Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200438
Name   oriT_ICEMsp.SymM7D in_silico
Organism   Mesorhizobium sp. M7D.F.Ca.US.005.01.1.1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP034453 (51993..52052 [+], 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  


Download         Length: 60 nt

>oriT_ICEMsp.SymM7D
AAAACGATGTGCAGACAAAGATTTAACCGCCTCCTGGAGGCGGTACCTTTATCTTGCCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   17026 GenBank   AZO39816
Name   t4cp2_EJ076_00715_ICEMsp.SymM7D insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 90448.92 Da        Isoelectric Point: 5.9950

>AZO39816.1 conjugal transfer protein TrbE [Mesorhizobium sp. M7D.F.Ca.US.005.01.1.1]
MLNLSEYRSKADRLADHLPWAALVAPGIVLNKDGSFQRTLRFRGPDLESATEAELVGICARANNALRRLG
SGWALFFEAERTEALGYPNSHFPDAASWLVDEERRAAFEGKVAHYESRYHLTLVFMPPPDAQARAESTLV
DSHYSRGERDWRQDLARFRDETNRVLDLFSGFMSEVRVLDDAQTLTYLHGTISPRRHPIMAPETPIYLDA
ILVDAPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDTLNHQDFAYRWMTRFIPLEKTEATKTLTRLRR
QWFAKRKSIVAILREVITNEPVPLVDSDADNKALDADEALQALGGDHVSFGYLTTTVTVWGEDRQAAAEK
LRAVERIINGLGFTTIREGVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPATNEHLAKV
TQTEAPPLFVAETSGSTPFRLSTHVEDVGHMLVVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHALGADGSLAFQPLRSINDQASRSWAAEWIASLVAHENVTVTPEVKEAIWSALASLATAP
AQERTLTGLSVLLQSNALKTALMPYTLDGPFGRLLDADHDGLALSDVQCFETEELMHSQSALLPVLTYLF
QRLEERFDGRPTLIMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVVFATQSLADIAGSGIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLSERQIELIARATPKRQYYLQSRRGNRLFELELGPIALALCGASDPA
TQTLIDRIMSEDGQGSFASQFLIARGLDWAGELLKQFPQPDKEQFS

  Protein domains


Predicted by InterproScan.

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)

TraG P-loop domain (P-loop_TraG)

(578-732)

  Protein structure



No available structure.



ID   17027 GenBank   AZO39821
Name   t4cp2_EJ076_00740_ICEMsp.SymM7D insolico UniProt ID   _
Length   674 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 674 a.a.        Molecular weight: 74667.88 Da        Isoelectric Point: 6.6481

>AZO39821.1 conjugal transfer protein TraG [Mesorhizobium sp. M7D.F.Ca.US.005.01.1.1]
MTPTKLLIGQIAVVCAIVIIGVWTATQWCAQMLTYQTPLGAPWFLFAGWPIYKPWKLFEWWFHFDAYAPE
VFDKAGTLAGASGFLGCAAAIAGSLLRARQRGSVTTYGSSRWATTHEVETAGLLRPAGVFLGRLNDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWTGSAIIHDIKGENWQLTSGWRSKFSYCLLFNPTDPRSARYN
PLLEVRKGPDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEDKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGTGHNPQVHPVVASAARELLNKSENERSGVLSTAMSFLGLYRDPTVAAATSSCD
WRIADLVDGERPLSLYLVVPPSDISRTKPFVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRSYLIAQSLNQVSKAYGENNAILDNCHVRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPSDELVLVSGLPPIRAKKLRYYQDQNFTDRVL
PAPVLHDGPYADCPASRPDGWTGQVCSVDSRLAADEESADAPVEDEGGVQQQRHPSLPEEDVVVSQEPDQ
ADLYKPADDDSEALADKRVMDRISTAARVYGINEGRGDDVIPGF

  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: 129224..138277

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EJ076_00670 124931..125674 - 744 AZO39808 Crp/Fnr family transcriptional regulator -
EJ076_00675 125827..127176 + 1350 AZO45940 oxygen-independent coproporphyrinogen III oxidase -
EJ076_00680 127287..128633 - 1347 AZO39809 IS5 family transposase -
EJ076_00685 128969..129211 - 243 AZO39810 DUF2274 domain-containing protein -
EJ076_00690 129224..130438 - 1215 AZO39811 TrbI/VirB10 family protein virB10
EJ076_00695 130435..131472 - 1038 AZO39812 P-type conjugative transfer protein TrbG virB9
EJ076_00700 131462..132193 - 732 AZO39813 conjugal transfer protein TrbF virB8
EJ076_00705 132194..133516 - 1323 AZO39814 P-type conjugative transfer protein TrbL virB6
EJ076_00710 133550..134275 - 726 AZO39815 P-type conjugative transfer protein TrbJ virB5
EJ076_00715 134272..136722 - 2451 AZO39816 conjugal transfer protein TrbE virb4
EJ076_00720 136716..136988 - 273 AZO39817 conjugal transfer protein virB3
EJ076_00725 136988..137296 - 309 AZO39818 conjugal transfer protein TrbC virB2
EJ076_00730 137309..138277 - 969 AZO39819 P-type conjugative transfer ATPase TrbB virB11
EJ076_00735 138274..138687 - 414 AZO39820 CopG family transcriptional regulator -
EJ076_00740 138804..140828 - 2025 AZO39821 conjugal transfer protein TraG -

Host bacterium

ID   389 Element type   ICE (Integrative and conjugative element)
Element name   ICEMsp.SymM7D GenBank   CP034453
Element size   7168230 bp Coordinate of oriT [Strand]   51993..52052 [+]
Host bacterium   Mesorhizobium sp. M7D.F.Ca.US.005.01.1.1 Coordinate of element   108613..527538

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixS, fixI, fixH, fixG, fixP, fixQ, fixO, fixN, nolX, nolW, nolB, nolT, nolU, nolV, nopC, 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   AcrIIA8