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
AP019378	Bordetella parapertussis Bpp01 DNA, complete genome	8 crisprs	csa3,DEDDh,cas3,DinG,RT	3	0	2	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: AP019378_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

AP019378_1

64056-64305

Orphan

Consensus_repeat	Method
CCACTGCGCTGCCCTGCGCGGCGGGTGCCTGGCACCTTGCCGCCACCCACGTGC	PILER-CR

2 spacers

The CRISPR arrays of AP019378_1

>merge|AP019378|1|64056-64305|PILER-CR
CCACTGCGCTGCCCTGCGCGGCGGGTGCCTGGCACCTTGCCGCCACCCACGTGCCAGGCACCCGCCGCATACACCGCGCTGCTCGCAGCGGCCATCGCAGCGGGTGCCTGGCACCCATGCAGGCACCGTCTCTTCCACGCCAACAACCACGACCGCAGCGGACCCGGGTGCCTGGCTCCCGCCACACCGGCCCGCGCCACTGCGCTGCCCTGCGCGGCGGGTGCCTGGCACCTTGCCGCCACCCACGTGC

>AP019378|1|1|64056-64305|PILER-CR
CCACTGCGCTGCCCTGCGCGGCGGGTGCCTGGCACCTTGCCGCCACCCACGTGC	CAGGCACCCGCCGCATACACCGCGCTGCTCGCAGCGGCCAT
CGCAGCGGGTGCCTGGCACCCATGCAGGCACCGTCTCTTCCACGCCAACAACCA	CGACCGCAGCGGACCCGGGTGCCTGGCTCCCGCCACACCGGCCCGCGCCACTGCGCTGCCCTGCGCGGCGGGTGCCTGGC
ACCTTGCCGCCACCCACGTGC

Protein	Signature genes	Signature genes Name	Protein_function
AP019378.1\|BBH96486.1\|68466_69264_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226862
AP019378.1\|BBH96487.1\|69260_69779_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226049
AP019378.1\|BBH96480.1\|62407_63313_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|372665
AP019378.1\|BBH96491.1\|73479_74013_+\|DUF2778-domain-containing-protein	unknown	unknown	unknown
AP019378.1\|BBH96478.1\|58778_61328_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|370755
AP019378.1\|BBH96472.1\|51327_51792_+\|oxidoreductase	unknown	unknown	gnl\|CDD\|224991
AP019378.1\|BBH96483.1\|65774_66338_+\|type-VI-secretion-system-associated-protein	unknown	unknown	gnl\|CDD\|226047
AP019378.1\|BBH96481.1\|63302_63914_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377450
AP019378.1\|BBH96474.1\|54208_55159_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176131
AP019378.1\|BBH96489.1\|71726_72386_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|371873
AP019378.1\|BBH96477.1\|58368_58782_+\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH96490.1\|72430_73483_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377755
AP019378.1\|BBH96476.1\|55958_58352_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|163676
AP019378.1\|BBH96473.1\|51788_54140_+\|aldehyde-dehydrogenase	unknown	unknown	gnl\|CDD\|224446
AP019378.1\|BBH96475.1\|55155_55866_-\|transcriptional-regulator	unknown	unknown	gnl\|CDD\|224332
AP019378.1\|BBH96485.1\|67931_68405_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377536
AP019378.1\|BBH96488.1\|69778_71692_+\|type-VI-secretion-system-protein-ImpG	unknown	unknown	gnl\|CDD\|377574
AP019378.1\|BBH96482.1\|64703_65732_+\|membrane-protein	unknown	unknown	gnl\|CDD\|274544
AP019378.1\|BBH96484.1\|66359_67862_+\|type-VI-secretion-protein-EvpB	unknown	unknown	gnl\|CDD\|226048
AP019378.1\|BBH96479.1\|61317_62175_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|224276

Protein	Function_ID	Function_description	E-value
AP019378.1\|BBH96486.1\|68466_69264_+\|hypothetical-protein	gnl\|CDD\|226862	COG4455, ImpE, Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only].	1.08358e-65
AP019378.1\|BBH96487.1\|69260_69779_+\|hypothetical-protein	gnl\|CDD\|226049	COG3518, COG3518, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport].	3.89545e-22
AP019378.1\|BBH96480.1\|62407_63313_+\|hypothetical-protein	gnl\|CDD\|372665	pfam13665, DUF4150, Domain of unknown function (DUF4150).	3.48044e-43
AP019378.1\|BBH96478.1\|58778_61328_+\|hypothetical-protein	gnl\|CDD\|370755	pfam09937, DUF2169, Uncharacterized protein conserved in bacteria (DUF2169). This domain, found in various hypothetical prokaryotic proteins, has no known function.	3.30347e-92
AP019378.1\|BBH96484.1\|66359_67862_+\|type-VI-secretion-protein-EvpB	gnl\|CDD\|226048	COG3517, COG3517, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport].	0
AP019378.1\|BBH96483.1\|65774_66338_+\|type-VI-secretion-system-associated-protein	gnl\|CDD\|226047	COG3516, COG3516, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport].	3.22609e-77
AP019378.1\|BBH96481.1\|63302_63914_+\|hypothetical-protein	gnl\|CDD\|377450	pfam05076, SUFU, Suppressor of fused protein (SUFU). SUFU, encoding the human orthologue of Drosophila suppressor of fused, appears to have a conserved role in the repression of Hedgehog signaling. SUFU exerts its repressor role by physically interacting with GLI proteins in both the cytoplasm and the nucleus. SUFU has been found to be a tumor-suppressor gene that predisposes individuals to medulloblastoma by modulating the SHH signaling pathway. Genomic contextual analysis of bacterial SUFU versions revealed that they are immunity proteins against diverse nuclease toxins in polymorphic toxin systems.	1.41634e-29
AP019378.1\|BBH96472.1\|51327_51792_+\|oxidoreductase	gnl\|CDD\|224991	COG2080, CoxS, Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion].	3.13747e-80
AP019378.1\|BBH96489.1\|71726_72386_+\|hypothetical-protein	gnl\|CDD\|371873	pfam12059, DUF3540, Protein of unknown function (DUF3540). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.	2.97486e-69
AP019378.1\|BBH96474.1\|54208_55159_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176131	cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to 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.	1.27165e-58
AP019378.1\|BBH96490.1\|72430_73483_+\|hypothetical-protein	gnl\|CDD\|377755	pfam06996, T6SS_TssG, Type VI secretion, TssG. This is a family of Gram-negative bacterial proteins that form part of the type VI pathogenicity secretion system (T6SS), including TssG. TssG is homologs to phage tail proteins and is required for proper assembly of the Hcp tube in bacteria.One other member in this family, SciB (Q93IT4) from Salmonella enterica, is thought to be involved in virulence.	8.00147e-108
AP019378.1\|BBH96476.1\|55958_58352_+\|hypothetical-protein	gnl\|CDD\|163676	cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain. 3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".	1.14907e-139
AP019378.1\|BBH96473.1\|51788_54140_+\|aldehyde-dehydrogenase	gnl\|CDD\|224446	COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion].	3.33897e-95
AP019378.1\|BBH96475.1\|55155_55866_-\|transcriptional-regulator	gnl\|CDD\|224332	COG1414, IclR, Transcriptional regulator [Transcription].	3.62923e-39
AP019378.1\|BBH96485.1\|67931_68405_+\|hypothetical-protein	gnl\|CDD\|377536	pfam05638, T6SS_HCP, Type VI secretion system effector, Hcp. HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head. Initially Hcp forms a hexameric structure with a central channel of 40 Angstroms. These hexamers pile up one on top of each other forming nanotubes resembling the gp19 tail phage tube.	4.30171e-49
AP019378.1\|BBH96488.1\|69778_71692_+\|type-VI-secretion-system-protein-ImpG	gnl\|CDD\|377574	pfam05947, T6SS_TssF, Type VI secretion system, TssF. This is a family of Gram-negative bacterial proteins that form part of the type VI pathogenicity secretion system (T6SS), including TssF. TssF is homologs to phage tail proteins and is required for proper assembly of the Hcp tube (the T6SS inner tube) in bacteria.	0
AP019378.1\|BBH96482.1\|64703_65732_+\|membrane-protein	gnl\|CDD\|274544	TIGR03363, VI_chp_8, type VI secretion-associated protein, ImpA family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812).	1.06758e-109
AP019378.1\|BBH96479.1\|61317_62175_+\|hypothetical-protein	gnl\|CDD\|224276	COG1357, COG1357, Pentapeptide repeats containing protein [Function unknown].	3.02847e-22

>AP019378.1|BBH96481.1|63302_63914_+|hypothetical-protein
MAPESKASAQPSPRHKAVARHALKVFGGTPVVHAYRHDQIDTLSIDMLAVDDSPDDGLVSYSTLGLFDLELRHDDGHPMATRVELCAEMPEDLQSWANVLATAAFGLMRSGQAVMPGSVLPDCVAEYYPDATVPHLYLCVPFSWQDGEFPRCDADGLLVNWLQAVPISETERQFIETAGPDAFEDELLEADPDIYDLSRPAVR
>AP019378.1|BBH96480.1|62407_63313_+|hypothetical-protein
MFADCQLMGMDLAFPDICKTPPALLPIPYPNFALGPMGIPNVWNVLLMAMPAHNLLTTIALSNGDNPGIGMGLISQTVMAQARRITCVPNVLFGCIPATRLTGVTVQNTINTVGMRVVPSQLKVVLLGGGGGGGAAKAAKSAKAGKGPGARAGATARRGAGGKGGAAGKGGQGGGKAAGSGKSGGGKGAKPRKPGDDPRYRRGKFRKGVRDKAWDQEARRSKDGVVRDPVSGKKMKKDEPWDMGHKPGYEHRKHVRSAKERDIDRKQFLDEYNDPSHYRPELPKSNRGHQGELKTDDYFGP
>AP019378.1|BBH96479.1|61317_62175_+|hypothetical-protein
MDAETLRDWVRQGRPLVGLDLRAAALQGADLAGALLQDCDLRGAALAGSRWRDSRFSGCRMEQADWRGADVAQCAFFRCELAEAVFAAAECAGASWVECRAAGADFRATPLHGSHFVQCALDGARLDQAEMREGGFAECTLEQASLAGAALRQTLFFRADLRTVDLAGARLERVVFVECDLSGQRLAGQFLGGSQFVEARMDGCDLREASMAQCNFKGASLRQACLAGASGARAMFAQADLSAADCSGARLPQSLWADAILDGAVFSGADLAQAMLHRARGRGAL
>AP019378.1|BBH96478.1|58778_61328_+|hypothetical-protein
MKIVKPLRLGLLSRPYRMRGRQRLGLAVFALATLDEQALLQPEADLWSLAGEALGEDGVLDLAVPKPCAEFLVSGAAYTAHQQDRTACMARVRVGELEKTLAVFGERYWLDGKPTPPAPFEAMPLDWAHAFGGPEYADNPHGRGAGDERIAGVRTRRLPNVEPARGRMQRPDQRPEPAGFGPVSPLWPRRFARAGQYHESWLDDGFPGFLDTLDPHFFNAAAPDQWWPGQPELAAGAPYALWNLHPRLACQQGALPRWRARCLLRRAGETALEDVALRLTTAWFFPDRERLLLIYHGATDIAQDDGADIELAMPALDAADAPRPLAHYEAVLAQRLDAQDGALHALRDKDLLPAQALGPWDALQAANPMEQPFAVNQRARGAAIRAQLGEQARAHGVDPRAYEPQPAPMPAAPQLDDLPDIARHMRQAAQEARIDALHARRRMAEALQARGAELPPAMGAAALAAAADGAGRGGPPSLHNHPALATLQELARAQPLGSDADRLDAGSVGARLREAQQQLGRLYLHAAHHQPPAEAARPARAARLRRRVQALMAGSRDLAGLDLTGADLSGLDLRGARCVGTWMEGVDLSGALLDDADLSQAVLARAHAEGGSWRRAVLAGANLGQAALDGVDLAGARLSSPVLDGIVLVDCALSASRWNDCHLAGAWLERCRFDQAELDTVTFWQGTLLRETGFAAARLARVTWLDCELDGLDFAGARLRRCAWVQSQCGAAPNWAGAELQTCCVVETDMPHAVFAGATLRECSLRDTVLDHADFTGAALWRCDLSQASLAEADLPGALLQKATLTHADLRGANLFRADLGLAVLDDTSDTRGAYTHLANTRPRARHGR
>AP019378.1|BBH96477.1|58368_58782_+|hypothetical-protein
MGSTAWWIAGTLATLAAVGLVALLVRGGARPYEAERALAAQLARTGRPAQAEVLALDRQPGGELYAAPMKLALRYADAMGRARQAELHVYIDSELLVNFMPGQAIHVRLDPSDAARIAVDRERSPTEIPAAWRRRHP
>AP019378.1|BBH96476.1|55958_58352_+|hypothetical-protein
MEKILISEVGPRDGLQNVQAVMPTEAKLQWIGALAAAGLREVEVGSFVHPKWLPQMADADAVVPRARAIAGLTVLALVPNLKGAQRALAAGAHKITVPVSASQTHNMANVRMTCEQSIEAIAAICAYRDEMAGAGPRVEVEAGIASAFGCSREGAVPERWVMEMAERLARAGVDSIGLSDSVGVAHPRQVKRMFGQLLRLLGERAGGAHLHNTRGQGLANAVAALEAGVTTLDASQGGLGGCPYAPGATGNIVTEDLVYLLESMGVDTGIDLERLLQAHGESVTGACNVRAFAPGYLFTLRNHPRPAENRQYLIAQAHYRIQEGGYASGAEDAVFDIDFRVLPATVPFRVARATPVPFRVARATPVPFRVARATPVPRTHGPQTATVVGQAGEEIWTDEYGRVKVHFHWDRYGKKNENSSCWVRVSSPWAGGGFGGIQLPRVGDEVIVDFIGGYPDRPIVIGRVYNASNMPPWDLPGNATQSGFLSRSKNGDRGTANALMFEDSAGAERIWLHAERDMDCEVEANESHTVDGNRTTLIGGNDTLTVRGTRTTTIDGLDTETFNAGATRTVTGEVSETTTGNETRTFNGDVTETVNGVETRTVNGDWKETITGEMTETRTGDETRTVTGAVTETITGDVTQTITGAVTQTQTGAHDITITGDQTSSITGAVSHTVTGAYTQTVTDPVTVNANTSMTVVTPSWTVSSASQQAFWTANTLRGTPARLTVVGAAADFWGVRQQVYGGINSQWSTVKIDLAAFKNGANGFESGQAGAQIKAIGAQIKTGGAAVISRVINLFT
>AP019378.1|BBH96475.1|55155_55866_-|transcriptional-regulator
MPRYPVRPADHAQSAEGGVTAVDRALTLLTAFRVTDQTLSLSELSERASLVPSTVLRLLASLMHFGFVLRRPDGRYALGPAAARLNRVYAASFNLQDVVLPALQELVGQTRESASFHVRQGAHRLVLYRVSSPQPLSDQSHAGDLLPLDRGTGGHVLMAFSDTPGEFYEALRLRGYMASPVSDRSPELAGISAPVFDAQGMLAGALTLTMPVHRYKDAHIPVLREAAARLSAALGA
>AP019378.1|BBH96474.1|54208_55159_+|LysR-family-transcriptional-regulator
MPSPSRSPATAYKKAPSLKGLPSIRQLRAFVAVYYTGTLSAAAEALSLTQPAVTILLKELEEKLGVRLFDRTTRALRRTTAALEAIAYAERVLGELDALSASMTDLADVRRGRLRVAATSTVAQTLLPKVVRRFLDLHPGVKLSVDDCAPAMFAEHVLSEQVDLGVGTLESAVPGLEQHQFLGDHLCAVATDAAFGHGRPMTWKQLSGLPVIVVQAGYGVRRSIERAAQQAGVELQVAFEVSLLTTALAMAASGLGVAVVPQSILAHTHYTNLVARRLVRPVVLRSTSVVFKEARALSPSAQAFAELLRREFSSPA
>AP019378.1|BBH96473.1|51788_54140_+|aldehyde-dehydrogenase
MNAFDRFAPSHAALADEPCGLAPASPARREWLRTAAALTGLVLVVGAGGVVRAAGEAAKEAKKYGGDGMPHGTVDDPLVFVSIAADGLVTIVAHRAEMGTGVRTSLPMVVADELEADWNRVRVIQAPGDEPRYGNQDTDGSRSTRHFFLPMRRVGAAARAMLEAAAARQWGVPVAEVAARQHEVVHEKSGRKLGYGELATAAAALPVPAEAALRLQQPAQFRYIGKPGARSVDIEDIVTGKTHFGIDTRLDGMLYASVARPAVLGGKVKAYKAEAALKVPGVVKVVELPAGPTPPVFAPLGGVAVIASDTWAALKGRQALEIEWDDGPHASYDSEAFRKTLSEGAGKPAKPVRNDGDAMQALAGAARRIEAEYYLPHLAHATMEPPAATARLADGKCEVWACVQSPYGTRENVARHLGLDIGAVTVHQTLLGGGFGRKSKSDFVVEAALLSKAMDGKPVKVTWSREDDLANDYFHTVSVERLEAGVDAQGKAVAWLHRTAAPTIGSTFAAGAEGQQPFELGMSAINIPFDIPNFRVESVPVPAHTRIGWFRSVSNIPHAFAVQSFVAEMAHALGRDPRDYLLELIGPPRRIAPAAMSDGWNYGESPELYPLDTGRMRHVIEVATGAAGWGRKLAAGRGLGVAVSYSFVTYIATVVEVEVGQDGAIAVPRVHVAVDCGPQVHPDRVRAQVEGACIMGLSLATRSEISFAQGRATQTNFHQYEVARMPEAPREIVVHLVEHGFDVPLGGVGEPAVPPFAPALCNAIFAATGKRIRALPIRDQLKA
>AP019378.1|BBH96472.1|51327_51792_+|oxidoreductase
MATLTINGKSQDVDAPDDMPLLWVIRDRLGMTGTKFGCGMALCGACTVHLDGQPVRSCITPVAAAAGKRIVTIEAVGEDEVGRAVQQAWTEIGVPQCGYCQSGQIMSATALIKSNPKPSDEDIDAAMSGNICRCGTYPRIRAAIKQVAVKGVAK
>AP019378.1|BBH96482.1|64703_65732_+|membrane-protein
MEFADLLKTLTPSLPCGEDLEYDADFLQLQQAAVGRSEQQFGATIIPAQAPDWRAVERLALGLLERTRDLRIIAYLTRAWTEMRGLPGYAEGVTLAAGTLEQYWDAVHPMLASGGEEDPMPRVNALASLGDPQGCVRGMRSACLLDDVHGRLSLRDAEALLDGGRSEADYPGGRTRLIENLRQARLRRDDAALAVGAAAGALRRIQQQATQRLGSAWCPDYAQALRALDALLRTWSDLDETAAAPAAAMPAEAHHAAPAPEPQPAPASWHDARIATREDAMAMLAKVSAYFETHEPSHPAPYLIRRVQQLIPLDFHDILRNLAPQGLAQFEAWTAREAASQS
>AP019378.1|BBH96483.1|65774_66338_+|type-VI-secretion-system-associated-protein
MATTLKGSGQKFIARNRAPRVQIEYDVEIYGAERKIQLPFVMGVLADLAGKSNTPQPEVGERKFLDVDIDNFDERMKSVAPRAAFQVANTLTGAGHLNVDITFESIDDFSPATVARKVGALNEMLEARTQLANLLTYMDGKTGAEELIGQVLQNPALLGALAAAPKPADAGPADADAESAQPGPQAR
>AP019378.1|BBH96484.1|66359_67862_+|type-VI-secretion-protein-EvpB
MTAVARRERAQAESSLAADDLSALLKKEFKPKTEQAREAVEHAVRTLAHQALENSGLGLSSDAYRTIQAIIAEIDRKLSEQINLVMHHPDFQQLEGAWRGLHYLVTNTETDELLKIRFMCLSKNELGRTLKRYKGVGWDQSPIFKRVYEEEYGQFGGEPIGCLVGDYSFDHSPPDVELLGEIARISAAAHCPFIAGASPNVMQMDSWQELSNPRDLTKIFTNTEYVAWRSLRELEDARYVGLAMPRFLARLPYGARTNPVDEFDFEEETDGANHDRYTWANSAYAMAANINRSFKLYGWCTSIRGVESGGAVENLPCHTFPTDDGGVDMKCPTEIAISDRREAELAKNGFMPLVHRKNSDFAAFIGAQSLQRPQEYHDADASANAKLAARLPYLFACCRFAHYLKCIVRDKIGSFRERSDMERWLNDWIMNYVDGDPANSSQETKARKPLAAAEVQVTEIEDNPGYYAAKFFLRPHYQLEGLTVSLRLVSKLPSLKQNEG
>AP019378.1|BBH96485.1|67931_68405_+|hypothetical-protein
MFMKIEGANGESKDANHKDWTDIVSFSWGATQPASLATGGGQGVGKASFNDLHVVARIDKAAPAVMKHCASGKHLGKIELSVCKAGGAQVEYSKVTLEDVLVTSVQIAADNGSEAVLVNYAFQAAKVRQQYWEQTESGGKGAESLVAWDIKQNKEIG
>AP019378.1|BBH96486.1|68466_69264_+|hypothetical-protein
MLAMPPRDGGLAGQAAAVQARIRRAPADADLRAQLFQLAAVQGDWRRAAEQLQLCARLNPLAQPMANLYLAAIHGELRREAVLAGQAEPGFLAERPCWCEPLLQALRAQASDPERAAMLRAQAFDAAQASAGTLEDAAAGQAGYAWICDGDSRLGPVCELILDGSYAWLPFAQVAAVHLPAPQGLCDLVWARAEIALADGAVVRGLVPARYPPSAGQDDGLRLGRATCWRPLGQDGYAGEGQKMWLTDAGEFALLDVRALRRQAP
>AP019378.1|BBH96487.1|69260_69779_+|hypothetical-protein
MRIADERVARDRLQPSLLDRLVDDEPWRRSEAPEAALLTHAGLRAAVLRDLRWLLNTVNLASSQDLAPYRHVPASSVNFGVRAMAGRRMSEIDWVDVETSIRDAIAAFEPRILESSVEVRCVSDTRTLEHHNVLSLEIRGMLWCVPHPREFLFRTDIDLESGHMDLRDLGGA
>AP019378.1|BBH96488.1|69778_71692_+|type-VI-secretion-system-protein-ImpG
MDARLLDYYNRELVYMRELGAEFARQHPKVAGRLGMHGTEVADPYVERLLEGFSFLAARIHLKMDAEFPRFTQRLLEVVHPHYLAPTPAMAVAQFSPSMNEGTLAGGFTLPRGTVLRGGLARGEQTPCEFMTGHALRLWPLRVTAAELTGAPTDLPLARLGLGGREAGVASALRLRLEVCGGVSLEELDLDQLVFYLNGSDAPMQRLLELIMCHTVAVLGHDSERPVSWINRLPADAVRHEGFADDQALLPTDTRVFQGYRLLQEYFAFARRYLFFSLNGLKQGLCTRRAAPAAAAGPAGTRRFDLTLLLSAAAPELEGAISAGNLALHCAPIVNLFPRRADRVAVTPRHHEYHVVVDRTRPLDFEVYSLTRVLGHMSAQRPEQEFRPFYGSFGADADDYGAYYSLRREPRLASDSARRHGTRTSYTGSEVYLSLVDRHEAPFADTLRHLGIDALCTNRDLALLLPLGGASDFSLRVSAPVGAIKVLHGPSRPAAAMADHGTAWQLISHLGLHYHSLTDLDETRGAQTLRELLNLYGNLADPVARKHISGVRHVRVEPMHHRLPVPGPIVYGRGVRIDLQVDETAFSGISPYLCGAVLEQFFARHVSINMMSALTLSTPQRGAVASWRPRMGRRPAV
>AP019378.1|BBH96489.1|71726_72386_+|hypothetical-protein
MQTRNARRLYPVYDPVHLIGTVARREDDGAWTVWCDGRPWRVRRAASCLLVPEEGDTALISGPDAERVYLIAVIEQADAAQATLELEGRVSLRSRTADVSLEAAGEVRLRGAQAVRVETEALSVKAGQAACAAARMHYVADEVEGAVGSMRLVGKVYEAVLDRLTQLARMAVRQTSEVEHVRAGTLDYQAEQSARVHAPYTMLTADALVKVDAKQIHMG
>AP019378.1|BBH96490.1|72430_73483_+|hypothetical-protein
MLPPAFWQALAAAPHGHDLFHVLRWIDARAGARAPLGRGASPRHEPVRMRQEPSLAFAPATLAAARAPGEGAAPELSIYSFGLFGPNGPLPLPLHLTEHARERRQHHGDHSLAAFADLFHHRLILLFYRAWADAQSTASLDRGQERFSGYVASLLHLGAPSLRRRDSVMDHAKYHMAGHLLRQTRNPEGLCQVLRAFFGLPVGVDEFVAQWIRLEAGQRLRLGAGGGLGGGAPLGVAVRDAQHKFRIRLGPLDWQDYLAFLPGSARARQLLHWVRLYVGVEFAWEVRPVLRRDAVRSVRLGAAAPLGLASWLGRRPPRLGDAAELLLDYEGRERQAARRAQAFHEKEQAA
>AP019378.1|BBH96491.1|73479_74013_+|DUF2778-domain-containing-protein
MIHDMSYDGQILAWPGHGQFRATSGMRGFQHPGQACTPDSGPVPPGLYRVLLADRGVALDDGRGVCNLAPAWGIQQVPRGAAAGECESYWANWGENRARMEPADAATRNRCAPARGGFYLHDSTKGFSHGCIEVEGRIFALLRSYARQRGRNAMILKVAYVADRATNGGTAGDGHAR

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Crispr_ID: AP019378_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

AP019378_2

132486-132642

Orphan

Consensus_repeat	Method
GGCATCTGCCCGTGCGTGTGCCTGTCCCCGCTGGGACAGGCACATTGCCGTA	PILER-CR

2 spacers

The CRISPR arrays of AP019378_2

>merge|AP019378|2|132486-132642|PILER-CR
GGCGTCTGCCCGTGCGTGTGCCTGTCCCCGCTGGGACAGGCACATTGCCGTACGCCATCCGGGGTGCCTGTCCCCGCAGGGGGACTGGCACCGGCAAGATTTCACGGCATCTGCCCGTGCGTGTGCCTGTCCCCGCTGGGACAGGCACATTGCCGTA

>AP019378|2|2|132486-132642|PILER-CR
GGCGTCTGCCCGTGCGTGTGCCTGTCCCCGCTGGGACAGGCACATTGCCGTA	CGCCATCCGG
GGTGCCTGTCCCCGCAGGGGGACTGGCACCGGCAAGATTTCACGGCATCTGC	CCGTGCGTGTGCCTGTCCCCGCTG
GGACAGGCACATTGCCGTA

Protein	Signature genes	Signature genes Name	Protein_function
AP019378.1\|BBH96549.1\|138925_140374_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377603
AP019378.1\|BBH96552.1\|143730_144630_-\|peptide-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224094
AP019378.1\|BBH96545.1\|133684_134896_+\|CoA-transferase	unknown	unknown	gnl\|CDD\|367110
AP019378.1\|BBH96544.1\|132874_133615_-\|GntR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|225097
AP019378.1\|BBH96542.1\|129116_129491_+\|glycine-cleavage-system-H-protein	unknown	unknown	gnl\|CDD\|234918
AP019378.1\|BBH96538.1\|124701_125907_+\|membrane-protein	unknown	unknown	gnl\|CDD\|367519
AP019378.1\|BBH96550.1\|140549_142025_-\|microcystinase-C	unknown	unknown	gnl\|CDD\|377823
AP019378.1\|BBH96540.1\|127234_127540_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|223505
AP019378.1\|BBH96534.1\|121132_121651_-\|N-acetyltransferase	unknown	unknown	gnl\|CDD\|372596
AP019378.1\|BBH96547.1\|135910_136723_+\|enoyl-CoA-hydratase	unknown	unknown	gnl\|CDD\|119339
AP019378.1\|BBH96539.1\|126009_126645_+\|superoxide-dismutase	unknown	unknown	gnl\|CDD\|223678
AP019378.1\|BBH96553.1\|144632_145574_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|223674
AP019378.1\|BBH96541.1\|127934_129035_+\|aminomethyltransferase	unknown	unknown	gnl\|CDD\|234742
AP019378.1\|BBH96551.1\|142068_143727_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224048
AP019378.1\|BBH96548.1\|136773_138798_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377603
AP019378.1\|BBH96546.1\|134927_135893_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|270234
AP019378.1\|BBH96543.1\|129550_132415_+\|glycine-dehydrogenase	unknown	unknown	gnl\|CDD\|235432
AP019378.1\|BBH96535.1\|121751_121922_+\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH96536.1\|121952_122201_+\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH96537.1\|122355_124626_+\|lysine-decarboxylase	unknown	unknown	gnl\|CDD\|224893

Protein	Function_ID	Function_description	E-value
AP019378.1\|BBH96549.1\|138925_140374_-\|hypothetical-protein	gnl\|CDD\|377603	pfam06097, DUF945, Bacterial protein of unknown function (DUF945). This family consists of several hypothetical bacterial proteins of unknown function.	1.75279e-118
AP019378.1\|BBH96552.1\|143730_144630_-\|peptide-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].	6.84311e-84
AP019378.1\|BBH96540.1\|127234_127540_+\|hypothetical-protein	gnl\|CDD\|223505	COG0428, COG0428, Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism].	8.92584e-16
AP019378.1\|BBH96544.1\|132874_133615_-\|GntR-family-transcriptional-regulator	gnl\|CDD\|225097	COG2186, FadR, Transcriptional regulators [Transcription].	1.4512e-42
AP019378.1\|BBH96542.1\|129116_129491_+\|glycine-cleavage-system-H-protein	gnl\|CDD\|234918	PRK01202, PRK01202, glycine cleavage system protein GcvH.	1.40219e-66
AP019378.1\|BBH96538.1\|124701_125907_+\|membrane-protein	gnl\|CDD\|367519	pfam03486, HI0933_like, HI0933-like protein.	2.36973e-170
AP019378.1\|BBH96550.1\|140549_142025_-\|microcystinase-C	gnl\|CDD\|377823	pfam07364, DUF1485, Metallopeptidase family M81. This is a family of proteobacterial metallo-peptidases.	8.85912e-105
AP019378.1\|BBH96545.1\|133684_134896_+\|CoA-transferase	gnl\|CDD\|367110	pfam02515, CoA_transf_3, CoA-transferase family III. CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.	7.1626e-149
AP019378.1\|BBH96534.1\|121132_121651_-\|N-acetyltransferase	gnl\|CDD\|372596	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain.	1.09696e-12
AP019378.1\|BBH96547.1\|135910_136723_+\|enoyl-CoA-hydratase	gnl\|CDD\|119339	cd06558, crotonase-like, Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.	1.79407e-70
AP019378.1\|BBH96546.1\|134927_135893_+\|hypothetical-protein	gnl\|CDD\|270234	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubacteria, at least three families of periplasmic binding-protein dependent transporters are known: the ATP-binding cassette (ABC) transporters, the tripartite ATP-independent periplasmic transporters, and the tripartite tricarboxylate transporters (TTT). Bug proteins are the PBP components of the TTT. Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter.	5.35441e-112
AP019378.1\|BBH96553.1\|144632_145574_-\|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].	9.53884e-123
AP019378.1\|BBH96539.1\|126009_126645_+\|superoxide-dismutase	gnl\|CDD\|223678	COG0605, SodA, Superoxide dismutase [Inorganic ion transport and metabolism].	6.82185e-105
AP019378.1\|BBH96541.1\|127934_129035_+\|aminomethyltransferase	gnl\|CDD\|234742	PRK00389, gcvT, glycine cleavage system aminomethyltransferase GcvT.	0
AP019378.1\|BBH96548.1\|136773_138798_-\|hypothetical-protein	gnl\|CDD\|377603	pfam06097, DUF945, Bacterial protein of unknown function (DUF945). This family consists of several hypothetical bacterial proteins of unknown function.	3.89582e-106
AP019378.1\|BBH96543.1\|129550_132415_+\|glycine-dehydrogenase	gnl\|CDD\|235432	PRK05367, PRK05367, aminomethyl-transferring glycine dehydrogenase.	0
AP019378.1\|BBH96551.1\|142068_143727_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|224048	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only].	0
AP019378.1\|BBH96537.1\|122355_124626_+\|lysine-decarboxylase	gnl\|CDD\|224893	COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism].	0

>AP019378.1|BBH96543.1|129550_132415_+|glycine-dehydrogenase
MSRAPDTHSDFIPRHIGPSDEDQATMLAAIGAASLDALIDEVVPPRIRSRAPLALPAARSETDVLQDLKRMAARNQIYRNYIGQGYYGTHTPNVVLRNVLENPAWYTAYTPYQPEISQGRLEALLNYQTMVADLTGLDISNASLLDEGTAAAEAMTLARRGSRSSSPVFFVSQHCHPQTLEVVRTRAEGLGIELVIGDESRGLPECFGVLLQYPHSLGGVADYRELAQAAHAQGAVVACVTDLLALALIEPPGQWGADIAVGSAQRFGVPFGFGGPHAGFMACRDAYKRNMPGRLVGVSKDAQGNPALRLALQTREQHIRREKATSNICTAQVLLAVMAGLYAVWHGPRGVRRIAERVQSLTGALRAALAGLGVKVANDTWFDTLLLETGVATPAILAAADCARTNLRQVDGARLAVSLDETVTLADLQALVNVFAAGLGKDEVALPAPQASLDGIPAAVRRQGPILSHPVFSSVQSETDMLRYLRKLADKDLALDRTMIPLGSCTMKLNATAEMIPITWPEFALIHPFAPASQTPGYRELIDGLSAQLCEITGYDGISLQPNSGAQGEYAGLLAIRAYHQANGQPQRNVCLIPASAHGTNPASAQLAGMDVVVVASDANGNVDLADLRARIAQVGERLAALMITYPSTHGVFEEAVTEICDAVHEAGGQVYLDGANMNAMVGVAQPGKFGSDVSHLNLHKTFCIPHGGGGPGVGPVAVRAHLAPYLPGVLDAQGRLDPEAKVGPVSAAPYGSAGILPIPYVYIALMGAEGLRRATEVAILNANYIAARLRDHYPVLYAGRNGRVAHECILDVRPLKETSGISAEDIAKRLMDYGFHAPTMSFPVAGTLMVEPTESEGLAELERFIEAMIAIRAEIAQIESGERDRDDNVLRNAPHTAQMLLAEEWHHDYPRQQAAYPVASLRENKYWPPVARVDNAYGDRNLVCACLPVEAYA
>AP019378.1|BBH96542.1|129116_129491_+|glycine-cleavage-system-H-protein
MSLPTDRKYTESHEWVQAEGDVFVVGITDNAQEQLGDLVFVGDVKVGATLKAGETAGVVESVKAASDIYAPVDGEIVAFNDELEANPSLINESAYTAWIFKIKPANAADLDKLLDAAGYQAVAG
>AP019378.1|BBH96541.1|127934_129035_+|aminomethyltransferase
MSAPLKRTPLAEEHLAAGARMVDFGGWDMPLAYGSQLEEHHAVRQDAGMFDVSHMLNVDVGGADATAFLRRLVANDVARLATPGRALYSCMLNPQGGIIDDLIIYYFAPDQWRVVVNAGTADKDIAWMQRVAAADGFDVAIAPRRDLAMVAVQGPNARAKVWAARPAWQAASEPLAPFSAAAVEAGTLVARTGYTGEDGFEIVLPADAVVQLWRDLLAQGVRPCGLGARDTLRLEAGMNLYGQDMDELVHPDQAGLSWTVALKDEARRFVGRDAIEQFAVPRAFVGLKLQERGVMRAHMPVRCAQGMGELTSGTMSPTLGVSVGFARVPVGVQPGDAVEVEIRGKWVPALVCKLPFVRHGKAVEHS
>AP019378.1|BBH96540.1|127234_127540_+|hypothetical-protein
MPEGLVVALALLAAGYSRAFSVALGMLSGLVEPLGAIVGAAVVGWSAAMLPWGLGFAAGAMLFVISHEIIPESHRKGHEVPATAGLMLGFVLMMLLDTALG
>AP019378.1|BBH96539.1|126009_126645_+|superoxide-dismutase
MPYVLPALSYAYDALEPHIDARTMEIHHTRHHQTYVNGLNAALEGAGLDSEEPVEQLLRRIPALPPGIHGAVRNHGGGHANHSLFWTVMSPSGGGRPDGRLAADIQAQLGGHDAFQAAFTQAALGRFGSGWAWLTVTPAGRLRVDSSANQDSPLMEGNTPILGLDVWEHAYYLQYQNRRPEYIEAFYRVVDWAEVARRYEIALAELGREAA
>AP019378.1|BBH96538.1|124701_125907_+|membrane-protein
MFDVAVIGAGAAGMMCAAVAGQRGLRVVLIDHAAKLAEKIRISGGGRCNFTNLGAGPANFLSDNPHFCRSALAGYTPQDFLGLLRRHRVHWHEKHRGQLFCDDSSETIIEVLRAECGQGGVAWRMPCRVDEIARREGGGFTLRTSTGAIDARAVVVATGGMAIPQLGATDYALKVARQFGLKVVEPRPALVPLTFDPAQWQPFAALSGVALEVTLSTGQGKGRAAFLEDLLFTHRGLSGPAILQISSYWKPGEAIVLDLAPGRDLAAELIGAKPGNRQQLHTVLAGLWPRRLADTWLDVAGRAVGADLAAARLADVPDRTLRALAALIHDWRLVPSGTAGYKKAEVMRGGVDTRALDQKSMQARGVPGLYFIGEAVDVTGWLGGYNFQWAWASGYACGNAL
>AP019378.1|BBH96537.1|122355_124626_+|lysine-decarboxylase
MKFRFPIFIIDEDYRSENASGLGIRALASAIEAEGVEVIGVTSYGDLSSFAQQQSRASAFILSIDDEEFDVDSPEDVAGAIKNLRTFIGELRFRNADIPIYLYGETRTSEHIPNDILRELHGFIHMFEDTPEFVARHIIREARSYVDGLLPPFFRELVKYAQDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGENMLRADVCNAVDELGQLLDHTGPVAESELNAARIFHADHCFFVTNGTSTSNKVVWHANVAAGDVVVVDRNCHKSILHAITMTGAIPVFLRPTRNHLGIIGPIPLDEFDPENIRRKIEANPFAREALNKKPRILTLTQSTYDGVIYNVEMIKEKLGTYVDTLHFDEAWLPHAAFHEYYRDMHAIGPDRPRSQDAMVFATHSTHKLLAGISQASQIIVQESESRKLDRNLFNEAYLMHTSTSPQYAIIASCDVAAAMMEPPGGTALVEESIREAMDFRRAMRKVASEFGKDDWWFKVWGPNRLAPEGIGHRDDWVLESGDHWHGFGDLAPGFNMLDPIKATIITPGLDMSGSFGESGIPAALVSKYLAEHGVVVEKTGLYSFFILFTIGITKGRWNTLLTALQQFKDDYDRNQPLWRILPEFCRGHRRYERMGLRDLCQQIHEAYRERDVARLTTEMYLSDMVPALKPSDAFARMAHREVERVEIDQLEGRVTGVLLTPYPPGIPLLIPGERFNRTIVQYLQFAREFNERFPGFETYIHGLADEEGPDGAKRYYVDCLKDAGEQ
>AP019378.1|BBH96536.1|121952_122201_+|hypothetical-protein
MQRVGAAAYLYEVARRRHGGLYEVCDDDDPVVLVTGEPEFDVCLCAIAKVERRIDAGPQEDLRPFFGRYEQAVAARRPDIIR
>AP019378.1|BBH96535.1|121751_121922_+|hypothetical-protein
MFGFRRKDTQQYDQEAQDAFVERVAAAARDFVAAVPAGAGLDYSPASIAALDAVLE
>AP019378.1|BBH96534.1|121132_121651_-|N-acetyltransferase
MNLSTIRPLTPEDAAEFQRVRLAALREAPEAFGSSYEEESVDTIAQWRARLAPREGYVLLGAFVDGALAGVGGVARGHTMKQRHKAEIWGIYVVPAQRRGGLARQLTEALLARAARMTGVRHVLLSVGADNGAAHALYASLGFAEYGREPDAMLVGGRLLANILMIRPLAAR
>AP019378.1|BBH96544.1|132874_133615_-|GntR-family-transcriptional-regulator
MKTVETNPNPLGPIKAVRSRDLLADALREQILSGARPSGVALPSERELTEETGLSRAAVRDALRVLESEGLIETRQGRYGGSVVKLPANDALARPVALFARARGISLQEMIEARVAIEPTIAELAALRRTPEDLQALIQATDLLQEALPRVEQFLDLNVRWYFALADACHNDLLRAFIVSIAGLILAATSREGQTPEPTRRLILQSHRRVVDAVIAGDAPAARRRMERHVAGYQEHYERLGLTPSA
>AP019378.1|BBH96545.1|133684_134896_+|CoA-transferase
MAAVSSSVPPTPLGGVRVLDLSKVLAGPLCTQYMADMGADVIKVEAAGQGDDTRGWPPFQDGQAAVFLSCNRNKRSIALDLKSAHGRAVVQRLAAWADVVVHSFGPGVAQKLGVDWEALSEINPRLVYCAISGFGPVGSLSHGKGFDVVLQAFCGMISITGETEGGAVRSPFSPVDQATGLHALIGILAALRQRDASGRGVTVDASLFDTALGFMGYFMQGYWARGTEPARAGAGHESLCPYQDFATADKPIILGIANDALWRAFCTLAGRPELVSDPRFATNAQRVANRAQTLAATRELLAARTRGEWLPALEQAGIPCSPIHTLAEVDAHPHTRESGMVFDYPETGADTGPLKGVAQPVRFDGMRLTTPKRPPSLNQDWASVLADAGYSDPEVRDLLQQMA
>AP019378.1|BBH96546.1|134927_135893_+|hypothetical-protein
MNVLIRRALCAAIASLAAAAAHAAYPEQPVRIVVAFAPGSGTDNVARYYATRLSEELKQPFVVENKPGANGSIAATQVARTQPDGYTLFLGSNSTLSAAPFLFKKLPYEPLKDFTAVARLSDIPSMLVVGADSPIRDFDQFIGKARAEPGRVTWANANTAHLAAGMALTKQAQLDMISVPYKSSPQALTDVIGGQVTAMVVDTSAGTAFVQQGKVRALAVTTARPVAAMPGVPSMSERFPGIDVYSWLGIVGPAGMPDEVVSVVNQAILKINASEDTVRFLRENAGAEPPPSSSPAEFTQFMHAQLEVWRKLLRDANVEPM
>AP019378.1|BBH96547.1|135910_136723_+|enoyl-CoA-hydratase
MSAPACVSEFVRYDVDAGVARITLDRPDRRNAIDVPMRAALLAAVQAATADPAVRAVVLTGAGGHFCSGGDVSTMRGASMSAEQGRDRMAPIGACARALLEMPKPVIAAVDGIAFGGGFGLCLCADLVLATPAARFCLSFMRIGLVPDFAAAFTLPRLVGLQRARQLIYTAAEIDGRQALEYGLVSELVDAGRLAPRAAEVATAMAGMPATAFALTKQALLRSSSSELAAMVEMEMTSQGVAFNTGYHQQAVERLLEKKPPLYSFPAPTA
>AP019378.1|BBH96548.1|136773_138798_-|hypothetical-protein
MKKSIGITAGVIVVLAGGWLGGTWYTGKRIETETQQRLGVLNEKLAAVVPGYTLRVDQLKYERGFFTTQARYGLSLSQDIKEESGTVTPLPLGSTEFDARFEHGPFPRSALASGQFLPQMAFVHAELARTELVKPLFELTKNAAPLWSDTIVSYSGNASTRSGLAPIDFTEDDVTLSFSGATLTSTFQRATRSGTARLDAEYVRFTADGDQDTQMSATGWSVDMRSHQGKHGFTLGESTMAIKRIAMIDKRESLDISLDDLSYRALATEDGDYIDIEAAYKTGPLTVNKIPFGSGELNVKVSRLDGQALKALSDGYNQLLRGYFATGETDEGLKDEQLTMLIENGGRLLAGGPSLSLGPVAWRTEKGESSLMSSIVLVKPATTSGELTPREYLEEAVKAIDVKMVVSKPMVRDLAIHYETSQGKTPEEAAKEADETIDAFAGMAEILNIGRNDGDKLVGTFTYAAGVAKLNGRDVPVNELFDNLYDSASASLDDDEHNHEDDAAMSAEAASEAVEAAAEAAAAEAAQEAADAAAWATEGDSLRSVNAGLLTSILAEGGYDSTTEEGASGPVIVIDANGLPLRDLRAELYCIDDDECMDVSMKASFGKRKTSLKALNAWNQKYRWTRAYLDDDNQAVLRMDLSAEGGVGRENLSIMVNTFMQMVGNFEDEVYAAR
>AP019378.1|BBH96549.1|138925_140374_-|hypothetical-protein
MKKSVAVTTGVIIVAVGGWLAGTWYTGQRIETESQTRLNEINAQLAAAFPEFPVRINQLKLERGFFTSQARYGVEVGKSEETGKPEATVEVDARIEHGPFAPGALARGKLMPQLAFVHAEVANTEDLKKVFEVTKGATPLWSDTVVAYNGDSTSTGGLAAIDYSGDEGKFAFSGATFDGSYQRATQAAIGSLKADSLALDASADDDGGPLLFTLDGLAVTVDSRMGKSGLSIGDSALSVKRLEVKQPEGDAHLTVADMAYAARIGEQDEFINGEISYGAGEITYNGIALGNGRAVFKAERLNAAAIKVVADEYNKAIKLQAEGKDPVPDNAEMRKLLMAQADTLLAGKPVLTLDPVQWKTAQGESVFNARVALSKPASSDLMAVDYFSQAIESIDASATLSKPMIKALMVGYLQSQEGMDAQQAAAAADQQVSSLAGMAEMMNLGKNEGDNIVSKFHYAAGTVDLNGRKMPADQLLGSILGG
>AP019378.1|BBH96550.1|140549_142025_-|microcystinase-C
MRWLLAMIKHETNTVSPVPTPLERFFRGSPEILAGERAIRAYENTDSGLGGYIEVARREGAEIVVPVAAESWPSAPTDRATYERLCGLVLDEARRGGFDAILLDLHGAMVAEGVEDAEGDLLRRLRDIAPAIPVGVTLDMHANIYDDIVRHATVISGFHTYPHVDIRAAGLRAANAIARTLRGEIKPVMSWANKPMLPHIMRQGTHAEPNKSLQARCKALESEGVIAASVFVGFPHADIREAGLSAVVCTDANLAQAEQYRDELLETAWRGRADWVFHAEPLAPTIARAKAIENGPVVLLDHYDNTGSGGTMDTTAVLAEILDQGLENVAFYAICDPQAAQQAAAAGVGATVTLPLGGKVAMPALRQASPPLHLTARVKLLFDGVYLNRGPMYRGVRNDTGLTVVLDTGKVEIVVVSRHQEPFDINCLLSAGIDPLQKRYVALKSRVHWRAGFADMATHVIECTGVGVTTSDYGQVEFRHVRRPVYPLDAI
>AP019378.1|BBH96551.1|142068_143727_-|ABC-transporter-ATP-binding-protein
MPYAPYPPAGDTSAAVLAIRNLSVSVCGAGNRVVRNLSLDVHAGETVCVVGESGSGKSVTSLAVMGLLPEGILEVSGGSARVLGEDIVTASARRRRELRATRMAMVFQEPMTALNPVHRVGSQVDEVLRLHRRMPRAQRRAKVLEMFRSVHLPDVERIYDAYPHQLSGGQRQRIVIAMALILEPKLLIADEPTTALDVTTQKQILALIRELQDRHQTAVLFITHDFGVVAEIADRIVVMNRSDLTEAGTRDEILARPSQNYTRRLVSSVPSLVPTQREAPGGEPVLRITGLGRTYAERRSLFGATRTVVAASEVDLTLRRGEILGIVGESGSGKSTVARCIVRLIEPSAGRMLLGETDIARLSGAGLRPLRRKVQIVFQDPYRSLNPRRAVGESIIEGLLNFGMPRAQALVRAARTLGVVGLGPDVMRRYPHQFSGGQRQRLCIARALVMDPEVLVADEAVSALDVSVQAQVLELIEQVRERTGVSVLFITHDLRVAAQVCDTIAVMQHGKVVETGAAQTVLTRPGHAYTRALIDAAPGRGWDFRNFRPLPA
>AP019378.1|BBH96552.1|143730_144630_-|peptide-ABC-transporter-permease
MPTHSDAVADGALPENEPPQAGAWRRVRREFSGAPVLAALAVLALVVGAALLAPWLGTVDPTAIDPGARLKPPFGDYLFGTDAFGRDIWSRVVYGARVSLVAGLGAALVSVTLGLVIGVIAGWFRTLDGLIMRTMDAVMAIPGILLAIALVSVTGASLATVLVAITIPEIPRVVRLVRGQILSVRGEPYVEAALALGTPLPLLLWRHLVPSTVAPLTVQGTYVFASAMLTEAILSFLGAGIPPEIASWGNIMSEGRMYFRMLPGLILFPGLFLSLTVLSVNILGDALRDALDPKMTRRT
>AP019378.1|BBH96553.1|144632_145574_-|ABC-transporter-permease
MLAFIARRLLATIPVLIMVAVVVFAILRASPGDPAIIMAGDAATPERIAQIRHVMGLDQPLVKQFFIWTGRLVRGDMGTSLMSGVPVTQLIGQRLEPSLSLAVITLAFTLAVAIPLGILAAWRRGRLLDRAVMGFSVLGFSVPVFVTGYVLIWAFAIKLGWFNVQGYTPLAQGFWPYLHRLVLPSLALSTVYVALIARITRTSIIEVMGEDFIRTARAKGLGETGVLLGHALRNAAVPIATVIGVGVALLISGVVVTESVFNIPGLGRLVVEAVMARDYPVIQGLTLFFAFVYVFINLVVDCAYTVFDPRIRY

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Crispr_ID: AP019378_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

AP019378_3

362435-362521

Orphan

Consensus_repeat	Method
CGTGGTGCCTGTCCCCGCGGGGAC	CRISPRCasFinder

1 spacers

csa3

The CRISPR arrays of AP019378_3

>merge|AP019378|3|362435-362521|CRISPRCasFinder
CGTGGTGCCTGTCCCCGCGGGGACGGATACCGTCTTAGGAGCGGGGAGGGTGGTGCGGGGGAACGTGGTGCCTGTCCCCGCGGGGAC

>AP019378|3|1|362435-362521|CRISPRCasFinder
CGTGGTGCCTGTCCCCGCGGGGAC	GGATACCGTCTTAGGAGCGGGGAGGGTGGTGCGGGGGAA
CGTGGTGCCTGTCCCCGCGGGGAC

Protein	Signature genes	Signature genes Name	Protein_function
AP019378.1\|BBH96758.1\|370319_370646_+\|transcriptional-regulator	csa3	COG0640_csa3_CAS-I-A	gnl\|CDD\|223713
AP019378.1\|BBH96754.1\|364675_366850_-\|ABC-transporter	unknown	unknown	gnl\|CDD\|274550
AP019378.1\|BBH96745.1\|350083_350776_+\|hydrolase	unknown	unknown	gnl\|CDD\|182251
AP019378.1\|BBH96759.1\|370642_371923_+\|arsenical-pump-membrane-protein	unknown	unknown	gnl\|CDD\|185342
AP019378.1\|BBH96756.1\|367053_368523_-\|outer-membrane-protein	unknown	unknown	gnl\|CDD\|273829
AP019378.1\|BBH96750.1\|354897_355581_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226198
AP019378.1\|BBH96757.1\|368874_370167_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|274820
AP019378.1\|BBH96753.1\|363230_364673_-\|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit	unknown	unknown	gnl\|CDD\|130902
AP019378.1\|BBH96747.1\|351132_352041_+\|aromatic-amino-acid-aminotransferase	unknown	unknown	gnl\|CDD\|181731
AP019378.1\|BBH96743.1\|347071_347440_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|225981
AP019378.1\|BBH96751.1\|355661_362309_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|333740
AP019378.1\|BBH96749.1\|352905_354882_-\|diguanylate-phosphodiesterase	unknown	unknown	gnl\|CDD\|379843
AP019378.1\|BBH96755.1\|366827_367043_-\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH96760.1\|371963_372968_-\|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270234
AP019378.1\|BBH96748.1\|352230_352857_+\|hydrolase	unknown	unknown	gnl\|CDD\|238494
AP019378.1\|BBH96746.1\|350848_351163_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|181731
AP019378.1\|BBH96752.1\|362543_363209_-\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|225107
AP019378.1\|BBH96744.1\|347539_350035_+\|copper-translocating-P-type-ATPase	unknown	unknown	gnl\|CDD\|319783
AP019378.1\|BBH96742.1\|345858_346785_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|379203
AP019378.1\|BBH96761.1\|372972_374109_-\|CoA-transferase	unknown	unknown	gnl\|CDD\|367110

Protein	Function_ID	Function_description	E-value
AP019378.1\|BBH96754.1\|364675_366850_-\|ABC-transporter	gnl\|CDD\|274550	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].	0
AP019378.1\|BBH96745.1\|350083_350776_+\|hydrolase	gnl\|CDD\|182251	PRK10119, PRK10119, putative hydrolase; Provisional.	2.80135e-80
AP019378.1\|BBH96759.1\|370642_371923_+\|arsenical-pump-membrane-protein	gnl\|CDD\|185342	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB.	0
AP019378.1\|BBH96756.1\|367053_368523_-\|outer-membrane-protein	gnl\|CDD\|273829	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family. Members of this model are outer membrane proteins from the TolC subfamily within the RND (Resistance-Nodulation-cell Division) efflux systems. These proteins, unlike the NodT subfamily, appear not to be lipoproteins. All are believed to participate in type I protein secretion, an ABC transporter system for protein secretion without cleavage of a signal sequence, although they may, like TolC, participate also in the efflux of smaller molecules as well. This family includes the well-documented examples TolC (E. coli), PrtF (Erwinia), and AprF (Pseudomonas aeruginosa). [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Porins].	1.98618e-74
AP019378.1\|BBH96750.1\|354897_355581_-\|hypothetical-protein	gnl\|CDD\|226198	COG3672, COG3672, Predicted transglutaminase-like cysteine proteinase [General function prediction only].	8.27062e-29
AP019378.1\|BBH96757.1\|368874_370167_-\|hypothetical-protein	gnl\|CDD\|274820	TIGR03862, flavo_PP4765, uncharacterized flavoprotein, PP_4765 family. This model describes a sharply distinctive clade of proteins within the larger family of flavoproteins described by pfam03486 and TIGRFAMs model TIGR00275. The function is unknown.	1.21991e-156
AP019378.1\|BBH96753.1\|363230_364673_-\|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit	gnl\|CDD\|130902	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. [Protein fate, Protein and peptide secretion and trafficking].	3.83731e-118
AP019378.1\|BBH96747.1\|351132_352041_+\|aromatic-amino-acid-aminotransferase	gnl\|CDD\|181731	PRK09257, PRK09257, aromatic amino acid transaminase.	0
AP019378.1\|BBH96743.1\|347071_347440_+\|hypothetical-protein	gnl\|CDD\|225981	COG3450, COG3450, Predicted enzyme of the cupin superfamily [General function prediction only].	1.25112e-24
AP019378.1\|BBH96751.1\|355661_362309_-\|hypothetical-protein	gnl\|CDD\|333740	NF012211, tand_rpt_95, tandem-95 repeat protein. This 95-amino acid repeat occurs in tandem in proteins that may be several thousand amino acids long.	1.20527e-16
AP019378.1\|BBH96749.1\|352905_354882_-\|diguanylate-phosphodiesterase	gnl\|CDD\|379843	pfam16448, LapD_MoxY_N, LapD/MoxY periplasmic domain. This domain is the N-terminal periplasmic domain of the LapD and MoxY receptor proteins.	3.66319e-38
AP019378.1\|BBH96758.1\|370319_370646_+\|transcriptional-regulator	gnl\|CDD\|223713	COG0640, ArsR, Predicted transcriptional regulators [Transcription].	2.26872e-12
AP019378.1\|BBH96760.1\|371963_372968_-\|ABC-transporter-substrate-binding-protein	gnl\|CDD\|270234	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubacteria, at least three families of periplasmic binding-protein dependent transporters are known: the ATP-binding cassette (ABC) transporters, the tripartite ATP-independent periplasmic transporters, and the tripartite tricarboxylate transporters (TTT). Bug proteins are the PBP components of the TTT. Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter.	1.37607e-113
AP019378.1\|BBH96748.1\|352230_352857_+\|hydrolase	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.	1.08247e-67
AP019378.1\|BBH96746.1\|350848_351163_+\|hypothetical-protein	gnl\|CDD\|181731	PRK09257, PRK09257, aromatic amino acid transaminase.	5.53287e-47
AP019378.1\|BBH96752.1\|362543_363209_-\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|225107	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription].	2.19301e-24
AP019378.1\|BBH96744.1\|347539_350035_+\|copper-translocating-P-type-ATPase	gnl\|CDD\|319783	cd02094, P-type_ATPase_Cu-like, P-type heavy metal-transporting ATPase, similar to human copper-transporting ATPases, ATP7A and ATP7B. The mammalian copper-transporting P-type ATPases, ATP7A and ATP7B are key molecules required for the regulation and maintenance of copper homeostasis. Menkes and Wilson diseases are caused by mutation in ATP7A and ATP7B respectively. This subfamily includes other copper-transporting ATPases such as: Bacillus subtilis CopA , Archeaoglobus fulgidus CopA, and Saccharomyces cerevisiae Ccc2p. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle.	0
AP019378.1\|BBH96742.1\|345858_346785_-\|hypothetical-protein	gnl\|CDD\|379203	pfam13468, Glyoxalase_3, Glyoxalase-like domain. This domain is related to the Glyoxalase domain pfam00903.	1.55135e-31
AP019378.1\|BBH96761.1\|372972_374109_-\|CoA-transferase	gnl\|CDD\|367110	pfam02515, CoA_transf_3, CoA-transferase family III. CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.	8.85561e-148

>AP019378.1|BBH96751.1|355661_362309_-|hypothetical-protein
MANSSPAVVTAVTGRAWIRNSDGSLTELHEGSKVPQGSDIVTASGSTVALQVDGGMPLVIGEGREVAVTPDLNGGGGDASEAAVALPTTTDSERLLAALQDGRDPFDELDPTAAVIGGSGDSAGSSFVRLAKILESTTPMDLAYPNPGRGEDGVRTFLGGATAGADDEAAPAPANQAPNALDDLGQTRQGQTLRGNLMLNDSDPDGDPLAVVSVNGRPMTSGGLTLPGSGGGTFTVQPDGSYTFVPGNEHQSLGEGQTTTTTITYTITDPSGATSTATLTVTVTGTNDAPTLTPGVTLDDQANDDGEAITPVDISGQFEDIDNGDTLTFTADGLPPGLTLDPATGIISGTLDNSASQGGNNGVYTVTITATDSGGKSVSQTFEWDVTNPAPTAVADTGATDEDTTLTVTDPAQGVLRNDTDPDNDDLHVSAVNGQPANVGAAIAGDNGGTFTLNADGTYTFNPGPDFQNLAKDATAETSITYTVSDGEGGTSSATLTITVAGGNDAPILTPGVTLDDQANDDGEAITPVDISGQFTDPDTGDTLTFTADGLPPGLTLDPATGIISGTLDNSASQGGANNDGVYTVEITATDANGASVSQTFEWDVNNPAPTAVADTGTTDEDTTLTVTDPAQGVLKNDTDPDNDDLHVSAVNGQPGNVGAAIAGDNGGTFTLNADGTYTFNPGPDFQNLAKDATAETSITYTVSDGEGGTSSATLTVTVTGTNDAPTLTPNVTLDDQANNDGEAITPVDISGQFEDVDNGDTLTFTADGLPPGLTLDPATGIISGTLDNSASQGGANNDGVYTVEITATDANGASVSQTFEWDVNNPAPTAVADTGTTDEDTTLTVTDPAQGVLRNDTDPDNDDLHVSAVNGQPANVGVAIAGDNGGTFTLNADGTYSFNPGNAFQHLAQGDSVETSISYTVSDGEGGTSTTTLTVTVTGVNDTGAISVNLGADDGKVYEAGLDNAADDSETTGGTITVSASDGISSVTIGGQTFTVAQLSGDLSSLPAINTTEGTLTITGYTPSADGKSADITFSYTLNEAQTHSQPGNDTITDNIGVTVTGNGDSETSSSFNITIVDDVPTFQTVTDTVLANEAGQTQTGTLEFESGADGVGSLNITGITGLPNDWTTSAMNNASVNIFSPDGTHVFTVTLNTDGTYTVDQLATRPGTTESVNMGSQITNSPQASYDFGIASVTVLHSNQQVQFNGKGSNVPNVSHEFGIGNTWFEGGESFQMTFESPMLNFNFGIATVNNPGSVKVTLFDGVNTLTLTVPVNAGDTSLSITQDQIQAAAAAAVPPISFGEFSTATLEGVGGLKVSLTTLSYTNSVPADDMDFTVHVTGTDGDGDPAQTEFDVTSGAEAAVVDAFNRVMEDSGDTVGGSVMLSTALAVVSVSVNGTDVTNATAGNPVTFHTGKGTLIVTGYDPQSGALSYTYTEKGQAHNHGNGKNSVHDDFTVTVTDSDGQERSGDLVIQILDSVPTAHADLDNVTEGVTQNVSAADGVLANDTSADGWHHAGAIVGVAAGDTGAISHGKVGQAIDGLYGKLTLNANGSYSYKANASGQGALPGDGQDVFTYTVRDADGDLTSTTLTINIDQFVAGSNDNNTITGGAGNDVMLGDQGGIKQNVTAGTSYNIALVLDLSDSMNDKWGSGSNKPTRLQTAKDALKALLENQLAVHDGEINVSLITFNGSSSALKKSITGLTPENVDEMVDILMGLKASSATPYGAAFDRTTQWFEGQPTVDSEGKPYKNLTFFLTDGEPSTEWSYNRDNEFAELAAISDVHGIGIGSGVSTSTLNKYDNTGGYYTGGQETHVNFSGNSNANNVNTWDKDGTGTVTKNDNAMRITDTTADGQAFKVTMNPDHRMNVTSAGGASFSFALSMGNKNPADKFEWVLMKWDGTQWNEVERGTDASTRTGIHGPGQYGFQFIVNDNSGGGQFYATVDTIRSYTSGRTGNSQTVLDPSDLESALIGGSQSTELAPVGNDKLYGGDGNDILFGDAINTDNLPWGVAGNPAKPADLPNGSGLEALKDFLFLKNGVQPTDADLHKYISENHALFDVDGDTRGGNDELHGGAGSDELHGGEGKDLLIGGQGDDILYGGDGSDTFKWELNDQGVVGAPARDTIKDFSNADIADGGDVLDLGELLQGENSGNLTQFLKFSSDGQDTVIQVNTQGHVNTQGADQTIVLENIDLTAGGTKDDAAIIQDLLSRHKLQVDQ
>AP019378.1|BBH96750.1|354897_355581_-|hypothetical-protein
MPLSTRPRKAPRLALAALLSLACGWGGVHALDVDTGKLQSLAASRYGARGARAVDDWLQLLRNDTSASEANQLARVNAFWNQRVLSGEDTHIWGRADYWATPLETLGKGAGDCEDYVIGKYFSLISLGVPTEKLRFIYVRARIGGPYSNQQIAHMVLGYYPTPNAVPLVLDSLISTIMPANERRDLTPVFSFNADGVYVDGKQASPVDRLSRWRDLLLRMEREGLRP
>AP019378.1|BBH96749.1|352905_354882_-|diguanylate-phosphodiesterase
MSILRRLLLSLTLAIGIILLGTLVLSINAARGYLSDQLQVQSTDAAVSLALSLSQPANNDPVTQELLVSALFDGGHFSLVRLADPQGAVMVERGAQPAASVPAWFQALAPLANRAASHAVSDGWRQIGEVTLVANDAYAWETLWASSLRMAALIMGAGVLWALFAFALVRWIEKRLLFQVSEQVRAIDSRASGEQAFARVAEFSGIVDALAQTRERVRATAEEQSSHIESLEVELNQDPVTGLANRKYFINEFRRALDEKPADSPALPAPLSSAGGHVLVFRQRDLTALNRHMPRQFIDQWLQSVCQRISALVTAQGLAQSLVARLNGSDFAVLLPHCAAPQAQVIADLVRAELRTLRIPVGEGGLCRWAMALADYAPGTQFNGVLARLDFGLTRAESAGDDHAVLVGPDNADPFSAAGQSAWMDALVTALDQQRFSLAFEPLHAVDGRLVRMEAMLMLHNDDAREPIPAMLFIPAAVRLNLSAECDLQAVRLALDWLAAQPGELAVRLSLPSLGKRSFLRQLELMLADRRAQVGRLYLEVDAHGLVDREGDVIALERIAAHFGAHVGLRRLAQQFGAMSRLHSLPLAYVKLGGGFVGGMSQSPGSRQLAGSVIDTARALNIDVYAEDVPDAATRDILASMGVEVMRGPGVTPPPAQE
>AP019378.1|BBH96748.1|352230_352857_+|hydrolase
MGKRYAKLDKNNVAVLMVDHQVGLLSLVRDIDPDKFKNNVLAVADLATYFKLPTILTTSFEDGPNGPLVQELKDQFPEAPYIARPGQINAWDNEDFVKAVKATGKKQLLIAGVVTEVCVAFPALSAIEEGYEVFVVTDASGTFNEVTRHSAWSRMEQAGAQLMTWFGVACELHRDWRNDIEGLGALFSSHIPDYRNLIAAYTTVKGGK
>AP019378.1|BBH96747.1|351132_352041_+|aromatic-amino-acid-aminotransferase
MQTLGGSGALKVGADFLKRYFPKSEVWVSDPSWENHRTIFEGAGFAVHTYPYYDDASGGLRFDEMLATVGGLPAGSVVLLHACCHNPTGVDLDRAQWDALIPVLRERGLIAFVDMAYQGFGDGLDDDAYAVRALAEAGVTCVVANSFSKNFSLYGERCGGLSVVCETAEQAGCVLGQLTSTIRAIYSNPPTHGARIVAQVLGTPALRQSWEAELGAMRERIQAMRRAIHDGLAGRVEPRMLQRYLSQRGMFTYTGLGAEQVETLRRDQGVYLLRSGRMCVAGLNRDNVAVAADAIASVLARG
>AP019378.1|BBH96746.1|350848_351163_+|hypothetical-protein
MFEHVQAYPGDPILSLNEDFQKDPRAGKVNLTIGIYFDEAGRIPVMAAAREAEAALLADIGPRPYLPMAGLPAYRDLVQELVFGAGSAAPAVSPRCRRWAGRAR
>AP019378.1|BBH96745.1|350083_350776_+|hydrolase
MTNPGDGAAGAVDCATLDHWRPRLAAIAAAAGQDDAAHDLGHLRRVWGAARAMLQAHPEADALVVLAASYLHDLVNLPKNHPERHLASRQAAAAARERLARAGFPAARLDAVAHAIEAHSFSAGIAPRTIEARIVQDADRLDALGPVGLARMFHVGGSLGRALAHPSDPLAAQRALDDSRYTLDHIEAKLARLPHGMQTEAGRRLGEQRLAWLRDFRAAFAAQWGGGQLR
>AP019378.1|BBH96744.1|347539_350035_+|copper-translocating-P-type-ATPase
MNASSLAGAPSTGAISLPIEGMTCASCVGRVERALKAVPGVSDAVVNLATERADVRFAGAPDVGAAVQAVEQAGYAVAASTMELAVSGMTCASCVGRVERALKAVPGVRAASVNLATERAHVEIAGAVAPQALVQAVAAAGYEARPLDPGGAAADVAARRQAAELQGLRRALIVAAVFALPVFVLEMGSHMIPAFHHAVAGSIGVQNSWYIQFVLASIVLFGPGLRFFRKGVPALLRGAPDMNSLVAVGTAAAYAYSVIATFAAGVLPPGTVNVYYEAAAVIVALILLGRYLEARAKGNTSEAIKRLMGLQAKTARVRRDGATVEVPIAQVAAGDVVEVRSGERVPVDGQVIEGTSFVDESMISGEPVPVEKQPGAEIVGGTVNQNGALALRATKVGGDTVLAQIIRMVEQAQGSKLPIQALVDRITMWFVPAVMAVALATFAIWFVFGPDPALTFALVNAVAVLIIACPCAMGLATPTSIMVGTGRAAQLGVLFRKGEALQALKDARVVAVDKTGTLTKGRPELTDLVLAEGFERAAVLGKVAAVEAKSEHPIARAIVDAAQVEGARPGAIEAFESITGYGVAARVDGARVEIGADRYMARLELDVAVFAAEAARLGDEGKTPLYAAIDGHLAAMIAVADPIKNTTAAAIRALHGLGLKVAMITGDNRRTGEAIARQLGIDEVIAEVLPDGKVDAVKRLKAEHGALAYVGDGINDAPALAEADVGIAIGTGTGTDVAIEAADVVLMSGDLGGVPNAIALSQATMANIRQNLFWAFAYNVALIPVAAGVLYPVNGSLLSPVFAAGAMALSSVFVLSNALRLRRFAAPFAAR
>AP019378.1|BBH96743.1|347071_347440_+|hypothetical-protein
MPQHDKSRLVRIDTGPMINPVAGKPSRPIAGDASFRTVTAFEGGQGKVESGVWESTSGSFQSNTTGYIEYCHIIEGEARLVDPDGTVHAVKAGDAFIMPEGYTGRWEVDRHVKKIYFVTHLA
>AP019378.1|BBH96742.1|345858_346785_-|hypothetical-protein
MTSHSTDHDTIGMPNLNLSLDHTGLIVFKLEDARQAFERLGFTLTPRSMHAGALTPGGPVVPWGSGNHCAMFRNGYFELLGLVEPDKPSTARRMLDRYEGLHIVAMDCESADAMHPQLTAAGVPAPAPATLERDAAFGPANDQTRRARFRNINLDGEAYPEARFIVIEHGTRDVLWQPHLLDHPNGATGLAAMYFAAADLSATLERFQRLLGTPSAHGDAYCFELRRGRFWVMSEAAMREHCPVLADGPVHRVAAACIEVRSLPALQEYLQARQIDYVAAPYLDGAAPSIWVAPAQASCAALQFIQAR
>AP019378.1|BBH96752.1|362543_363209_-|helix-turn-helix-transcriptional-regulator
MHATPVLLVTDDDLLWQHWRGLDAARWLPARGRGLASLQQWQGQGRQLVVLDASVARLPAWDAPQWQELTVGLRLVVASSRPSDAQGTQVFAAGAYGYCHSHAPLASLMQVLEVVSGGGIWMGRSLVTRLLKLVDERVPSAPAPWQHDRLTERENAVALRAAHGDSNADIAGELGITERTVKAHLSAAFEKLGVSDRLQLALCVHGISTRTPAPRTGTDGR
>AP019378.1|BBH96753.1|363230_364673_-|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit
MQNTQNATLAAPPARQGSLLGALWRVPRGWIMGLFDRLLDGAERKDGPSPANYVGNAEWAIRQADARGSRVLLWASLLATLALLLWAGFGYIDEVVRGEGKVVPSRQVQIVQSLDGGIVEEILVRPGEAVETGQVLLKIDPTRFASSLGENNAEYLSLLAKAARLKALATGEPFVAPEKVLQEAPAIVEMERNTWQARTSELNATVNVAREQLKQREEELRETIAKRDQASASCGLTSRELQVTRPLLKSGAVSEVDLLRLQRDVARYCGEQKGAEAQIDRIGASIKEAQSKLQEAELNIRNQARSELSETNTKLATLREGQAALADRVKLADIRSPVRGTVKSLFSNTVGGVVQPGKDIIEIVPTDDTLLLEVRVLPRDIGFLHPDQKAEVKFTAYDFAIYGGLEGHVEQIGADTVTDEKGNSFYIVRVRTNSATLGDRKLPIIPGMVAEVHILTGKRTVLQYLLKPILRAKENAFTER
>AP019378.1|BBH96754.1|364675_366850_-|ABC-transporter
MTTDKFSDPATRSWRADPHASHEDPLLDCLVELTRIHGVPATAQAPSSGLPLVEHRLTPALLPRAAARAQMSARTVKRTLDEISPELLPAILLLRGERACLLLGTAPGGKYLISHPELGASAVEMDADLLQEDYTGLACFVRPQFRFDARAPEVVKVRSRHWFWAAIAENRRLYRDALIAALLINVFAMAMPLFTMNVYDRVVPNNAIETLWVLALGIGLVVLFNLVLTTARAHVVDSASKRVDIRLSAQIMERVLDLRMEGRPVSVGSFAANLRSFESIRDFIASASITTLVDLPFTLLFLAALAWISPWLIAPPLVAIALILLVSLAAQARMETLTMASYQASAQRNATLVEALAGFEAVKTLNGQGAIQRNWERSTEFIAQNGGKLKLISASTVGFVQAMQQLVSVAVVIIGVFQAQESAMSMGGIIAASMIAGRCLTPFGQVAALLMQYQNARTSLGSIDNYMNLPVERPAGTEFLHRPVFQGGIEFRDVTFAYPGASQPALKKVSFKLAPGEKVGVIGRIGSGKTTLEKLALALYQPTEGAVLVDGVDVRQIDPADLRRAIGHVPQDPVLFYGSLRHNLAMGAPHADDASILAAANAAGVTEFANVHPNGFDMMIGERGESLSGGQRQSVAIARALINDPPILLLDEPSSNMDHQSESQLRKRLKAASADKTILLVTHRTALLDLVERLIVIDNGHIVADGPKEQVVEALRQGRVGRGS
>AP019378.1|BBH96755.1|366827_367043_-|hypothetical-protein
MSASNDNGFSKLDADFVRVLEDLIDALIKNGTLRLTDLPPQAQRKLTERKRHRARLAEDLDLLDDDDGQVL
>AP019378.1|BBH96756.1|367053_368523_-|outer-membrane-protein
MPTFSFKRTTAIVAVLFAPAAYAQQQAGTTLNQVVEQTLLSNPEIQAKYHDFRASMEGQNVARGGLRPQVNAQGFVGKEWRSNVPDRGSYNWSRPGYSVELRQLIFDGFRTSNDVKQAGYDKLGRFYELLATSDSTAYSAVQAYVDLQRYREMELLARQNYSLHEDTLKQIREHAESGVGRRVDLEQAGGRLALAQTNLMTESANLIDVQQRFQRITGMTPAVDLQPVPDVAGKLPQQPANFDDSLRMNPSFLAKQAYLQAANAGVASAKGAFSPKFEFVAATGRDREQPEPQYRDVQSSSVQLVMSYNLYRGGADSARVRQTAEQSYAARDVRDYTCRNVQQDLAVAWNNIVRLREQIPFLRDHEIATAKVRNAYREQFQIGQRSLLDLLDTENELFESRRALANGMADLQLAQYRWLALSHKILPALSVQPARDEMPEENAVLETTDEVLKLCNSPVPDVSRLAPVQVIYNSGAKPPTFVPADKARP
>AP019378.1|BBH96757.1|368874_370167_-|hypothetical-protein
MSPDSLSAVAAPQAGAPSPRAARVAIIGAGPAGLMAAETLAGHGLRIDVYDAMPSVGRKFLLAGRGGLNLTHSEAPQAFGARYGARADWVAQWLAQWDAQALRAWAHGLGVETFVGTSGRVFPREMKAAPLLRAWLARLRGAGVGFHMRHRWLGWPAGEPASPQALRFGTPDGALAVRADAVVLALGGASWARLGSDGAWTATLREHGVAVAPLRPANCGFEADWSEPMRQRATGQPAKAVAMALAPDGPWRRGEFVVTDSGIEGSLVYACSAGLRDAIDVRGAATAWLDLLPDWPAERVAAAVMHPRGARSMSSHLQSRLGIKGVKAALLRECAGAEAYADAGLLARRIKALPLRLLRTRPIDEAISSAGGVERAALDARLMLAKAPDVFCAGEMLDWEAPTGGYLLTAVMASGVVAGRGVLAWLRDGL
>AP019378.1|BBH96758.1|370319_370646_+|transcriptional-regulator
METNAAIKALVVLGHASRLTAFRLLVQAGAEGVAAGQLAQAMGIAPSSLSFHLKELVQAGLLEARQDGRFVIYAARYDTMAGLIAYLTDNCCQGAPCDAAPCTREPRA
>AP019378.1|BBH96759.1|370642_371923_+|arsenical-pump-membrane-protein
MITAAVIFLFTLTLVIWQPRGLGIGWSACLGAAISLATGVVHWSDIPVVWGIVWNATAAFIAIIIVSLLLDEAGFFEWAALHVARWGRGRGRMLFAWIVLLGAAVSALFANDGAALILTPIVMAMLAALGFGAGATLAFVMAAGFVADTASLPLIVSNLVNIVSADYFGIGFNRYAAVMIPVTLVSVAATLAVLLLRFGASVPARYDASQLKAPRAAIRDPRTFRAGWMVLALLLVGFFGLEPLGVPVSATAAAAAAVLLAVAGRGHFISTRKVMREAPWHIVVFSLGMYLVVFGLRNAGLTQSLADLFGWFASHGLWAATYGVGLVTALLSSVMNNLPTVLVGALSIDASSASGAAREAMVYANVIGSDLGPKITPIGSLATLLWLHVLARKGVRISWGYYFKVGIVLTLPVLLLTLGALALRLS
>AP019378.1|BBH96760.1|371963_372968_-|ABC-transporter-substrate-binding-protein
MPIPIPIKHRRPLMHSFKSALLASAVLALAAGTAGAADTYPGDKPIKIVAAFSPGSATDTSARIIAEELRKDLGANVIVENKPGAQGLIGTEYAVRQPGDGYTLTIASSSLNSINPGLFKKLPYDAQKDFTHISRLTTMPMLVLVRGDGDIKTLDQLVQKAKAGSLNYGYGSPGGQVGAVAFNNIAGIRAEGVPYKSQPPALTDLAGGQVDYVLGDLSVATPLLRAGKIRALAVSTEQRLPDLPEVPTFAETDYKAFDLVVWVGLSGPAGIPPEVAQRLNDSVNKALARPEIQEKFKGLGMTTAPNTLAQQQQFVQSQLDTWGRRMREANIQPE
>AP019378.1|BBH96761.1|372972_374109_-|CoA-transferase
MQSSDSGGALAGLRVIDASRVLAGPFCGQMLGDHGAEVIKIESPEGDECRGFGPPFVDGASAYFRAVNRNKRSMVLDLNSEAGRETLWQLLETADVLIENFKASTLRAWGIADPAEITARFPRLVHCRITGFGDDGPLGQLPGYDAAVQAIAGLLSINGEAGGPPVRLGVPVVDLTTGMNAAIAVLLALQARHRTGRGQMADVALYDSAVSVAHPFLTNYLASGKTPGPSGNGHPNIVPYNVYRTRTCPLFIAVANDRLFAKLCAQLGVAELAADARFATNGQRVVNREALDAALSQAFAQVDGEPFGQQLLAQNVPAAPILDIAAVAAAPHTAHRRMVVQQPDYTGPGIPIKLSHTPAAIRRGPPALGEMAAPPPKR

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Crispr_ID: AP019378_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

AP019378_4

1508965-1509051

Orphan

Consensus_repeat	Method
AGTGTGCCTGTCCCCGCAGGGACAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of AP019378_4

>merge|AP019378|4|1508965-1509051|CRISPRCasFinder
AGTGTGCCTGTCCCCGCAGGGACAGATACCGTCTTGGCGGGCTAGCGTCGATGGCGTACGGCAGTGTGCCTGTCCCCGCGGGGACAG

>AP019378|4|2|1508965-1509051|CRISPRCasFinder
AGTGTGCCTGTCCCCGCAGGGACAG	ATACCGTCTTGGCGGGCTAGCGTCGATGGCGTACGGC
AGTGTGCCTGTCCCCGCGGGGACAG

Protein	Signature genes	Signature genes Name	Protein_function
AP019378.1\|BBH97880.1\|1508137_1508902_+\|short-chain-dehydrogenase	unknown	unknown	gnl\|CDD\|235910
AP019378.1\|BBH97877.1\|1502275_1503103_+\|deoxyribonuclease	unknown	unknown	gnl\|CDD\|238635
AP019378.1\|BBH97876.1\|1501546_1502242_+\|lipoprotein-releasing-system-ATP-binding-protein-LolD	unknown	unknown	gnl\|CDD\|213222
AP019378.1\|BBH97889.1\|1519514_1520384_-\|transposase	unknown	unknown	gnl\|CDD\|289759
AP019378.1\|BBH97878.1\|1503408_1506615_+\|serine-protease	unknown	unknown	gnl\|CDD\|377133
AP019378.1\|BBH97882.1\|1509737_1510637_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|223656
AP019378.1\|BBH97875.1\|1500273_1501554_+\|lipoprotein-releasing-system-protein	unknown	unknown	gnl\|CDD\|274034
AP019378.1\|BBH97871.1\|1495612_1496368_-\|short-chain-dehydrogenase	unknown	unknown	gnl\|CDD\|180796
AP019378.1\|BBH97873.1\|1497604_1499305_-\|single-stranded-DNA-specific-exonuclease	unknown	unknown	gnl\|CDD\|182944
AP019378.1\|BBH97874.1\|1499286_1500228_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226706
AP019378.1\|BBH97885.1\|1513552_1514998_-\|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270236
AP019378.1\|BBH97890.1\|1520604_1521168_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|198171
AP019378.1\|BBH97883.1\|1510684_1511770_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|226361
AP019378.1\|BBH97886.1\|1515131_1516445_+\|pyrimidine-permease	unknown	unknown	gnl\|CDD\|132655
AP019378.1\|BBH97888.1\|1518736_1519213_+\|transcription-elongation-factor-GreA	unknown	unknown	gnl\|CDD\|234693
AP019378.1\|BBH97872.1\|1496397_1497279_-\|peptide-chain-release-factor-2	unknown	unknown	gnl\|CDD\|234799
AP019378.1\|BBH97879.1\|1506735_1507956_-\|ISL3-family-transposase	unknown	unknown	gnl\|CDD\|225995
AP019378.1\|BBH97887.1\|1516475_1518107_-\|methyl-accepting-chemotaxis-protein	unknown	unknown	gnl\|CDD\|185001
AP019378.1\|BBH97884.1\|1511766_1513476_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224099
AP019378.1\|BBH97881.1\|1509082_1509727_-\|phosphoglycerate-mutase	unknown	unknown	gnl\|CDD\|366010

Protein	Function_ID	Function_description	E-value
AP019378.1\|BBH97880.1\|1508137_1508902_+\|short-chain-dehydrogenase	gnl\|CDD\|235910	PRK07024, PRK07024, SDR family oxidoreductase.	4.78988e-141
AP019378.1\|BBH97877.1\|1502275_1503103_+\|deoxyribonuclease	gnl\|CDD\|238635	cd01310, TatD_DNAse, TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.	1.42767e-89
AP019378.1\|BBH97876.1\|1501546_1502242_+\|lipoprotein-releasing-system-ATP-binding-protein-LolD	gnl\|CDD\|213222	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein. This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of lipoproteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyzes the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.	2.7791e-114
AP019378.1\|BBH97889.1\|1519514_1520384_-\|transposase	gnl\|CDD\|289759	pfam13011, LZ_Tnp_IS481, leucine-zipper of insertion element IS481. This is the upstream region of the conjoined ORF AB of insertion element 481. The significance of IS481 in the detection of Bordetella pertussis is discussed in. The B portion of the ORF AB carries the transposase activity in family rve, pfam00665.	2.93696e-24
AP019378.1\|BBH97878.1\|1503408_1506615_+\|serine-protease	gnl\|CDD\|377133	pfam03797, Autotransporter, Autotransporter beta-domain. Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type V pathway was first described for the IgA1 protease. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C-terminus of the proteins it occurs in. The N-terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs.	1.21965e-46
AP019378.1\|BBH97882.1\|1509737_1510637_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|223656	COG0583, LysR, Transcriptional regulator [Transcription].	7.08863e-33
AP019378.1\|BBH97875.1\|1500273_1501554_+\|lipoprotein-releasing-system-protein	gnl\|CDD\|274034	TIGR02212, releasing_system_transmembrane_protein_lolC., lipoprotein releasing system, transmembrane protein, LolC/E family. This model describes the LolC protein, and its paralog LolE found in some species. These proteins are homologous to permease proteins of ABC transporters. In some species, two paralogs occur, designated LolC and LolE. In others, a single form is found and tends to be designated LolC. [Protein fate, Protein and peptide secretion and trafficking].	9.67778e-160
AP019378.1\|BBH97871.1\|1495612_1496368_-\|short-chain-dehydrogenase	gnl\|CDD\|180796	PRK07023, PRK07023, SDR family oxidoreductase.	5.47641e-103
AP019378.1\|BBH97873.1\|1497604_1499305_-\|single-stranded-DNA-specific-exonuclease	gnl\|CDD\|182944	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ.	0
AP019378.1\|BBH97874.1\|1499286_1500228_-\|hypothetical-protein	gnl\|CDD\|226706	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown].	1.75258e-20
AP019378.1\|BBH97885.1\|1513552_1514998_-\|ABC-transporter-substrate-binding-protein	gnl\|CDD\|270236	cd13518, PBP2_Fe3_thiamine_like, Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. On the other hand, thiamin is an essential cofactor in all living systems. Thiamin diphosphate (ThDP)-dependent enzymes play an important role in carbohydrate and branched-chain amino acid metabolism. Most prokaryotes, plants, and fungi can synthesize thiamin, but it is not synthesized in vertebrates. These periplasmic domains have high affinities for their respective substrates and serve as the primary receptor for transport. After binding iron and thiamine with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The iron- and thiamine-binding proteins belong to the PBPI2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.	6.57311e-40
AP019378.1\|BBH97890.1\|1520604_1521168_-\|hypothetical-protein	gnl\|CDD\|198171	smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.	1.07852e-27
AP019378.1\|BBH97883.1\|1510684_1511770_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|226361	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism].	3.76041e-148
AP019378.1\|BBH97886.1\|1515131_1516445_+\|pyrimidine-permease	gnl\|CDD\|132655	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the uracil-xanthine permease family defined by TIGR00801. As well as the The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40).	0
AP019378.1\|BBH97888.1\|1518736_1519213_+\|transcription-elongation-factor-GreA	gnl\|CDD\|234693	PRK00226, greA, transcription elongation factor GreA; Reviewed.	7.10406e-83
AP019378.1\|BBH97872.1\|1496397_1497279_-\|peptide-chain-release-factor-2	gnl\|CDD\|234799	PRK00578, prfB, peptide chain release factor 2; Validated.	0
AP019378.1\|BBH97879.1\|1506735_1507956_-\|ISL3-family-transposase	gnl\|CDD\|225995	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	1.13968e-78
AP019378.1\|BBH97887.1\|1516475_1518107_-\|methyl-accepting-chemotaxis-protein	gnl\|CDD\|185001	PRK15041, PRK15041, methyl-accepting chemotaxis protein.	1.67757e-117
AP019378.1\|BBH97884.1\|1511766_1513476_-\|ABC-transporter-permease	gnl\|CDD\|224099	COG1178, ThiP, ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism].	3.58657e-90
AP019378.1\|BBH97881.1\|1509082_1509727_-\|phosphoglycerate-mutase	gnl\|CDD\|366010	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1). The histidine phosphatase superfamily is so named because catalysis centers on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches. The larger branch 1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase. The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases. The bacterial regulatory protein phosphatase SixA is also in branch 1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in branch 1 members.	5.12316e-70

>AP019378.1|BBH97880.1|1508137_1508902_+|short-chain-dehydrogenase
MQHVFITGASSGLGQALARRYAADGARLGLLGRRAQALEALASSLPGQHRCYAVDVRDRAALHAAAQDFIAHCGGRVDVVIASAGVSAGTLTEAGEDYAVFKEIVDTNLLATVATFEPFIAGMRAARAGRLVGIASVAGVRGLPGAGAYSASKAAVATYCESLRLELAQAGVRVVTIAPGYVKTAMTAHNPYAMPFLMEADAFAGRAHAAIARGVSYRVIPWQMGVVAKLMRLLPDAVYDRLARDAPRKPRRGQ
>AP019378.1|BBH97879.1|1506735_1507956_-|ISL3-family-transposase
MLDRKLLESLGGWQGYGVERVEWPEDPGRTLSIYLKPTAKVMLCEQCGARCRQVHETTVRRVRDLPLFEYRVVLHVPRRRLWCEQCGGPRLERLAWLGRYQRVTDRLAQACSQLLQSSNVQAVARFFELGWHTVKTLDKARLRASVREPDWSKIEYLAMDEFALHKGHRYATVVVDPISRQVLWIGPGRSRETARAFFEQLPPGAAQRIKAVAIDMTTAYELEIQAHSPQAEIVYDLFHVVAKYGREVIDRVRVDQANQLRQDRPARRIIKSSRWLLLRNRDNLDRQQAVRLDELLQANQPLLTVYVLRDELKRLWFYQRPAWARQAWNHWYKQAEQSGIAALNTFAQRLKGYLHGILARCRHPLNTSIVEGINNTIKVIKRRAYGYRDQEYFSLKIRAAFPGNAR
>AP019378.1|BBH97878.1|1503408_1506615_+|serine-protease
MGLRITSLAAALLGVYGAAGAAENRLECIGACPPGQPVAGAHYSGTNLSANREWVVYGEGSNAVFTLQGGSVTASGGLMGAVNAADGARVYLNQVSVRTDAGNGWEAPGVRAEYGALVNVRGGSIATVGGGSYGVQSLDSGTMIELNGTDIRTTDAYSDGLRAEFGGSIRAVGLTINTTGEHAVGAMGADDGTIALRDSRITTSGVDAYGLGTESQVLSPGGVLQVSNTAIQTSGKNAHGVYLQGGSSLNMSGGSIRTTGSGAAGLRVSNGSSVALNGVEVVASGPSLLSTLSATRQQSIVVGAGSNLTRNDGRLLLVRRVAGGELGQVTLTLKSGSYAAGNIENLAADGSRESSALTIVDVQSGAQWAGLVIDDTTAIVNGSQSGQHSGFSTAGDMVLEGGSAPVTFTGVSNIGGSSSLGAGSQTTFGGATTIGQSLAVLPGGSVAFNGPLTIGESVTGGQGTALSFNAPAIIGANVQGAGGAAFTFSGPAQVGGSVQGLDGASFRFSTSAPTAIAGGLSLAGGSSLGGGSPTTPIVVTGGADAVSGAILGGNLDIGGALRMTGASLAPGNSIGTVTVGSVGALSGSTYLAEVNAKGQSDLLVVRSGNVDLAGVSLVVGQENGTGGYVLNHDYTIIKTEAGKIVGEFAAASLDESLASTLVKLDPVKYGAQATQVSLSPDADKLAAARAGLTRNQSAVLDGALSVAGRNASADAVMLMSDTGQRAGALDQLSGEVHGSAVSALYSNTQLLNRTVARRMSANLGAGLLAGAPTAQAAGPAAASAMPGTAAYPLWADVVGNWSSFDAKDNAAKAKSNTAGLFIGGDVAVGAGWRVGGALGFTDGRIKADAVDSRSDVTSYTAALYGGNSWAAGKGKLNFLAGVGYTHHDIDSRRSVDVGGAQTLKADYKANTTQLFAELGYQVPVGASSSVEPYAGLAWFNNHSDSFDEDGGPAALHGSGQTDQITTFTLGLRGNTALQLGATETRLSAGLGWRHANGDVDATRKLAFIQGGGTAFTVAGSPVARDAAVLDLAAEVDVGRNAALGLAYGGQFGNGNKENTGSLYLKVRF
>AP019378.1|BBH97877.1|1502275_1503103_+|deoxyribonuclease
MLIDTHCHLDAAEFDADRMAVARAAREAGVQAIVIPAVERANFATVRQLAHAVDSGAYALGIHPLYVARARDEDLDSLRRAIESALPDPRFVAIGEIGLDFFVAEIASGAPRERQERFYAAQLDLAAEYGLPVLLHVRRSQDILLKHLRRRPGVPGGIAHAFNGSAQQAGAFVEQGFALGLGGAMTYPRALQIRRHAADIGLDHLVLETDAPDIPPAWLYEPERRNTPGQLPRIAAELAALRGQAVADVARATTTTALRVLPRLGALLQDRAATP
>AP019378.1|BBH97876.1|1501546_1502242_+|lipoprotein-releasing-system-ATP-binding-protein-LolD
MTEPNDTGPALQAEHLGKVYDEGPARIEVLSDVSLSVARGEMVAIVGASGSGKSTLLHILGLLDVPSSGTVSVDGVPAAGLSEKRKSALRNRSLGFVYQFHHLLPEFSALDNVAMPLIVRRENRDRARAQAREVLELVGLAAREEHFPGQLSGGERQRVALARALVTRPACVLADEPTGNLDRHTAHNMFELLTRVNRESGTAFVIVTHDPELAARADRQLHMENGRLQPD
>AP019378.1|BBH97875.1|1500273_1501554_+|lipoprotein-releasing-system-protein
MLKIPYELWIGARYAGMARIRQRRGRRDRFISFIAATSMAGIALGVAALIVVLSVMNGFQKEVRDRMLSVLPHIELYIPGAAPERVLQQWRQFAQAARANPEVKGEAPFVAAQGMLVRGQALRGVQVRGIDPATEGNVSNIPRQMVSGKLSDLVAGGFGAVLGSDLADGLGVKTGDTVLMLAPQGSISPAGFAPRMRQFTVVGIFSSGHYEYDSTLVFIDDEDAAKVFRESGTAGVRLRVADMQRAPEVAAELTKVLPPYVMAADWSRNNRTWFAAVQTEKRMMFLILALIVAVAAFNLLSSLVMAVKDKQSDIAILRTLGAGPGEVARIFLVQGALIGVVGTLLGVAGGIAIAYNVDVIVPFIERLLGVQFLPREVYFISALPSDPQADDIITIGLTSLVLSLLATLYPSWRASRLQPAQVLRHD
>AP019378.1|BBH97874.1|1499286_1500228_-|hypothetical-protein
MLIVIPGALPAAAVAPELARLLPQHAPTLHGWLQAASARVQAFDAARQGCTPFEGWQLEQAGYQPQPGLPLGAGLGPLRAAGGTPGQPVWLADLAHLMLGADQAALLDPALLDLRADESAQLFEAAAPLFADSGFGATPIDAARWRLTLPAGMAPQTASPAAVAGQRLRAWWTQDVAMRPWRRLLNEIQMVWYEHPVNEARAARGAAPINALWLYGGATPWPAGAPAPARVCDELAAAQRAGDWAAWLDALAVLDAAQLAPLAGPHGRPVQPLQLLLLGDDRRAALTLKPRAGLARWLPAPKHNWNAWWSRPV
>AP019378.1|BBH97873.1|1497604_1499305_-|single-stranded-DNA-specific-exonuclease
MVSPRLIIRTADLQACQHLEAAGIHPLLSRLWAARGVIHPEQTRMAWPALLPPDRLTHSAHAAAVLADAIEQGKRLLIVADYDCDGATACAVGLRALSAMGADVDFLVPNRFETGYGLSPAVVELACRHRRGKPDIIITVDNGIASVDGVAAANAAGIGVVITDHHLPGDTLPEALAIVNPNQPGCGFGSKHLAGVGVIFYMMLALRAELRRRGVYAPDGGPRLDALSDLVALGTVADVVKLDANNRLLVTQGLQRMRAGRMQPGVRALFAVAGREPRTASGFDLGFALGPRINAAGRLADMSLGIACLTTDDEAQALEMARELDNINRERRTIEAEMRDQALAAMEAPDAAAGATVCVFDPGWHQGVVGLVASRLKEKFWRPTLAFAPAGEDELRGSGRSIPDVHLRDALDLVSKRHPGLIRKFGGHAMAAGLTLGSGDFAAFAPAFDAAVRELTGRDRFEPLLETDGSLESGYANAEVAGLLQQQVWGAGFAAPLFLDEFTVRSQRLVGGKHLKLALERGHQRFDAIWFGHDQSLPERIQAAYRLEQNIWNGMVSVQLVIEHAA
>AP019378.1|BBH97872.1|1496397_1497279_-|peptide-chain-release-factor-2
MGSGLADSCELVELALADSDDATLEAIEHDVDRFQEKLETLEFRRMFANPADPLNCFVDIQAGAGGTEAQDWASMLLRQYLKYAERKGFKAEILEESEGDVAGLKSATIKIEGEYAFGYLRTETGVHRLVRKSPFDSSGGRHTSFASVFVYPEVDESFEVEVNPADLRIDTYRASGAGGQHINKTDSAVRITHAPSGIVVQCQNDRSQHRNRAEAMQMLKSKLYELEMRNRMTEQQKLEDSKTDVGWGHQIRSYVLDQSRIKDLRTNVEISNTQKVLDGDLDPFIQASLKQGV
>AP019378.1|BBH97871.1|1495612_1496368_-|short-chain-dehydrogenase
MTDTVAILTGASRGLGAALARGLLAPGTRLITLARRADPDLEAAARTRGASLEQVQVDLSDPAAAGAAAKRLCAALPRDARRYLLINNAGTVSPVAQAAGLTDGAAIAGALNLNVTAVVLLTARFVAALQGLPADRRVLNISSGAGRNPNAGWGVYCAAKAALDMYSRVLKQEQGQDGVRVVALAPGIVDTDMQGAIRASDPADFPALERFREFHATGKLSAPADVAARILAYLDRDDFGTTEIDDIRNYQ
>AP019378.1|BBH97881.1|1509082_1509727_-|phosphoglycerate-mutase
MTEIWFIRHGETDWNRQRRLQGWQDIPLNESGREQARLLAERLRDTASEHPFAALYSSDLKRAHDTAASLSAALQLRVRTEPGIRERGFGVLEGLEMENLEQQAPQAAQAWRSRDPLRALEGGETLGQFQARIIATVDDLAARHASERILAVTHGGALDIIWRHASGVPLDAPRYAALLNVSINRVAIAQRKWEVLGWGDVEHIGAETGNDVTP
>AP019378.1|BBH97882.1|1509737_1510637_-|LysR-family-transcriptional-regulator
MEIYQIRAFVTVARLGNLTKAAEALSLTQPAVTAQLKALEQSLGVALFDRAAGRLSLAKAGEALLPTAEALLVLGAQLKSEARQLQGQLQGVIDLGVPSEQPDFLRLGELAAALRQRLPLVELKTHVLPSTALLEQVGTARLAGALTIVAHPPRGVTWHALRSVRYRIALPASLADTLKRAGWRDIAQLPWLDGPSGSHLHLLLRDMFERHGLAPRVVMQNDDQSNLDALVRAGAGCALLREETALAGAAAGDFIVWGQARADATLGFIAPPEQAGEPMLVALISMIQKIWKPGAAVAT
>AP019378.1|BBH97883.1|1510684_1511770_-|ABC-transporter-ATP-binding-protein
MKKVSVECRNIRLSYGRNEVLKDISIHIEPGEFFALLGPSGSGKSTLLRLIAGFNRQSHGQLLVDGRDIGATPPWDRNIGMVFQNYALWPHMTVWDNVAFGLVERRLPRAEIRDKVAAALELVGLADFGRRRPNQLSGGQQQRVALARTIVIEPQVLLLDEPLSNLDKKLRVQMRQDLLSLQRRLGITTIFVTHDQEEAMTTADRMAVLDHGVVQQIGAPSTLFDYPVNRFVANFVGTMNVLEGEVRERSRGGVVLAVDGVGELHLPVNGDAPQAGRLAASFRPHTVLIEMADGTGDARYVWLPGVVESSEFLGEFTRYQVQVGEQRLTADQHHLAGLSPFPVGAPVAVGLEPTQIRLLAA
>AP019378.1|BBH97884.1|1511766_1513476_-|ABC-transporter-permease
MTSTGTFRLPAGPALAALLVLAFLALFLVFPVGTVFYTAFVNADGSFTLGHFGAVFNQPLMKEAFFNSLYVAGWSSLLASLIAVPLAYFTVRFEFRGALLIQTLGVLPLIMPPFVGAMAMQLIFGRSGSVNLLLDDWLGITLPFMDGLNGVIFVESLHYFPFILMNLVVALRNIDGSMEEAAFNLGSRGFRLFCRIIFPLALPGYLAGTSLVFVKVFDDLGTPLVLGTTNMLAPQAYLRITQVGLEDPLGYVISVIMIGFSILALWLSARVLKGKDYSTLQKGGNAIHKRRLRPVESVLAYAWIGAVLLLVLSPHLGVLLLSLASVWSYAPLPDGYTLAHYTAVFTESQGMIANTLLYCGLAAGVDVVLGTAIAYLMLRTRLPARQWLDFIASAALAIPGIVLAIGYLRTFRGVEIPGTGVLLTSSWVLIMIAYSVRRLPYALRSCVAALQQINVSLEEAAESLGASRLRTIRRIVVPLMAGGMLAGFVTSFITAAVELSATIMLVTRDSQAPMSYGIYLYMQSAAGRGPGAALGVLAVVAVGIGTYVSHLLVERASARQRPARSGESS
>AP019378.1|BBH97885.1|1513552_1514998_-|ABC-transporter-substrate-binding-protein
MTVSSVSSRISAGAFDQYARQLRDRAAASGAKDEAGSPAAEALQALQRQLAAIMAACAPALAGTVTVITSFPKDLTQAYKAAFEKAHPDIKLEILNKNTVSGIAFVRATPAGQRPEVFWASAPDAFEVLGRDKLLAKAPDVANPAVPDKIGSYPINDPSGMYMGQALAGYGIIYNTRYIKANKLPAPVEWKDLLAPHWFGHVGITAPSRSGTMHLTVETILQGEGWNDGWGTLLRMSGNASAVTERSFGVPDGVNNGQFGAGPVIDFFGLSSKYSKFPVDFVYPSETAIVPANIALIEGAKNTEEGKKFIAFTLSQAGQELLLEPKISRLPVLPYAALAGKIPPGYPDPAEIAKRSKVHFDADLSQARYYVVQSLFDQTITFRLKELQAATKAIYDAEAKLGERAGQGKAAELLAQARQLAWTPLVDAQRAADPAFLKLFAGNKKDAAVNQQITQLEGEWNGKARANYEQAQKLAREAAAL
>AP019378.1|BBH97886.1|1515131_1516445_+|pyrimidine-permease
MSNTYFPRWRLADDTVPGAVIAPDERLSWPKNIAMGAQHVVAMFGSTVLAPLLMGFDPNVAILMSGIGTLIFFLFVGGRVPSYLGSSFAFIGGVVAVTGYVAPGANANIGVALGAIIACGLVYALIGLVVWAASARGNGARWIEAMMPPVVTGAVVAVIGLNLAPIAAKGAMGSSGFEASMALMTILCVGGIAVYTRGMVQRLLILVGLVLACVIYAVCANGLGLGAPMDFAKVAAAPWFGLPSFAAPVFEPQAMGLIVPVAIILVAENLGHVKAVAAMTGQDLDRCVGRAFVGDGVATMVSGAVGGTGVTTYAENIGVMAVTRIYSTLVFVVAAVIALVLGFSPKFGALIQTIPGPVLGGMSVVVFGLIAIAGARIWVVNQVDFSDNRNLIVAAVTLVLGAGDFSVKLGDFSMNGIGTATFGAIILYALLGLARRR
>AP019378.1|BBH97887.1|1516475_1518107_-|methyl-accepting-chemotaxis-protein
MLERIKVRTAMVAVFACFLAVLMLSGALTWRNAGRSAAEIEGLNQVAVNQVDPLFEASGAALRARVALLEALANLQANHLDPVATLHQQAGAAQRQAATQFQRYVDVPKEPAAAELAATLQTRWRAYQSVLDELAAAVDAGQAEPALAAMNRAQQAEHAFQRDMEAFLARVQAHSDEVRSGAEDTHVVARWSAIALAALGVLLTLAGWLFVRRAVLRPLLEAGHHFDRIADGDLTARIEVRSANEIGALFAALKRMQEGLTRTIAVMRRGVDEINVGAAEISAGNANLSSRTEEQAAALEETAATMEELATTVKQNADNAAQANQLAAVSMQVAQRGGESVAQVVQTMHGISASSRQIADIVTVIDGIAFQTNILALNAAVEAARAGEQGKGFAVVAGEVRSLAQRAAQAAKEIKALIESSVATVRAGSQQVASAGGTMDEVVASVQRVADIMGEISAASAQQASGIDQVSLAISQMDETTQQNTALVEQAAAAATAMEEQARHLAAAAAVFRTQGGAIIDVAAAPLAGPAGGHAALPPAAAR
>AP019378.1|BBH97888.1|1518736_1519213_+|transcription-elongation-factor-GreA
MSAIPLTVRGAERLQQELHRLKTVERPAVISAIAEARAQGDLSENAEYDAARERQGFIEGRISELEGTLSNAHLIDPTALDAEGRAVFGATVEIEDLDSGDRLTYQIVGDVEADIKSNLISVSSPVARALIGKSEGDVVEVKVPAGVREYEVIGVRYL
>AP019378.1|BBH97889.1|1519514_1520384_-|transposase
MRQASQAAGVSLRTGYKWLARFRSEGLDGLLDRSSRPHRSPKACAPEQVEHFAQQRRQRLPLWRIAREAGRSLATVARYMERIGLSRLASLEPPAPVRRYERASPGELLHIDTKRLGRIRGVGHRITGDRAQNRNRGIGWDAVHLAIDDFSRVSFARILDDEGGDQCAEFLRQATAYYASLGVRIDRVMTDNGSGYVSRTFRAVCVELGIRHIRTRPYTPKTNGKAERLVQTCLREWAYARPYTSSAERQAALQPFIDRYNWCRPHSALGHQPPITRIPDVNNLLRIDT
>AP019378.1|BBH97890.1|1520604_1521168_-|hypothetical-protein
MRSAAHPLRPVVLIGDNGLTDAVLKEIDLALTAHELIKVRAGGDDREAREAMLATICDTLSCAAVHHLGKTLILFRPDLRAAAAKAAADTPAKRRPSEPHTPKKMAAEGKRLTKTRPARKAAEAAAPAAGARPGRDDLNQAGRPARPSTRKASPGHAIPRRSGSALSLRAGARGGLAGRKPARANKQ

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Crispr_ID: AP019378_5

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

AP019378_5

2401579-2401675

Orphan

Consensus_repeat	Method
GTGCCTGTCCCGGCGGGGACAGGCACCC	CRISPRCasFinder

1 spacers

The CRISPR arrays of AP019378_5

>merge|AP019378|5|2401579-2401675|CRISPRCasFinder
GTGCCTGTCCCGGCGGGGACAGGCACCCAGCCGCAGATGTCAGTCCCCATGCCGCTGGCGCATGACGGCGTGCCTGTCCCGGCGGGGACAGGCACCC

>AP019378|5|3|2401579-2401675|CRISPRCasFinder
GTGCCTGTCCCGGCGGGGACAGGCACCC	AGCCGCAGATGTCAGTCCCCATGCCGCTGGCGCATGACGGC
GTGCCTGTCCCGGCGGGGACAGGCACCC

Protein	Signature genes	Signature genes Name	Protein_function
AP019378.1\|BBH98734.1\|2392283_2393639_-\|amidase	unknown	unknown	gnl\|CDD\|223232
AP019378.1\|BBH98737.1\|2396110_2397055_-\|peptide-ABC-transporter	unknown	unknown	gnl\|CDD\|223674
AP019378.1\|BBH98735.1\|2393635_2395243_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224048
AP019378.1\|BBH98751.1\|2413377_2415573_+\|1,4-alpha-glucan-branching-enzyme-GlgB	unknown	unknown	gnl\|CDD\|235445
AP019378.1\|BBH98736.1\|2395262_2396093_-\|peptide-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224094
AP019378.1\|BBH98749.1\|2410039_2411851_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|274140
AP019378.1\|BBH98744.1\|2403183_2404593_+\|RNA-polymerase-sigma-54-factor	unknown	unknown	gnl\|CDD\|235648
AP019378.1\|BBH98743.1\|2401736_2402957_-\|ISL3-family-transposase	unknown	unknown	gnl\|CDD\|225995
AP019378.1\|BBH98746.1\|2405295_2406828_+\|glycogen-synthase	unknown	unknown	gnl\|CDD\|273969
AP019378.1\|BBH98750.1\|2411875_2413381_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|274141
AP019378.1\|BBH98738.1\|2397107_2398682_-\|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|173867
AP019378.1\|BBH98748.1\|2409188_2410028_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|200482
AP019378.1\|BBH98752.1\|2415577_2417194_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|131155
AP019378.1\|BBH98745.1\|2404621_2405038_-\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH98742.1\|2400554_2401505_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176131
AP019378.1\|BBH98740.1\|2399081_2399279_-\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH98747.1\|2406839_2409176_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|200482
AP019378.1\|BBH98739.1\|2398729_2399089_-\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH98741.1\|2399288_2400458_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377804
AP019378.1\|BBH98733.1\|2391344_2392106_-\|lipoprotein	unknown	unknown	gnl\|CDD\|132874

Protein	Function_ID	Function_description	E-value
AP019378.1\|BBH98734.1\|2392283_2393639_-\|amidase	gnl\|CDD\|223232	COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis].	6.98538e-115
AP019378.1\|BBH98737.1\|2396110_2397055_-\|peptide-ABC-transporter	gnl\|CDD\|223674	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].	1.35623e-122
AP019378.1\|BBH98735.1\|2393635_2395243_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|224048	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only].	0
AP019378.1\|BBH98751.1\|2413377_2415573_+\|1,4-alpha-glucan-branching-enzyme-GlgB	gnl\|CDD\|235445	PRK05402, PRK05402, 1,4-alpha-glucan branching protein GlgB.	0
AP019378.1\|BBH98736.1\|2395262_2396093_-\|peptide-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].	1.14667e-85
AP019378.1\|BBH98749.1\|2410039_2411851_+\|hypothetical-protein	gnl\|CDD\|274140	TIGR02456, Trehalose_synthase, trehalose synthase. Trehalose synthase interconverts maltose and alpha, alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor (). [Energy metabolism, Biosynthesis and degradation of polysaccharides].	0
AP019378.1\|BBH98744.1\|2403183_2404593_+\|RNA-polymerase-sigma-54-factor	gnl\|CDD\|235648	PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.	0
AP019378.1\|BBH98743.1\|2401736_2402957_-\|ISL3-family-transposase	gnl\|CDD\|225995	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	5.26988e-80
AP019378.1\|BBH98750.1\|2411875_2413381_+\|hypothetical-protein	gnl\|CDD\|274141	TIGR02457, trehalose_synthase, trehalose synthase-fused probable maltokinase. Three pathways for the biosynthesis of trehalose, an osmoprotectant that in some species is also a precursor of certain cell wall glycolipids. Trehalose synthase, TreS, can interconvert maltose and trehalose, but while the equilibrium may favor trehalose, physiological concentrations of trehalose may be much greater than that of maltose and TreS may act largely in its degradation. This model describes a domain found only as a C-terminal fusion to TreS proteins. The most closely related proteins outside this family, Pep2 of Streptomyces coelicolor and Mak1 of Actinoplanes missouriensis, have known maltokinase activity. We suggest this domain acts as a maltokinase and helps drive conversion of trehalose to maltose. [Energy metabolism, Biosynthesis and degradation of polysaccharides].	0
AP019378.1\|BBH98738.1\|2397107_2398682_-\|ABC-transporter-substrate-binding-protein	gnl\|CDD\|173867	cd08502, PBP2_NikA_DppA_OppA_like_16, 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.	0
AP019378.1\|BBH98748.1\|2409188_2410028_+\|hypothetical-protein	gnl\|CDD\|200482	cd11344, AmyAc_GlgE_like, Alpha amylase catalytic domain found in GlgE-like proteins. GlgE is a (1,4)-a-D-glucan:phosphate a-D-maltosyltransferase, involved in a-glucan biosynthesis in bacteria. It is also an anti-tuberculosis drug target. GlgE isoform I from Streptomyces coelicolor has the same catalytic and very similar kinetic properties to GlgE from Mycobacterium tuberculosis. GlgE from Streptomyces coelicolor forms a homodimer with each subunit comprising five domains (A, B, C, N, and S) and 2 inserts. Domain A is a catalytic alpha-amylase-type domain that along with domain N, which has a beta-sandwich fold and forms the core of the dimer interface, binds cyclodextrins. Domain A, B, and the 2 inserts define a well conserved donor pocket that binds maltose. Cyclodextrins competitively inhibit the binding of maltooligosaccharides to the S. coelicolor enzyme, indicating that the hydrophobic patch overlaps with the acceptor binding site. This is not the case in M. tuberculosis GlgE because cyclodextrins do not inhibit this enzyme, despite acceptor length specificity being conserved. Domain C is hypothesized to help stabilize domain A and could be involved in substrate binding. Domain S is a helix bundle that is inserted within the N domain and it plays a role in the dimer interface and interacts directly with domain B. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.	1.60943e-119
AP019378.1\|BBH98752.1\|2415577_2417194_+\|hypothetical-protein	gnl\|CDD\|131155	TIGR02100, Glycogen_operon_protein_GlgX_homolog, glycogen debranching enzyme GlgX. This family consists of the GlgX protein from the E. coli glycogen operon and probable equivalogs from other prokaryotic species. GlgX is not required for glycogen biosynthesis, but instead acts as a debranching enzyme for glycogen catabolism. This model distinguishes GlgX from pullanases and other related proteins that also operate on alpha-1,6-glycosidic linkages. In the wide band between the trusted and noise cutoffs are functionally similar enzymes, mostly from plants, that act similarly but usually are termed isoamylase. [Energy metabolism, Biosynthesis and degradation of polysaccharides].	0
AP019378.1\|BBH98746.1\|2405295_2406828_+\|glycogen-synthase	gnl\|CDD\|273969	TIGR02095, Glycogen_synthase, glycogen/starch synthase, ADP-glucose type. This family consists of glycogen (or starch) synthases that use ADP-glucose (EC 2.4.1.21), rather than UDP-glucose (EC 2.4.1.11) as in animals, as the glucose donor. This enzyme is found in bacteria and plants. Whether the name given is glycogen synthase or starch synthase depends on context, and therefore on substrate. [Energy metabolism, Biosynthesis and degradation of polysaccharides].	0
AP019378.1\|BBH98742.1\|2400554_2401505_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176131	cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to 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.	1.58441e-67
AP019378.1\|BBH98747.1\|2406839_2409176_+\|hypothetical-protein	gnl\|CDD\|200482	cd11344, AmyAc_GlgE_like, Alpha amylase catalytic domain found in GlgE-like proteins. GlgE is a (1,4)-a-D-glucan:phosphate a-D-maltosyltransferase, involved in a-glucan biosynthesis in bacteria. It is also an anti-tuberculosis drug target. GlgE isoform I from Streptomyces coelicolor has the same catalytic and very similar kinetic properties to GlgE from Mycobacterium tuberculosis. GlgE from Streptomyces coelicolor forms a homodimer with each subunit comprising five domains (A, B, C, N, and S) and 2 inserts. Domain A is a catalytic alpha-amylase-type domain that along with domain N, which has a beta-sandwich fold and forms the core of the dimer interface, binds cyclodextrins. Domain A, B, and the 2 inserts define a well conserved donor pocket that binds maltose. Cyclodextrins competitively inhibit the binding of maltooligosaccharides to the S. coelicolor enzyme, indicating that the hydrophobic patch overlaps with the acceptor binding site. This is not the case in M. tuberculosis GlgE because cyclodextrins do not inhibit this enzyme, despite acceptor length specificity being conserved. Domain C is hypothesized to help stabilize domain A and could be involved in substrate binding. Domain S is a helix bundle that is inserted within the N domain and it plays a role in the dimer interface and interacts directly with domain B. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.	1.17971e-107
AP019378.1\|BBH98741.1\|2399288_2400458_-\|hypothetical-protein	gnl\|CDD\|377804	pfam07287, AtuA, Acyclic terpene utilisation family protein AtuA. This family consists of several bacterial and plant proteins of around 400 residues in length. One member of this family has been characterized in Pseudomonas citronellolis as AtuA, a member of a gene cluster that is essential for the acyclic terpene utilisation (Atu) pathway.	4.47053e-161
AP019378.1\|BBH98733.1\|2391344_2392106_-\|lipoprotein	gnl\|CDD\|132874	cd06911, VirB9_CagX_TrbG, VirB9/CagX/TrbG, a component of the type IV secretion system. VirB9 is a component of the type IV secretion system, which is employed by pathogenic bacteria to export virulence proteins directly from the bacterial cytoplasm into the host cell. Unlike the more common type III secretion system, type IV systems evolved from the conjugative apparatus, which is used to transfer DNA between cells. VirB9 was initially identified as an essential virulence gene on the Agrobacterium tumefaciens Ti plasmid. In the pilin-like conjugative structure, VirB9 appears to form a stabilizing complex in the outer membrane, by interacting with the lipoprotein VirB7. The heterodimer has been shown to stabilize other components of the type IV system. This alignment model spans the C-terminal domain of VirB9. CagX is a component of the Helicobacter pylori cag PAI-encoded type IV secretion system. Some other members of this family are involved in conjugal transfer to T-DNA of plant cells.	6.01599e-30

>AP019378.1|BBH98742.1|2400554_2401505_+|LysR-family-transcriptional-regulator
MRPQADLSTRQLRAFVMLADLRHFTKAAQACHLSQPAFSALIQSLEATLAMQLFDRSTRRVVLTQEGELFEPLARRLLADLGHAMTHIASFVELRRGRVHVAALPSLAAGWLPKVLHEFHAEHPDIELMLSDVLSDECIELVRSGQADFALASRGIRASDPAVLHARELCSDTFHLICRKDHPLAREPRLTLKHLAPWPFIHLTRNSSVRQTVEAALRPQVAKTILEVAQLATVAGMIEAGLGISVVPTFTLYQFERPGLLIRPISLPGLTRQIYIVRRQEERLSIAAQALYDLVVAKLGTPAAAKPRRRRTEKGR
>AP019378.1|BBH98741.1|2399288_2400458_-|hypothetical-protein
MRSLPSLLIGCAAGFSGDRVDAAGPVVDTLIARLGGVPANGRAFLIFETLAERTLALAQLRKRADAQAGYEPLLEDMLGPVLARCLAHGIRIVSNFGAANPEGAARHILRMAARLGLRKPRIAVVKGDDVSGAQHAGMLAEYLGEQYDPSSIVSANAYLGSEQIRDALDHGAEIVVCGRVADPSLTVGPAMSYFGWQADDWDRIGRATMAGHLLECGAQVCGGYYADPGYKDVPGLEQVGFPVAEIDEDGHCIIGKSDGTGGLVDEATVIEQLLYEVHDPAGYLTPDVVADISQAEVRRVADNQVRLTGVRGHPRPAAYKVNVCLEGGWLAEGEISYAGPRAEARARLAAEVVCKRLADLRIRTDLIGHVSIFGDDAGRLLAGAPAGDG
>AP019378.1|BBH98740.1|2399081_2399279_-|hypothetical-protein
MRLAAHAVTRQDAMRLTREVTALYCCGPAGGGGVRTTLTPRLDMVSCLLPRDLVRAGFEMVDADV
>AP019378.1|BBH98739.1|2398729_2399089_-|hypothetical-protein
MSDVLVPLFRVAHARTGDKGDRSNISVIAWDRALYPLLVEQLTPEVVLAQFAHRRPAGAQRYLLPKLGAMNFVLDAVLDGGVNGALNLDAHGKALSYLILKTEIAVPSDLVCRLAGSPG
>AP019378.1|BBH98738.1|2397107_2398682_-|ABC-transporter-substrate-binding-protein
MRYLKSTYAAVLLAIGTAVPHATTLAQEVKVAAEAPLRLLDPVGTTAYITRNHAYMVYDTLFALDAQLKPQPQMVSTWSVSPDKLVYRFTLRDGLKFHDGSPVTAADCVASIKRWAQRDLTGLRMMAAAKEITAKDDKTFEIVLEQPFGAVIEGLSKASSLPAFIMPKRIADAPASQAITEVIGSGPFRFVASEYRPGLQVVYERNTDYVPRSEPPSGLAGGKVVNVDRVVWLSLPDIQTEANALAKGEVDYVQTVYPDVVQTLQASKDVVIQKLASTTTPTLRLNWLQPPFNNQKVRQALLHAVSQRDYMDAQVGDPKAYRVCWAMFGCDSPLASTAGVVSQDDEADLNAAKALLKESGYKNEKAVVLHATDYPPTSAIAPFTAQILRSIGMKAEVQSMDWATFLTRRGKQDPVEKGGWSVAYGSWNTLDLMSPIANLNLDGRGKEGYAGWTESAEMESLRTQYAQATEPASRQQIAAKIQQLAYDQVFYIPLGTYSNYAARRSNVTPLLDAPVTVFWGISKN
>AP019378.1|BBH98737.1|2396110_2397055_-|peptide-ABC-transporter
MQILRLLFLRLASAIPVVLVVVTVVFLLVRLTGDPATILAGDMASPEVVASVRADLGLDRPLLGQYAQWLWDLLQGNLGTSIVTKQPVATLIGERLESTLVLSLSALVVTVLLAVPLGVLAAWRHNTLVDRVVMIYAVIGFSLPSFVVGYLLILMFSVWLGWLPVQGYVSITDDIWLAAQHLVLPTLALAIFYMSLISRVTRASVLEALNEDFVRTAKAKGVPSLRILSQHVLRNAAIPIVTVIGIGLAFLISGVVITESVFNLPGLGRLTIDAVLSRDYPVVQGVILFFACVYILVNLLIDMLYVVIDPRIRY
>AP019378.1|BBH98736.1|2395262_2396093_-|peptide-ABC-transporter-permease
MTSILRHNRLALLGGGVLLLMVAISVAASWIASMDPAMMQPRMRLTPPGEAFLLGTDALGRDVYSRVVHGSRMSLAIGALVVVITIAIGTLIGLVAGASRIMDRVLMRIMDGVMAIPGILLAVALVSLFGASLASVVIAIAVPEIPRVVRLVRSVVLSVREEPYVEAAVGLGVPYPKVVWRHILPNCFAPLIVQASYVFAAAILLEAVLGFLGVGFPPEIPTFGNILAEARPVFQRAPWATVAPGLLLAVTVLAVNLLGDGLRDSLDPKLARRAND
>AP019378.1|BBH98735.1|2393635_2395243_-|ABC-transporter-ATP-binding-protein
MLEVSGLAIRAGARTLVQDVTLSLAQGEILCLVGESGSGKSLTASAVMGLLPGNLGVSAGSIRLDGEDLTAASPARMQALRGDRMAMVFQEPMTSLNPLMRVGRQIAEVLQVHRPDLGAGQVRARVLELMGDVRLPTPEALMDAFPHQLSGGQRQRIMIAMALALEPALIIADEPTTALDVTTQAQVLKLFRQLLAKHSSAVLFITHDFDVVRDIADHVAVMQLGRIVEQGPAGQVLDAPRHDYTRKLLAAVPSGVPKTQQNASSDELLSVSGLNLVYESRGLLGPARRTHAVADVGFTLKKGETLGVVGESGSGKSTLGRCITRAHAPTSGRIVFDGVDIAGLSGKALRAVRRRVQMVFQDPYRSLNPRRRILHALIEGPIESGVDRKAACARAAELMALVGLPADGLQRYPHQFSGGQRQRICIARALAMEPDLIVADEAVSALDVSVQAQVLELFEDLQKRLGFAMIFITHDLRVAAQVCDRIGVMQKGRLLELGPVRQVIHAPQHPYTRHLFDSLPGRVGQAAEPAMELQA
>AP019378.1|BBH98734.1|2392283_2393639_-|amidase
MTSTDQHIARAGVAELARGIARGAFTPAEVTDVFLRRIQDLNPAIGAFVAVYEDEARHAARQATQALAQGQRLSPLHGIPFAVKDIVDVAGRFTTYGSRTGAGRQAGATAEYVRALLDAGMILLGKTHTVEFAFGGWGTNQRMGTPRNPLRADVPCATGGSSSGSGAAVGAQMVPFAVGTDTGGSIRIPSAFCGLTGMRPSMGRHSGAGVMSLSHTLDTIGPLARTVEDVQMLDDLLTGKTATDTAQPGSQAVARVRDARIGVLGAQWLGAIEPEVAHAYAQSLRAFEAMGATLVELALPFDREAFAQLTSTLIACEGLQFAGKYVHDPLSGMDEDVRARFLVGDRYDAAAYAELLGRRSAMIDTFTQAMAGVKALLMPTTPCVAQPLAGLEQSPYNPAVYTRMPAWLGCCALAVPNGSGAHGLPTSLQIVGLPESDRLVMSLGRAYQEYA
>AP019378.1|BBH98733.1|2391344_2392106_-|lipoprotein
MVRSLSIVCLLAVLQACAGPRPAAVAAAWDEAPAGQYRFDWQLSGDPAVAPLQVFDDARRIWLQFAPGQPIPAIFAHGAGGERPVPYLRRDPYIVVDGAWPALSLRGGRYVARIQRSGAPIPAGAPVVRAEGPAPVPATPSAVAPAEAAEAAPPAPRFRAAPPDLTLRAVLARWARAAGWTFEAEHWALDVDIPLAGKAELPGDFKTAVRALLAATELSEPPAQPCFYANRVLRVVPLAQACDRTRAAAPGLT
>AP019378.1|BBH98743.1|2401736_2402957_-|ISL3-family-transposase
MLDRKLLESLGGWQGYGVERVEWPEDPGRTLSIYLKPTAKVMLCEQCGARCRQVHETTVRRVRDLPLFEYRVVLHVPRRRLWCEQCGGPRLERLAWLGRYQRVTDRLAQACSQLLQSSNVQAVARFFELGWHTVKTLDKARLRASVREPDWSKIEYLAMDEFALHKGHRYATVVVDPISRQVLWIGPGRSRETARAFFEQLPPGAAQRIKAVAIDMTTAYELEIQAHSPQAEIVYDLFHVVAKYGREVIDRVRVDQANQLRQDRPARRIIKSSRWLLLRNRDNLDRQQAVRLDELLQANQPLLTVYVLRDELKRLWFYQRPAWARQAWNHWYEQAEQSGIAALNTFAQRLKGYLHGILARCRHPLNTSIVEGINNTIKVIKRRAYGYRDQEYFFLKIRAAFPGNAR
>AP019378.1|BBH98744.1|2403183_2404593_+|RNA-polymerase-sigma-54-factor
MSHVLQDLRLRQQTTLAPRLQQSIHLLQMSALEFTTTVQQALATNPFLEDADETEAQDDAPAPPAASEPPATSEPPPEPPSYAGDYPTRSAAAQPGVASDAAAWVPATLSLHERLSQALGAYVLSERDRALAEFIVDGLDDDGYLRQELAQLAGVADFDPPPDASEWQAALHLVQQLDAPGLAARDLPECLALQIRACSRLDPAVRDAALAIVAAHLPRLARSDYPGMRRALRCSEPVLRQACGVIRGLDPKPGRRYAHEPPSYVVPDVVVSKQRQQWLVVPNRGAMPHARLHQAYADLFRRARMDERSPMAQELQEARWLVRNVEQRYATIRRVAEAIVQRQQMFFEFGQIALRPLMLREVADELEMHESTVSRATANKYMSTPRGVFEFRHFFSRELSTESGGTCSAAAVRALIREYIDAEDPRMPLSDVTLAKRLAGDGIVVARRTVSKYRLQLRLPAADTRRQYY
>AP019378.1|BBH98745.1|2404621_2405038_-|hypothetical-protein
MADRHAACEMEGPYLEDIDMKQRSLIYLVAGAMAALLAHGGALAQSGTAPTTPSTTPNDSTAVPPNRPVPPGQVPPAPGTTTHDGMPKTPQQHMNEHRGNDTRGDMPRRQPDINDNPPATPAQGASPPPGYPNTGGSK
>AP019378.1|BBH98746.1|2405295_2406828_+|glycogen-synthase
MTTIRTLVVAAEAFPLAKTGGLGDAVSGMVQALGHRPGGVDVQCELLMPAYRGTLDMVYRPRTVARLGGLPGGPASLVRGHCPGSGLSVLLLRNDALYDRPGIYVDDSGQGYPDNARRYAALAHAAARLAQGLPGLRPPHVVHAHDWHAALAPLLIHAAGLHYVKTLLTIHNLAFQGTFPAELASALGIPLACRHDDGALSDDSVNFLKAGIRYATRVTTVSRAYAREILTPAFGCGLHGLLRARGADLSPVPNGIDTALWNPAADPHLGGLRFDALDMRNKACCKAALQAELGLQPRADATVLAMGSRLTGQKMADVAIAALPALLEAHEHLQFALIGRGEPALETALRALAARYPGRCAVHIGYDEPLAHRLHAGADLLLHGSRFEPFGLTPLYAMRYGTLPVASRVGGMVDTIRDPGPAVEESCAGQGTGFLFDGSEPADMQLAVARALRALAKPAVCDAMRRNAMQADFSWRASAQAYAGLYASLASAPQRGRVPAPTLPLLANAA
>AP019378.1|BBH98747.1|2406839_2409176_+|hypothetical-protein
MVRRAAARLDRDAHLLAFHAAAIALARDTPAGSFAAWQTLCVRLRRCGFNAVCLTPPWQCPDDIQGAPADVDHADARWGGGAMDATLARLAREAAAQGLTLLLDLEPDRVARDAAPRTAQAQWLESPADEPAGDPRQPAARHGVRYVRGRPAPAAFLQAWQSRLAGWLDAGVAGFRCTAPQRLDPSDWRALFEPLRASRPALRLLAWTAGLTPAQSAALAGVGFDGVFGSIPWWSPDATWLDAESQRLREIAPLLAAPLAPAGGAPLAPASAAAHAALRALWVAALWGDGLLVGSELQRMMPAVARALRWRRQAAPRGRPVLLCGRDGWATLIIRPGPPGTSHVLALDPQAAHEPRVDWSAGAALLPAGVPRHLADPVEHCALYRVAAERPVRATAGALLPGPPSACDRDARVVFEHVAPSVAHGSLAAKALAHVPVEVGVDLISDGHEQLAGELQWRAVDQAGWHGVPLAPGDNDRWHARFAPRRIGLHEFRVCAWRDTWLTFCRELRLKHEADQDIALDLAEGAAHLRTALARRQARGDARRAPIEAALSMLNGGPAPADAVAALLRDGLAQAMRALAARPFMHTSASRPLWVDRAAAGHGSWYELFPRSQAVPAGAHGTFDDVIARLPALRAMGFDVLYLPPIHPIGQSQRKGRNNALQAAADDPGSPYAIGSPDGGHDAIHPQLGTRADFARLVQAAAAHGMEVALDFAIQCSPDHPWLQRHPDWFEHRADGSIRHAENPPKRYEDIVNVSFYDQASGRPRRALWRALRDVLLY
>AP019378.1|BBH98748.1|2409188_2410028_+|hypothetical-protein
MRIFRVDNPHTKPLPFWQWLIADVHARHPDVVFLSEAFTRPRMMYRLAKLGFTQSYTYFTWRNTRHELDSYLRELSRPPVCEWFRPNFFVNTPDINPYFLQASGRAGFLIRAALATAGSGLWGMYSGFELCEAQPVPGKEEYLDSEKYQLRQRDWHAPGNVTAEIAALNRIRRANPALHSHLGYVPLQCANEQVLTFCKATPNRASVVLAAVSLDPWAPQSVRVALPRWLFGLDDSADLHGEDLLDGARASWREVALDLELTPQRPYRLWRLWSRPLSS
>AP019378.1|BBH98749.1|2410039_2411851_+|hypothetical-protein
MPATHPAPDPLWYKDAVIYQLHVKSFFDANDDGVGDFAGLLAKLDYIVELGVNSIWLLPFYPSPRRDDGYDIADYRGVHPDYGSLADARRLVRAAHARGLRVITELVINHTSDQHPWFQRARAARPGSAHRAYYVWSDDDKAYAGTRIIFCDTEKSNWTWDPVAGAYFWHRFYSHQPDLNYDNPQVLREVLGAMRYWLDMGVDGLRLDAVPYLVEREGTNNENLPETHAILRRIRRVIDSEYPGRMLLAEANQWPEDAQEYFGAGDECHMAFHFPLMPRMYMAIAQEDRLPVTDIIRQTPSIAPQCQWAIFLRNHDELTLEMVTSRERDYLWNVYAAEPRARINLGIRRRLAPLLERDRRRIELMNSLLLSMPGTPVLYYGDELGMGDNIHLGDRDGVRTPMQWSPDRNGGFSRADPERLPLPLLMGPLYGYEAVNVEAQQRDPHSLLNWTRRMLAKRRQSHVFGRGELSFLYPGNRKILAYLRTWEDTVVLCVANLSQAAQPVELHLSEYAGRVPVEMLGGTAFPQIGELPYLLTLPPFGFYWLDLSAGAAPPAWHSELPPQMPESITLVSRGAGAALRLTEASRRQLEADVLPAYLQRQRW
>AP019378.1|BBH98750.1|2411875_2413381_+|hypothetical-protein
MRLAYSVPLNDDVESYYEAEIEVSDDGPPRRFHTPVALAWQDDTAAQYPLARVRRGAQLGTLTDASLQPGYARVLLAALTAGRDIQAGGEPAVRLRFLPEPGLADLALRDDSKVRALSADQSNSSLLVGERVVFKLLRELHAGPHPEAEMTRYLTQAGYAHTPALLGEVVRVQGDQAPHTLALAHAYVVNEGDAWNWTVAYLKRTVDAAMLTGASADDYQQELAGYEVLAGTIGQRLAQMHSVLARAGELPGFAPRPASERDAALAGEHAVAQLDRALQALRACESGLAPASHACAQWLFEHRDRLAAHIMTLAQAETGALRIRVHGDFHLGQILVAQTDAYLIDFEGEPARPMAERRQLSSPFKDVAGILRSFDYAVAELSRDDPLGGAPRDFNTGVAEPADPASAPRETREALLARFRQRAGAALLASYGNAIDPVLALPPERAQALTCLYLLEKAAYEICYESAYRPERLPVPIHGLAETARAALLAAAVDHDEGPAP
>AP019378.1|BBH98751.1|2413377_2415573_+|1,4-alpha-glucan-branching-enzyme-GlgB
MMRDSPSIQGTLDAATQHALLAGRHADPFSVLGPHQAGAHTVVRVLAPGARTVMAVLPGGQRTPLLPMQPGLFENTVPGLQPGAPAAYRLCIEWEGGIQHTADPYAFGPVLDTAQLDHCAAGGWRYLAGLLGAHAASVDGCAGTRFALWAPNARRVAVVGDFNGWDGRRHAMRLRYPAGVWELFLPDVGPGARYKFQVLGADGHTVLKADPLARQAEAPPATASIVPDERPFAWTDEAWMEQRAARQRCDAPISIYEVHAGSWFDDAGAPRWQSLAARLPEYARSLGFTHIELLPVMAHPFGGSWGYQPLGLFAPAAAHGAPADFAHFVDRCHEAGLGVILDWVPAHFPDDAHGLARLDGTPLYEHADPHEGRHPDWNTLIYNYGRREVRAFLIASAIHWLRHYHVDGLRVDAVASMLYRDYSRPAGQWIPNRHGGRENLEAIDFLRELNAAVGVQCPGAITVAEESTAWPGVTAPVANGGLGFDYKWNMGWMHDTLRYMRRDPIHRRHHHHDLSFGMVYAYAERFVLPLSHDEVVHGKGSLLGKMPGERAAQLAQLRLYYAFMWAHPGKKLLFMGGEFGQQGEWNHDAMLQWSLLDDPAHRGLQRLVADLNHVYATLPELHCRDADPSGFAWIVGDDADNSVLAFARVDASHCLVAVCNFTPVPRPGYRFGVPHAGDWRVRVDTGATRYGGAGGGPPICLRSEPIPAHGHPQSLVLDLPGFTALYLRHSE
>AP019378.1|BBH98752.1|2415577_2417194_+|hypothetical-protein
MYPSLPDRLLPGLPAPLGATSDGLGVNFAVFSANAARIELCLFDARGRKELARLPMPECTDEVWHGYLPDAQPGLVYGYRAHGPYNPRAGHRFNPHKLLLDPYATALTGALRWSDALFGYRMQHPRADLSMDRRDSAAGVPKAVVTEPAFHWGATRRPAAAWAHTVIYEAHVRGVSMLRSDLREPIRGTCAALADPRFIDHLHRLGVTALELMPVHAFLQDRTLVERGLRNYWGYNTLAYFAPEPAYLADGQPHDLRRAIRRLHAAGIEVILDVVYNHTCEGNELGPTLSWRGLDNASYYRLVPGDERRYIDDTGTGNTLNLSHPRVLQMVMDSLRYWAVHYRVDGFRFDLGVTLGREGTGFDAGSGFFDALLQDPVLARVKLISEPWDVGPDGYQLGRHPPGMAEWNDQFRDTARRFWRGDPGMAGALATRLTASRDVFDHRHRRPWSSINFAAAHDGFTLQDVVSFAERHNEANGEDGADGHGENYSSNWGVEGAASSASRWPRPTACRRARQRSRRRSDGGNCRRARSGCRPRPA

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Crispr_ID: AP019378_6

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

AP019378_6

3077428-3077509

Orphan

Consensus_repeat	Method
CTGTCCCCGCCGGGACAGGCACC	CRISPRCasFinder

1 spacers

The CRISPR arrays of AP019378_6

>merge|AP019378|6|3077428-3077509|CRISPRCasFinder
CTGTCCCCGCCGGGACAGGCACCCGTCGTGCGCCATGAGCGCCACTGCCAAGACGGCGTCTGTCCCCGCCGGGACAGGCGCC

>AP019378|6|4|3077428-3077509|CRISPRCasFinder
CTGTCCCCGCCGGGACAGGCACC	CGTCGTGCGCCATGAGCGCCACTGCCAAGACGGCGT
CTGTCCCCGCCGGGACAGGCGCC

Protein	Signature genes	Signature genes Name	Protein_function
AP019378.1\|BBH99344.1\|3072100_3073273_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226346
AP019378.1\|BBH99346.1\|3073868_3074243_-\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH99339.1\|3068367_3069624_-\|isocitrate-dehydrogenase-[NADP]	unknown	unknown	gnl\|CDD\|180792
AP019378.1\|BBH99353.1\|3082174_3083263_-\|ferrochelatase	unknown	unknown	gnl\|CDD\|234585
AP019378.1\|BBH99357.1\|3087048_3088269_-\|ISL3-family-transposase	unknown	unknown	gnl\|CDD\|225995
AP019378.1\|BBH99348.1\|3077516_3078650_-\|chaperone-protein-DnaJ	unknown	unknown	gnl\|CDD\|236757
AP019378.1\|BBH99349.1\|3078750_3080676_-\|chaperone-protein-DnaK	unknown	unknown	gnl\|CDD\|234715
AP019378.1\|BBH99350.1\|3080766_3081147_-\|thiol-reductase-thioredoxin	unknown	unknown	gnl\|CDD\|239245
AP019378.1\|BBH99338.1\|3067187_3068093_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|340821
AP019378.1\|BBH99340.1\|3069826_3070252_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|370177
AP019378.1\|BBH99352.1\|3081850_3082093_-\|hypothetical-protein	unknown	unknown	unknown
AP019378.1\|BBH99355.1\|3084439_3085339_+\|NAD-kinase	unknown	unknown	gnl\|CDD\|179379
AP019378.1\|BBH99351.1\|3081154_3081709_-\|protein-GrpE	unknown	unknown	gnl\|CDD\|237621
AP019378.1\|BBH99341.1\|3070302_3070665_-\|cytochrome	unknown	unknown	gnl\|CDD\|225418
AP019378.1\|BBH99356.1\|3085354_3087016_+\|DNA-repair-protein-RecN	unknown	unknown	gnl\|CDD\|223571
AP019378.1\|BBH99343.1\|3071119_3072079_+\|ATP-binding-protein	unknown	unknown	gnl\|CDD\|223786
AP019378.1\|BBH99347.1\|3074575_3077326_+\|peptidase-M16	unknown	unknown	gnl\|CDD\|223685
AP019378.1\|BBH99345.1\|3073276_3073831_-\|N-acetyltransferase	unknown	unknown	gnl\|CDD\|224168
AP019378.1\|BBH99354.1\|3083320_3084325_-\|heat-inducible-transcription-repressor-HrcA	unknown	unknown	gnl\|CDD\|234621
AP019378.1\|BBH99342.1\|3070677_3071013_-\|cytochrome-c	unknown	unknown	gnl\|CDD\|225418

Protein	Function_ID	Function_description	E-value
AP019378.1\|BBH99344.1\|3072100_3073273_+\|hypothetical-protein	gnl\|CDD\|226346	COG3825, COG3825, Uncharacterized protein conserved in bacteria [Function unknown].	0
AP019378.1\|BBH99356.1\|3085354_3087016_+\|DNA-repair-protein-RecN	gnl\|CDD\|223571	COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair].	0
AP019378.1\|BBH99339.1\|3068367_3069624_-\|isocitrate-dehydrogenase-[NADP]	gnl\|CDD\|180792	PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.	0
AP019378.1\|BBH99353.1\|3082174_3083263_-\|ferrochelatase	gnl\|CDD\|234585	PRK00035, hemH, ferrochelatase; Reviewed.	7.84073e-159
AP019378.1\|BBH99357.1\|3087048_3088269_-\|ISL3-family-transposase	gnl\|CDD\|225995	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	6.63558e-80
AP019378.1\|BBH99348.1\|3077516_3078650_-\|chaperone-protein-DnaJ	gnl\|CDD\|236757	PRK10767, PRK10767, chaperone protein DnaJ; Provisional.	0
AP019378.1\|BBH99349.1\|3078750_3080676_-\|chaperone-protein-DnaK	gnl\|CDD\|234715	PRK00290, dnaK, molecular chaperone DnaK; Provisional.	0
AP019378.1\|BBH99350.1\|3080766_3081147_-\|thiol-reductase-thioredoxin	gnl\|CDD\|239245	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functional TRXs have been reported in most organisms; in eukaryotes, they are located in the cytoplasm and the mitochondria. Higher plants contain more types (at least 20 TRX genes have been detected in the genome of Arabidopsis thaliana), two of which (types f amd m) are located in the same compartment, the chloroplast. Also included in the alignment are TRX-like domains which show sequence homology to TRX but do not contain the redox active CXXC motif. Group II proteins, in addition to either a redox active TRX or a TRX-like domain, also contain additional domains, which may or may not possess homology to known proteins.	1.07863e-05
AP019378.1\|BBH99338.1\|3067187_3068093_-\|hypothetical-protein	gnl\|CDD\|340821	cd03789, GT9_LPS_heptosyltransferase, lipopolysaccharide heptosyltransferase and similar proteins. Lipopolysaccharide heptosyltransferase (2.4.99.B6) is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family also contains lipopolysaccharide 1,2-N-acetylglucosaminetransferase EC 2.4.1.56 and belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.	2.0024e-14
AP019378.1\|BBH99340.1\|3069826_3070252_+\|hypothetical-protein	gnl\|CDD\|370177	pfam08897, DUF1841, Domain of unknown function (DUF1841). This family of proteins are functionally uncharacterized.	1.92899e-74
AP019378.1\|BBH99355.1\|3084439_3085339_+\|NAD-kinase	gnl\|CDD\|179379	PRK02155, ppnK, NAD kinase.	0
AP019378.1\|BBH99351.1\|3081154_3081709_-\|protein-GrpE	gnl\|CDD\|237621	PRK14139, PRK14139, heat shock protein GrpE; Provisional.	1.18525e-78
AP019378.1\|BBH99341.1\|3070302_3070665_-\|cytochrome	gnl\|CDD\|225418	COG2863, COG2863, Cytochrome c553 [Energy production and conversion].	2.60442e-23
AP019378.1\|BBH99343.1\|3071119_3072079_+\|ATP-binding-protein	gnl\|CDD\|223786	COG0714, COG0714, MoxR-like ATPases [General function prediction only].	1.77814e-45
AP019378.1\|BBH99347.1\|3074575_3077326_+\|peptidase-M16	gnl\|CDD\|223685	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only].	3.06874e-64
AP019378.1\|BBH99345.1\|3073276_3073831_-\|N-acetyltransferase	gnl\|CDD\|224168	COG1247, COG1247, Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane].	1.00531e-60
AP019378.1\|BBH99354.1\|3083320_3084325_-\|heat-inducible-transcription-repressor-HrcA	gnl\|CDD\|234621	PRK00082, hrcA, heat-inducible transcription repressor; Provisional.	1.1274e-145
AP019378.1\|BBH99342.1\|3070677_3071013_-\|cytochrome-c	gnl\|CDD\|225418	COG2863, COG2863, Cytochrome c553 [Energy production and conversion].	9.14682e-23

>AP019378.1|BBH99347.1|3074575_3077326_+|peptidase-M16
MRLPLLSRRLNALLVSSFLAFQAGAASLPAGVSEVSSIEGITEYRLANGLRVLLAPDASKPTTTVNMTYLVGSRNENYGQTGMAHLLEHMLFKGTPAIRNALGEFSRRGLQANGSTSSDRTNYFASFAANPETLKWYLGWQADAMVNSLIAKEDLDSEMTVVRNEMESGENNPFRVLMQKMQAAAYQWHNYGKSTIGARSDVENVDIAQLRAFYHEYYQPDNAVLIVAGKFDPQTALADIQSSLGKLPKPKRTLPPEYTVEPVQDGERSVTLRRAGGTPLVAAMYHLPAAGSPDFVGLDLAATILADTPSGRLYHALVPTKLASGVFGFTMDQLDPGLAMFGAQLQPGMDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVRDAKLDDVQRAAVAYLVRSNRTEGRYIPTEKPQRAPLAQRADLAAVFKDYKGDPNFKAVEAFDPSPANIDKRTLRRTLDLPNGQVELALLPKATRGDRVQAELLIQFGDAEALRGQRVPLAAAAALLDRGTDKLSRQAIQDRLDQLQAEAAINGSGTNLVVNISTLGKNLPDVMALVLDVVRNASFPQDQVEEYKRQAITMVQDAMTDPTALASRALARHNNPWPADDVRYVPTFDEALEQLRSLSRDDLAAVSGKLYGAGRIKFSAVGEFDPAAVEAVLRKGLDGWRSAPAYTRLPDPYRAVPAQQFDIATPDKANAFYISRMPLQLQDTNADYPALYLANFLLGTSETSRLWHRVRETEGLSYNVRSNLSVSSYEPSANWTIYAIYAPQNRARLEKAISEELARALKDGFTDQEVRDGVVALLNYRNLARAQDDVLADTWVNYMQTGRSFQWSADMDRKLEALTPDQVNAALRKYLKPDAFSTAVAGDFTKKSAP
>AP019378.1|BBH99346.1|3073868_3074243_-|hypothetical-protein
MLTDIVTRALSQLLGNSLSGDVIKGRFRYAYASDDGRFVAILGHDLTTYVVDVDAQRYFAECAGVPCGFAGHVLEMEGAQEHGHPWPAVNDLFDLDMDGDEIAWRRCPGAVALAATRQAQSRVA
>AP019378.1|BBH99345.1|3073276_3073831_-|N-acetyltransferase
MNATPSPAPTGATLVDCTHDRHAAAILDIFNDAILTSTALYDYQPRALASMEAWFLAKRQGGFPVVGFEDAAGVLMGFASYGTFRAWPAYKYSVEHSVYVDRRYRGRGLGEALLRALIERARLQQVHVLVGGIDATNAGSVALHRKLGFVHAGTITQAGFKFGRWLDLAFYQLTLDTPLRPVDG
>AP019378.1|BBH99344.1|3072100_3073273_+|hypothetical-protein
MLIDFFYHLRAHKLPVSVQEYLTLLEALRQRLMAPTLDDFYFLARTALVKDESLYDRYDAAFGAYYRGIAAALPADRDIPLDWLIKEFEKTLTPEEKAAIEAHGWDKLMELFKQRLEEQQERHAGGSKWIGTGGTSPFGNGGYHPEGIRVGGDSAGNRTAVKVWDMRQFRDYDDQLELGTRNFKVALRRLRRFARQGADLELDLDDTIASTARNAGHLDLRLVPERRNTVKVLMLLDVGGSMDDHIARVEELFSAARSEFRHLDVYYFHNCPYENLWQNNRRRQNERFDTWDVLRKYNADWRLIIVGDATMSPYEILQPGGSVEHYNKEAGAVWLRRLLDAWPKAAWLNPEPTASWRYRQSIALLRDIMQDRMYPVTVAGLEQAMRQLSK
>AP019378.1|BBH99343.1|3071119_3072079_+|ATP-binding-protein
MYDNCRKTIPYHASALSRLIDCHSMPTSASSSSAPAQPARFEGTDRYVATDDLKLAVNAALTLQRPLLIKGEPGTGKTILAEEVARALDRPLLQWHIKSTTKAHQGLYEYDAVSRLRDSQLGDEKVRDIRNYIVQGTLWQAFEAPEPVVLLIDEIDKADIEFPNDLLRELDRMEFHVYETRQTVQARHRPLVIITSNNEKDLPDAFLRRCFFHYIRFPDRDTMRDIVGVHYPDIRQDVLRAALDTFFALREAPGLKKKPSTSELLDWLRLLLAEAIPAAEIDAHAATAVPVLAGALLKNEQDVHLLERLGAMARGAQRR
>AP019378.1|BBH99342.1|3070677_3071013_-|cytochrome-c
MTRTVSVLAVLASCAIAGPAAAADAAPVGNAQNARDKVSMCIGCHGIPGYKASFPELYHVPMIAGQNAKYIEAALNEYRKGARSHPTMDAVAGSLSDQDIADLAAYYSSLK
>AP019378.1|BBH99341.1|3070302_3070665_-|cytochrome
MKRFTFALAGIVLATAGVSAQAQDVVAGKAVFDKFNCASCHGADAKTSVQPEYPVLAGQHADYLAHALKAYKRGAAGSAATANVRKNPIMGAFAAQLSDQDIRNVAAWLAAQPSDLGVRQ
>AP019378.1|BBH99340.1|3069826_3070252_+|hypothetical-protein
MFNPSRDQVREFFIETWRKHRATEVLTPLESMALDWILEHPEYHGDLESPEAMTAEYPVEHGRTNPFLHLSMHLAIAEQLSIDHPRDIRAAYQRLVGRGDAHQAAHEIMECLGQVVWEAQRLGTPLDSDAYIELIRQRAER
>AP019378.1|BBH99339.1|3068367_3069624_-|isocitrate-dehydrogenase-[NADP]
MSYQHIKVPTGGQKITVNADYSLNVPDQVIIPVIEGDGTGADITPVMIKVVDAAVQKAYAGKRKIHWMEVYAGEKATKVYGPDVWLPEETLDAVKDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVRYFKGVPSPVREPEKTDMVIFRENSEDIYAGIEYMAESEQAKDLIQYLQTKLGATKIRFPNTSSIGIKPVSREGTERLVRKALQYAIDNDRASVTLVHKGNIMKFTEGGFRDWGYALAQNEFGAQPIDGGPWCKFKNPKTGREIIVKDSIADAFLQQILLRPAEYDVIATLNLNGDYISDALAAQVGGIGIAPGANLSDSVAMFEATHGTAPKYAGKDYVNPGSEILSAEMMLRHMGWTEAADLIIASMEKSILSKKVTYDFARLLEGATQVSCSGFGQVMIDNM
>AP019378.1|BBH99338.1|3067187_3068093_-|hypothetical-protein
MALLMAPRLGDTLLMMNMARNLAAHGREVSIFGDYIHGLRDWFPGLDIRPSLSEEQAGQVLPGYDCAAQMHVGWPYALHAHQPNYFYYDAHVVITGRGFVKLFQIRDFCREQLGLAQAGADNGLRPPPQVQPHRSHPRRVALHPTSTGAQRCWAPRHFKELGLRLLHEGYEPNYIVAPHERAEWSWVLDHGLHLPQFPSLSEVAGFIHASGWFIGNESGIGHLASNVGVPTLSLTGRPTRTRAWRPAWSTSRIVYPALIPGGRWRDRLWREWLSPRRVMSAFHKLQADDRRQPVGVPWGKI
>AP019378.1|BBH99348.1|3077516_3078650_-|chaperone-protein-DnaJ
MAKRDYYEVLGVAKNASDEDLKKAYRKLAMKYHPDRNPDSKEAEEKFKEAKEAYEVLGDEQKRAAYDRYGHAGVDPNAAGMGGGMGGGMGGGFADAFGDIFGEIFGAGRRGGGGPQVYRGADLKYALEITLEQAASGFDTEIRVPSWENCDTCHGSGAKAGTSPKTCRTCGGSGAVRMQQGFFSVQQTCPTCHGTGKEITDPCPSCDGVGRTRRNKTLQVKIPAGIDDGMRIRSSGNGEPGINGGPPGDLYVEIHIKQHKIFQRDGDDLHCELTIPFTTAALGGELQVPTLGGKAEISIPEGTQSGKTFRLRAKGIRGVRGSYPGDLYCHVVVETPVRLSDEQKAILRQFEASLNDGGDRHSPQSKSWTDRVKEFFS
>AP019378.1|BBH99349.1|3078750_3080676_-|chaperone-protein-DnaK
MSKIIGIDLGTTNSCVAVLDGGQVKIIENAEGARTTPSIVAYMDDGETLVGAPAKRQAVTNPKNTLYAVKRLIGRKFDEKAVQKDIDLMPYSIVKADNGDAWVEVHGKKLAPPQVSAEVLRKMKKTAEDYLGEEVTEAVITVPAYFNDSQRQATKDAGRIAGLEVKRIINEPTAAALAFGLDKTEKGDRKIVVYDLGGGTFDVSIIEIADVDGEMQFEVLSTNGDTFLGGEDFDQRIIDYIISEFKKEQGVDLSKDVLALQRLKEAAEKAKIELSSSQQTEINLPYITADASGPKHLNLKITRAKLEALVEELIERTIEPCRVAIKDAGVKVSDIDDVILVGGMTRMPKVQDKVKEFFGREPRKDVNPDEAVAAGAAIQGSVLSGERKDVLLLDVTPLSLGIETLGGVMTKMIQKNTTIPTRYSQTFSTADDNQPAVTIKVFQGEREIAAGNKGLGEFNLEGIPPAPRGLPQIEVTFDIDANGILHVSAKDKGTGKENKITIKANSGLSEDEIQRMVKDAEANAEEDHRLAELAQARNQADALVHATRKSLTEYGEKLEAAEKESIEAAIKDLEDILKTGDKAEIDAKVEALSTASQKLGEKMYADMQAQQQAQQQQAADNAKPVDDNVVDADFKEVKRDQ
>AP019378.1|BBH99350.1|3080766_3081147_-|thiol-reductase-thioredoxin
MAAAPFDPAEVFQVFGMRRVDSASFDEQVVQAPGDDLRCVFLWGQDCYNCGIFKQTALLQRQALLALELSWFEADVYADEALGRRFSLHGVPTFVLYRSGKRLGRVTGWPGLPQFSAAMQRLRDGT
>AP019378.1|BBH99351.1|3081154_3081709_-|protein-GrpE
MTAPQEPVDSTPESGENAATPGLEDDLSAELAALRAELEAAQATVKAQQEQVLRAAAEAENVRRRAQEDVAKARKFGIESFAESLVPVKDSLEAALAQPDQAAQAWREGVEVTLKQLTAAFERNLLKEIAPAQGDKFDPHLHQAISSVPADQPANTVLQLLQKGYVIADRTLRPALVVVSAGQG
>AP019378.1|BBH99352.1|3081850_3082093_-|hypothetical-protein
MNPPRKPTIGTSGPPGHANLEEDQLERELDEALLETFPASDPIAITSEDERDEPDDKVDEALEDTFPASDPPAPAQPGKK
>AP019378.1|BBH99353.1|3082174_3083263_-|ferrochelatase
MFLRLFKYLWPERYLPEIPAQDPFDENPPPCGPGRVGVLLVNLGTPDEPTRGAIRRYLGEFLSDPRVIEIPRYLWMPILHGLVLAMRPKKLAPRYAGIWMEEGSPLLVYSQRQAAGVRQGLAARGVHAEVELAMRYGKPSIPAAITALRERGCDHILAVPLYPQYAASTTATVVDAVTRHAGRLRDQPALRFVKRFHNDPAYVEAQAGRIAEFWQAHGRPQKLVMSFHGLPRYSIELGDPYYRDCLDTARLLRERLGLREDEVEVTFQSRFGSARWLEPYTEPTLAELARQGVTEVDVVCPGFVADCLETLEEISQECRDAFVAAGGRQFRYIPALNDCPPWIEGLTDLVERQLRGWPTGNP
>AP019378.1|BBH99354.1|3083320_3084325_-|heat-inducible-transcription-repressor-HrcA
MDDRARALLKALIERYIADGQPVGSRTLSKVFDLSPATIRNVMADLEELGLIHSPHTSAGRVPTPRGYRMFVDSLLAVRAYQFEPAHIGELLPVSEPSRAVNAAAALLSNLTQFAGVVLTPKRTQIFRQIEFIRLSDKRVLLIIVTPEGDVQNRILSAQRDYTEAELLEAGNFFNVHFSGKSFDAVRRTLSTELAQLRDDISRLMQAAVEAGAEAADDGEAVVISGERKLLDVTDIASDMDRLRKMFSLFEKKTDLLQLLDVSSRAQGVQIYIGGDSQLVPMEEVSVITAPYGVDGKVIGTLGVIGPTRMAYERVIPIVDITARLLSNALSHNQ
>AP019378.1|BBH99355.1|3084439_3085339_+|NAD-kinase
MYFPIVALIGRYQDTGLDAPLTALAQMLTQAGRRVLVEAETARNAGVSGYPVADWDEIGRTATLAVVMGGDGTVLGAARHLAPYGVPLIGINHGRLGFITDIPLQDAHDALGRVLEGNYQAEDRMLLQGGVWRGEQQMYSASAVNDVVLNRAGRGGMIEVRVELDGAFMYTQRADGLIIATPTGSTAYSLSANGPILHPGMNAMVLVPVAPQTLSNRPIVIPDSGVLNMTLTAMGRVEIGASVHFDMQTWSDLQPGDRITVQRAPHTIRFVHPEGYSFFSTLRRKLHWNLMPQATDNLE
>AP019378.1|BBH99356.1|3085354_3087016_+|DNA-repair-protein-RecN
MLRTLHIRDFVIVEQTELHFGDGFTVFSGETGAGKSILIDALALTLGERGDASMLREGAARADITAVFDAPPALRDWLAERELDSGDELALRRVIDSQGRSRAYINGMPATIAQLRELGDGLVDIHGQHAHQSLMRPEAQRDLLDAHGGHAELRQTVAQAWKQWRALARQLDTAEQDAEALAAERDRLQWQSDELDRLGLGPDEWDALQTEHTRLSHAQSLLDGASRILEALDGEHDSAQYRLNGAAHQLQQMLRHDPALQGIGDELESARIAITEAVSDLNNYVSRVELDPQRLADVEARLSAVFETARKFKCEPHGLPALRDSLHGKLAEMQAASDVQALRAQAEAAQARYEAAAARLSAARRKIAKDLGKQVTQAMQTLSMQGGRFEAALTGGAPSAHGSEQVEFLVAGHAGSTPRPLAKVASGGELSRISLALSVIASRAARVPTLIFDEVDSGVGGAVAEAVGKLLRELGQRHQVLCVTHLPQVAACAHAQYRVSKVESGGSTRSRIAELDAEARVEEVARMLGGIKITATTRDHAREMLGGHTAPAA
>AP019378.1|BBH99357.1|3087048_3088269_-|ISL3-family-transposase
MLDRKLLESLGGWQGYGVERVEWPEDPGRTLSIYLKPTAKVMLCEQCGARCRQVHETTVRRVRDLPLFEYRVVLHVPRRRLWCEQCGGPRLERLAWLGRYQRVTDRLAQACSQLLQSSNVQAVARFFELGWHTVKTLDKARLRASVREPDWSKIEYLAMDEFALHKGHRYATVVVDPIGRQVLWIGPGRSRETARAFFEQLPPGAAQRIKAVAIDMTTAYELEIQAHSPQAEIVYDLFHVVAKYGREVIDRVRVDQANQLRQDRPARRIIKSSRWLLLRNRDNLDRQQAVRLDELLQANQPLLTVYVLRDELKRLWFYQRPAWARQAWNHWYEQAEQSGIAALNTFAQRLKGYLHGILARCRHPLNTSIVEGINNTIKVIKRRAYGYRDQEYFFLKIRAAFPGNAR

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Crispr_ID: AP019378_7

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

AP019378_7

3230453-3230537

Orphan

Consensus_repeat	Method
CTGTCCCCGCGGGGACAGGCACC	CRISPRCasFinder

1 spacers

The CRISPR arrays of AP019378_7

>merge|AP019378|7|3230453-3230537|CRISPRCasFinder
CTGTCCCCGCGGGGACAGGCACCCTGTCATACGCCATGAACGCTTGACGGCCAAGACGGTATCTGTCCCCGCGGGGACAGGCACC

>AP019378|7|5|3230453-3230537|CRISPRCasFinder
CTGTCCCCGCGGGGACAGGCACC	CTGTCATACGCCATGAACGCTTGACGGCCAAGACGGTAT
CTGTCCCCGCGGGGACAGGCACC

Protein	Signature genes	Signature genes Name	Protein_function
AP019378.1\|BBH99491.1\|3231849_3232551_+\|DnaA-regulatory-inactivator-Hda	unknown	unknown	gnl\|CDD\|236347
AP019378.1\|BBH99482.1\|3221235_3222219_-\|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270295
AP019378.1\|BBH99488.1\|3227614_3229504_+\|DNA-mismatch-repair-protein-MutL	unknown	unknown	gnl\|CDD\|234630
AP019378.1\|BBH99492.1\|3232547_3233246_+\|phosphoserine-phosphatase	unknown	unknown	gnl\|CDD\|319796
AP019378.1\|BBH99494.1\|3234598_3235090_+\|2-amino-4-hydroxy-6--hydroxymethyldihydropteridine-pyrophosphokinase	unknown	unknown	gnl\|CDD\|172582
AP019378.1\|BBH99485.1\|3224894_3225431_+\|bifunctional-alanine-racemase/tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-ATPase-subunit-type-1-TsaE	unknown	unknown	gnl\|CDD\|223873
AP019378.1\|BBH99486.1\|3225361_3226747_+\|N-acetylmuramoyl-L-alanine-amidase	unknown	unknown	gnl\|CDD\|182376
AP019378.1\|BBH99480.1\|3218413_3220168_-\|gamma-glutamyltranspeptidase	unknown	unknown	gnl\|CDD\|223482
AP019378.1\|BBH99493.1\|3233246_3234602_+\|poly(A)-polymerase-I	unknown	unknown	gnl\|CDD\|130997
AP019378.1\|BBH99497.1\|3237482_3239585_-\|membrane-protein	unknown	unknown	gnl\|CDD\|129868
AP019378.1\|BBH99487.1\|3226889_3227528_-\|membrane-protein	unknown	unknown	gnl\|CDD\|182775
AP019378.1\|BBH99498.1\|3239755_3240796_+\|C4-dicarboxylate-ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270320
AP019378.1\|BBH99481.1\|3220274_3221171_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176107
AP019378.1\|BBH99483.1\|3222423_3223335_+\|membrane-protein	unknown	unknown	gnl\|CDD\|223751
AP019378.1\|BBH99489.1\|3229500_3230442_+\|tRNA-dimethylallyltransferase	unknown	unknown	gnl\|CDD\|234626
AP019378.1\|BBH99499.1\|3240938_3241583_+\|GntR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224715
AP019378.1\|BBH99496.1\|3236091_3237480_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377179
AP019378.1\|BBH99495.1\|3235108_3236065_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|270296
AP019378.1\|BBH99490.1\|3230547_3231573_-\|phosphoribosylformylglycinamidine-cyclo-ligase	unknown	unknown	gnl\|CDD\|235439
AP019378.1\|BBH99484.1\|3223351_3224743_-\|fumarate-hydratase-class-II	unknown	unknown	gnl\|CDD\|234779

Protein	Function_ID	Function_description	E-value
AP019378.1\|BBH99491.1\|3231849_3232551_+\|DnaA-regulatory-inactivator-Hda	gnl\|CDD\|236347	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.	8.14329e-101
AP019378.1\|BBH99482.1\|3221235_3222219_-\|ABC-transporter-substrate-binding-protein	gnl\|CDD\|270295	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter.	3.25651e-157
AP019378.1\|BBH99488.1\|3227614_3229504_+\|DNA-mismatch-repair-protein-MutL	gnl\|CDD\|234630	PRK00095, mutL, DNA mismatch repair endonuclease MutL.	0
AP019378.1\|BBH99492.1\|3232547_3233246_+\|phosphoserine-phosphatase	gnl\|CDD\|319796	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C. This family includes Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C, PgpC (previously named yfhB) which catalyzes the dephosphorylation of phosphatidylglycerol-phosphate (PGP) to phosphatidylglycerol (PG). This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.	3.35754e-64
AP019378.1\|BBH99494.1\|3234598_3235090_+\|2-amino-4-hydroxy-6--hydroxymethyldihydropteridine-pyrophosphokinase	gnl\|CDD\|172582	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.	1.33001e-89
AP019378.1\|BBH99485.1\|3224894_3225431_+\|bifunctional-alanine-racemase/tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-ATPase-subunit-type-1-TsaE	gnl\|CDD\|223873	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only].	5.46598e-54
AP019378.1\|BBH99486.1\|3225361_3226747_+\|N-acetylmuramoyl-L-alanine-amidase	gnl\|CDD\|182376	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA.	1.25625e-84
AP019378.1\|BBH99480.1\|3218413_3220168_-\|gamma-glutamyltranspeptidase	gnl\|CDD\|223482	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism].	0
AP019378.1\|BBH99493.1\|3233246_3234602_+\|poly(A)-polymerase-I	gnl\|CDD\|130997	TIGR01942, pcnB, poly(A) polymerase. This model describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell. This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well. Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase (cca).	7.39002e-147
AP019378.1\|BBH99497.1\|3237482_3239585_-\|membrane-protein	gnl\|CDD\|129868	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit. The Tripartite ATP-independent Periplasmic Transporter (TRAP-T) Family (TC 2.A.56)- DctM subunit TRAP-T family permeases generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. Only one member of the family has been both sequenced and functionally characterized. This system is the DctPQM system of Rhodobacter capsulatus (Forward et al., 1997). DctP is a periplasmic dicarboxylate (malate, fumarate, succinate) binding receptor that is biochemically well-characterized. DctQ is an integral cytoplasmic membrane protein with 4 putative transmembrane a-helical spanners (TMSs). DctM is a second integral cytoplasmic membrane protein with 12 putative TMSs. These proteins have been shown to be both necessary and sufficient for the proton motive force-dependent uptake of dicarboxylates into R. capsulatus. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids].	2.19046e-96
AP019378.1\|BBH99487.1\|3226889_3227528_-\|membrane-protein	gnl\|CDD\|182775	PRK10847, PRK10847, DedA family protein.	1.10927e-69
AP019378.1\|BBH99498.1\|3239755_3240796_+\|C4-dicarboxylate-ABC-transporter-substrate-binding-protein	gnl\|CDD\|270320	cd13602, PBP2_TRAP_BpDctp6_7, Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold. DctP6 and DctP7 groups of the TRAP transporters that involved in pyroglutamic acid transport. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.	1.18155e-85
AP019378.1\|BBH99481.1\|3220274_3221171_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176107	cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to 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.	1.752e-38
AP019378.1\|BBH99483.1\|3222423_3223335_+\|membrane-protein	gnl\|CDD\|223751	COG0679, COG0679, Predicted permeases [General function prediction only].	1.49124e-41
AP019378.1\|BBH99489.1\|3229500_3230442_+\|tRNA-dimethylallyltransferase	gnl\|CDD\|234626	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed.	1.00887e-155
AP019378.1\|BBH99499.1\|3240938_3241583_+\|GntR-family-transcriptional-regulator	gnl\|CDD\|224715	COG1802, GntR, Transcriptional regulators [Transcription].	1.22341e-42
AP019378.1\|BBH99496.1\|3236091_3237480_-\|hypothetical-protein	gnl\|CDD\|377179	pfam03972, MmgE_PrpD, MmgE/PrpD family. This family includes 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyzes the third step of the 2-methylcitric acid cycle.	4.46056e-107
AP019378.1\|BBH99495.1\|3235108_3236065_-\|hypothetical-protein	gnl\|CDD\|270296	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold. Bug27 binds non-carboxylated solute nicotinamide, in contrast to BugD (aspartic acid transporter) and BugE (glutamate transporter) which both bind aliphatic carboxylated ligands. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a large functional diversity.	6.01101e-118
AP019378.1\|BBH99490.1\|3230547_3231573_-\|phosphoribosylformylglycinamidine-cyclo-ligase	gnl\|CDD\|235439	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional.	0
AP019378.1\|BBH99484.1\|3223351_3224743_-\|fumarate-hydratase-class-II	gnl\|CDD\|234779	PRK00485, fumC, fumarate hydratase; Reviewed.	0

>AP019378.1|BBH99489.1|3229500_3230442_+|tRNA-dimethylallyltransferase
MTPRAIICLAGPTAAGKSASTLALAQRWPLEIINVDSATIYRGMDIGTAKPSAAERAQVPQHLLDIRDPAQSYSAAKFRADALRLIAEIHARGRIPLLAGGTMLYYKALREGLDDLPQADPALRAELEARAARLGWPALHAELALLDPATAARLSPNDSQRIQRALEICRLAGQPMSALLQGERRGDAPSPYRYVTLSLEPSERAALHARIAQRFDAMLAAGLVEEVRGLHARPDLHPGLPSVRCVGYRQMWSYLDGDIDLDTAREQGVAATRQLAKRQLTWLRAQPERVIIDCLAGDAVARTVDAMARALPD
>AP019378.1|BBH99488.1|3227614_3229504_+|DNA-mismatch-repair-protein-MutL
MSDRRPIATLPDLLISQIAAGEVIERPASVLKEILENAIDAGARAIEVRLEGGGIRRIAVTDDGSGIPPEELPLALTRHATSKIRSLDELESVASMGFRGEALASIASVADLTIISRTRGAEHAWQIDGGSLQVSPASGPPGTTIDVRQLFDRVPARRKFLRSEATEFGHCVDAMERIALAHPEVAFRLFHHDRAQRQWLPADHGQRIRDVLGAEFVDHVLPVQAAAGAIALMGMVTRPTAARARADRQYLYVNGRFVRDRTVSHALRSAYADVLHGDRQPAYVLYLDIDPGAVDVNVHPAKHEVRFRDSGAVHRFVSQVVGQTLAQTGGAEAVPAGVPDGAAPDAAYAGEPAAAAPGLAEPRAPYPAAYPSPGQSPYQGSPARPHTQVPFRLHGEPAGIPATDWQSLYRPLPGDAAPAATALRAAPATPLPTADEHPLGQALAQLHGIYILAQNSRGLVLVDMHAAHERVVYEQLKRALDDRALPRQDLLVPVVFHAAEKDVALVEEHETQLNELGFEMRPSGPASIAVRSVPALLARGDIESLARAVLRDLGAVGVSRLLTEQRNELLSTMACHGSVRANRRLTLEEMNALLRQMEITERADQCNHGRPTWVQWSVNDLDKLFLRGQ
>AP019378.1|BBH99487.1|3226889_3227528_-|membrane-protein
MLDFFNMVLHIDQTLGIWVEQYGVWVYLVLFLIVFAETGLVVLPFLPGDSLLFIAGAFGATGHMDPVLTAALLIVAAISGNTVNYTIGRYIGPRVFSMNLRFLDRNALMRTHAFYEKHGGKTIVMSRFIPVIRTFAPFVAGVADMRLARFQLFNIGGALLWVISLVAAGYFFGNIPLVREHLNTIVLIGLGAAIVPVVIGALVRLLQVRRGQ
>AP019378.1|BBH99486.1|3225361_3226747_+|N-acetylmuramoyl-L-alanine-amidase
MVERDCPPAHGALSPRAAARRRLISVAATLLVLPVVPRLAHAATILAVRTWPADEYTRVTLELDSELKAEHFTLENPHRLVVDIEGLSVNAALNDLVSKVRHDDPYIQGLRVAQNRPNVVRLVFDLKQSVAPQVFTLKPVADYQYRLVLDLYPKVAQDPLMAILNKQSGPDVDDPLARVLDEIARNQPAPDQPAAPLARGQEPAPALPAPPIKPLPAPGRSASRKRMLTIALDPGHGGEDPGAIGRSGLREKDVVLRIARRLKTLIDAQPYMRAYLTRDDDYFVPLHVRVQKARRVRADLFVSIHADAFIKPTANGSSVFALSERGASSTQARWLADKENAADLIGGVNLGSHDRQVAKVLLDLSTTAQINDSLKVGSAFLDEIKKINRLHKNRVEQAGFAVLKAPDIPSILVETAFISNPKEEALLRSAAHQEKLAQAMMTGIDRYFTANPPLARVGDVS
>AP019378.1|BBH99485.1|3224894_3225431_+|bifunctional-alanine-racemase/tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-ATPase-subunit-type-1-TsaE
MSAPPTTLCLHLPDEAATEDLARQLAPLVDGRRGGQPGGQIHLQGDLGAGKTAFTRALLRECGIQGRIKSPSYALLESYKVSNLYFYHLDFYRFSDSREWLDAGFRDLLRDDAVVLIEWPERAAGLLPPPDLLISLAYADQGRDASLTAHTARGQTWLNAIVPPPTARSLPAPPPADA
>AP019378.1|BBH99484.1|3223351_3224743_-|fumarate-hydratase-class-II
MKTRTEKDTFGPIEVPEQHLWGAQTQRSLHFFAISTEKMPVPLVAAMARLKRAAAKVNAELGELDPQVADAIMRAADEVVAGKWPDEFPLSVWQTGSGTQSNMNMNEVLANRASELLGGERGEGRKVHPNDHVNRGQSSNDTFPTAMHVAAAVEVEHRVLPALKALRGTLAAKSAAFYDIVKIGRTHLQDATPLTLGQEISGYVAQLDLAEQQIRATLAGLHQLAIGGTAVGTGLNAHPQFSAKVSAELAHDTGSAFVSAPNKFQALASHEALLFAHGALKTLAAGLMKIANDVRWLASGPRSGLGEISIPENEPGSSIMPGKVNPTQCEAVTMLAAQVMGNDVAINVGGASGNFELNVFKPLVIHNFLQSVRLLADGMVSFDKHCAAGIEPNRERITELVERSLMLVTALNPHIGYDKAAQIAKKAHKENLSLKEAALALGHLTEAQFAEWVVPGDMTNARR
>AP019378.1|BBH99483.1|3222423_3223335_+|membrane-protein
MSVALLVLPDFMLVALGWALRHKLGFSREFFAGTERMVYFVLFPALLFQSILRTPISAGHAMQLLQATAALMACGVALAWLAGPVLRPAPVALASAAQCGYRFNTYIGLALAASLAGGPGQTIMALIVGFAVPMANVAAVYGLARHSGNGLLRELARNPLLVSTLLGLACNLAGLSLPGPIDTVMARLGAAALALGIMCVGASLAWEGGKGHGRLIGWMLAVKLAAMPSAALGIAWALGLPALETRMLVLFSALPTASAAYVLAMRMGGDGRMVAVLISLGTLASAATIPLWLTAAAGLGAPN
>AP019378.1|BBH99482.1|3221235_3222219_-|ABC-transporter-substrate-binding-protein
MNKVRTLVQAIAVATGLVAAAGAQAADAYPSKAIRVIVPFAPGGSTDIIARLVTQRMSQELGQPMVVENKGGAGGAIGASEAARAEPDGYTLSIATVSTMAVNPACRPKDLPYDPIKDFQPVTNFANTANVVAVNPKFPAKDFKGFLEELKKNPGKYSYGSLGTCGVLHLMGESFKMATGTDIVHVPYKGSGPAVADAVGGQIELIFDNLPSSMPQIQAGKLRAMAIAWPTRIDAIKDVPTFADAGFPVLNQPVWYGLLAPKGTPMDVVNKLRDAAVVALKDPKVIKALDDQGSAPSGNTPEEFAKEIKEQYDWAQDVVKKQNIKLD
>AP019378.1|BBH99481.1|3220274_3221171_+|LysR-family-transcriptional-regulator
MRLRHIEIFEAIRRTGSLTEAAALHISQPAASKLLAHAEAQLGFKLFERVKGRLVATRETEILAPEVARLNQDLGSVRRLAASLRDRPHGHLRLGCAPALGLGLLPGVVRASRDAQPGITFDIHTHHSAELVQGLLAHELDLAITFDANDHPGLTRTSLGHTELVHLSRRPGAGTTRLQELGGETLIVLDARDASGSLLQMALDAQGLAPRVAIQVQTHYVACALAEAGCGDAVVDAITARAMLRPGMALRRLEPALRVPISVMTRSQDALSTLHHDFIERLRQACSVLQAQPAPQPE
>AP019378.1|BBH99480.1|3218413_3220168_-|gamma-glutamyltranspeptidase
MPLRTLLAALCAAAICQAPAWAREAPGVAREDVNPEIASARSERAQAHAQRYMIATANPLASEAGYRILRAGGSATDAIIAAQLVLNLVEPQSSGIGGGAFMVHYDRGAGELRVYDSRETAPAAARPDRFLREGKPLSYAESVNNGRAVGTPGLLRGLELAHRQHGKLPWQALFEPAIAMAEQGFAVSPRLHESIAGDKALAAQPAAARYFYGPDGQAWPVGHRLRNPEFAATLRSIAREGADAFYRGPIARDIVAAVRAHPTPGDLAEADLAGYRAVVREPVCGLYRGYRLCGAPPPSSGPLAVLQMLGELEQYPLARMRPGSVEAVHYFSEAGRLAFADRDFYVADPAFVDVPVRALLDPAYLRQRGALIRPDRSMKTALPGDPQGLLAERARDDAIEVPSTSHLVAVDAAGNVVSMTSTIEAAFGSKIFVRGFLLNNEMTDFSSSYRDPEGRLVANRVEPGKRPRSSMAPMIVFRAGKPVLALGSPGGSAIINYVAKTLVGVLDWKLDVQQAIALPNLGSRNKETELERGTALEALAPALRRMGHEVRITDFPSGIQGIVIGPHGLAGGADPRREGLALGD
>AP019378.1|BBH99490.1|3230547_3231573_-|phosphoribosylformylglycinamidine-cyclo-ligase
MTYRDAGVDIDAGDALVDRIKPLAARTMRPGVLVGIGGFGALFEVPKKFREPVLVSGTDGVGTKLRLAFDWNRHDTVGIDLVAMSVNDILVQGAEPLYFLDYFACGKLSVDTAAAVVGGIARGCELAGCALIGGETAEMPGMYPDGEYDLAGFAVGAVDKSAIIDGKSIQPGDVVLGLASSGAHSNGYSLVRKILERAGARPDQDFHGQPLVDVVMAPTRIYVKQVLAALDRHGPAIKGLAHITGGGLLDNVPRILQPGMAAQLQRDGWEMPKLFQWLQQQGSVADAEMHRVFNCGIGMVLVVAADQADAVAATLREQGEIVNRIGEIVPQQDGMAQTVVV
>AP019378.1|BBH99491.1|3231849_3232551_+|DnaA-regulatory-inactivator-Hda
MNRQLLLDVLPAPAPTLNNYIAGPNGQALAAAHALTAGRAIYLWGPAGCGRTHLLRGLSARPEAIYIDAARAAQSLRELAEADSTAPMPRLVAVDDVHRMDDARQAGLFALYNRWRESAATGRAFALAVSGDRAPMSLPLREDLRTRLGWDLVFRLDPLSDADKLAALTAQAAERGLQLAPEVINWMLTHHERDIRKLAALLDALDRYSLATGRPITTPLLRAMLADPHSQAT
>AP019378.1|BBH99492.1|3232547_3233246_+|phosphoserine-phosphatase
MTTRRLALFDLDHTLLPLDSDYQWADFLARTGRAGDPAEARRRNDDLMERYNRGELTAEQAAEFMLGLLAAHSPVELAAWHEEFMRDVIRPSLTAQAVDVVRGHLAAGDLCALVTATNSFVTAPIARAFGVQHLIATDPEYRDGRYTGRIEGTPSFREGKVVRVNQWLAGMGLALGDFAESYFYSDSVNDVPLLEAVTRPIAANPSPGLREIAQARGWQVIDLFDHLEDAKS
>AP019378.1|BBH99493.1|3233246_3234602_+|poly(A)-polymerase-I
MITETIRKFVGRLFAPALRGPQRIGAERHGIDRRNVSRHAIKVCDVLRQHGYEAYIVGGAVRDLIVGLEPKDFDVATNATPEQIRPLFRRARIIGRRFQLVHVVFGQEIIETSTFRAPASDDQETDEHGRILRDNVFGSQEEDAARRDFTMNALYYDPHTEEVIDYHQGVQDLKKRQVRIIGDPVKRYREDPVRMLRAVRFAAKLNGSIDTATRQPIRTMASLIENVPASRLFDEMLKLLTCGHAMDCLRQLRNDGLHHGLLPLLDVVLEQPGGENFVELALERTDARVRAGKTISPSFLFAALLWQLVDVRWKQLRAQGEHNIPALVQAADSVLDEQTEKLAIQRRFSSDMREIWFMQPRFERRAGKTIYRMLEQPRFRAACDFLQLRAAAGEFDSVLAQWWMDLANGDDATRAEMIEETAHLPREASDAPAQKRRRPRRRPSNRPREPQ
>AP019378.1|BBH99494.1|3234598_3235090_+|2-amino-4-hydroxy-6--hydroxymethyldihydropteridine-pyrophosphokinase
MNGSPASALAYVGLGANLGDAAATLRSVLAELAAAPGILACKASRLYRTAPVDAQGPDFVNAVAALDTTLAPLDLLDLLQALEQRHGRERPYRNAPRTLDLDLLLYGEQAIDHPRLSVPHPRIHERAFVLAPLCELAPGLRLAQGDCAALLAALEDQAIEPLR
>AP019378.1|BBH99495.1|3235108_3236065_-|hypothetical-protein
MKKRIWGTLLAAAMTVGSGAAHAGYPDKAVRIVVPFAAGGGVDALARPFAKELGDILGQSIVVENKPSNTGQIGATDVARAAADGYTLLLSSAAFATTPAFYPQVPYDPVKDFSPVMIMAAAPQVLVASNRFKAASLPDVLAQARQSDRINFALSASTGIQALATAMLAGQGGVTFMTIPYKGAGAAFMDLISGEVDLMIDNPASSLVHVRAGKLRVLATTGSKRMAILPDVPTVAETLPGFEARNWFVLAAPQGTPPAVIQKLNEASARALNTPAMRQMLERDGIDLVADSPAHAAAFLQDEIAKWGKVVKEGNLQP
>AP019378.1|BBH99496.1|3236091_3237480_-|hypothetical-protein
MNQAVSPLAGTPAVSAELARFAATSRWEDVPQAVRHEGRRSLLNYFAVALAAARDPVLDTATRTYARFASDARASLVGRARRLDMLNAAALNAMAANVYDFDDTHHPTIIHPTAPVAPALFALAETRPLSGAQLLHAFVLGVEATCRIGNAMSPGHYARGWHITSTCGVFGAALGAARCLGLPGDAMVAALGCAAVQAGGLVETLGTAAKSISVGNAARNGLLSALLAAEGFDGPPQPLEGVRGYLRVAADAPDIAAVSAGLGERWEVLNNTYKPYPCGVVLNPVIDACLALAADPRIAGGGWAAIERIELTGHPLLKQRTDRPGVATGRQSQVSAQHAVAVALVRGRAGLPEFSDEAVADAGLRALGLRLGFRDDASMSVDAVKVRIAFQDGTLLEREVQAARGSRERPLQDGEIEEKLRELCRHGGARVDADRLIEAVWTLDEAGDAAAVMRLAAEQPAA
>AP019378.1|BBH99497.1|3237482_3239585_-|membrane-protein
MSSIEMPAPVMPIEPAELAGASPYPLAIDQDFCLIRWMAAISRACGALATVALLLMALSMCYEIFSRYLFNAPTAWATEISGYLLVATVFFGLAAAQASNSHVQVELWIDRLSAPVRLRVELLCQWLALLFCVVLGWQMASFNVREYLNDTRDWGLLSTPQWMPELAVSVGIVVFCMSILVDIYRLSPPAQAWRRWLTPTLLALLAAALVALGANAVPMAAGGRFDWGMALIVAALLACAWAWSGVRTLAHVVLVVGGCAVLYGLARGQSLGWVAFLLVASMMLLLFLGVRIGVALGLVGLFGVYFLLSRPQLSLLAERAWSSTNTFTLTAVPMFIFMGGLLLRSGITAGMFDALVRWFGRAPGGLAHASAGASAVFAAVSGSSLATAATLGKVACPDMIERGYSPRLTYGVAAAGATLGILIPPSIPMIIYGTTVGASVTHLFLAGMLPGLLLMACFMLGALVWALAVPGSAPVARAYTLREKLSASRGMVPFVAIIGAVLGSMYTGVATPTEAAAIGAVSAFVLCLVRRQLSWRALFEIAHDSAKVTALLLLIVVGAGIFSWVFDYLRLPREVVNLIQGADLSPALIVAAMVLAYLVLGMFVESIAMMLMTLPVTYPIAMSLGLDPIWFGVFLVLMIELGLITPPVGMVLFVLRSMNEKARFTDIIRGALPFVLIILLFLCLIYIYPQIVMWLPQQVK
>AP019378.1|BBH99498.1|3239755_3240796_+|C4-dicarboxylate-ABC-transporter-substrate-binding-protein
MSQRFPLPRGFQAALAAAALCTASWSGAAAQTYDLTMAVITSPGDGYSILTASVPERVAKATDGKVKVTVSDSLVPPAQIATAVREGRVDMSAALHTYLAADEPRMGIFNLPGLINNIQEYKQVCDAFWCEDTRKIWKDKWNAIVLAEGAWCTQQLFSKDPIHKVEDFKGKRLRVHNPQTAEVVNALGGKPVAMPTTEIFPALERGVIDGLFISTCVGGSLEFWRIAKNVQNWSLGPINGWAILANPDSWQKLPADVQKQVQGAMDALQQEAFGNYDTFVSNAQQEMMKKGVTFWVAPEEERAKLMQQQYIGPSYEAWNKRAKQVGFDGPAYLDRVRTTLGKSASN
>AP019378.1|BBH99499.1|3240938_3241583_+|GntR-family-transcriptional-regulator
MTESIRNAILVGRFRPGERLPERELCEMTGVSRTLVREALRQLESEGLIVVIPHRGPVVERLSPEQARGIYQVREELEGLACQLFAEHATEPQLAALQEAFQALKRALTRGTPLEQIAAKNAFYQQLLDGAGNEALTTTLRLLNSRVMLLRSTSMQAPGRAKHSVAELSNLLQALVARDGKAARKAGSLHVRNAASVAIAILQDSLADAAATAE

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Crispr_ID: AP019378_8

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

AP019378_8

3441110-3441203

Orphan

Consensus_repeat	Method
GTGCCTGTCCCCGCCGGGACAGGCAC	CRISPRCasFinder

1 spacers

The CRISPR arrays of AP019378_8

>merge|AP019378|8|3441110-3441203|CRISPRCasFinder
GTGCCTGTCCCCGCCGGGACAGGCACCCGGGCCCAGGAAAACCCCCACGCTGCGCCCGCTGTGCGGGCGTGCCTGTCCCCGCCGGGACAGGCAC

>AP019378|8|6|3441110-3441203|CRISPRCasFinder
GTGCCTGTCCCCGCCGGGACAGGCAC	CCGGGCCCAGGAAAACCCCCACGCTGCGCCCGCTGTGCGGGC
GTGCCTGTCCCCGCCGGGACAGGCAC

Protein	Signature genes	Signature genes Name	Protein_function
AP019378.1\|BBH99682.1\|3433207_3434125_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176106
AP019378.1\|BBH99679.1\|3429535_3430729_-\|acetyl-CoA-acetyltransferase	unknown	unknown	gnl\|CDD\|180775
AP019378.1\|BBH99693.1\|3445135_3446110_+\|multidrug-DMT-transporter-permease	unknown	unknown	gnl\|CDD\|223769
AP019378.1\|BBH99694.1\|3446106_3446766_+\|membrane-protein	unknown	unknown	gnl\|CDD\|224199
AP019378.1\|BBH99686.1\|3437380_3438136_-\|membrane-protein	unknown	unknown	gnl\|CDD\|223930
AP019378.1\|BBH99681.1\|3431849_3433010_-\|acyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|173841
AP019378.1\|BBH99698.1\|3449172_3449568_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377229
AP019378.1\|BBH99687.1\|3438246_3438765_+\|Mg(2+)-transporter	unknown	unknown	gnl\|CDD\|224204
AP019378.1\|BBH99692.1\|3443606_3445052_-\|GntR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224089
AP019378.1\|BBH99697.1\|3448236_3449238_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|212118
AP019378.1\|BBH99680.1\|3430794_3431823_-\|acyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|366103
AP019378.1\|BBH99690.1\|3442603_3443074_-\|universal-stress-protein	unknown	unknown	gnl\|CDD\|366180
AP019378.1\|BBH99691.1\|3443162_3443507_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|225984
AP019378.1\|BBH99695.1\|3446855_3447779_+\|peptidase	unknown	unknown	gnl\|CDD\|378820
AP019378.1\|BBH99685.1\|3435955_3437185_-\|CoA-transferase	unknown	unknown	gnl\|CDD\|367110
AP019378.1\|BBH99683.1\|3434135_3435107_-\|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270234
AP019378.1\|BBH99696.1\|3447784_3448240_-\|membrane-protein	unknown	unknown	gnl\|CDD\|226610
AP019378.1\|BBH99688.1\|3438761_3440879_-\|elongation-factor-G	unknown	unknown	gnl\|CDD\|234569
AP019378.1\|BBH99684.1\|3435173_3435959_-\|enoyl-CoA-hydratase	unknown	unknown	gnl\|CDD\|181723
AP019378.1\|BBH99689.1\|3441240_3442461_-\|ISL3-family-transposase	unknown	unknown	gnl\|CDD\|225995

Protein	Function_ID	Function_description	E-value
AP019378.1\|BBH99682.1\|3433207_3434125_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176106	cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain 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 substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.	1.19908e-60
AP019378.1\|BBH99679.1\|3429535_3430729_-\|acetyl-CoA-acetyltransferase	gnl\|CDD\|180775	PRK06954, PRK06954, acetyl-CoA C-acetyltransferase.	2.86943e-175
AP019378.1\|BBH99693.1\|3445135_3446110_+\|multidrug-DMT-transporter-permease	gnl\|CDD\|223769	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only].	1.6581e-12
AP019378.1\|BBH99694.1\|3446106_3446766_+\|membrane-protein	gnl\|CDD\|224199	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism].	4.25651e-32
AP019378.1\|BBH99686.1\|3437380_3438136_-\|membrane-protein	gnl\|CDD\|223930	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism].	1.14565e-78
AP019378.1\|BBH99681.1\|3431849_3433010_-\|acyl-CoA-dehydrogenase	gnl\|CDD\|173841	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26. Putative acyl-CoA dehydrogenases (ACAD). Mitochondrial 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 ACD 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. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position.	2.9679e-84
AP019378.1\|BBH99698.1\|3449172_3449568_+\|hypothetical-protein	gnl\|CDD\|377229	pfam04138, GtrA, GtrA-like protein. Members of this family are predicted to be integral membrane proteins with three or four transmembrane spans. They are involved in the synthesis of cell surface polysaccharides. The GtrA family are a subset of this family. GtrA is predicted to be an integral membrane protein with 4 transmembrane spans. It is involved is in O antigen modification by Shigella flexneri bacteriophage X (SfX), but does not determine the specificity of glucosylation. Its function remains unknown, but it may play a role in translocation of undecaprenyl phosphate linked glucose (UndP-Glc) across the cytoplasmic membrane. Another member of this family is a DTDP-glucose-4-keto-6-deoxy-D-glucose reductase, which catalyzes the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is involved in the biosynthesis of the serotype-specific polysaccharide antigen of Actinobacillus actinomycetemcomitans Y4 (serotype b). This family also includes the teichoic acid glycosylation protein, GtcA, which is a serotype-specific protein in some Listeria innocua and monocytogenes strains. Its exact function is not known, but it is essential for decoration of cell wall teichoic acids with glucose and galactose.	8.84202e-15
AP019378.1\|BBH99687.1\|3438246_3438765_+\|Mg(2+)-transporter	gnl\|CDD\|224204	COG1285, SapB, Uncharacterized membrane protein [Function unknown].	1.18053e-44
AP019378.1\|BBH99692.1\|3443606_3445052_-\|GntR-family-transcriptional-regulator	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].	6.70342e-111
AP019378.1\|BBH99697.1\|3448236_3449238_-\|hypothetical-protein	gnl\|CDD\|212118	cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins from bacteria. This subfamily contains many hypothetical proteins, and belongs to the YdjC-like family of uncharacterized proteins from bacteria. The YdjC-family is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. The molecular function of this subfamily is unclear.	1.99725e-92
AP019378.1\|BBH99680.1\|3430794_3431823_-\|acyl-CoA-dehydrogenase	gnl\|CDD\|366103	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain. C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.	1.19321e-12
AP019378.1\|BBH99690.1\|3442603_3443074_-\|universal-stress-protein	gnl\|CDD\|366180	pfam00582, Usp, Universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, though UspA lacks ATP-binding activity.	9.38587e-30
AP019378.1\|BBH99691.1\|3443162_3443507_-\|hypothetical-protein	gnl\|CDD\|225984	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown].	3.40043e-35
AP019378.1\|BBH99695.1\|3446855_3447779_+\|peptidase	gnl\|CDD\|378820	pfam12146, Hydrolase_4, Serine aminopeptidase, S33. This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. The majority of the members in this family carry the exopeptidase active-site residues of Ser-122, Asp-239 and His-269 as in UniProtKB:Q7ZWC2.	6.02976e-19
AP019378.1\|BBH99685.1\|3435955_3437185_-\|CoA-transferase	gnl\|CDD\|367110	pfam02515, CoA_transf_3, CoA-transferase family III. CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.	6.62375e-118
AP019378.1\|BBH99683.1\|3434135_3435107_-\|ABC-transporter-substrate-binding-protein	gnl\|CDD\|270234	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubacteria, at least three families of periplasmic binding-protein dependent transporters are known: the ATP-binding cassette (ABC) transporters, the tripartite ATP-independent periplasmic transporters, and the tripartite tricarboxylate transporters (TTT). Bug proteins are the PBP components of the TTT. Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter.	2.06741e-117
AP019378.1\|BBH99696.1\|3447784_3448240_-\|membrane-protein	gnl\|CDD\|226610	COG4125, COG4125, Predicted membrane protein [Function unknown].	1.97335e-52
AP019378.1\|BBH99688.1\|3438761_3440879_-\|elongation-factor-G	gnl\|CDD\|234569	PRK00007, PRK00007, elongation factor G; Reviewed.	0
AP019378.1\|BBH99684.1\|3435173_3435959_-\|enoyl-CoA-hydratase	gnl\|CDD\|181723	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein.	3.47115e-155
AP019378.1\|BBH99689.1\|3441240_3442461_-\|ISL3-family-transposase	gnl\|CDD\|225995	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	6.63558e-80

>AP019378.1|BBH99688.1|3438761_3440879_-|elongation-factor-G
MTRRTSIERYRNIGISAHIDAGKTTTTERILFYTGITHKLGEVHEGAATMDWMEQERGITITSAATTAFWRGMAGNYPEHRINIIDTPGHVDFTIEVERSMRVLDGACMVYDSVGGVQPQSETVWRQANKYGVPRIAFVNKMDRVGADFFRVQRQIVERLKGDAVPIQIPVGAEDHFEGVVDLVKMKAIIWDDASQGVRFEYRDIPPELQAQAEQWREKMIEKAAEANEALLEKYLSGQPLSEDEIKSGLRARTVANEIVPMLCGSAFKNKGVQAMLDAVIDYLPSPADVPAIIGHDERDREIERHPADDEPFSALAFKIMTDPFVGQLVFFRVYSGVVKSGDSVLNPLKSKKERLGRILQMHANERREISEVYAGDIAAAVGIKEITTGDTLTDPAHVIILERMTFPEPVISQAVEPRTKADQEKMGIALNRLAQEDPSFRVRTDEESGQTIISGMGELHLEILVDRMKREFGVEANVGKPQVAYRETIRSTVTDVEGKFVKQSGGRGQYGHVVLKLEPQEQGKGYEFVDAIKGGVVPREFIPAVDRGVRETLNTGVLAGYPVVDVKVTLVFGSYHDVDSNENAFRMAASMAFKEGMRRAKPVLLEPMMHVEVETPEDFTGNVMGDLSSRRGMVQGMEDIAGGGGKLVRAEVPLAEMFGYSTSLRSLTQGRATYSMEFKHYAEAPRQVAEQIIAARGSGAAARG
>AP019378.1|BBH99687.1|3438246_3438765_+|Mg(2+)-transporter
MDTVWMEIWTTVRNEFADIPDVAEATRIVLRLGMAVALGGLLGYERERSGKAAGLRTHMLVALGAALFVLVPLQGGMEVGDLSRVLQGVIAGIGFLGAGAIIKLGNEGEIRGLTTSAGIWLTAAIGVAAGMGREATALASTLIALFVLAALRHLEKRIAARDDKRVVAQPPP
>AP019378.1|BBH99686.1|3437380_3438136_-|membrane-protein
MDYLVSLAQQPAAWAALATLIAMEVVLGIDNLIFISILTNKLPPQHQTKARRIGIGMALILRLALLGTVAFIVQLTQPVFELFGHGFSWRDVILVAGGLFLVWKATKEIHHHVDPNPGDDMFGGKAATLGFAAAVAQILMLDLVFSIDSIITAVGMTEHIPIMFVAVIVAVAVMLLAAEPLARFIERNPTVVMLALAFLMMIGMTLIAEGFGAHVPKGYIYAAMAFSALVEGLNMMARRAREGRGAGAAGG
>AP019378.1|BBH99685.1|3435955_3437185_-|CoA-transferase
MSGPLEGVRILDVTTVLMGPYATQILGDLGADVIKVEPPAGDNVRGIGPGRHADMGGIFLHANRSKRSIALDLKNPAGREALLKVAATCDVLVYNVRPQAMARLGLSYAEVAQANPSILYVGMYGYDQRGPYAARAAYDDLIQGAVGIPSLSVEAGSDIPRYAPSAMVDRIVGISAANAVTAGLYHRARTGQGQAIDVPMFETMAHLILGDHMMGQTFEPPLGPPGYPRILNADRRPYATRNGHICVLLYADKHWKAFFELIGQPGRDAADPRFRDIGTRTQHIHAIYRLVSDAIASRTTEEWLAAFEAADIPAMPVHTMASLLRDPHLEAIGFFGMVDHPSEGAVRMMAVPSRWSGTPPQPRGHAPRLGEHSVDVLKEAGYDDEAIAALVRNGAGHRRGPPASGGNRS
>AP019378.1|BBH99684.1|3435173_3435959_-|enoyl-CoA-hydratase
MTDFLRHERHGGVLLLTMDRERTRNALSDADAVEALVQACARIGADLSVRAVVLTGSHGVFSSGGNLKTLSDTVGAGLGEPVHSRQAYRSGIQRIPLALYNLEVPTIAAVNGPAIGAGCDLACMCDIRLAARQASFAESFVKLGLTPGDGGAWLLPRIVGMSRACELAFTGRSIDAARARELGLVPEVFDADALLPAALALAQEIAQHSGHALRLTKRLLREGQHTRLDTLLELSAGFQALAHHTQEHAGALDAHLSRKRG
>AP019378.1|BBH99683.1|3434135_3435107_-|ABC-transporter-substrate-binding-protein
MHSRTLALALLSVAALAQGGSARAASDYPAHPVKIIVSLPPGSGADTTARFLSKHLAERFKQPFVVENRPGGNSFIAAQAVATAPPDGYTLFVASNSPMTTNAAVFKNLPYDAVKDFAPVAPIARFPMALVVPANSPYRSVADLVAAARAAPGQLNFASGTATYQVVLELFHEQNGIKATHVPYKGTSAALADVAGGVVQYSVADVSAALPLIRGGKLRPLAVTSTRRIKDLPDVPTMQESGNKGFEAYAWTAAFFPAKVDPAIVARVSDAVQALVRSQEGKAFMEQLGGEPFVGGPDTLAAFQRDELASMRRIAKLANIQQE
>AP019378.1|BBH99682.1|3433207_3434125_+|LysR-family-transcriptional-regulator
MELRQLKQLLVLSETLNFHRAAERLHMAQPPLSTAIKKLEQELGVQLFERLPAGLQPTPAAEVVLRYARATLFYADEIQRAAQEGASGKQGMLKVGFVGSSIYSLMPQLLSAFRKDYPRVDLVIEESTTVDLLRRLDAHTLDVALVRFPVLEPSTARITLLQADHLMLAVPAGSRYAQRDDVALDELADEPFIGYSRTHVPGMHALIMYAFQQYGVVPHIAQEAIQVQTILSLVESGLGLAIVPKVACRQAGSGVRLVNVPQLAETIKVGIALAVHPDNATPTTANFVDMACRLMQTEPAAGQAR
>AP019378.1|BBH99681.1|3431849_3433010_-|acyl-CoA-dehydrogenase
MGTIIEALQLAAIPAHDEALRPAVRAFLDEALREMPADRRARSWMGHDAEFSRALARQGWLGLTLPVEYGGAGRSNFARFVLSEELLAAGAPVSAHWIADRQTAPLILRFGSPAQRAFYLPRIIRGEAFFAIGMSEPDTGSDLASVRTRATPVADGWLLNGRKIWTTNAHRSHYMCALVRTSGASEDRHRGLSQMIFDLALPGIEIRPIRDIAGDAHFCEVLFDNVLLPHDALVGEEGSGWRQVMAELALERSGPERIYSSMVLLDGWLAHLRRDAAPQRAQVCLAGRLAARLAVLRSMSLAVSQRLEQGADASLAAVLVKDLGTEFEQAVPELIGQALHASPQPAPDDVLMRTLAYLTLINPTFSLRGGTRHILRGIIARELGLR
>AP019378.1|BBH99680.1|3430794_3431823_-|acyl-CoA-dehydrogenase
MVSTMQQDLYETFARALAGLCPLERVRELEAAADPRAGAARAWNEVDALGYGDALSPAEHGGAGLSLADAEGLLRAAGAMALPFPFADTLLARALLRAAGQAVPDGPIALGVALPHGAGWRCAPIAGVALAQAVAVEHDGCLALWPAPDAVQPGLFRPRASGAPAWRGTPAQAGRAGAPAGAVQAWRNAADAAGMAGAMQAVLDRCVAYVQERQQFGRALGRFQAVQQDISMLAEQVAAVAMAARLACASGALFPDPALAACARLRACEAVPVVCALAHAVHGAIGITEELPLGLYTARLHEWRATGMSEDDCAELLGRRVLADGERTLLDVVRGMVSAAHA
>AP019378.1|BBH99679.1|3429535_3430729_-|acetyl-CoA-acetyltransferase
MSVHPDPVVIVAARRTPIGAFQGALAHYSAPQLGAHALAAAVRQAGLQPDAAQEALMGCCLFAGLGQAPARQAVLGAGLPTDVQATTLSKMCGSGMKAAMLAHDMLRAGSADVVLAGGMESMSNAPHLIPKARQGYRLGDGQLLDHMYRDGLQDAYEGRLMGHYADLAAREYGFSREQQDAYAHESVLRAQRSVAEGEFAEEIAPIAGLARRGAPAAMVAVDETPGLCDVSRLASLKPVFNADGTVTAGNASSISDGAAALVLTRQAHAERLGLAPQARIVGHATAALPPGQFPAAPVRAIARLFERVGWDRDSVDLFEINEAFAVVTMIALRELGLPAERVNVNGGACALGHPVGATGARLIVTLMHALRRRGLRRGVACLCLGGGEATAIAIERA
>AP019378.1|BBH99689.1|3441240_3442461_-|ISL3-family-transposase
MLDRKLLESLGGWQGYGVERVEWPEDPGRTLSIYLKPTAKVMLCEQCGARCRQVHETTVRRVRDLPLFEYRVVLHVPRRRLWCEQCGGPRLERLAWLGRYQRVTDRLAQACSQLLQSSNVQAVARFFELGWHTVKTLDKARLRASVREPDWSKIEYLAMDEFALHKGHRYATVVVDPIGRQVLWIGPGRSRETARAFFEQLPPGAAQRIKAVAIDMTTAYELEIQAHSPQAEIVYDLFHVVAKYGREVIDRVRVDQANQLRQDRPARRIIKSSRWLLLRNRDNLDRQQAVRLDELLQANQPLLTVYVLRDELKRLWFYQRPAWARQAWNHWYEQAEQSGIAALNTFAQRLKGYLHGILARCRHPLNTSIVEGINNTIKVIKRRAYGYRDQEYFFLKIRAAFPGNAR
>AP019378.1|BBH99690.1|3442603_3443074_-|universal-stress-protein
MFKKILIPTDGSPLSAQAANAGICFARSTGAEVVALHVTQPFAATIGFDGMAAAYAITDEDYEKASAEQAEKYLKLILDRAETAGVKAESRAVSNFNVADGIVQAAGEAGCDLIFIGSHGRSGLSRLLLGSVTAKVLSLAHTAVLVYRVKEDKDKK
>AP019378.1|BBH99691.1|3443162_3443507_-|hypothetical-protein
MSAAIKPLTENFAVAPQLGPADMADVAAAGYKSVIINRPDFEGGPDQPTAADVSQAAQALGLQVEYQPVVGSAMTAADVARFAELLRTMPGPVLAYCRTGTRCTNLFAAAQQLG
>AP019378.1|BBH99692.1|3443606_3445052_-|GntR-family-transcriptional-regulator
MTVATSSPSGAGWQPVRQADATLVTQLADDLARRIDEHGLRPGTRLPSIRRMAEQSGVSRFTVVEAYDRLVARGLVQSRRGAGFFVRARSASLTALASARVPQAAPETPVRVDVSWLLRNMFRETAAGMPGGAGLLPPEWLDPDMVAAAVRAVGRTVRGNLVSYGSPQGYAPLRQQLASMLQADGVPAHPERNLLTTNGVTHGLDIVARHLIKPGDTVLVEDPAWFVIFGRLAAFGARPVGVPRGPDGPDLAMLDRLAAEHKPRLYIINGAVHNPTGHTLSAGAAYDILRLAERHDFMVVEDDTYADLHPGGAMKLAALDRLERVILVGGFSKMLAASLRVGYIAAGAETLQRLTDLKMLAGLTSPELGERVVHRVLVEGQYRRHIERVRARVNEARLRSIQALQQLGLSVPHEPHAGMFVWADCGRDSEPVARNAAERGMLLAPGTLFSPSGAPSTMLRFSVAMVDTPGIWQSIAAVMAQ
>AP019378.1|BBH99693.1|3445135_3446110_+|multidrug-DMT-transporter-permease
MRRHGKPGRPLSPIQRQIFPMSPPSAQASAPSASPHAPSWEGYGYGLIGVLVFALTLPMTRLAVGELSPLLVGLGRALLAAVPAAALLWLTRSRRPDRAEWSGIVLAAVGIVVGWPVASTLAMASVPAAHGAVFNGLLPLSTAVFAAWRSGERPSPAFWSFAVLGAVLVAGYALRQGHGALQPGDLWLLLAVVLGGMGYAEGARASRTLGGWRTICWALVVSVPALLPAVLWLAHDAAWPSLPVAGAFAYLAFGSMFLGFFAWYRGLAIGGIARVGQIQLLQPFLTVVAAALLFNEQVEPITYVFAVAVVLVIAGGRRAMVRKA
>AP019378.1|BBH99694.1|3446106_3446766_+|membrane-protein
MIGSDLSSLDQAPLASLSVLMPLVLFTLVNSLTPGPNNVMLASSGLTFGFRRTIPHLLGISVGFSIMLLMVGLGLGATLERLPWLYSTLKYGGAAYLLYLAWKIATSGPMESGAERGKPLTFIQAALFQWVNPKAWVMIVSVVATYTPQHGYFANLIIATLVCGVVNLPSVGVWAAFGMALRRWLHRPAAVRAFNVGMAVLLVVSLYPVGLDLLALYTG
>AP019378.1|BBH99695.1|3446855_3447779_+|peptidase
MVCLPFRLSWRRMAAVLLLAAGALGFNQLDAWQRQAIFSPQTDQQRWWREPPAGTEVFDLALPNGDKVHAWYWQSPRRDAPTVLYLHGARWNLNGSAFRMEGWTGMGYSMLAIDYRGFGQSTPLLPSEQSASQDAAAALQELARRQPDPARRFIYGHSLGGAIAIDLAARPDLPPFAGLIVESSFTSIGAMLGTMKWGWVPGATLLVTQPFASVDKLAALTTLMLLLHGTADRVVPHTMSDELYRAAQQVPADLKRLVKIEGASHSGAIRSGRIYEDAVADFVRDAGRGYAGRQGAPTPLTASRPGT
>AP019378.1|BBH99696.1|3447784_3448240_-|membrane-protein
MSSSSKQTPKTIKERFLHAFFFEIIAIGLSAPVAAWAMDQPLFDMGVLTAVIAWIALLWNMVYNAGFERLERRFGVVRTMPVRVAHAVGFELGLVLIIVLLAAWWLAISFWEAFMLDIGLLMFYLPYAFFYNLAYDKLRARWWGRIEPAGA
>AP019378.1|BBH99697.1|3448236_3449238_-|hypothetical-protein
MGGGRGASDGNEPGNLSQQAAHVEEVSPLRNQAGDVRCRRIAVCGDDFGMNEAIDGALIELAGAGRLSAVSCMPLAPAFAADAPALARLDVDLGVHVDFTEAFAGAAPAAPGLAALLWRAYAGQLDPDWIDARLASQFDAFERAFGRAPDYVDGHQHVHQLPGILPRLRALLKRRYAGQRIWLRHTAPGLQFGLPLAEAAKARLIGALGAGALARAAGQEGWQTNRRMLGVYGFTGGPRRYAGLLHHWLMNARDGDLLMCHPGWPQVHGAAHASQRAAEYEVLAHPELGTWLARNGLRIVRLSQVRGRQASQESGKVRNVPHSGSFRRLASRL
>AP019378.1|BBH99698.1|3449172_3449568_+|hypothetical-protein
MRGLLRQIAWFIAVGCAAAATHWAVAVACVEWAGLPPLGANVVGWLLAFVVSFTGHFRLTFRHLAASWTIAARRFFLVSALGFAINELSYAWLLHATSLPYDVLLALVLIGLAFLTFVASRLWAFRHRHAP

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
AP019378_1	1.1\|64110\|41\|AP019378\|PILER-CR	64110-64150	41	AP019378.1	64306-64346	0	1.0
AP019378_2	2.2\|132600\|24\|AP019378\|PILER-CR	132600-132623	24	AP019378.1	132462-132485	0	1.0
AP019378_2	2.2\|132600\|24\|AP019378\|PILER-CR	132600-132623	24	AP019378.1	132672-132695	0	1.0
AP019378_1	1.2\|64205\|80\|AP019378\|PILER-CR	64205-64284	80	AP019378.1	64368-64447	20	0.75
AP019378_1	1.2\|64205\|80\|AP019378\|PILER-CR	64205-64284	80	AP019378.1	63976-64055	20	0.75

1. spacer 1.1|64110|41|AP019378|PILER-CR matches to position: 64306-64346, mismatch: 0, identity: 1.0

caggcacccgccgcatacaccgcgctgctcgcagcggccat	CRISPR spacer
caggcacccgccgcatacaccgcgctgctcgcagcggccat	Protospacer
*****************************************

2. spacer 2.2|132600|24|AP019378|PILER-CR matches to position: 132462-132485, mismatch: 0, identity: 1.0

ggactggcaccggcaagatttcac	CRISPR spacer
ggactggcaccggcaagatttcac	Protospacer
************************

3. spacer 2.2|132600|24|AP019378|PILER-CR matches to position: 132672-132695, mismatch: 0, identity: 1.0

ggactggcaccggcaagatttcac	CRISPR spacer
ggactggcaccggcaagatttcac	Protospacer
************************

4. spacer 1.2|64205|80|AP019378|PILER-CR matches to position: 64368-64447, mismatch: 20, identity: 0.75

atgcaggcaccgtctcttccacgccaacaaccacgaccgcagcggacccgggtgcctggc	CRISPR spacer
atgcaggcaccgtctcttccacgccaacaaccacgaccgcagcggacccgggtgcctggc	Protospacer
************************************************************

5. spacer 1.2|64205|80|AP019378|PILER-CR matches to position: 63976-64055, mismatch: 20, identity: 0.75

atgcaggcaccgtctcttccacgccaacaaccacgaccgcagcggacccgggtgcctggc	CRISPR spacer
atgcaggcaccgtctcttccacgccaacaaccacgaccgcagcggacccgggtgcctggc	Protospacer
************************************************************

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1454836 : 1520384

uncultured_Caudovirales_phage(11.76%)

protease,transposase,tRNA

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
BBH97830.1\|1454836_1455490_+\|protease	ATP-dependent Clp protease proteolytic subunit	A0A223W000	Agrobacterium_phage	6.8e-56	57.5
BBH97831.1\|1455594_1456899_+\|protease	ATP-dependent Clp protease ATP-binding subunit ClpX	G3M9Z9	Bacillus_virus	5.4e-129	53.8
BBH97832.1\|1457087_1459541_+\|protease	Lon protease	A0A0R6PGP8	Moraxella_phage	2.3e-221	52.1
BBH97833.1\|1459672_1460623_-	LysR family transcriptional regulator	NA	NA	NA	NA
BBH97834.1\|1460850_1462074_+	CoA transferase	NA	NA	NA	NA
BBH97835.1\|1462139_1463111_+	ABC transporter substrate-binding protein	NA	NA	NA	NA
BBH97836.1\|1463115_1463580_+	oxidoreductase	NA	NA	NA	NA
BBH97837.1\|1463599_1464397_+	enoyl-CoA hydratase	NA	NA	NA	NA
BBH97838.1\|1464393_1464825_+	hypothetical protein	NA	NA	NA	NA
BBH97839.1\|1464821_1465979_+	thiolase	NA	NA	NA	NA
BBH97840.1\|1466000_1466777_+	3-oxoacyl-ACP reductase	NA	NA	NA	NA
BBH97841.1\|1466773_1467937_+	acyl-CoA dehydrogenase	NA	NA	NA	NA
BBH97842.1\|1468069_1468519_-	hypothetical protein	NA	NA	NA	NA
BBH97843.1\|1468571_1468955_+	hypothetical protein	NA	NA	NA	NA
BBH97844.1\|1468951_1469668_+	3-oxoadipate CoA-transferase subunit A	NA	NA	NA	NA
BBH97845.1\|1469660_1470302_+	3-oxoadipate CoA-transferase subunit B	NA	NA	NA	NA
BBH97846.1\|1470336_1471299_+	exported protein	NA	NA	NA	NA
BBH97847.1\|1471686_1473255_+	autotransporter	NA	NA	NA	NA
BBH97848.1\|1473639_1474290_-	LexA repressor	A0A2H4JG58	uncultured_Caudovirales_phage	3.3e-10	50.7
BBH97849.1\|1474418_1475621_-	aminotransferase	NA	NA	NA	NA
BBH97850.1\|1475699_1477727_+	UvrABC system protein B	NA	NA	NA	NA
BBH97851.1\|1478081_1478480_+	phosphotyrosine protein phosphatase	NA	NA	NA	NA
BBH97852.1\|1478695_1479208_+	Fe-S cluster assembly transcriptional regulator IscR	NA	NA	NA	NA
BBH97853.1\|1479225_1480437_+	cysteine desulfurase IscS	NA	NA	NA	NA
BBH97854.1\|1480470_1480881_+	iron-sulfur cluster assembly scaffold protein IscU	A0A218MKD1	uncultured_virus	7.5e-53	79.0
BBH97855.1\|1480882_1481206_+	iron-sulfur cluster assembly protein IscA	A0A2H4N7N5	Lake_Baikal_phage	6.8e-25	52.8
BBH97856.1\|1481208_1481721_+	co-chaperone protein HscB	NA	NA	NA	NA
BBH97857.1\|1481799_1483713_+	chaperone protein HscA	A0A0N9QXN8	Chrysochromulina_ericina_virus	9.1e-101	42.2
BBH97858.1\|1483722_1484064_+	ferredoxin, 2Fe-2S type, ISC system	NA	NA	NA	NA
BBH97859.1\|1484063_1484258_+	Fe-S assembly protein IscX	NA	NA	NA	NA
BBH97860.1\|1484384_1485278_+	methylglyoxal synthase	NA	NA	NA	NA
BBH97861.1\|1485302_1486112_-	enoyl-CoA hydratase	NA	NA	NA	NA
BBH97862.1\|1486381_1487206_+	ABC transporter ATP-binding protein	A0A2R8FG22	Brazilian_cedratvirus	2.3e-08	22.2
BBH97863.1\|1487205_1488084_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA
BBH97864.1\|1488087_1489125_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA
BBH97865.1\|1489162_1490341_+	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA
BBH97866.1\|1490348_1491164_+	ABC transporter ATP-binding protein	W6JKT0	Anomala_cuprea_entomopoxvirus	5.7e-12	23.7
BBH97867.1\|1491175_1493026_+	long-chain-fatty-acid--CoA ligase	A0A1V0SBX8	Catovirus	4.1e-50	23.5
BBH97868.1\|1493104_1493737_+	TetR family transcriptional regulator	NA	NA	NA	NA
BBH97869.1\|1493733_1494069_-	hypothetical protein	NA	NA	NA	NA
BBH97870.1\|1494085_1495606_-\|tRNA	lysine--tRNA ligase	A0A1V0SAC0	Catovirus	2.9e-81	35.6
BBH97871.1\|1495612_1496368_-	short-chain dehydrogenase	NA	NA	NA	NA
BBH97872.1\|1496397_1497279_-	peptide chain release factor 2	NA	NA	NA	NA
BBH97873.1\|1497604_1499305_-	single-stranded-DNA-specific exonuclease	A7KV88	Bacillus_phage	4.5e-51	28.4
BBH97874.1\|1499286_1500228_-	hypothetical protein	NA	NA	NA	NA
BBH97875.1\|1500273_1501554_+	lipoprotein releasing system protein	NA	NA	NA	NA
BBH97876.1\|1501546_1502242_+	lipoprotein-releasing system ATP-binding protein LolD	G9BWD6	Planktothrix_phage	7.0e-35	38.6
BBH97877.1\|1502275_1503103_+	deoxyribonuclease	NA	NA	NA	NA
BBH97878.1\|1503408_1506615_+\|protease	serine protease	NA	NA	NA	NA
BBH97879.1\|1506735_1507956_-\|transposase	ISL3 family transposase	A4PE56	Ralstonia_virus	8.1e-196	80.8
BBH97880.1\|1508137_1508902_+	short-chain dehydrogenase	NA	NA	NA	NA
BBH97881.1\|1509082_1509727_-	phosphoglycerate mutase	NA	NA	NA	NA
BBH97882.1\|1509737_1510637_-	LysR family transcriptional regulator	NA	NA	NA	NA
BBH97883.1\|1510684_1511770_-	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	6.4e-27	37.7
BBH97884.1\|1511766_1513476_-	ABC transporter permease	NA	NA	NA	NA
BBH97885.1\|1513552_1514998_-	ABC transporter substrate-binding protein	NA	NA	NA	NA
BBH97886.1\|1515131_1516445_+	pyrimidine permease	Q9KX94	Enterobacteria_phage	2.3e-148	66.8
BBH97887.1\|1516475_1518107_-	methyl-accepting chemotaxis protein	A0A2H4J162	uncultured_Caudovirales_phage	6.7e-12	30.2
BBH97888.1\|1518736_1519213_+	transcription elongation factor GreA	NA	NA	NA	NA
BBH97889.1\|1519514_1520384_-\|transposase	transposase	NA	NA	NA	NA

DBSCAN-SWA_2

2604349 : 2612415

uncultured_Mediterranean_phage(28.57%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
BBH98909.1\|2604349_2605234_-	peptidase	A0A292GJG6	Xanthomonas_phage	4.6e-15	49.5
BBH98910.1\|2605251_2606031_-	protein-L-isoaspartate O-methyltransferase	A0A1B1IU40	uncultured_Mediterranean_phage	4.8e-32	46.9
BBH98911.1\|2606015_2606774_-	5'-nucleotidase SurE	A0A1B1ITZ2	uncultured_Mediterranean_phage	6.2e-69	51.2
BBH98912.1\|2606911_2607547_+	glycerol-3-phosphate acyltransferase	NA	NA	NA	NA
BBH98913.1\|2607591_2608632_-\|tRNA	tRNA N6-adenosine threonylcarbamoyltransferase	A0A0R6PI74	Moraxella_phage	7.9e-91	51.3
BBH98914.1\|2608766_2610059_+	permease	A0A0R6PHV4	Moraxella_phage	1.9e-65	35.8
BBH98915.1\|2610264_2611290_+	hypothetical protein	NA	NA	NA	NA
BBH98916.1\|2611425_2611809_+	thiol reductase thioredoxin	V9SJ74	Achromobacter_phage	1.8e-08	25.8
BBH98917.1\|2611827_2612415_-	thymidylate synthase	A0A1X9I5T8	Streptococcus_phage	2.1e-16	46.8

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. AP019378

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

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