fluidity. While HUFAs may be required for cold tolerance in bacteria, plants and fish, the primary role of HUFAs in mammals is cell signaling. These enzymes are described as front-end desaturases because they introduce a double bond between the pre-exiting double bond and the carboxyl (front) end of the fatty acid. Various substrates are involved, with both acyl-coenzyme A (CoA) and acyl-lipid desaturases present in this CD. Acyl-lipid desaturases are localized in the membranes of cyanobacterial thylakoid, plant endoplasmic reticulum (ER), and plastid; and acyl-CoA desaturases are present in ER membrane. ER-bound plant acyl-lipid desaturases and acyl-CoA desaturases require cytochrome b5 as an electron donor. Most of the eukaryotic desaturase domains have an adjacent N-terminal cytochrome b5-like domain. This domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain the residues: HXXXH, HXX(X)HH, and Q/HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homolog, stearoyl CoA desaturase.	7.84115e-50
NC_013739.1\|WP_012932892.1\|1482064_1483105_+\|alpha-keto-acid-dehydrogenase	gnl\|CDD\|240661	cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and (R)-2-Hydroxyglutarate Dehydrogenase-like proteins, NAD-binding and catalytic domains. This group contains various putative dehydrogenases related to D-lactate dehydrogenase (LDH), (R)-2-hydroxyglutarate dehydrogenase (HGDH), and related enzymes, members of the 2-hydroxyacid dehydrogenases family. LDH catalyzes the interconversion of pyruvate and lactate, and HGDH catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. Despite often low sequence identity within this 2-hydroxyacid dehydrogenase family, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain.	1.63447e-169
NC_013739.1\|WP_012932885.1\|1476738_1477101_+\|hypothetical-protein	gnl\|CDD\|226318	COG3795, COG3795, Uncharacterized protein conserved in bacteria [Function unknown].	1.37507e-27
NC_013739.1\|WP_049793197.1\|1480138_1481290_-\|HAMP-domain-containing-histidine-kinase	gnl\|CDD\|223715	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms].	1.20928e-44
NC_013739.1\|WP_041730208.1\|1481282_1481978_-\|response-regulator-transcription-factor	gnl\|CDD\|223816	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription].	4.23702e-64
NC_013739.1\|WP_012932878.1\|1464746_1466756_+\|PKD-domain-containing-protein	gnl\|CDD\|238084	cd00146, PKD, polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.	1.46046e-08
NC_013739.1\|WP_041730204.1\|1464134_1464338_+\|hypothetical-protein	gnl\|CDD\|227721	COG5434, PGU1, Endopygalactorunase [Cell envelope biogenesis, outer membrane].	0.00276674
NC_013739.1\|WP_049793194.1\|1470256_1472005_+\|hypothetical-protein	gnl\|CDD\|376421	pfam00932, LTD, Lamin Tail Domain. The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated hydrolases of the metallo-beta-lactamase,synaptojanin, and calcineurin-like phosphoesterase superfamilies.	3.39495e-12
NC_013739.1\|WP_012932880.1\|1468065_1469157_-\|ferredoxin-reductase	gnl\|CDD\|99812	cd06216, FNR_iron_sulfur_binding_2, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.	1.09833e-103
NC_013739.1\|WP_049793196.1\|1478501_1479398_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|223656	COG0583, LysR, Transcriptional regulator [Transcription].	3.12101e-29
NC_013739.1\|WP_012932889.1\|1479428_1480142_-\|FadR-family-transcriptional-regulator	gnl\|CDD\|225097	COG2186, FadR, Transcriptional regulators [Transcription].	5.92801e-41
NC_013739.1\|WP_012932873.1\|1460916_1461189_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|376540	pfam01381, HTH_3, Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within Neisseria gonorrhoeae NGO_0477, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family.	7.7255e-10
NC_013739.1\|WP_148261263.1\|1477114_1477660_-\|dihydrofolate-reductase	gnl\|CDD\|223340	COG0262, FolA, Dihydrofolate reductase [Coenzyme metabolism].	2.52741e-19
NC_013739.1\|WP_012932876.1\|1462133_1464062_+\|endopygalactorunase	gnl\|CDD\|227721	COG5434, PGU1, Endopygalactorunase [Cell envelope biogenesis, outer membrane].	7.21957e-15
NC_013739.1\|WP_012932874.1\|1461185_1461530_+\|hypothetical-protein	gnl\|CDD\|227054	COG4710, COG4710, Predicted DNA-binding protein with an HTH domain [General function prediction only].	0.00408421
NC_013739.1\|WP_012932893.1\|1483097_1484138_+\|D-alanine--(R)-lactate-ligase	gnl\|CDD\|184750	PRK14568, vanB, D-alanine--D-lactate ligase; Provisional.	0
NC_013739.1\|WP_012932887.1\|1477800_1478550_+\|glucose-1-dehydrogenase	gnl\|CDD\|235816	PRK06500, PRK06500, SDR family oxidoreductase.	1.35424e-77
NC_013739.1\|WP_012932884.1\|1475998_1476721_+\|dihydrofolate-reductase	gnl\|CDD\|223340	COG0262, FolA, Dihydrofolate reductase [Coenzyme metabolism].	1.93942e-19
NC_013739.1\|WP_012932881.1\|1469392_1469965_+\|collagen-like-protein	gnl\|CDD\|189968	pfam01391, Collagen, Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxy-proline. Collagens are post translationally modified by proline hydroxylase to form the hydroxy-proline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure. The family includes bacterial collagen-like triple-helix repeat proteins.	0.000451937

>NC_013739.1|WP_049793194.1|1470256_1472005_+|hypothetical-protein
MAATAAAACAVLAVGVAPASAVTTRLTDVKINEVESNGDAVHGDWIELYNTGRVVNDEVDLSGVILSDSDNTHRVLIPARTFLGVGEWAAFRVDDPAVSGNFGLGAADSARLFPAGTVNLGSTTPADSYSWTAHAATTYGRNPDGTGTFQTTAAATFGDANDFGLPSIGNITGIKLNEVESNGDATNGDWAELYNTTGSAINIDGAIITDSDPAHQFVIPSSTPDLPAGGYVAFRVDDPAVAGNFGLGAADAVKLYAPNDVTLSRVVDQVTWSSHATITWGRTVAGAGSWAQTSVSTFGAVNQFSGVTAPNLTGVVVNEAESHGDDTNGDWIELKNTTGTRVNLDDAILSDNDNSHVFRIPAATPDLAAGAVAAFRVDDPALGDGQFGLGDADSARLFRADAVDLAAAPAVSRQSWSTHALQTLGLNGSGVFAATNKGTFAAANDFTSTVTPDISYVVLNEVVSTGDVTNGDWVELYNTSGVTIDIGGAIIADSTNANTYTIPARTTIAAGRTFVLRTEATAGFGLGSDDAVRLYRAGGTVGTSIPVDHFEWSQHAAGSYARQSSGLGIWTVDATPSYDAAN
>NC_013739.1|WP_012932881.1|1469392_1469965_+|collagen-like-protein
MAPGRHRWAGRGPRERLRGDHGPGFVDVPMSGTGGGASAGPQGDPGPQGAPGQQGVAGAQGAPGADGGQGPRGTPGANGSQGPQGTAGQAGAVGPTGPAGPTGPAGKAGRDARVTCTTETVKRKPKTTCKVTYPPSARQPRSATARLTRGGRTYAAGSATRLTGTRKLPRGTYALRVTHGGRTMTATVKL
>NC_013739.1|WP_012932880.1|1468065_1469157_-|ferredoxin-reductase
MRVFAEHRRRARGRLWDAASLLTTPLLPDDFLGLVNPLWSRRQLAGRVVAVRHETADSATIAIRPGAGWRDHRAGQHVTVGVEVDGVRHQRSYSLTSPPRAADGCIAITVKAVRDGVVSSHLVRRTSPGAVVYLGEATGDFVLPDDDSERLLFITAGSGVTPVMGMLRTLARSNAPRDVTVVHIDREPDSVIFASELRRLAGQRRLALHEHHTSRLGRPSAATIVGLVRDWRQRETWACGPGELLDGLEAHFAASGARSRLRTERFQSSVAAGAGAAAAPGGSVTFTRSGVTVNADGATTLLAAGEAAGALLPSGCRAGVCRTCVGPLRAGFVRDLRTGAVGAPGDMVQTCVSVAAGPVEIEL
>NC_013739.1|WP_148260920.1|1466971_1468108_-|acyl-CoA-desaturase
MRVRRGRAGRDRAVTPPAQETPVLDPDAANPLDRLTPDDLDAIARELDAIRDAVRADLGERDAAYIRRVVSVQRTLEASARILLIAGRSRPAVASGTALLTVAKILENMEIGHNVMHGQWDWMRDPRIHSATWEWDAVSTAQSWKHAHNYQHHTFTNVVGKDRDLGYSAIRVHPDQPWHPAYLLQPLYAVALAFVFEWAIAIYDMELDAVRNGTKPASQARREVRAFMRKAGRQFAKDYVLFPALSGRSARRTALANLTANVLRSVWTHTIVFMGHLPEGAETFSEEQLEDESRGGWYVRQLLGSCNLDGSRLFHLMSGHLSFQIEHHLFPDLPSNRYPEIAPRVRAVCERHGLPYASGRLGRQYRSVAKKVLRFALP
>NC_013739.1|WP_012932878.1|1464746_1466756_+|PKD-domain-containing-protein
MRRLRSAAVAALTAVAAAAGAASAQAAWLPGPTYGDGGLAGLVGIGADASGATTVAWLQRTGAFDDPSQVRVQRISSGGAAGTARTVGMAGGPVGSVPSSASVAVARSGAAVVAWVTPDGDAQLVALGADGAPGPIRTLAADVAPGTVRTGVDETGNATVAWIGDADAPSGPTLRVRRIAADGNAGAPVDLGEPADARPALAVAPGGQAYVAWRAEVPPATDAVVRVARLGAGGTLASGPATVSAPNRKTVAVTVSASASGAIVDWAETVEDDTTYGRTTRLRDSGGVVGVALRQLEMAGIGPGGAASTIADDGTVTTVWYQNTTLGAGELSARRVSADGTESIRTLMTTTSMTEVELLPAIASAPDGGAFLTTVGIESFDGLTPTFKLLARKLAADGTASAPQTLGRVEAGLAFLAGSASIAADGHGSATVGWYVGAAPDNLSFTTANYDAHPPTVDATIPATATVGEDVVFSARASDPSGVTGFAWEFGDGSGARGETVRHAYARPGAYPIELTVTDRSGDAAVVRRTLTVTAAATPPGSPQPPGLPQPPAREAPRAATGLKLTKALRSGAKVTVAGTISRHSGGHVTIAYRAKVGRKTVMKRGTARIVRGRFVATVRLPRALARSRARATVTVTYSGDADTRPATARRAVALARRAPARRGAARKR
>NC_013739.1|WP_012932877.1|1464491_1464668_+|hypothetical-protein
MSLWRAAKDHESGPAHAFPLDLHEVSHLGLNDVRDAIVITAWTPERGVWTVARRQQGA
>NC_013739.1|WP_041730204.1|1464134_1464338_+|hypothetical-protein
MIPAGKTFLTGSLRIGSGTTLRVDGTLLQSQDTAHYSPAVERGHDRAVPRAQWDHMWLANQPFLFYA
>NC_013739.1|WP_012932876.1|1462133_1464062_+|endopygalactorunase
MRRLLVGAVLAVLLGCLLPAAASALDVDVTAAPYSAAGDGVTNDRLAIQSAIDAVNAAGGGTVTLPASRTFLSGNLRLKSNVELIIARGATLKQSQTVAHYDYTPLRGMIIDLTIPWNFTFYRNFPLVYAASARNVKVTGRGTIEMTHLPNVADTILNDAIGLYQVTGFELADLHVIGGGVPYIGIYFSDNGSMHDMTLNEPYKDPVSGLELISSQHVVVEDNVMRNPDGRPGVTDDGIALGTIHRDPRSTGWWRSDVSEPLSDVIVRNNIVETECCSALAFIPWASVTADKRDGEMRNILIENNVLNAPATWDSVKCWCDNPWNGPGGAAYTATDSDQAQMTNIRFSGNTYAGRVNEFIRANIAGVRGAPFHPGEPFIQNPGFETTGTSSWSTVGTASQVGATDGLSVGQSGRFYGYIQDFRTGYTALGQGVGLAASTSYRYRARVQTSGANVRLFVHNQCTNTTVAVLNVSATSWTTYDLPFTTTTACSNYEIGIDPAGSTSGWARIDDVELHGPAMDEGDPKFTYSGMWQQWLDPVDFGGTHLTTSSAGATANVTFYGTEARWRGTRGPNMGYADIWLDGVFRGTVDLYSGSFATGADLWSTGTVARGWHVLGIRAQGARNPLSSADYVAIDSVAVSGY
>NC_013739.1|WP_012932874.1|1461185_1461530_+|hypothetical-protein
MRATTFRADDDTLARLSTVSERLGIAKAAFVREATIARIASVEATEGLAGEHVERVVRERVNEAVLPLHARLRRLELHIAHRPRRGAPHSAFSIAGTPFIKWNSCVMKPTSLRR
>NC_013739.1|WP_012932873.1|1460916_1461189_+|helix-turn-helix-transcriptional-regulator
MPQKRSRAVLGPEFVALGRAAREVRARRDLSQEVLGSRGGLHRNYVGAIERGEINPTFRVLSKLAYGLDVPLSELFLLYEARQREEAIRR
>NC_013739.1|WP_012932884.1|1475998_1476721_+|dihydrofolate-reductase
MTKVTAQMSVSLDGFYTGPRDTRNPKEMSGWMRGPEAPGFFRITRWAVDAMGWRERMGFAGGEQSINSEIIEETFAAAGAYVMGRRMFDAGEVPWGEEPPFHAPVFVVTHRTRDVLERQGGTSFTFVTEGLERAVELARDAAGSKDVAVAGGGELLRQVLSAGLLDQLELHIAPVLLGDGQRLFDPSLGLGADDGIELVPTRVVEAPEVTHIRYTVTGRSKLVLDDRGASGDLVGPAQPE
>NC_013739.1|WP_012932885.1|1476738_1477101_+|hypothetical-protein
MKYMLLIYGNEEAFNSVGAETLAEIIRETDALNRELVESGELVGGYGVADQVNAKMVRVTAGTPVVTDGPYAEAKEYLGSFTILDCDSMERALEIAARNPSARYWGVEVRPLVHEADVER
>NC_013739.1|WP_148261263.1|1477114_1477660_-|dihydrofolate-reductase
MQVSLDGFMEAPGHDISWTAPDPEAHTYMNEMEAATVVSLYGRRLFELMESYWPTADEDPNAAPEVAQYARVWRESPKVVFSNTLDAVTGNARLVRGDAAEEVARIKRETDGLITVGGAHLAASLMRAELVDQIEVLVYPVLIGEGTPLLPELRDRVGLELEATRTFRQSGVVSLRYRVRR
>NC_013739.1|WP_012932887.1|1477800_1478550_+|glucose-1-dehydrogenase
MEFTDKIALVTGGTSGMGLAAARRLLDGGATVVITGRDDARLAAAALELGDPQRLLTVRADVSVAADADRTTAAIAERFGHLDIVFANAGIALFKPFDVLGDAEADRLLDINVKGVLLTLRRSLPLLADGGAIVLNASWTAHRGLAGGSVYAASKAAVASLARSLAAELAPRGIRVNAVSPGYIRTDMFVTAVPDNVAEGAVRKQIALGRIGTAEEVADAVAFLASEQARYVTGQELIIDGGLLGAVAA
>NC_013739.1|WP_049793196.1|1478501_1479398_-|LysR-family-transcriptional-regulator
MTLTQLAYFVAVVETGSFTGAARREHVAQPSLSQQIRALERELGGPLLERLPQGVRLTAAGRALLPKARVAVQAVADGRTLAGNALVDGPDALCVAVVGGTPLEPVARAIASLRAARPQLTVRLHVHADAARLHELILEGERVVAVGPPPAAWEGPVTALGERELVLATAADADDERLHDGVALADLADRTWIALDQDGDRATAALADAGVEPGTLLLASHLDALLALVAAGAGVALVDPAALAGRDGLRGVPVAEAPTCLCAAFGNGPWTPAARELVDRLAAQAATAPSSPPSMISS
>NC_013739.1|WP_012932889.1|1479428_1480142_-|FadR-family-transcriptional-regulator
MTFAPQQLERRPVYEQVADALREAILSGEMPPGSALPPERELCERFGVGRTTVREALRALQTRGLAVATGPTLPLRVVAPDALTTEPLRDTLVHLLRLGRVPLDDLIGLGATLEGAGAEQVATSDPQPDLTTVRDQIALMRAAGADVEAFELADMRFHLELVRASGSEALTIVMLAVRDTVSKALLSHLKSLADPRPTLAQLIAEHEGILQAVLDRDGDAARRLSGEHLRRFYIGSA
>NC_013739.1|WP_049793197.1|1480138_1481290_-|HAMP-domain-containing-histidine-kinase
MDRASDLSVRLKLALSYAGFLMVAGAWLLAAVWVFLLRGYPKSSIVPRLSDFPRVLDPSNFGPRVFGAATVVVLVFLLVFGLVGGWILAGRMLAPLGRITDATRMAAGGSLSHRIRLQGPRDEFRELADAFDSMLARLEAHVAEQQRFAANASHELRTPLAITQALLDVARNDPDHADGELVDRLHFVNTRAIDLTEALLVLSRADQRSFTREHVDLSLIAEEATETLLPLAEGRGLTIETSGNAAPASGSPALLLQLATNLVHNAIVHNLPDHGTVWVTTSASSENVALTIENTGEQLTPQLVTMLAEPFQRGSKRIRSDHGGVGLGLAIVKSIAQAHDGTLTLSPRAAGGLSVTVQLPAAPVDQHGRTAPTSAAADDVPPP
>NC_013739.1|WP_041730208.1|1481282_1481978_-|response-regulator-transcription-factor
MRVLIVEDEPYMAEAIRDGLRLEAIAADIAGDGDAAVELLSVNAYDIAVLDRDIPGPSGDEIAQRIVASGSGMPILMLTAADHLDDKTTGFELGADDYLTKPFELQELVLRLRALDRRRAHHRPPVREIAGLRLDPFRREVYRDGRYVALTRKQFAVLEVLVAAEGGVVSSEELLERAWDQNADPFTNAVRITVSALRRRLGEPWIIATVAGSGYRIDAAPGAGDGGGDGG
>NC_013739.1|WP_012932892.1|1482064_1483105_+|alpha-keto-acid-dehydrogenase
MIRSEPAPPAARRIRSPASSPSSAASTTGITVYGCGEDEAAVFGAMAPRLGVVPTITEEAVAEGTVDLARGNRCISIGHKTHVTNSTLRALSEAGVRYISTRSVGCNHVDVHHARSVGIAVETVAYSPDSVADYTLMLMLMAVRHAKSVIRRADVHDYTLSGIRGKELRDLTVGVIGTGRIGGAVIDRLSGFGCRTLAHDTRPTTAADYVALGALLEQSDIVTLHTPLTAETHHLLDRRRIERMKHGAVVVNTGRGALVDTEALVSALERGSLGGAALDVLEGEEGIFYADCSDRPIESPLLLRLHTLPNVLITPHTAYYTDHALSDTVENSLINCLRFEGRDQHA
>NC_013739.1|WP_012932893.1|1483097_1484138_+|D-alanine--(R)-lactate-ligase
MHRLKTGVIFGGCSEEHPISVKSAQEVARHLDPARYEPFYIGITTSGAWKLCDGPDADWENGRCRPATLSPDRSARGLLVLEYGRYETISLDVVLPVLHGKLGEDGAMQGLLELSGIPYAGCDVQSSALCMDKSLTYTVARAAGIATPRFWTVTANEHVDPDQLPYPVFVKPARSGSSFGVSKVSGRDELPGALDVARRYDSKVLVEEAVVGSEIGCAILGNGLDLLAGEVDQIALSHGFFRIHQEDEPERGSDNSSVTVPAAISQEARALVQETAKAAYRALGCRGLSRVDMFLTADGDVVLNEVNTLPGMTSYSRYPRMMAAAGLPFAEVIDRIVALALTGDGR

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Crispr_ID: NC_013739_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_013739_4

3488865-3488965

Orphan

Consensus_repeat	Method
GACGTCGACGGCGCCCATCACGGCGA	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_013739_4

>merge|NC_013739|4|3488865-3488965|CRISPRCasFinder
GACGTCGACGGCGCCCATCACGGCGATCGCGGTGATCTGCACCTCGCCGCTCTCGAGGATCGCGTTGCGCAGGTCGACGTCGACGCCGCCCATCACGGCGA

>NC_013739|4|4|3488865-3488965|CRISPRCasFinder
GACGTCGACGGCGCCCATCACGGCGA	TCGCGGTGATCTGCACCTCGCCGCTCTCGAGGATCGCGTTGCGCAGGTC
GACGTCGACGCCGCCCATCACGGCGA

Protein	Signature genes	Signature genes Name	Protein_function
NC_013739.1\|WP_148261043.1\|3495187_3497200_+\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_081425391.1\|3485156_3486296_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|270619
NC_013739.1\|WP_012934749.1\|3489362_3490469_+\|alcohol-dehydrogenase-catalytic-domain-containing-protein	unknown	unknown	gnl\|CDD\|176260
NC_013739.1\|WP_049793303.1\|3478925_3479747_+\|HAD-IIA-family-hydrolase	unknown	unknown	gnl\|CDD\|223720
NC_013739.1\|WP_012934759.1\|3498948_3499371_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|367450
NC_013739.1\|WP_049793304.1\|3493785_3494034_-\|MoaD/ThiS-family-protein	unknown	unknown	gnl\|CDD\|340452
NC_013739.1\|WP_081425390.1\|3482647_3483439_+\|glutamine-amidotransferase	unknown	unknown	gnl\|CDD\|225974
NC_013739.1\|WP_012934751.1\|3491235_3491841_+\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_012934738.1\|3479759_3480629_+\|diacylglycerol-kinase-family-lipid-kinase	unknown	unknown	gnl\|CDD\|224513
NC_013739.1\|WP_081425392.1\|3487430_3488042_+\|DUF2384-domain-containing-protein	unknown	unknown	gnl\|CDD\|378249
NC_013739.1\|WP_012934753.1\|3492452_3493784_-\|acetamidase/formamidase-family-protein	unknown	unknown	gnl\|CDD\|376984
NC_013739.1\|WP_012934747.1\|3488111_3488561_-\|transcriptional-repressor	unknown	unknown	gnl\|CDD\|223806
NC_013739.1\|WP_012934750.1\|3490592_3491204_+\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_041732723.1\|3494056_3495040_-\|aldo/keto-reductase	unknown	unknown	gnl\|CDD\|381302
NC_013739.1\|WP_012934758.1\|3497714_3498965_+\|MFS-transporter	unknown	unknown	gnl\|CDD\|340883
NC_013739.1\|WP_012934739.1\|3480628_3482005_+\|Mur-ligase-family-protein	unknown	unknown	gnl\|CDD\|223840
NC_013739.1\|WP_012934743.1\|3484491_3485103_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|376764
NC_013739.1\|WP_012934752.1\|3491864_3492464_+\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_012934740.1\|3482001_3482718_+\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|379312
NC_013739.1\|WP_012934742.1\|3483726_3484473_-\|SOS-response-associated-peptidase	unknown	unknown	gnl\|CDD\|376837

Protein	Function_ID	Function_description	E-value
NC_013739.1\|WP_012934758.1\|3497714_3498965_+\|MFS-transporter	gnl\|CDD\|340883	cd17325, MFS_MdtG_SLC18_like, bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily of transporters. This family is composed of eukaryotic solute carrier 18 (SLC18) family transporters and related bacterial multidrug resistance (MDR) transporters including several proteins from Escherichia coli such as multidrug resistance protein MdtG, from Bacillus subtilis such as multidrug resistance proteins 1 (Bmr1) and 2 (Bmr2), and from Staphylococcus aureus such as quinolone resistance protein NorA. The family also includes Escherichia coli arabinose efflux transporters YfcJ and YhhS. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. The SLC18 transporter family includes vesicular monoamine transporters (VAT1 and VAT2), vesicular acetylcholine transporter (VAChT), and SLC18B1, which is proposed to be a vesicular polyamine transporter (VPAT). The MdtG/SLC18 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement.	3.43179e-24
NC_013739.1\|WP_081425391.1\|3485156_3486296_-\|hypothetical-protein	gnl\|CDD\|270619	cd14486, 3D_domain, 3D domain, named for 3 conserved aspartate residues, is found in mltA-like lytic transglycosylases and numerous other contexts. This family contains the 3D domain, named for its 3 conserved aspartates. It is found in conjunction with numerous other domains such as MltA (membrane-bound lytic murein transglycosylase A). These aspartates are critical active site residues of mltA-like lytic transglycosylases. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. MltA has 2 domains, separated by a large groove, where the peptidoglycan strand binds. The C-terminus has a double-psi beta barrel fold within the 3D domain, which forms the larger A domain along with the N-terminal region of Mlts, but is also found in various other domain architectures. Peptigoglycan (also known as murein) chains, the primary structural component of bacterial cells walls, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc); lytic transglycosylases (LTs) cleave this beta-1-4 bond. Typically, LTs are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, membrane-bound lytic murein transglycosylase E (MltE) is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane- bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and family 4 of bacteriophage origin. While most LTs are related members of the lysozyme-like lytic transglycosylase family, MltA represents a distinct fold and sequence conservation.	7.33658e-31
NC_013739.1\|WP_012934749.1\|3489362_3490469_+\|alcohol-dehydrogenase-catalytic-domain-containing-protein	gnl\|CDD\|176260	cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding.	3.83951e-174
NC_013739.1\|WP_049793303.1\|3478925_3479747_+\|HAD-IIA-family-hydrolase	gnl\|CDD\|223720	COG0647, NagD, Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism].	7.84215e-58
NC_013739.1\|WP_012934759.1\|3498948_3499371_-\|hypothetical-protein	gnl\|CDD\|367450	pfam03330, DPBB_1, Lytic transglycolase. Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N-terminus of pollen allergen. Recent studies show that the full-length RlpA protein from Pseudomonas Aeruginosa is an outer membrane protein that is a lytic transglycolase with specificity for peptidoglycan lacking stem peptides. Residue D157 in UniProtKB:Q9X6V6 is critical for lytic activity.	8.82021e-13
NC_013739.1\|WP_049793304.1\|3493785_3494034_-\|MoaD/ThiS-family-protein	gnl\|CDD\|340452	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins. MoaD, also termed molybdopterin synthase sulfur carrier subunit, or MPT synthase subunit 1, or MPT synthase small subunit, or molybdopterin-converting factor small subunit, or molybdopterin-converting factor subunit 1, is a conserved small sulfur carrier protein that has beta-grasp ubiquitin-like (Ubl) fold involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. MoaD is activated in an ATP-dependent manner by sulfurtransferases similar to the activation mechanism of ubiquitin-activating enzyme E1.	1.84258e-15
NC_013739.1\|WP_081425390.1\|3482647_3483439_+\|glutamine-amidotransferase	gnl\|CDD\|225974	COG3442, COG3442, Predicted glutamine amidotransferase [General function prediction only].	1.22647e-76
NC_013739.1\|WP_012934738.1\|3479759_3480629_+\|diacylglycerol-kinase-family-lipid-kinase	gnl\|CDD\|224513	COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].	5.34835e-74
NC_013739.1\|WP_081425392.1\|3487430_3488042_+\|DUF2384-domain-containing-protein	gnl\|CDD\|378249	pfam09722, DUF2384, Protein of unknown function (DUF2384). Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. The function is unknown.	0.00474647
NC_013739.1\|WP_012934753.1\|3492452_3493784_-\|acetamidase/formamidase-family-protein	gnl\|CDD\|376984	pfam03069, FmdA_AmdA, Acetamidase/Formamidase family. This family includes amidohydrolases of formamide EC:3.5.1.49 and acetamide. Methylophilus methylotrophus FmdA forms a homotrimer suggesting all the members of this family also do.	7.40212e-66
NC_013739.1\|WP_012934747.1\|3488111_3488561_-\|transcriptional-repressor	gnl\|CDD\|223806	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism].	1.43216e-37
NC_013739.1\|WP_041732723.1\|3494056_3495040_-\|aldo/keto-reductase	gnl\|CDD\|381302	cd19076, AKR_AKR13A_13D, AKR13A and AKR13D families of aldo-keto reductase (AKR). Schizosaccharomyces pombe aldo-keto reductase YakC is a founding member of aldo-keto reductase family 13 member A1 (AKR13A1). It catalyzes the reversible reduction of ketones to the respective alcohols using NADP(+) as a hydride donor. Rauvolfia serpentina PR is a founding member of aldo-keto reductase family 13 member D1 (AKR13D1). It catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. This family also includes Arabidopsis thaliana aldo-keto reductases, ALKR1-6.	0
NC_013739.1\|WP_012934739.1\|3480628_3482005_+\|Mur-ligase-family-protein	gnl\|CDD\|223840	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane].	7.24019e-62
NC_013739.1\|WP_012934743.1\|3484491_3485103_-\|hypothetical-protein	gnl\|CDD\|376764	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II. This family consists of cytochrome bd type terminal oxidases that catalyze quinol-dependent, Na+-independent oxygen uptake. Members of this family are integral membrane proteins and contain a protohaem IX centre B558. One member of the family, Klebsiella pneumoniae CydB, is implicated in having an important role in micro-aerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae. The family forms an integral functional unit with subunit I, family Bac_Ubq_Cox, pfam01654.	0.00488058
NC_013739.1\|WP_012934740.1\|3482001_3482718_+\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|379312	pfam13649, Methyltransf_25, Methyltransferase domain. This family appears to be a methyltransferase domain.	4.19705e-16
NC_013739.1\|WP_012934742.1\|3483726_3484473_-\|SOS-response-associated-peptidase	gnl\|CDD\|376837	pfam02586, SRAP, SOS response associated peptidase (SRAP). The SRAP family functions as a DNA-associated autoproteolytic switch that recruits diverse repair enzymes onto DNA damage. We propose that the human protein Q96FZ2:UniProtKB, the eukaryotic member of the SRAP family, which has been recently shown to bind specifically to DNA with 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, is a sensor for these oxidized bases generated by the TET (tetrahedral aminopeptidase of the M42 family) enzymes from methylcytosine. Hence, its autoproteolytic activity might help it act as a switch that recruits DNA repair enzymes to remove these oxidized methylcytosine species as part of the DNA demethylation pathway downstream of the TET enzymes.	1.87334e-104

>NC_013739.1|WP_012934747.1|3488111_3488561_-|transcriptional-repressor
MTTDLESVDNDLIERLRARGQRVTSQRLVINRMLRSRDQHVTAEEVLGAVTRTLPGTSLPTVYATLELFEQLGIVRRVNSGGGAVLFDSRTVDHHHVICRTCGRVQDLDARVELGAVMDAARAAGFAPDRAALVVDGVCASCGAAASAG
>NC_013739.1|WP_081425392.1|3487430_3488042_+|DUF2384-domain-containing-protein
MGTRTRSSEGDARRIAENASSAGDDRRPGAERSMDEPPGRAVTQAFQARTTRLREWRQRFVTARAGSLQARLQLLAAFGLSDRDIARTIEKTQPRSVRRWRTEGVATPRAGARWEPVDDLCAIIGYFLTDGTYDEEGIVAWLRSRQTALGNQRPLDVLRERGDTGFREVQQAAEQHLTAAEATADDQLILPRADSAGRRQRSH
>NC_013739.1|WP_081425391.1|3485156_3486296_-|hypothetical-protein
MQHDRVRLAESRRHERHDPSVVRAIDGVRGGCRVAGWAARPGDRALKLRQRAGGLTARRASPLKHRLPWSIACRERTGGSESRSLRRSFWRVPVLMHHVTRTRTLLLLIALAFTVTASAAQAKPIRRAGWLRSVTVTEYYPAPEWWFVGKKVQTPGLDRLSRIDWLYSSTGMSMEGDGIGLDGDRYHIAGLGSGGWVTERGKPSVPGHRGWKGGSPFWRAGGYWLSSDKYVTFPLDGGGWSNGPGRRYRELPGVSFGEGPSRPLKYYRSVAVDPDLIPLGSKVYIAAYQTSAGGGWFTAEDVGGAIIGRHVDVYRTPPARADIGGSHLQDQRIYVQPPGTRAARNSPPKSSGKGTATPSPPVPQPPATLSDPSGGAGAP
>NC_013739.1|WP_012934743.1|3484491_3485103_-|hypothetical-protein
MAKQQKQRPMRMEQRGSLAAMQQLETRTDEQLEAETKFKAAALAILGARAAERYDARATRAYYSRAIAAARPQERLQLRRMADASIALAERRAGDLKDAVTKLGQRPPSNRQLLILRFMGLLAPPPGSGILLRLRGIAIVLGIVIVLLALGFGIAKLIALPFGGVGTIGGLLLGLIVIIAVFAVLALLGRRRQARARARAAAG
>NC_013739.1|WP_012934742.1|3483726_3484473_-|SOS-response-associated-peptidase
MCGRFTLATTTADELRHRFPLGESAVDLRQRFNVAPGDEVVTVAARDGVATGRMLRWGLIPPWARDPSVGYKMINARAETVAEKPAYRDPFAKRRCLIVADGFYEWQRQGRAKQPFHITRTDGAPFAFAGLWTGWKNPEDDEWLRSCTIVTTEANDKISGIHPRMPVILDPADEQTWIDPETPVARLQELLRPLPADGTNARAVSRAVNNARYDGPDCLADAEPDDLKAFAEAVNAAQAAPASQEGLF
>NC_013739.1|WP_081425390.1|3482647_3483439_+|glutamine-amidotransferase
MPAAGGSRRPRNTSAARWCCSVADTLRVCALYPDLMNIYADRGNLLLLQRRCEWRGLGFELSASGLGEPLDPDAADLFYIGGGQDRDQKLCALDLAEVKREGIHAAAERGAALLAVCGGYQLLGHSYQLGEETLPGIGLVDLTTVRSDGPRLIGNVAIEVDLGDGPRVLAGFENHGGRTRLGAAEQPLGRVLRGHGNDGRSGVEGVRRGNVIGTYLHGPLLPKNAWLADWLIARALGRDTPLPPLDDALENAAHVEARRAAGA
>NC_013739.1|WP_012934740.1|3482001_3482718_+|class-I-SAM-dependent-methyltransferase
MSEVIWHDLECGGYDADLPLWRELAAAEGGPVLDLGAGTGRVALDLARAGFEVVAVDLEAEFLEALRARAGELPIETLLADARTFALPGRRFPLILAPMQTVQLLGGPDGRAAFLHSVAAHLAPGGLLAASLADAMDGFDAEHTEPPLPDIVERDGWVYVSQPVAVRPGPAGISIERIRQIVSPAGRRTAEGDEIHLDTLDGDTLAAEGVAAGLRDAGRRRIEATEEHVGSEVVLLRG
>NC_013739.1|WP_012934739.1|3480628_3482005_+|Mur-ligase-family-protein
MAGLPLGPKLAVARAVGSVARRAGRGGGTSLPGKVLMKLDPHAIGALASRLPEGSVAISATNGKTTTAAMVASVLERRGTPLVHNRAGANMAGGIASTLLGAAQGKGIDGRLGLFEVDEFWLGGLVEQLRPRKLLLGNLFRDQLDRYGELETIADRWAEIVARHGSSTQLVLNADDPLVADLGREQPRVVYFGVQDDTMALPQMQHASDSKHCRRCGHAYEYDAIYLGHLGRYHCPNCGQRRPEPAVVGERIELRGTRGARFTLRTPEGSARVELPLPGLYNVYNALGAAALCLSLGVPLAEVVSGLEQVAAAFGRAETIALDGRDLSILLIKNPAGANEVLRTLALEDGAVDLLAVLNDNTADGRDISWVWDADFELLAGRVRRVTCSGTRAAELALRMKYAGVDEERLVVVPELEAALDEARRDGDGTLFALPTYTALLALKELLARRGLAPEYWR
>NC_013739.1|WP_012934738.1|3479759_3480629_+|diacylglycerol-kinase-family-lipid-kinase
MDRNVALIVNPVAGGGRGLRMLPGVERWLRVHGVAYHVERTRDIEHARELARRAAADGEVAAAFGGDGIVGAVAGALAGTDGILAVLPGGRGNDFARAAGIPKSPVAACTVFESARERRIDIGAVGERRFVGIASCGFDSDANRIANATRVPGEAAYAYAAIRALASWKPATFGVEIDGVANSHTGYSVAVANGPAYGGGMFLAPDAQLDDGLFDVVTIAGVSKFRLLSQLPKVFKGTHVRNPEIEIRRGREVRIEADRPFTLYADGDPIGELPATVRTLPGAVRMLVP
>NC_013739.1|WP_049793303.1|3478925_3479747_+|HAD-IIA-family-hydrolase
MSQTSPPPLTSLLRSYDHVLLDLDGCLWVGGAATRDAPRALDALRAAGKHVAFVTNDTRSTAEEYVRKLWSLGFKAALEEVVTVGGALQHQLAERHGARRATAYVIGTPAILKHVADAGLRVVNGTPHAPQAEVVVAAGHDALVFEELRIATQALLAGADFVAAGRDRTFPMPDGMWPATGALVAALEYASGRTALSVGKPEPEIFATALDRLGPGRALVVGDRLDSDLGGAHAAGLDGAIVLTGATTHSEAHAASDPAPVAIAPDLATLVLG
>NC_013739.1|WP_012934749.1|3489362_3490469_+|alcohol-dehydrogenase-catalytic-domain-containing-protein
MEIRAAVLEEFGAPLVVQTVELAEPGPGEVLVRLVACGVCHTDMYTASGADPSGYAPCVLGHEGAGVVERVGSDVTLVRPGDHVVTLFSPQCGECVHCLSPKTNLCMKIREQQNKGYLPDGTTRLRRGGQELRHFMGTSTFAEYTVMPEIALAKIDPEAPLEGAALFACGLSTGLGAALRTAKVEPGSTAVVFGAGMVGLGAVAGARMAGAERIVCVDLSQDRLELARGQGATDLIVGGPDTVQQILDMTGGFGADYTFEATGLVSVMRQAVESARMGWGLCTVAGVAGKGEHLEVIPRWLIQGRRIAGSSFGGLKGRDDVPALIDRWMAGELDVDPFISHRISLDQVNEGFDLMHAQDGIRSVIAFD
>NC_013739.1|WP_012934750.1|3490592_3491204_+|hypothetical-protein
MRKSTAVAATLVAALLLAVGAGASSATTIGIANQTPLTQQVGQLTFFNGSVNFNCTVVLRKQLIVGLILVRTTSLTRLGRVTSGQINCPAGPAALLNLPLQLGGTPPIGPLPTSWDVSFLGSDLVTGEMLFGILDFQVRLPNNCLYRGTLLGRLSRDGRVLRFLGNPPLLLAGGPTGCQPQIGVGGTLNDNPPINFILLNIGV
>NC_013739.1|WP_012934751.1|3491235_3491841_+|hypothetical-protein
MRTSLAAVLAAVVLMLLGSSAASAAPLGIVINGPALTTQVGALRLTAGPVMLTCQVVLRKELVLGLTPVNPTGLTRLGRITAGRLFGCPSTLLNLPPELGAIPPIGPLPNSWDISYLTSDPLTGDLLFGILDFQISLGVPPGCLYRGTLLGRLSRDGRTLTITGSVPIDFPTPGCAGSASITGTLNDTPPIQYFLLPGPPA
>NC_013739.1|WP_012934752.1|3491864_3492464_+|hypothetical-protein
MRKTAAAAVVLVTTLLLGLAAGSGSAATIGITNATPLTTQQGNLTFFGGGFSATCAVQLRKRLRTGLIPVLASLTRLGRVEAGQLGAACPAAFLDLPLQLGGLPPIGPTPTSWDVSFLGSDPITGELLFGILDFQIKFNNGCLYRGTLLGRLSRDGRVLRFLGQPPLPLIAGGPECPPQIGVQGVLNDNPPIIYTLLII
>NC_013739.1|WP_012934753.1|3492452_3493784_-|acetamidase/formamidase-family-protein
MAVEPTTATTAHRTVFVETFTNGLLGPDVPMLGPVADGGHVVVNTAPGCWGPMITPAIRGGHEVAQPVAVEGARVGDAIAIRIKDISVTSLATSSGNDQAMDGRFNGDPYCAAVCPGCGDEWPATTLDGIGPTAVRCARCGADATPFTFTNGYTIAFDEQHAVGVTVGREAAERFAREAARAAALPDGSVQNPILTFAPHDVVALATRLRPFMGQLGTTPSTTIPDSHNAGDFGSFLVGAPHRYALTAQELQQHKTDGHLDVDAVRAGAILICPVKVDGGGVYMGDMHALQGDGEIAGHTADVSGTVTLQVEVVKGLGIDGPILLPVAEDLPFLAKPLTASERARAAALGARYGVAELEESLPISVIGTGPDLNSATDNGLARAAELLGMSVPEVMNRATIAGAIEIGRHPGVVQVTFRAPAERLAARGLLAYAREQYGSSDD
>NC_013739.1|WP_049793304.1|3493785_3494034_-|MoaD/ThiS-family-protein
MRVKVRFAAALARLAAAPQLTLDLPDGATVGQLLDRLAGEQPELAPALGAALPVRAGSHVAHDDALADGDEVALLIPVAGGS
>NC_013739.1|WP_041732723.1|3494056_3495040_-|aldo/keto-reductase
MKQRRLGTQGLTVSAEGLGCMGMSEFYGTTDEAEGIATIHRALELGVTLLDTADVYGPHTNEQLVGRAIADRRDQVVLATKFGIVRDPADPARRGMDGSPEYVRRSIDASLRRLGVEHVDLYYQHRVDPRTPIEETVGAMAELVAAGKVRYLGLSEASPATIRRAHAVHPISAVQTEYSLWSRDPEAEILPALRELGIGFVPYSPLGRGFLTGTIRSLADLEDGDVRRHNPRFAADALAANLALVERVREIAEEKGVTPGQLALAWVLAQGEDVVPIPGTKRRSYLEQNVAAAAIPLSSEELARLDAAAPVGAAAGDRYPDMSFVDG
>NC_013739.1|WP_148261043.1|3495187_3497200_+|hypothetical-protein
MSSKRSDRVRRLRRGGLLATLGALLVMAGGSPAQAVFGPPGEVTISFWCPPPQQFIPDAASAQQRMQQIKDAGFNLVTTNACDLGEWPVEVTRRALVAADAVGLKALVHDERFRRAAETGDTSGVPGVARDFAGYPAVAGYEVIDEPSYGFIPVAAEMVRTLRTLDPAHASYINLLPSWDPNLPVPYTRYVGDYLNAVDPVLLSYDNYLWPTMYTNLITIRDEARRRGIPFWNVVLATAHGRFPDQPTAPQMLWEGMQTLAYGGTGILWFVYWDMIDPDFREAMIDARGNETPLYAETAAINAKLRTIGRPLVGARHVRTFQTGPDPLPAGGVRRQPQTPVFGDDNAPMTIGVFEDDSYVYSLVTSRDTASARTANTRLKYNATLPQRLTGPGSWTTVSPTSTGGGLAAVSASLAPGDAVLYRVAKPLARVDDEVVIGRVRNNHGTLHSVDSAGGVTYMGPAPWGTCPPGYGEAGRYERPNGFWVCTRSDLAGRGVYVGNVVNNGSELVRVQNGNALPLGPKAWSGCTNTSRFVAQLLESNGFWVCLDAADRRGPEAVVGLVRANDGQLYATDYANGTYHVGSGGWGACPGGYGYVGKYEAVNGFWLCARSDLVPRTFLVGNVVANAATLFSVTWGAVSAIHYPAAWNDCRGGRLLGNLVVSNGFWLCQQ
>NC_013739.1|WP_012934758.1|3497714_3498965_+|MFS-transporter
MAADPRTSQVHERRAIWLLGLPTFGLALSITVVTTYLPLIAQEFTDSSIVVGVLIGSEGLLALALPLVVGTWSDQLKSPIGGRLPFLLVATPPLAISLALLGFAGSLVIALGLVWLFFAAYFVAYEPYRALYPDLVSDANAGKSQSVQAIWRGAATGLALVAGGLLFDLEPWIPFVVSAVVTAAVMFVFLHIMVRAPGRRWHEPEHPKPLGAAVRELRSLVEGRPGLQAYLAANALWEASLGALKTFVLLYVTVGLGIDVADAALIVGAAATFVLGGAVVSGILADRYGQLPVLRVTLIVYGFGLLIPAVTTATLPLALIAPLAAFGGGTLMTLPYALLMPHMPAGSHGALTGFYSLSRGIGTMLGPLLTGLAVQLLRGPFDGTEGYQAMWLVCGGTVLASLFFVRRMSAALRAAT
>NC_013739.1|WP_012934759.1|3498948_3499371_-|hypothetical-protein
MYPSVVRRRLLAALVLSGLAAVAFATGLSLARGEPAEADRTFVQGDQTLREAGWQHDLASRFDDYGQELACGGTLAPDQLGVASRTLPCGTIVTFTYRGRTVQVPVIDRGPWIDGREWDLTGAAAEALGFPGLAVVTWRL

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Crispr_ID: NC_013739_5

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_013739_5

4880374-4881053

Orphan

Consensus_repeat	Method
GGCGCCAAGGGCGACACCGGCGACCA	CRISPRCasFinder

11 spacers

The CRISPR arrays of NC_013739_5

>merge|NC_013739|5|4880374-4881053|CRISPRCasFinder
GGCGCCAGAGGCGCCACCGGCGCGACGGGCCCCGCCGGTCCTGCCGGCCCGATCGGCCCGGTCGGCCCCGCCGGCCCGCAGGGCGCCGCCGGCCCCCAGGGACCGCAGGGCGAGAGAGGCGCGGCCGGCGCCGACGGCAGAAACGGCGCGAACGGCCTCAAGGGCGACACCGGCGCTGCCGGCACCGGCGCCAAGGGCGACACCGGCGACCAGGGCATCCAGGGCATCCAGGGCGTCAAGGGCGATACCGGCGGCCAAGGCATCCAGGGCGCCAAGGGCGACACCGGCGGCCAAGGCATCCAGGGCGATACCGGCGGCCAAGGCATCCAGGGCGCCAAGGGCGACACCGGCGACCAAGGCACCCAAGGCGTCAAGGGCGACAAGGGCGACACCGGCGACCAAGGCACCCAAGGCGTCAAGGGCGACCAAGGCACCCAGGGCATCCAGGGCGACGTCGGCCCCGAGGGGCCGCAGGGCCCCATCGGTCCGAATGGCCTCCAGGGCGTCAAGGGCGATAAGGGCGACAAGGGCGACGACGGTGCCGCTGGTGGCGACGGCGCGGCTGGCGCAACCGGCGCGGCTGGCGGCACGGGCGCGACCGGCGCTCAGGGTCCGCAGGGCGAGACCGGTCCGATCGGTCCGCAGGGTCCCGCAGGCCCGCAGGGCGATAAGGGCGACCC

>NC_013739|5|5|4880374-4881053|CRISPRCasFinder
GGCGCCAGAGGCGCCACCGGCGCGAC	GGGCCCCGCCGGTCCTGCCGGCCCGATCGGCCCGGTCGGCCCCGCC
GGCCCGCAGGGCGCCGCCGGCCCCCA	GGGACCGCAGGGCGAGAGAGGCGCGGCCGGCGCCGACGGCAGAAAC
GGCGCGAACGGCCTCAAGGGCGACAC	CGGCGCTGCCGGCACC
GGCGCCAAGGGCGACACCGGCGACCA	GGGCATCCAGGGCATCCAG
GGCGTCAAGGGCGATACCGGCGGCCA	AGGCATCCAGGGCGCCAAGGGCGACACCGGCGGCCAA
GGCATCCAGGGCGATACCGGCGGCCA	AGGCATCCAGGGCGCCAAG
GGCGACACCGGCGACCAAGGCACCCA	AGGCGTCAAGGGCGACAAG
GGCGACACCGGCGACCAAGGCACCCA	AGGCGTCAAGGGCGACCAAGGCACCCAG
GGCATCCAGGGCGACGTCGGCCCCGA	GGGGCCGCAGGGCCCCATCGGTCCGAAT
GGCCTCCAGGGCGTCAAGGGCGATAA	GGGCGACAAGGGCGACGACGGTGCCGCTGGTGGCGACGGCGCGGCTGGCGCAACCGGCGCGGCT
GGCGGCACGGGCGCGACCGGCGCTCA	GGGTCCGCAGGGCGAGACCGGTCCGATCGGTCCGCAGGGTCCCGCA
GGCCCGCAGGGCGATAAGGGCGACCC

Protein	Signature genes	Signature genes Name	Protein_function
NC_013739.1\|WP_148261364.1\|4885590_4887276_-\|RNB-domain-containing-ribonuclease	unknown	unknown	gnl\|CDD\|273947
NC_013739.1\|WP_012936035.1\|4872566_4873832_-\|NADH:flavin-oxidoreductase/NADH-oxidase-family-protein	unknown	unknown	gnl\|CDD\|240084
NC_013739.1\|WP_160165558.1\|4887392_4888595_-\|PDZ-domain-containing-protein	unknown	unknown	gnl\|CDD\|223864
NC_013739.1\|WP_012936037.1\|4874484_4875273_+\|SDR-family-NAD(P)-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|212491
NC_013739.1\|WP_012936051.1\|4890418_4891408_-\|cell-division-ATP-binding-protein-FtsE	unknown	unknown	gnl\|CDD\|225438
NC_013739.1\|WP_012936040.1\|4877508_4878582_+\|phosphotransferase-family-protein	unknown	unknown	gnl\|CDD\|270703
NC_013739.1\|WP_012936033.1\|4869714_4871202_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|237940
NC_013739.1\|WP_041730858.1\|4883036_4884512_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|129794
NC_013739.1\|WP_012936049.1\|4888662_4889484_+\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|379312
NC_013739.1\|WP_012936031.1\|4868165_4869326_-\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_012936046.1\|4885097_4885580_-\|SsrA-binding-protein-SmpB	unknown	unknown	gnl\|CDD\|376590
NC_013739.1\|WP_148261365.1\|4889528_4890392_-\|FtsX-like-permease-family-protein	unknown	unknown	gnl\|CDD\|225088
NC_013739.1\|WP_012936032.1\|4869429_4869645_-\|flagellar-biosynthesis-anti-sigma-factor-FlgM	unknown	unknown	unknown
NC_013739.1\|WP_012936052.1\|4891531_4892785_+\|insulinase-family-protein	unknown	unknown	gnl\|CDD\|223685
NC_013739.1\|WP_012936039.1\|4876288_4877512_+\|acyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|173844
NC_013739.1\|WP_012936038.1\|4875269_4876265_+\|NADPH:quinone-oxidoreductase-family-protein	unknown	unknown	gnl\|CDD\|176203
NC_013739.1\|WP_012936045.1\|4884601_4884988_+\|MarR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|197670
NC_013739.1\|WP_012936043.1\|4882003_4882921_+\|site-2-protease-family-protein	unknown	unknown	gnl\|CDD\|100081
NC_013739.1\|WP_012936041.1\|4878618_4879674_-\|hypothetical-protein	unknown	unknown	unknown
NC_013739.1\|WP_012936036.1\|4873858_4874461_+\|TetR/AcrR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|366102

Protein	Function_ID	Function_description	E-value
NC_013739.1\|WP_012936052.1\|4891531_4892785_+\|insulinase-family-protein	gnl\|CDD\|223685	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only].	1.11286e-78
NC_013739.1\|WP_012936035.1\|4872566_4873832_-\|NADH:flavin-oxidoreductase/NADH-oxidase-family-protein	gnl\|CDD\|240084	cd04733, OYE_like_2_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.	1.38304e-170
NC_013739.1\|WP_160165558.1\|4887392_4888595_-\|PDZ-domain-containing-protein	gnl\|CDD\|223864	COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer membrane].	2.38323e-89
NC_013739.1\|WP_012936037.1\|4874484_4875273_+\|SDR-family-NAD(P)-dependent-oxidoreductase	gnl\|CDD\|212491	cd05233, SDR_c, classical (c) SDRs. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.	1.32263e-55
NC_013739.1\|WP_012936051.1\|4890418_4891408_-\|cell-division-ATP-binding-protein-FtsE	gnl\|CDD\|225438	COG2884, FtsE, Predicted ATPase involved in cell division [Cell division and chromosome partitioning].	6.30201e-112
NC_013739.1\|WP_012936040.1\|4877508_4878582_+\|phosphotransferase-family-protein	gnl\|CDD\|270703	cd05154, ACAD10_11_N-like, N-terminal domain of Acyl-CoA dehydrogenase (ACAD) 10 and 11, and similar proteins. This subfamily is composed of the N-terminal domains of vertebrate ACAD10 and ACAD11, and similar uncharacterized bacterial and eukaryotic proteins. ACADs are a family of flavoproteins that are involved in the beta-oxidation of fatty acyl-CoA derivatives. ACAD deficiency can cause metabolic disorders including muscle fatigue, hypoglycemia, and hepatic lipidosis. There are at least 11 distinct ACADs, some of which show distinct substrate specificities to either straight-chain or branched-chain fatty acids. ACAD10 is widely expressed in human tissues and highly expressed in liver, kidney, pancreas, and spleen. ACAD10 and ACAD11 are both significantly expressed in human brain tissues. They contain a long N-terminal domain with similarity to phosphotransferases with a Protein Kinase fold, which is absent in other ACADs. They may exhibit multiple functions in acyl-CoA oxidation pathways. ACAD11 utilizes substrates with carbon chain lengths of 20 to 26, with optimal activity towards C22CoA. ACAD10 may be associated with an increased risk in type II diabetes. The ACAD10/11-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K).	4.51675e-93
NC_013739.1\|WP_012936033.1\|4869714_4871202_-\|hypothetical-protein	gnl\|CDD\|237940	PRK15313, PRK15313, intestinal colonization autotransporter adhesin MisL.	1.33945e-11
NC_013739.1\|WP_041730858.1\|4883036_4884512_-\|MFS-transporter	gnl\|CDD\|129794	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Other].	4.1849e-51
NC_013739.1\|WP_012936049.1\|4888662_4889484_+\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|379312	pfam13649, Methyltransf_25, Methyltransferase domain. This family appears to be a methyltransferase domain.	2.77815e-17
NC_013739.1\|WP_012936046.1\|4885097_4885580_-\|SsrA-binding-protein-SmpB	gnl\|CDD\|376590	pfam01668, SmpB, SmpB protein.	2.84682e-81
NC_013739.1\|WP_148261365.1\|4889528_4890392_-\|FtsX-like-permease-family-protein	gnl\|CDD\|225088	COG2177, FtsX, Cell division protein [Cell division and chromosome partitioning].	4.55358e-54
NC_013739.1\|WP_148261364.1\|4885590_4887276_-\|RNB-domain-containing-ribonuclease	gnl\|CDD\|273947	TIGR02063, Ribonuclease_R, ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA].	2.03761e-147
NC_013739.1\|WP_012936039.1\|4876288_4877512_+\|acyl-CoA-dehydrogenase	gnl\|CDD\|173844	cd01155, ACAD_FadE2, Acyl-CoA dehydrogenases similar to fadE2. FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACAD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. ACAD's are generally homotetramers and have an active site glutamate at a conserved position.	0
NC_013739.1\|WP_012936038.1\|4875269_4876265_+\|NADPH:quinone-oxidoreductase-family-protein	gnl\|CDD\|176203	cd08241, QOR1, Quinone oxidoreductase (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction.	8.81943e-131
NC_013739.1\|WP_012936045.1\|4884601_4884988_+\|MarR-family-transcriptional-regulator	gnl\|CDD\|197670	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein.	1.31751e-11
NC_013739.1\|WP_012936043.1\|4882003_4882921_+\|site-2-protease-family-protein	gnl\|CDD\|100081	cd06160, S2P-M50_like_2, Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.	1.06989e-27
NC_013739.1\|WP_012936036.1\|4873858_4874461_+\|TetR/AcrR-family-transcriptional-regulator	gnl\|CDD\|366102	pfam00440, TetR_N, Bacterial regulatory proteins, tetR family.	4.56982e-08

>NC_013739.1|WP_012936041.1|4878618_4879674_-|hypothetical-protein
MTPVEAEPSQQSAAPAGNDGDAGEAPRTPNRLTRWLLPAVALVAAVVVGIVLLAGGGDDEKPAAARRALAVAASLERLAAASAGAGHPVYWAGARDGTTYELSETRDGRIFIRYLPAGVSVGASEARYLTVATYPQARAFQTLLATARAQGVEAVTVPGGGRAFQDRNRAESAYVAFPGSNVQIEIFDATAGEALRLARSGAIVPVRAAVASGEPRAVSPQQLAQTATQAGHPVYWAGAEEQTTYELTEERDGRIYVRYLPSGVAVGDDSPRFLTVGTYPQPDPLASLRRAAADSGSATFEVEGGTAYADAAHPKSVYVAYRDSGVQVEVYDPVDGRARTLLTSGRIVPAR
>NC_013739.1|WP_012936040.1|4877508_4878582_+|phosphotransferase-family-protein
MTGTARAEDRAVRAEDAFDVDAVDAWLRAAAGVALPPGEPDVRQFAGGASNLTYLLRYADRDLILRRPPPGTKASSAHDMAREHRIQAALKPAFPYVPEMVALCTDEAVLGSDFYVMERVPGVIPRASMPPEVGTDPALMRALGERFVDLLVELHAIEPAAAGLADIGRGAGYVERQVAGWTERYARARTWNVPSFARVMRWLDERRPADVRTCVIHNDFRLDNIVLDAAEPLRVRAVLDWELATLGDPLMDLGSSLAYWVEPGDGRLMQRFRRQPSNLPGMPTRREIVERYCAATGLRADDWPFYEVFGMFRLAGIAQQIYFRYARGQTTNPAFKRFWLAAWVLERRCRTVMRAAA
>NC_013739.1|WP_012936039.1|4876288_4877512_+|acyl-CoA-dehydrogenase
MDFEPSDRAKEYQERLQAFMDEKVYPAERVYIAQVRAADSPHVHPPVMEELKEEARRRGLWNLFLPDPAHGPGLSYLEYAPLAEIMGRTMIAAEATNCNAPDTGNMEVLHQFGSDAQKERWLQPLLDGEIRSGFAMTEPDVASSDATNVQMSMVREGDELVLNGRKWWTTGALHERCRILIVMGKTDPDAHVYAQQSMVLVPLDTPGLEIVRSLPVFGYHDPEGHAELKFTDVRVPAENVIAQPGAGFLIAQARLGPGRIHHCMRAVGAAERALELMCARADARETFGKPVSTRSNIRDWIAEARIELEMLRLLVLKTAWLVDRVGGKNARVEVAAIKVAAPNIALKIIDRAIQVHGGAGVSDDTPLAYMYAHMRTLRLADGPDEVHKLSIARRELRRQRGEEAPVL
>NC_013739.1|WP_012936038.1|4875269_4876265_+|NADPH:quinone-oxidoreductase-family-protein
MRALQITELTGPRSALAFAELPDPEPPHMLTPDGGVVVEVHAAGVSFPELLQSRGQYQLKPPLPFVPGSEVAGIVRSAPDGAAVRAGDRVAAFCALGGFAEVAVAPEFLTFALPGALSFAQGAGLILNYHTAYFALKLRGRLAPGETVLIHGGAGGVGTAAIQVANGLGARTIAVVSSDEKEHVARTAGADEVVRSDGAWKDAAKELTDGAGVDVVLDPVGGDRFTDSLRALREDGRLVVVGFTAGSIPEVRVNRLLLGNTSVVGAGWGAYAMGKPAACREIGAALDVMIRDGVVSPIVGALLPLERAAEALELLDGRRAVGKVVLAVREA
>NC_013739.1|WP_012936037.1|4874484_4875273_+|SDR-family-NAD(P)-dependent-oxidoreductase
MPETNSSPPDLSGLRDRVALVTGGASGIGRATALALAAAGVEVVVADLDAAQAQEVARQVGGHAFEADVSDLDANRAAVAFAQERCGGLDLAFLNAGVTSGCGVGEDFDLALYRRAMGVNLDGVVFGTHAALPALRARGGGAIVATASLAGLVGVPLEPIYTANKHAVVGLTRSLGPTLAAEGIRFNAVCPGFAETPLIADFRDGLRDAGFELLSPEVVAETAVHLFAGEMSGECWFVQVGREPAPFGFRGIPGPRTTEVPK
>NC_013739.1|WP_012936036.1|4873858_4874461_+|TetR/AcrR-family-transcriptional-regulator
METPVAIEGARERLVCGMNAAVAEKGYAPTTIADVVRHARVSKRTFYEHFGDKRACFLAAYDTASAHVLGAMRAASEAAAGAPWSERVERVVVAYLEAMAAKPELTQTFLIEILGAGPLALAHRRETMERFADQLVALCADLRRAEPQLRPVSRSLATAVVGGINELVLGAVEQGRASELAQLRRPAAELIRSVLTGPEP
>NC_013739.1|WP_012936035.1|4872566_4873832_-|NADH:flavin-oxidoreductase/NADH-oxidase-family-protein
MDTTTLASPLTLPCGAVLANRIAKAAMSEQLSDRANSPTVRIDRLYERWAAGGSGLVITGNVMIDRRHVGEPRQVVVEDERDLPALRRWAAAGRANGTTLWVQVNHPGRQAMRIAGSRPVAPSAIAPRIPGAVTPQALTGAQIEEIVGRFARTAAVFREAGFDGVQLHGAHGYLISQFLSPLANRRDDEWGGDAARRQRFVLEVVRATRAAVGPDFPVGIKLNSADFQRGGFSEEESGDVVAALAAAGVDLIEISGGTYESPAMMGDATGTASSAAAASAAVPARASTRAREAYFLDYAVRVRDRAPDVPLMVTGGFRSAAAMREAVASGACNVIGLGRPLALHPDASAALLDGSRARIDAGSRSIGVRKLDSVIDLWWHTRQLHRIGRGREPWAGERALHTLATFLLVNGWGAARRKRGG
>NC_013739.1|WP_012936033.1|4869714_4871202_-|hypothetical-protein
MDERTLDTTPLARIAARRRALRGALVALTAAAALGAAPAGVLAADVGGAQAPDSQALAAPSTEQPATAAAPQDTSQAAAAPQDTSQVAAAPQDTAPAATAPQESAPPAAAPQDTAPAATAPQESTPPAADGASGETPPAADGASGETPPADPGSGAPQTPADGQTPTEPAPTEPGPVDPGPVDPGPVDPGPVDPGPVDPGPVNPGPVDPGPVNPGPVDPGPVDPGPVDPGPVDPGPVDPAPVDPAPVDPGPVDPAPADNPSPRTPSRPADTSDTPDTHPKPPVNGGTLRPPTVEAPAPPVAPTTTPVTAPAPVVSAPVTLPQPAATAPPESTAKDDAEQAAARAAEKQRGVRKVLARLGFGPAQTAAELPRAAASIDPAGALCAPIVVATATTTADGTTPAPVDRDQVRKTRNAEEPGSVRGPPAPSDAPVSPVSASAAAAAATAGAGGISFFAILVGSVSAGLAQAESVAPPCSFESNPATPTSHDAARAPPAS
>NC_013739.1|WP_012936032.1|4869429_4869645_-|flagellar-biosynthesis-anti-sigma-factor-FlgM
MVATNDRIQRLTTARRDRITRSSRVRLLAKQVAAGEYVVDPDRIAEVLVERAQFHQRVKADLLTQRSPTEL
>NC_013739.1|WP_012936031.1|4868165_4869326_-|hypothetical-protein
MRRRLILAICTAALAATIVASPAGAATFQGTLTIAPPVVQADGTVVVNASGTTASQCAPQEYCGYFPLVTTVPAAQSCQAEITGSSWVGTDVYDDTRGRVPQSFAPTWKEWPSLYAGPKRACLYISAGSSETFVAEATYEVPGDPGSPPPTSPPPGDGSDIVRAPIPRSVGKRNPFPYRLSTANVPSGVDATRFEQLTRIAARRWGLRAVGTTPRAPRAGDGRDTVGFARDVPRAALGVTRIRSVRYYRRDGRGRQRFVFERVLERDLALAYGVPWHAGPGIPPRDRVDLQTVIVHELGHYAGNDHVRNCTNSPMWVGLRAGEWWWSRADWFQVGCRNAPSTPAVATAAAVRDAAAARAATRARSAAPGPPRPLLVQRSVRRVVLG
>NC_013739.1|WP_012936043.1|4882003_4882921_+|site-2-protease-family-protein
MEQRADWLPPTSPTPASTPAPPATPAVWETPPPHDPQPQQEPPRGRSRLRRLFGPLIVGGALVLRLLGPLKGLLLALPKLKLLSTSGSMLVSVAAYSLIWGWQFALGFVLLLLVHEMGHVIQLRREGIPASAPMFIPFLGAVVAAKSLGDNAAAEARVGLAGPILGSLGAALLVPVWLATGNEFWQALAFTGFFLNLFNLLPVVPLDGGRAMAAMSPWMWFVGLFAIVGVAFAFPNPIIILIALLAAYETWRRWKALREGGERAAAYYRVTRGQRIAVVVVYIGLIVALAVGMDLTHLERALSDA
>NC_013739.1|WP_041730858.1|4883036_4884512_-|MFS-transporter
MTALASPPEAPRESEASQAQHWDARLWGALFVLCGALFLDGLDVSMVGVALPSIGADLGLSTGDLQWVVSGYVLGYGGLLLLGGRTADILGRRSVFLAAVAVFAVASLLGGIASDGGVLIATRFIKGVAAAFTVPAGLSIVTTTFAEGPARNRALSIYAACGATGFSAGLIFGGLLTEIGWRWTFIVPGPIALLVLLAGIRLIPRDKVDPAERQGFDLLGAISVSAAMLLLVRTVVTAPEVGWGAGEVLGGFAISAALMITFVLIERRVKHPLVRLGILRSGSLVRANLAAVAVFGSYVAFQFIATLYLQNLLEWSALQTALAFLPAGLLVATVAPRIGKVADRIGTAPILVVGFVAFVSGYLLFMRIDASPTYIVDILPTMLLLGIGFAFCFPALNMQATAGVADHEQGLASGLVNTSFQVGGAVVLAIAAAIVTSQAGVSTDPQTLLDAYRPALGVVAGISAAGLLVSLSGVLVRQRQSAVAVASADES
>NC_013739.1|WP_012936045.1|4884601_4884988_+|MarR-family-transcriptional-regulator
MAPMTRDDTALVERWRELLDCHARTCGALEKVLQERHQLGVSEFEVLERLAGCDKEMHRMQGLADNVHLSQSALSRLIGRLEADGLVVRNMCSDDRRGIFACLTDAGRERYDAAKPTQRQVLAELLLD
>NC_013739.1|WP_012936046.1|4885097_4885580_-|SsrA-binding-protein-SmpB
MAKGKGKKKFAPGDVATNRQARFRFRLLDTFEAGMVLTGTEVKSLREGGAQMKDAYALVRGGEVWLVNMHIPPYASAYRDNHLPERDRKLLLHRREIERLVGKTRERGLTLVPTRIYFRGARAKCEIALAQGKDQFDKRQSIKSREQAREMQRATREYQR
>NC_013739.1|WP_148261364.1|4885590_4887276_-|RNB-domain-containing-ribonuclease
MLEKRGRHLVGEPYFQRGPRLIVDRDRRASLGDLVLLRAGQRGKGHAKVVRRIGRPDVARDVIEALMLDRGLRRRFDPAVERAAREPRAVDVPGRRDLRDLTTFTIDPATAKDFDDAISAEQTGPDRWRIWVHIADVSAYVRPGDLIDREAYRRGTSVYVPAKVEPMLPEGLSNVACSLRPGEDRLAVTAELELHGPSVARASFYRSTIRSDERLDYDRVDRIFAGAEPALEPWAQPLAAARGAAAALAARRDAQGALAIESVEPEFAFDREGHVTAAAGVVQTESHRLIEHLMILANEQVARLLSERKVPTLYRVHERPDGSAAERLIAQLASLGVPTPPLPEQPTPQQGAEAIAVASHLVAAYVRRSRRGGIGLNSLVLRALKQARYDPRNLGHTGLGLTHYCHFTSPIRRYPDLVCHRALLSAVGAGEDAPQASRLPGAGDWASARERDAMQVERAADDVARCFLLERTLFETGFDQDFDGEVTGVIGAGAFVAFGDGYEGMLPVRKLHGEWWELNEEGTILNGTRTGKAIRIGDAVRVQVDRVDAPRGRVDLFPVEL
>NC_013739.1|WP_160165558.1|4887392_4888595_-|PDZ-domain-containing-protein
MPRRASRIPLVLAGALIAVVMLGVGIYLGGHASNLPDPIRSALVDDDESQLMQQAIDTISDAYYRPVSRDELVNKSVEGAVNSLDDQFSHYFDPRTYERFQHATNPRFSGIGVTVQGTPRGLRVAHVIDDTPAAKAGLRDGDMIVAVGRSTLAGHPASYGISLVKGEPGTTVELTIERDGRRRVQTIERAEIVEPVVEGRMVQTRAGRFGVVVFTSFTSNSSAQVRAAVDRLLARGARGIVLDLRGNGGGLLNEAVDTASIFIPDGTIVSTDGRARERHVYTATGGAIRSSVPVVVLVDRNTASSSEIVTGALQDRRRAEVVGTRTYGKGVFQEIRELPNGGALDITVGQYFLPSGKNIGGRGVREGDGIQPDVQARDDPDTRRDEGLDAALRALATESR
>NC_013739.1|WP_012936049.1|4888662_4889484_+|class-I-SAM-dependent-methyltransferase
MSIDRRIADYYELGAEHERLETISRVEGVRTRELLDRLLPAPPAVVLDVGGAAGIYALPLAAAGYEVHLLDPVLLHVQQAREASAAQAAAGGDPLMETVVGDARALPWSDGAADAVLLLGPLYHLDADGRASALAEARRVLRPGGLVLAAAISRFASTLDGIHARALADPAFAQVAAHDVRTGEHRNDPHERPEWFTTAYFHHPDELWEEVAVAGFAVEGVLAVEGVASFLRDEAWWLEDEQRRAALLDAIRSVEQEPSVLGASAHLLAVGRA
>NC_013739.1|WP_148261365.1|4889528_4890392_-|FtsX-like-permease-family-protein
MRSLGRNAAPSFAALATVLLTMLVVGVFIPIVQATTGAANDVRKRVLVDVYLRRDATQRDAARVRAMLAGTPNVKRVEFISKQEAYEQQVKKDPEAFELLGANPLPDTFRITPEDPDTVLALKSELAPAAAGGTRTPVDSAIDEVRDRREDTTKILQVTRFVKLMAGTLALLLVAASIFLIANTIRLSLYARRREVEVMKLVGATDWFIRWPFVIEGVIVGALGTTLAILLLAVGKIAIIDPLASDFALISAPETIGFGVLIAVMMGAGITISAIGSGLSLRRFLKV
>NC_013739.1|WP_012936051.1|4890418_4891408_-|cell-division-ATP-binding-protein-FtsE
MALSVRRPSLGRRAVPAHPPKHVAASQSAPAASRRGTPVIDFKAVEKHYDVGAVGLDQASFSVQRGEFVFLVGSTGSGKSTIMRLLIKELEPTGGTIGVAGRDLSEITRRRVPYYRRNIGAVFQDFKLLPNRTVYDNVAYALQVTGGSRKDIRAKVPDILRLTGLSTKLHNYPDQLSGGEQQRVAIARAFVNHPPLLLADEPTGNLDPETSIGIMQLLYRINKTGTTVLVATHDHGMVDKMRRRVIELSKGRIVRDEATGLYARDESTREFAARLRNDAPVAPETMAVEASRGSRTARFREAAAARETAEAEATAAREAAAQDPTPSRK
>NC_013739.1|WP_012936052.1|4891531_4892785_+|insulinase-family-protein
MTAISSSTAPNGLPIHRVQLDGTRAVTALVAFDAGARTERAEENGMAHFLEHLVFKGGEKYVTYRDVNETAENLGAQLNAYTSHDLVAFHITARAEKALEAIDLLTDFVGRPRLDGEELDRERGVVIQEIARSNDQPSTVAEHVIDRAAFGDHPLGRPVLGPEEHLRDTFTREAIVAFRQRQWAGSRGGAFVVGNLEHLPANGALDELFDRFPDLPAPPPYEPAPGFAPRTLVEERDSNQSHLRMMYRPAIDATDRRARAALAIYSTLLGGSMGSRLFDEIREQRGLAYSVYALSHAFSDVPILQLSAGLESGKAVEAYTRMREIVAELRTEGPTVEEVERARAYAAGARVLAFENTNAVARHAANQTIVFGEEVDPDAAIAALDAVTYDEVAEVARGIADELAIGVVGPHTVADFA

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
NC_013739_5	5.3\|4880544\|16\|NC_013739\|CRISPRCasFinder	4880544-4880559	16	NC_013739.1	1446137-1446152	0	1.0
NC_013739_5	5.3\|4880544\|16\|NC_013739\|CRISPRCasFinder	4880544-4880559	16	NC_013739.1	2410784-2410799	0	1.0
NC_013739_5	5.7\|4880739\|19\|NC_013739\|CRISPRCasFinder	4880739-4880757	19	NC_013739.1	6249107-6249125	2	0.895

1. spacer 5.3|4880544|16|NC_013739|CRISPRCasFinder matches to position: 1446137-1446152, mismatch: 0, identity: 1.0

cggcgctgccggcacc	CRISPR spacer
cggcgctgccggcacc	Protospacer
****************

2. spacer 5.3|4880544|16|NC_013739|CRISPRCasFinder matches to position: 2410784-2410799, mismatch: 0, identity: 1.0

cggcgctgccggcacc	CRISPR spacer
cggcgctgccggcacc	Protospacer
****************

3. spacer 5.7|4880739|19|NC_013739|CRISPRCasFinder matches to position: 6249107-6249125, mismatch: 2, identity: 0.895

aggcgtcaagggcgacaag	CRISPR spacer
aggcgacaagggcgaccag	Protospacer
***** ********** **

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_013739_5	5.4\|4880586\|19\|NC_013739\|CRISPRCasFinder	4880586-4880604	19	MG298964	Streptomyces phage Alsaber, complete genome	18459-18477	0	1.0
NC_013739_5	5.4\|4880586\|19\|NC_013739\|CRISPRCasFinder	4880586-4880604	19	MG298964	Streptomyces phage Alsaber, complete genome	18468-18486	0	1.0
NC_013739_5	5.4\|4880586\|19\|NC_013739\|CRISPRCasFinder	4880586-4880604	19	MN908687	Gordonia phage Skog, complete genome	81716-81734	0	1.0
NC_013739_5	5.4\|4880586\|19\|NC_013739\|CRISPRCasFinder	4880586-4880604	19	MT711978	Streptomyces phage Endor1, complete genome	18914-18932	0	1.0
NC_013739_5	5.4\|4880586\|19\|NC_013739\|CRISPRCasFinder	4880586-4880604	19	MK977696	Gordonia phage SCentae, complete genome	51364-51382	0	1.0
NC_013739_5	5.4\|4880586\|19\|NC_013739\|CRISPRCasFinder	4880586-4880604	19	MH271302	Gordonia phage Margaret, complete genome	22911-22929	0	1.0
NC_013739_5	5.4\|4880586\|19\|NC_013739\|CRISPRCasFinder	4880586-4880604	19	MK977695	Gordonia phage Pupper, complete genome	51218-51236	0	1.0
NC_013739_5	5.7\|4880739\|19\|NC_013739\|CRISPRCasFinder	4880739-4880757	19	MT639639	Gordonia phage LittleFella, complete genome	27093-27111	0	1.0
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MH047632	Mycobacterium phage Puppy, complete genome	2022-2049	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	KY083059	Mycobacterium phage Achebe, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	KX550442	Mycobacterium phage Badger, complete genome	2076-2103	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MN284905	Mycobacterium phage AbbysRanger, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MK359322	Mycobacterium phage Datway, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MK359310	Mycobacterium phage Katalie136, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MK279898	Mycobacterium phage Cici, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MK875799	Mycobacterium phage Xena, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MK494115	Mycobacterium phage Bumblebee11, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	NC_042308	Mycobacterium virus Backyardigan, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MF668278	Mycobacterium phage Morpher26, complete genome	2075-2102	4	0.857
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	NC_023709	Mycobacterium phage Wile, complete genome	2076-2103	4	0.857
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	MT498035	Gordonia Phage Barsten, complete genome	52436-52468	5	0.848
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	MH051259	Mycobacterium phage TNguyen7, complete genome	2020-2047	5	0.821
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	KY464936	Mycobacterium phage Idleandcovert, complete genome	2022-2049	5	0.821
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	NZ_CP007130	Gemmatirosa kalamazoonesis strain KBS708 plasmid 2, complete sequence	76690-76722	6	0.818
NC_013739_5	5.8\|4880784\|28\|NC_013739\|CRISPRCasFinder	4880784-4880811	28	MK279857	Mycobacterium phage IronMan, complete genome	4586-4613	6	0.786
NC_013739_5	5.8\|4880784\|28\|NC_013739\|CRISPRCasFinder	4880784-4880811	28	NC_016113	Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCAT, complete sequence	209353-209380	6	0.786
NC_013739_5	5.8\|4880784\|28\|NC_013739\|CRISPRCasFinder	4880784-4880811	28	NC_017585	Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCATT, complete sequence	1603768-1603795	6	0.786
NC_013739_5	5.8\|4880784\|28\|NC_013739\|CRISPRCasFinder	4880784-4880811	28	MK448671	Streptococcus phage Javan115, complete genome	32494-32521	6	0.786
NC_013739_5	5.8\|4880784\|28\|NC_013739\|CRISPRCasFinder	4880784-4880811	28	MK875791	Gordonia phage Yakult, complete genome	22210-22237	6	0.786
NC_013739_5	5.9\|4880838\|28\|NC_013739\|CRISPRCasFinder	4880838-4880865	28	NZ_CP029358	Azospirillum sp. CFH 70021 plasmid unnamed3	96275-96302	6	0.786
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	NZ_CP032344	Azospirillum brasilense strain MTCC4038 plasmid p5, complete sequence	15015-15047	7	0.788
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	NC_020548	Azoarcus sp. KH32C plasmid pAZKH, complete sequence	189259-189291	7	0.788
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	NZ_CP033317	Azospirillum brasilense strain Sp 7 plasmid p5, complete sequence	87274-87306	7	0.788
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	NZ_CP033323	Azospirillum brasilense strain Cd plasmid p5, complete sequence	244282-244314	7	0.788
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	NZ_CP012919	Azospirillum brasilense strain Sp 7 plasmid ABSP7_p5, complete sequence	19739-19771	7	0.788
NC_013739_5	5.5\|4880631\|37\|NC_013739\|CRISPRCasFinder	4880631-4880667	37	KU761559	Mycobacterium phage ArcherNM, complete genome	4622-4658	7	0.811
NC_013739_5	5.8\|4880784\|28\|NC_013739\|CRISPRCasFinder	4880784-4880811	28	KY092484	Streptomyces phage Raleigh, complete genome	17488-17515	7	0.75
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	NZ_CP022541	Antarctobacter heliothermus strain SMS3 plasmid pSMS3-1, complete sequence	257124-257156	8	0.758
NC_013739_5	5.5\|4880631\|37\|NC_013739\|CRISPRCasFinder	4880631-4880667	37	MG655270	Erwinia phage vB_EamM_Mortimer, complete genome	257935-257971	8	0.784
NC_013739_1	1.1\|466323\|33\|NC_013739\|CRISPRCasFinder	466323-466355	33	NZ_AP014705	Methylobacterium aquaticum strain MA-22A plasmid pMaq22A_1p, complete sequence	529638-529670	9	0.727

1. spacer 5.4|4880586|19|NC_013739|CRISPRCasFinder matches to MG298964 (Streptomyces phage Alsaber, complete genome) position: , mismatch: 0, identity: 1.0

gggcatccagggcatccag	CRISPR spacer
gggcatccagggcatccag	Protospacer
*******************

2. spacer 5.4|4880586|19|NC_013739|CRISPRCasFinder matches to MG298964 (Streptomyces phage Alsaber, complete genome) position: , mismatch: 0, identity: 1.0

gggcatccagggcatccag	CRISPR spacer
gggcatccagggcatccag	Protospacer
*******************

3. spacer 5.4|4880586|19|NC_013739|CRISPRCasFinder matches to MN908687 (Gordonia phage Skog, complete genome) position: , mismatch: 0, identity: 1.0

gggcatccagggcatccag	CRISPR spacer
gggcatccagggcatccag	Protospacer
*******************

4. spacer 5.4|4880586|19|NC_013739|CRISPRCasFinder matches to MT711978 (Streptomyces phage Endor1, complete genome) position: , mismatch: 0, identity: 1.0

gggcatccagggcatccag	CRISPR spacer
gggcatccagggcatccag	Protospacer
*******************

5. spacer 5.4|4880586|19|NC_013739|CRISPRCasFinder matches to MK977696 (Gordonia phage SCentae, complete genome) position: , mismatch: 0, identity: 1.0

gggcatccagggcatccag	CRISPR spacer
gggcatccagggcatccag	Protospacer
*******************

6. spacer 5.4|4880586|19|NC_013739|CRISPRCasFinder matches to MH271302 (Gordonia phage Margaret, complete genome) position: , mismatch: 0, identity: 1.0

gggcatccagggcatccag	CRISPR spacer
gggcatccagggcatccag	Protospacer
*******************

7. spacer 5.4|4880586|19|NC_013739|CRISPRCasFinder matches to MK977695 (Gordonia phage Pupper, complete genome) position: , mismatch: 0, identity: 1.0

gggcatccagggcatccag	CRISPR spacer
gggcatccagggcatccag	Protospacer
*******************

8. spacer 5.7|4880739|19|NC_013739|CRISPRCasFinder matches to MT639639 (Gordonia phage LittleFella, complete genome) position: , mismatch: 0, identity: 1.0

aggcgtcaagggcgacaag	CRISPR spacer
aggcgtcaagggcgacaag	Protospacer
*******************

9. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MH047632 (Mycobacterium phage Puppy, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
ggggccgcagggtcccatcggtcctcag	Protospacer
************.***********  *

10. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to KY083059 (Mycobacterium phage Achebe, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

11. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to KX550442 (Mycobacterium phage Badger, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

12. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MN284905 (Mycobacterium phage AbbysRanger, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

13. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MK359322 (Mycobacterium phage Datway, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

14. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MK359310 (Mycobacterium phage Katalie136, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

15. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MK279898 (Mycobacterium phage Cici, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

16. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MK875799 (Mycobacterium phage Xena, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

17. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MK494115 (Mycobacterium phage Bumblebee11, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

18. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to NC_042308 (Mycobacterium virus Backyardigan, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

19. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MF668278 (Mycobacterium phage Morpher26, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

20. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to NC_023709 (Mycobacterium phage Wile, complete genome) position: , mismatch: 4, identity: 0.857

ggggccgcagggccccatcggtccgaat	CRISPR spacer
gggcccgcagggccccatcggcccgcaa	Protospacer
*** *****************.*** *

21. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to MT498035 (Gordonia Phage Barsten, complete genome) position: , mismatch: 5, identity: 0.848

-cggcgatcgagcgtcgcgtcggcgcgccgctcg	CRISPR spacer
gcgacggtc-agcgtcgagtcggcgcgtcgctcg	Protospacer
 **.**.** ******* *********.******

22. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to MH051259 (Mycobacterium phage TNguyen7, complete genome) position: , mismatch: 5, identity: 0.821

ggggccgcagggccccatcggtccgaat	CRISPR spacer
agggccgcagggtcccatcggtcctcag	Protospacer
.***********.***********  *

23. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to KY464936 (Mycobacterium phage Idleandcovert, complete genome) position: , mismatch: 5, identity: 0.821

ggggccgcagggccccatcggtccgaat	CRISPR spacer
agggccgcagggtcccatcggtcctcag	Protospacer
.***********.***********  *

24. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to NZ_CP007130 (Gemmatirosa kalamazoonesis strain KBS708 plasmid 2, complete sequence) position: , mismatch: 6, identity: 0.818

cggcgatcgagcgtcgcgtcggcgcgccgctcg	CRISPR spacer
tgccgcacgagcgtgccgtcggcgcgccgctcg	Protospacer
.* **  *******  *****************

25. spacer 5.8|4880784|28|NC_013739|CRISPRCasFinder matches to MK279857 (Mycobacterium phage IronMan, complete genome) position: , mismatch: 6, identity: 0.786

aggcgtcaagggcgaccaaggcacccag	CRISPR spacer
aggcgacaagggcgaccaaggcgagatg	Protospacer
***** ****************.    *

26. spacer 5.8|4880784|28|NC_013739|CRISPRCasFinder matches to NC_016113 (Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCAT, complete sequence) position: , mismatch: 6, identity: 0.786

aggcgtcaagggcgaccaaggcacccag	CRISPR spacer
cgtcgtcgagggcgaccgaggcaccctt	Protospacer
 * ****.*********.********

27. spacer 5.8|4880784|28|NC_013739|CRISPRCasFinder matches to NC_017585 (Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCATT, complete sequence) position: , mismatch: 6, identity: 0.786

aggcgtcaagggcgaccaaggcacccag	CRISPR spacer
cgtcgtcgagggcgaccgaggcaccctt	Protospacer
 * ****.*********.********

28. spacer 5.8|4880784|28|NC_013739|CRISPRCasFinder matches to MK448671 (Streptococcus phage Javan115, complete genome) position: , mismatch: 6, identity: 0.786

aggcgtcaagggcgaccaaggcacccag	CRISPR spacer
aggccccaagggcgaccaaggcatacct	Protospacer
**** .*****************. *

29. spacer 5.8|4880784|28|NC_013739|CRISPRCasFinder matches to MK875791 (Gordonia phage Yakult, complete genome) position: , mismatch: 6, identity: 0.786

aggcgtcaagggcgaccaaggcacccag	CRISPR spacer
cgtgctcaagggcgaccagggcatccag	Protospacer
 *   *************.****.****

30. spacer 5.9|4880838|28|NC_013739|CRISPRCasFinder matches to NZ_CP029358 (Azospirillum sp. CFH 70021 plasmid unnamed3) position: , mismatch: 6, identity: 0.786

ggggccgcagggccccatcggtccgaat	CRISPR spacer
ctggccggacggccccatcggtccgagc	Protospacer
  ***** * ****************..

31. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to NZ_CP032344 (Azospirillum brasilense strain MTCC4038 plasmid p5, complete sequence) position: , mismatch: 7, identity: 0.788

cggcgatcgagcgtcgcgtcggcgcgccgctcg	CRISPR spacer
agaccatcgagcgtcgcgtcgacccgccggccg	Protospacer
 *.* ****************.* ***** .**

32. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to NC_020548 (Azoarcus sp. KH32C plasmid pAZKH, complete sequence) position: , mismatch: 7, identity: 0.788

cggcgatcgagcgtcgcgtcggcgcgccgctcg	CRISPR spacer
cggcgatcgtgcgccgcgtcggcgaggagcgct	Protospacer
********* ***.********** *  ** *

33. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to NZ_CP033317 (Azospirillum brasilense strain Sp 7 plasmid p5, complete sequence) position: , mismatch: 7, identity: 0.788

cggcgatcgagcgtcgcgtcggcgcgccgctcg	CRISPR spacer
agaccatcgagcgtcgcgtcgacccgccggccg	Protospacer
 *.* ****************.* ***** .**

34. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to NZ_CP033323 (Azospirillum brasilense strain Cd plasmid p5, complete sequence) position: , mismatch: 7, identity: 0.788

cggcgatcgagcgtcgcgtcggcgcgccgctcg	CRISPR spacer
agaccatcgagcgtcgcgtcgacccgccggccg	Protospacer
 *.* ****************.* ***** .**

35. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to NZ_CP012919 (Azospirillum brasilense strain Sp 7 plasmid ABSP7_p5, complete sequence) position: , mismatch: 7, identity: 0.788

cggcgatcgagcgtcgcgtcggcgcgccgctcg	CRISPR spacer
agaccatcgagcgtcgcgtcgacccgccggccg	Protospacer
 *.* ****************.* ***** .**

36. spacer 5.5|4880631|37|NC_013739|CRISPRCasFinder matches to KU761559 (Mycobacterium phage ArcherNM, complete genome) position: , mismatch: 7, identity: 0.811

aggcatccagggcgccaagggcgacaccgg--cggccaa	CRISPR spacer
gggcatccaaggccccaagggcgacaccggacctgct--	Protospacer
.********.*** ****************  * **.

37. spacer 5.8|4880784|28|NC_013739|CRISPRCasFinder matches to KY092484 (Streptomyces phage Raleigh, complete genome) position: , mismatch: 7, identity: 0.75

aggcgtcaagggcgaccaaggcacccag	CRISPR spacer
gggcgtcaagggcgaccagggcgtacct	Protospacer
.*****************.***.. *

38. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to NZ_CP022541 (Antarctobacter heliothermus strain SMS3 plasmid pSMS3-1, complete sequence) position: , mismatch: 8, identity: 0.758

cggcgatcgagcgtcgcgtcggcgcgccgctcg-	CRISPR spacer
tccggatcgagcggcgcgtctgcgcgcc-cgcgt	Protospacer
.   ********* ****** ******* * **

39. spacer 5.5|4880631|37|NC_013739|CRISPRCasFinder matches to MG655270 (Erwinia phage vB_EamM_Mortimer, complete genome) position: , mismatch: 8, identity: 0.784

aggcatccagggcgccaagggcgacaccggcggccaa	CRISPR spacer
tggtaatgacggcgccaagggcgacaccggcgccaaa	Protospacer
 **.* . * ********************** * **

40. spacer 1.1|466323|33|NC_013739|CRISPRCasFinder matches to NZ_AP014705 (Methylobacterium aquaticum strain MA-22A plasmid pMaq22A_1p, complete sequence) position: , mismatch: 9, identity: 0.727

cggcgatcgagcgtcgcgtcggcgcgccgctcg	CRISPR spacer
gccggatcgagcgtcgcgtgggcgcggcgcatc	Protospacer
    *************** ****** *** .

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

688888 : 698911

Cronobacter_phage(16.67%)

The bacterium proteins that are colored denote the protein is present at specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin' and 'tRNA')

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_012932133.1\|688888_691567_-	ATP-dependent chaperone ClpB	K4FB40	Cronobacter_phage	1.2e-119	31.8
WP_012932134.1\|691570_691906_-	hypothetical protein	NA	NA	NA	NA
WP_012932135.1\|691906_692920_-	DnaJ domain-containing protein	A0A0P0YMJ9	Yellowstone_lake_phycodnavirus	3.5e-11	48.4
WP_012932136.1\|692920_693487_-	nucleotide exchange factor GrpE	NA	NA	NA	NA
WP_012932137.1\|693464_695351_-	molecular chaperone DnaK	A0A0N9QXN8	Chrysochromulina_ericina_virus	2.8e-142	47.9
WP_012932138.1\|695364_695538_-	hypothetical protein	NA	NA	NA	NA
WP_041730050.1\|695835_696672_+	sigma-70 family RNA polymerase sigma factor	A0A1W6DY88	Aeromonas_phage	1.0e-08	29.6
WP_012932140.1\|696728_697181_+	thioredoxin	A0A1J0GW78	Streptomyces_phage	4.1e-12	35.2
WP_012932141.1\|697204_698911_-	FAD-dependent oxidoreductase	G3MA85	Bacillus_virus	8.8e-31	29.5

DBSCAN-SWA_2

4883036 : 4892785

Mycobacterium_phage(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_041730858.1\|4883036_4884512_-	MFS transporter	A0A0M3UL24	Mycobacterium_phage	1.3e-54	34.3
WP_012936045.1\|4884601_4884988_+	MarR family transcriptional regulator	NA	NA	NA	NA
WP_012936046.1\|4885097_4885580_-	SsrA-binding protein SmpB	W5RAM5	Staphylococcus_phage	1.7e-32	48.6
WP_148261364.1\|4885590_4887276_-	RNB domain-containing ribonuclease	Q0GXV6	Lactococcus_phage	6.7e-47	29.4
WP_160165558.1\|4887392_4888595_-	PDZ domain-containing protein	A0A0R6PIZ1	Moraxella_phage	1.8e-17	26.5
WP_012936049.1\|4888662_4889484_+	class I SAM-dependent methyltransferase	NA	NA	NA	NA
WP_148261365.1\|4889528_4890392_-	FtsX-like permease family protein	NA	NA	NA	NA
WP_012936051.1\|4890418_4891408_-	cell division ATP-binding protein FtsE	G9BWD6	Planktothrix_phage	3.9e-31	39.3
WP_012936052.1\|4891531_4892785_+	insulinase family protein	G3MBJ8	Bacillus_virus	3.8e-31	28.2

Anti-CRISPR protein detection

Acr ID	Acr position	Acr size	Homology with known anti	Neighbor HTH/AcRanker	Neighbor Aca	In prophage	Protospacer in prophage

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NC_013739

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection