Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200425
• Name: oriT_ICEMsp.SymM1A-α
• Organism: Mesorhizobium sp. M1A.F.Ca.IN.022.06.1.1
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP034455 (41769..41829 [+], 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.SymM1A-α
AAAACGATGTGCAGACAAAGATTTAACCGCCTCCTGGAGGCGGTACCTTTATCTTGCCTTA

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_EJ078_08760_ICEMsp.SymM1A-α

• ID: 17001
• GenBank: AZO63183
• Name: t4cp2_EJ078_08760_ICEMsp.SymM1A-α
• UniProt ID: _
• Length: 816 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 816 a.a.
• Molecular weight: 90160.73 Da
• Isoelectric Point: 5.9222

>AZO63183.1 conjugal transfer protein TrbE [Mesorhizobium sp. M1A.F.Ca.IN.022.06.1.1]
MLNLSEYRSKADRLADHLPWAALVAPGIVLNKDGSFQRTLRFRGPDLESATEAELVGICGRANNALRRLG
SGWALFFEAERIEALGYPNSHFPDAASWLVDEERRAAFEGKVAHYESRYHVTLVFMPPPDAQARAESALV
DSHYSQGERDWRQDLARFRDETNRVLDLFSGFMPEVRVLDDAQTLTYLHGTISPRRHPIMVPETPIYLDA
ILVDAPLAGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLEKTEATKTLTRLRR
QWFAKRKSIVAILREVITNEPVPLVDSDADNKALDADEALQALGGDHVSFGYLTTTVTVWGEDRQAAAEK
LRAVERIINGIGFTTIREGVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPATNEYLAKV
TQTEAPPLLVAETSGSTPFRLSTHVEDVGHMLAVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHALGADGSLAFQPLRSINDQASRSWAAEWIASLIAHENVTVTPEVKEAIWSALASLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADHDGLALSDVQCFETEELMHSQGALLPVLTYLF
QRLEERFDGRPTLIMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVVFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLSERQIELIARATPKRQYYLQSRRGNRLFELGLGPIALALCGASDPA
TQTLIDRILSEDGQGSFASQFLIARGLDWAGELLKQFPQPDKEQLA

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) (307-389)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (182-289)

Protein structure

No available structure.

t4cp2_EJ078_08785_ICEMsp.SymM1A-α

• ID: 17002
• GenBank: AZO59390
• Name: t4cp2_EJ078_08785_ICEMsp.SymM1A-α
• UniProt ID: _
• Length: 676 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 676 a.a.
• Molecular weight: 74790.09 Da
• Isoelectric Point: 6.7079

>AZO59390.1 conjugal transfer protein TraG [Mesorhizobium sp. M1A.F.Ca.IN.022.06.1.1]
MTPTKLLIGQIAVVCAIVIIGVWTATQWCAQMLTYQTPLGAPWFLFAGWPIYKPWKLFEWWFHFDAYAPE
VFDKAGTLAGASGFLGCAAAIAGSLLRARQRGSVTTYGSSRWATTHEVETAGLLRPAGVFLGRLNDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWTGSAIIHDIKGENWQLTSGWRSKFSYCLLFNPTDPRSARYN
PLLEVRKGPDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLQRMMTTNHLGTGHNPQVHPVVASAARELLNKSENERSGVLSTAMSFLGLYRDPTVATATSSCD
WRIADLVDGERPLSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRSYLIAQSLNQVSKAYGENNAILDNCHVRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPSDELVLVSGLPPIRAKKLRYYQDQNFTDRVL
PAPVLRDGPYADCPASRPDGWTGQVCSVDSRLAADDESADAPVEDEGGVQQQRHPSLPVEDVVVSQEPDQ
ADLLKPADDDSEALADKRVMDRISTAARAYGINEGRGDDKDVIPGF

Protein domains

Predicted by InterproScan.

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

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1773447..1782501

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
EJ078_08715	1768592..1770211	-	1620	AZO59381	cytochrome-c oxidase, cbb3-type subunit I	-
EJ078_08720	1770711..1771454	-	744	AZO59382	Crp/Fnr family transcriptional regulator	-
EJ078_08725	1771606..1772955	+	1350	AZO63181	oxygen-independent coproporphyrinogen III oxidase	-
EJ078_08730	1773192..1773434	-	243	AZO59383	DUF2274 domain-containing protein	-
EJ078_08735	1773447..1774661	-	1215	AZO59384	TrbI/VirB10 family protein	virB10
EJ078_08740	1774673..1775697	-	1025	Protein_1736	P-type conjugative transfer protein TrbG	-
EJ078_08745	1775731..1776417	-	687	Protein_1737	conjugal transfer protein TrbF	-
EJ078_08750	1776418..1777740	-	1323	AZO59385	P-type conjugative transfer protein TrbL	virB6
EJ078_08755	1777774..1778499	-	726	AZO63182	P-type conjugative transfer protein TrbJ	virB5
EJ078_08760	1778496..1780946	-	2451	AZO63183	conjugal transfer protein TrbE	virb4
EJ078_08765	1780940..1781212	-	273	AZO59386	conjugal transfer protein	virB3
EJ078_08770	1781212..1781520	-	309	AZO59387	conjugal transfer protein TrbC	virB2
EJ078_08775	1781533..1782501	-	969	AZO59388	P-type conjugative transfer ATPase TrbB	virB11
EJ078_08780	1782498..1782911	-	414	AZO59389	CopG family transcriptional regulator	-
EJ078_08785	1783028..1785058	-	2031	AZO59390	conjugal transfer protein TraG	-

Host bacterium

• ID: 379
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEMsp.SymM1A-α
• GenBank: CP034455
• Element size: 6278406 bp
• Coordinate of oriT [Strand]: 41769..41829 [+]
• Host bacterium: Mesorhizobium sp. M1A.F.Ca.IN.022.06.1.1
• Coordinate of element: 1756939..2286188

Cargo genes

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