Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 108769
• Name: oriT_pDR208
• Organism: Pseudomonas viridiflava strain JACO-C-5
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP097287 (17796..18148 [+], 353 nt)
• oriT length: 353 nt
• IRs (inverted repeats): 103..109, 113..119 (GCCGCGC..GCGCGGC)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 353 nt

>oriT_pDR208
GTATAGCAAATGTAATACACAAAAAGCTTGATTTAGCTGGGCTAGATGGTAGTTTTGTATAGCAAGTGTATAGCGCAAGAAACTACACGCATTTCGCTGTAGGCCGCGCTCTGCGCGGCTTGCGCCTCCCGCTAGGGGGGTGCGTGATGTGTATTGAGATTTTGACCCTGTTAAGGGGAAAAATCGAAGCTCTTGTTAAGGGCGTATCCACTGTTTAGGCCGAAGGCCGTAGGGTGGTATGCAGAAAGGGTGCAGGAAGGGTGCTATAAGAGTGCAGGAGCAGTGCAACTTGACTACAGGTAGGGGGCAGGTAAGATGCACATAGAGTGCAACAGGGGTGCAGGTAGGGTGCA

oriT secondary structure

Predicted by RNAfold.

Relaxase

mobF_M4X66_RS27060_pDR208

• ID: 5879
• GenBank: WP_054076663
• Name: mobF_M4X66_RS27060_pDR208
• UniProt ID: _
• Length: 981 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 981 a.a.
• Molecular weight: 109217.07 Da
• Isoelectric Point: 9.9333

>WP_054076663.1 MULTISPECIES: MobF family relaxase [Pseudomonas]
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLEGPIDQQELAKLFDGKLPNGEMMPKP
VNKETGEIVTRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQTRRKEHGKSMLER
TGNLIIGKFRHELSRAKDPQLHTHAVVMNATRRADGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGY
EIRVLDKDGNFELAHISRDQIEAFSSRAKVIEDALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVK
EYWVTKARELGIEFGGRSQLDNREYGRRSESIHAEHNLPEGISAGQAVVQYAINHLTEREQVVGESDLRT
AALRRAVGLASPTEVDDEIKRLVKQGSLIESPPAYRMATAPDGAALSPAGWRALLKEQKGWSEKEAQQYV
KKAIDRGSLVEVEKRYTTQRALKREKAILAIERTGRGQVTPLLTKEQVAKALEGSTLSAGQYQAVEVIVS
TSNRFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERSTTTDATFRVVALAPYGNQVTALKNEGLDAHTL
ASFFHTKDKKLDERTIVVLDEAGVVGARQMEQLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGM
ETARIKEIQRQKNQELKIAVQHAAEGNPGKSLAHVNHVEEFRDPALRHEAIVRDYVSLTPEERKEVLIVA
GTNKDRKQINTMTREALGLVGKGLELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRAGLSRGELYTV
DQALPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNVNG
VIELASVKERDGKPERVVTLPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSRTTSQNLWYVAISRA
RYEARIYTDKIAHLPAAIANRYDKTTALSLQQERERQRKEPIKPRTVLDGKAMEKKQRTALDGASAGKSG
V

Protein domains

Predicted by InterproScan.

• AAA domain (AAA_30) (476-666)

• Viral (Superfamily 1) RNA helicase (Viral_helicase1) (872-918)

• TrwC relaxase (TrwC) (15-289)

Protein structure

No available structure.

T4CP

t4cp2_M4X66_RS27065_pDR208

• ID: 6318
• GenBank: WP_054076662
• Name: t4cp2_M4X66_RS27065_pDR208
• UniProt ID: _
• Length: 518 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 518 a.a.
• Molecular weight: 58181.56 Da
• Isoelectric Point: 8.9119

>WP_054076662.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Pseudomonas]
MHKREVDSATMTAGFGLPIAGWGAGVYLAQMPLTPFPAAFKETLHNGWHNPIVLGATIATSVAAASLVYY
LQEYCDDGFRGEQYQEFLRGSQIKNWHTVKAKVNRRNAQTNRERKKKGLAKSDPIMIGKLPMPLHLEDRN
TMICASIGAGKSVTMEGMIASALKRGDRMAVVDPNGTFYSKFSFKGDYILNPFDVRSAGWTIFNEIRGIH
DFNRMAKSIIPPQVDPSDEQWCAYARDVLSDTMRKLKETNNPNQDTLVNLLVREDGDTIRAFLANTDSEG
YFRDNAEKAIASIQFMMNKYIRPLRYMSKGEFSIYQWVNDPNAGNLFITWREDMRDTMKPLVATWIDTIC
ATILSSEPMTGKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF
RNYVILAAANAKNAGMASEILGSHDVKRWRKSLTAGKLTRTEEVTRDEPVVQASEISNLPDLVAYVKFGE
DFPITKVKTPYIDYKERAQAIMITGQAA

Protein domains

Predicted by InterproScan.

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (125-499)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46..17349

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
M4X66_RS26985	46..2688	+	2643	WP_081003828	type VI secretion protein	virb4
M4X66_RS26990	2688..3371	+	684	WP_042934861	type IV secretion system protein	virB5
M4X66_RS26995	3399..3611	+	213	WP_017124976	hypothetical protein	-
M4X66_RS27000	3604..4008	+	405	WP_054076671	hypothetical protein	-
M4X66_RS27005	3996..4859	+	864	WP_017124978	type IV secretion system protein	virB6
M4X66_RS27010	4859..5524	+	666	WP_054076670	type IV secretion system protein	virB8
M4X66_RS27015	5551..6342	+	792	WP_054076669	TrbG/VirB9 family P-type conjugative transfer protein	virB9
M4X66_RS27020	6345..7628	+	1284	WP_054076668	TrbI/VirB10 family protein	virB10
M4X66_RS27025	7638..8666	+	1029	WP_017124982	P-type DNA transfer ATPase VirB11	virB11
M4X66_RS27030	8650..9552	+	903	WP_054076667	lytic transglycosylase domain-containing protein	virB1
M4X66_RS27035	9582..9911	+	330	WP_054076666	TrbM/KikA/MpfK family conjugal transfer protein	-
M4X66_RS27040	9901..10506	+	606	WP_081003826	phospholipase D family protein	-
M4X66_RS27045	10521..11003	+	483	WP_054076665	hypothetical protein	-
M4X66_RS27050	11048..11686	+	639	WP_054076664	hypothetical protein	-
M4X66_RS27055	12009..12764	-	756	WP_230847846	hypothetical protein	-
M4X66_RS27060	12837..15782	-	2946	WP_054076663	MobF family relaxase	-
M4X66_RS27065	15793..17349	-	1557	WP_054076662	type IV secretion system DNA-binding domain-containing protein	virb4
M4X66_RS27070	17342..17734	-	393	WP_017124989	hypothetical protein	-
M4X66_RS27075	18151..18606	+	456	WP_169880829	conjugal transfer protein TraD	-
M4X66_RS27080	18603..19322	+	720	WP_054076660	StbB family protein	-
M4X66_RS27085	19326..19712	+	387	WP_054076659	hypothetical protein	-
M4X66_RS27090	19845..20648	+	804	WP_054076658	SprT-like domain-containing protein	-
M4X66_RS27095	21387..21650	-	264	WP_081003825	antirestriction protein ArdR	-
M4X66_RS27100	21905..22177	-	273	WP_054076656	hypothetical protein	-

Host bacterium

• ID: 9204
• GenBank: NZ_CP097287
• Plasmid name: pDR208
• Incompatibility group: -
• Plasmid size: 42253 bp
• Coordinate of oriT [Strand]: 17796..18148 [+]
• Host baterium: Pseudomonas viridiflava strain JACO-C-5

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -