Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200439
• Name: oriT_ICEMsp.SymM8A
• Organism: Mesorhizobium sp. M8A.F.Ca.ET.057.01.1.1
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP034454 (362568..362627 [-], 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.SymM8A
AAAACGATGTGCAGACAAAGATTTAACCGCCTCCTGGAGGCGGTACCTTTATCTTGCCTT

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_EJ077_02350_ICEMsp.SymM8A

• ID: 17028
• GenBank: AZO52463
• Name: t4cp2_EJ077_02350_ICEMsp.SymM8A
• 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

>AZO52463.1 conjugal transfer protein TraG [Mesorhizobium sp. M8A.F.Ca.ET.057.01.1.1]
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_EJ077_02375_ICEMsp.SymM8A

• ID: 17029
• GenBank: AZO52468
• Name: t4cp2_EJ077_02375_ICEMsp.SymM8A
• 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

>AZO52468.1 conjugal transfer protein TrbE [Mesorhizobium sp. M8A.F.Ca.ET.057.01.1.1]
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: 535997..545049

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
EJ077_02350	533446..535470	+	2025	AZO52463	conjugal transfer protein TraG	-
EJ077_02355	535587..536000	+	414	AZO52464	CopG family transcriptional regulator	-
EJ077_02360	535997..536965	+	969	AZO52465	P-type conjugative transfer ATPase TrbB	virB11
EJ077_02365	536978..537286	+	309	AZO52466	conjugal transfer protein TrbC	virB2
EJ077_02370	537286..537558	+	273	AZO52467	conjugal transfer protein	virB3
EJ077_02375	537552..540002	+	2451	AZO52468	conjugal transfer protein TrbE	virb4
EJ077_02380	539999..540724	+	726	AZO52469	P-type conjugative transfer protein TrbJ	virB5
EJ077_02385	540758..542080	+	1323	AZO52470	P-type conjugative transfer protein TrbL	virB6
EJ077_02390	542081..543838	+	1758	AZO52471	P-type conjugative transfer protein TrbG	virB9
EJ077_02395	543835..545049	+	1215	AZO52472	TrbI/VirB10 family protein	virB10
EJ077_02400	545062..545304	+	243	AZO52473	DUF2274 domain-containing protein	-
EJ077_02405	545540..546889	-	1350	AZO57542	oxygen-independent coproporphyrinogen III oxidase	-
EJ077_02410	547042..547785	+	744	AZO52474	Crp/Fnr family transcriptional regulator	-
EJ077_02415	548282..549901	+	1620	AZO52475	cytochrome-c oxidase, cbb3-type subunit I	-

Host bacterium

• ID: 390
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEMsp.SymM8A
• GenBank: CP034454
• Element size: 6629336 bp
• Coordinate of oriT [Strand]: 362568..362627 [-]
• Host bacterium: Mesorhizobium sp. M8A.F.Ca.ET.057.01.1.1
• Coordinate of element: 152947..563716

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, nolT, nolB, nolW, nodX, fixN, fixO, fixQ, fixP, fixG, fixH, fixI, fixS
• Anti-CRISPR: -