Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200435
• Name: oriT_ICEMsp.SymM3A
• Organism: Mesorhizobium sp. M3A.F.Ca.ET.080.04.2.1
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP034451 (348547..348606 [-], 60 nt)
• oriT length: 60 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: 60 nt

>oriT_ICEMsp.SymM3A
AAAACGATGTGCAGACAAAGATTTAACCGCCTCCTGGAGGCGGTACCTTTATCTTGCCTT

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_EJ074_19415_ICEMsp.SymM3A

• ID: 17020
• GenBank: AZO11004
• Name: t4cp2_EJ074_19415_ICEMsp.SymM3A
• 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

>AZO11004.1 conjugal transfer protein TraG [Mesorhizobium sp. M3A.F.Ca.ET.080.04.2.1]
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_EJ074_19440_ICEMsp.SymM3A

• ID: 17021
• GenBank: AZO11009
• Name: t4cp2_EJ074_19440_ICEMsp.SymM3A
• UniProt ID: _
• Length: 816 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 816 a.a.
• Molecular weight: 90415.89 Da
• Isoelectric Point: 5.9950

>AZO11009.1 conjugal transfer protein TrbE [Mesorhizobium sp. M3A.F.Ca.ET.080.04.2.1]
MLNLSEYRSKADRLADHLPWAALVAPGIVLNKDGSFQRTLRFRGPDLESATEAELVGICARANNALRRLG
SGWALFFEAERTEALGYPNSHFPDAASWLVDEERRAAFEGKVAHYESRYHLTLVFMPPPDAQARAESALV
DSHYSRGERDWRQDLARFRDETNRVLDLFSGFMSEVRVLDDAQTLTYLHGTISPRRHPIMAPETPIYLDA
ILVDAPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDTLNHQDFAYRWMTRFIPLEKTEATKTLTRLRR
QWFAKRKSIVAILREVITNEPVPLVDNDADNKALDADEALQALGGDHVSFGYLTTTVTVWGEDRQAAAEK
LRAVERIINGLGFTTIREGVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPATNEHLAKV
TQTEAPPLFVAETSGSTPFRLSTHVEDVGHMLVVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHALGADGSLAFQPLRSINDQASRSWAAEWIASLVAHENVTVTPEVKEAIWSALASLATAP
AQERTLTGLSVLLQSNALKTALMPYTLDGPFGRLLDADHDGLALSDVQCFETEELMHSQGALLPVLTYLF
QRLEERFDGRPTLIMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVVFATQSLADIAGSGIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLSERQIELIARATPKRQYYLQSRRGNRLFELELGPIALALCGASDPA
TQTLIDRIMSEDGQGSFASQFLIARGLDWAGELLKQFPQPDKEQFS

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) (182-389)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 4084456..4093509

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
EJ074_19415	4081905..4083929	+	2025	AZO11004	conjugal transfer protein TraG	-
EJ074_19420	4084046..4084459	+	414	AZO11005	CopG family transcriptional regulator	-
EJ074_19425	4084456..4085424	+	969	AZO11006	P-type conjugative transfer ATPase TrbB	virB11
EJ074_19430	4085437..4085745	+	309	AZO11007	conjugal transfer protein TrbC	virB2
EJ074_19435	4085745..4086017	+	273	AZO11008	conjugal transfer protein	virB3
EJ074_19440	4086011..4088461	+	2451	AZO11009	conjugal transfer protein TrbE	virb4
EJ074_19445	4088458..4089183	+	726	AZO11010	P-type conjugative transfer protein TrbJ	virB5
EJ074_19450	4089217..4090539	+	1323	AZO11011	P-type conjugative transfer protein TrbL	virB6
EJ074_19455	4090540..4091271	+	732	AZO11012	conjugal transfer protein TrbF	virB8
EJ074_19460	4091261..4092298	+	1038	AZO11013	P-type conjugative transfer protein TrbG	virB9
EJ074_19465	4092295..4093509	+	1215	AZO11014	TrbI/VirB10 family protein	virB10
EJ074_19470	4093522..4093764	+	243	AZO11015	DUF2274 domain-containing protein	-
EJ074_19475	4094000..4095349	-	1350	AZO13098	oxygen-independent coproporphyrinogen III oxidase	-
EJ074_19480	4095502..4096245	+	744	AZO11016	Crp/Fnr family transcriptional regulator	-
EJ074_19485	4096742..4098361	+	1620	AZO11017	cytochrome-c oxidase, cbb3-type subunit I	-

Host bacterium

• ID: 386
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEMsp.SymM3A
• GenBank: CP034451
• Element size: 6165597 bp
• Coordinate of oriT [Strand]: 348547..348606 [-]
• Host bacterium: Mesorhizobium sp. M3A.F.Ca.ET.080.04.2.1
• Coordinate of element: 3715425..4112178

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, nopC, nolV, nolU, nolT, nolB, nolW, nolX, fixN, fixO, fixQ, fixP, fixG, fixH, fixI, fixS
• Anti-CRISPR: -