Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200426
• Name: oriT_ICEMsp.SymM1B
• Organism: Mesorhizobium sp. M1B.F.Ca.ET.045.04.1.1
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP034448 (303023..303082 [-], 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.SymM1B
AAAACGATGTGCAGACAAAGATTTAACCGCCTCCTGGAGGCGGTACCTTTATCTTGCCTT

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_EJ071_07745_ICEMsp.SymM1B

• ID: 17003
• GenBank: AZO27325
• Name: t4cp2_EJ071_07745_ICEMsp.SymM1B
• 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

>AZO27325.1 conjugal transfer protein TraG [Mesorhizobium sp. M1B.F.Ca.ET.045.04.1.1]
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_EJ071_07770_ICEMsp.SymM1B

• ID: 17004
• GenBank: AZO32667
• Name: t4cp2_EJ071_07770_ICEMsp.SymM1B
• 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

>AZO32667.1 conjugal transfer protein TrbE [Mesorhizobium sp. M1B.F.Ca.ET.045.04.1.1]
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: 1596157..1605210

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
EJ071_07745	1593606..1595630	+	2025	AZO27325	conjugal transfer protein TraG	-
EJ071_07750	1595747..1596160	+	414	AZO27326	CopG family transcriptional regulator	-
EJ071_07755	1596157..1597125	+	969	AZO27327	P-type conjugative transfer ATPase TrbB	virB11
EJ071_07760	1597138..1597446	+	309	AZO27328	conjugal transfer protein TrbC	virB2
EJ071_07765	1597446..1597718	+	273	AZO27329	conjugal transfer protein	virB3
EJ071_07770	1597712..1600162	+	2451	AZO32667	conjugal transfer protein TrbE	virb4
EJ071_07775	1600159..1600884	+	726	AZO27330	P-type conjugative transfer protein TrbJ	virB5
EJ071_07780	1600918..1602240	+	1323	AZO27331	P-type conjugative transfer protein TrbL	virB6
EJ071_07785	1602241..1602972	+	732	AZO27332	conjugal transfer protein TrbF	virB8
EJ071_07790	1602962..1603999	+	1038	AZO27333	P-type conjugative transfer protein TrbG	virB9
EJ071_07795	1603996..1605210	+	1215	AZO27334	TrbI/VirB10 family protein	virB10
EJ071_07800	1605223..1605465	+	243	AZO27335	DUF2274 domain-containing protein	-
EJ071_07805	1605701..1607050	-	1350	AZO32668	oxygen-independent coproporphyrinogen III oxidase	-
EJ071_07810	1607203..1607946	+	744	AZO27336	Crp/Fnr family transcriptional regulator	-
EJ071_07815	1608443..1610062	+	1620	AZO27337	cytochrome-c oxidase, cbb3-type subunit I	-

Host bacterium

• ID: 380
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEMsp.SymM1B
• GenBank: CP034448
• Element size: 7779814 bp
• Coordinate of oriT [Strand]: 303023..303082 [-]
• Host bacterium: Mesorhizobium sp. M1B.F.Ca.ET.045.04.1.1
• Coordinate of element: 1272644..1623878

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: -