Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200437
• Name: oriT_ICEMsp.SymM6A
• Organism: Mesorhizobium sp. M6A.T.Cr.TU.016.01.1.1
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP034452 (369053..369113 [-], 61 nt)
• oriT length: 61 nt
• IRs (inverted repeats): 26..34, 36..44 (ACCGCCTCC..GGAGGCGGT)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 61 nt

>oriT_ICEMsp.SymM6A
AAAACGATGTGCAGACAAAGATTTAACCGCCTCCTGGAGGCGGTACCTTTATCTTGCCTTA

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_EJ075_17140_ICEMsp.SymM6A

• ID: 17024
• GenBank: AZO69493
• Name: t4cp2_EJ075_17140_ICEMsp.SymM6A
• UniProt ID: _
• Length: 674 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 674 a.a.
• Molecular weight: 74605.81 Da
• Isoelectric Point: 6.6481

>AZO69493.1 conjugal transfer protein TraG [Mesorhizobium sp. M6A.T.Cr.TU.016.01.1.1]
MTPTKLLIGQIAVVCAIVIIGVWTATQWCAQMLTYQTPLGAPWFLFAGWPIYKPWKLFEWWFHFDAYAPE
VFDKAGTLAGASGFLGCAAAIAGSLLRARQRGSVTTYGSSRWATTHEVETAGLLRPAGVFLGRLNDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWTGSAIIHDIKGENWQLTSGWRSKFSYCLLFNPTDPRSARYN
PLLEVRKGPDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEDKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGTGHNPQVHPVVASAARELLNKSENERSGVLSTAMSFLGLYRDPTVAAATSSCD
WRIADLVDGERPLSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRSYLIAQSLNQVSKAYGENNAILDNCHVRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPSDELVLVSGLPPIRAKKLRYYQDQNFTDRVL
PAPVLHDGPYADCPASRPDGWTGQVCSVDSRLAADEESADAPVEDEGGVQQQRHPSLPEEDVVVSQEPDQ
ADLYKPADDDSEALADKRVMDRISTAARAYGINEGRGDDVIPGF

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (133-560)

Protein structure

No available structure.

t4cp2_EJ075_17165_ICEMsp.SymM6A

• ID: 17025
• GenBank: AZO66467
• Name: t4cp2_EJ075_17165_ICEMsp.SymM6A
• UniProt ID: _
• Length: 816 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 816 a.a.
• Molecular weight: 90304.81 Da
• Isoelectric Point: 5.9043

>AZO66467.1 conjugal transfer protein TrbE [Mesorhizobium sp. M6A.T.Cr.TU.016.01.1.1]
MLNLSEYRSKADRLADHLPWAALVAPGIVLNKDGSFQRTLRFRGPDLESATEAELVGICARANNALRRLG
SGWALFFEAERIEALGYPNSHFPDAASWLVDEERRAAFEGKVAHYESRYHLTLVFMPPPDAQARAESALV
DSHYSQGERDWRQDLARFRDETNRVLDLFSGFMSEVRVLDDAQTLTYLHGTISPRRHPIMAPETPIYLDA
ILVDAPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDTLNHQDFAYRWMTRFIPLEKTEATKTLTRLRR
QWFAKRKSIVAILREVITNEPVPLVDSDADNKALDADEALQALGGDHVSFGYLTTTVTVWGEDRQAAAEK
LRAVERIINGLGFTTIREGVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLIPLSSVWAGPATNEHLAKV
TQTEAPPLFVAETSGSTPFRLSTHVEDVGHMLVVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHALGADGSLAFQPLRSINDQASRSWAAEWIASLVAHENVTVTPEVKEAIWSALASLATAP
AQERTLTGLSVLLQSNALKTALMPYTLDGPFGRLLDADHDGLALSDVQCFETEELMHSQGALLPVLTYLF
QRLEERFDGRPTLIMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVVFATQSLADIAGSGIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLSERQIELIARATPKRQYYLQSRRGNRLFELELGPIALALCGASDPA
TQTLIDRIMSEDGQGSFASQFLIARGLDWAGELLKQFPQPDKEQLA

Protein domains

Predicted by InterproScan.

• TraG P-loop domain (P-loop_TraG) (578-732)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (182-290)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (307-389)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3573800..3582856

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
EJ075_17140	3571249..3573273	+	2025	AZO69493	conjugal transfer protein TraG	-
EJ075_17145	3573390..3573803	+	414	AZO66463	CopG family transcriptional regulator	-
EJ075_17150	3573800..3574768	+	969	AZO66464	P-type conjugative transfer ATPase TrbB	virB11
EJ075_17155	3574781..3575089	+	309	AZO66465	conjugal transfer protein TrbC	virB2
EJ075_17160	3575089..3575361	+	273	AZO66466	conjugal transfer protein	virB3
EJ075_17165	3575355..3577805	+	2451	AZO66467	conjugal transfer protein TrbE	virb4
EJ075_17170	3577802..3578527	+	726	AZO69494	P-type conjugative transfer protein TrbJ	virB5
EJ075_17175	3578561..3579883	+	1323	AZO66468	P-type conjugative transfer protein TrbL	virB6
EJ075_17180	3579884..3580615	+	732	AZO66469	conjugal transfer protein TrbF	virB8
EJ075_17185	3580605..3581630	+	1026	AZO66470	P-type conjugative transfer protein TrbG	virB9
EJ075_17190	3581642..3582856	+	1215	AZO66471	TrbI/VirB10 family protein	virB10
EJ075_17195	3582869..3583111	+	243	AZO66472	DUF2274 domain-containing protein	-
EJ075_17200	3583348..3584697	-	1350	AZO69495	oxygen-independent coproporphyrinogen III oxidase	-
EJ075_17205	3584849..3585592	+	744	AZO66473	Crp/Fnr family transcriptional regulator	-
EJ075_17210	3586094..3587713	+	1620	AZO66474	cytochrome-c oxidase, cbb3-type subunit I	-

Host bacterium

• ID: 388
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEMsp.SymM6A
• GenBank: CP034452
• Element size: 6784580 bp
• Coordinate of oriT [Strand]: 369053..369113 [-]
• Host bacterium: Mesorhizobium sp. M6A.T.Cr.TU.016.01.1.1
• Coordinate of element: 3180370..3602318

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: nodF, nodE, nodA, nodB, nodC, nodI, nodJ, nodH, nodD, nifA, fixU, nifZ, nifB, fixX, fixC, fixB, fixA, nifW, nifS, nifQ, nifH, nifD, nifK, nifE, nifN, nifX, mlr6097, nolV, nolU, nolT, nolB, nolW, nodX, fixN, fixO, fixQ, fixP, fixG, fixH, fixI, fixS
• Anti-CRISPR: -