Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200358
Name   oriT_ICEMcSym1192 in_silico
Organism   Mesorhizobium ciceri strain CC1192
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP015062 (52001..52060 [+], 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_ICEMcSym1192
AAAACGATGTGCAGACAAAGATTTAACCGCCTCCTGGAGGCGGTACCTTTATCTTGCCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   16885 GenBank   AMX95308
Name   t4cp2_A4R28_20765_ICEMcSym1192 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

>AMX95308.1 conjugal transfer protein TrbE [Mesorhizobium ciceri]
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   16886 GenBank   AMX95312
Name   t4cp2_A4R28_20790_ICEMcSym1192 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

>AMX95312.1 conjugal transfer protein TraG [Mesorhizobium ciceri]
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: 4237029..4246082

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
A4R28_20720 4232736..4233479 - 744 AMX95299 transcriptional regulator -
A4R28_20725 4233632..4234981 + 1350 AMX95300 coproporphyrinogen III oxidase -
A4R28_20730 4235092..4236438 - 1347 AMX95301 transposase -
A4R28_20735 4236774..4237016 - 243 AMX95302 transposase -
A4R28_20740 4237029..4238243 - 1215 AMX95303 conjugal transfer protein TrbI virB10
A4R28_20745 4238240..4239277 - 1038 AMX95304 P-type conjugative transfer protein TrbG virB9
A4R28_20750 4239267..4239998 - 732 AMX95305 conjugal transfer protein TrbF virB8
A4R28_20755 4239999..4241321 - 1323 AMX95306 conjugal transfer protein TrbL virB6
A4R28_20760 4241355..4242080 - 726 AMX95307 conjugal transfer protein TrbJ virB5
A4R28_20765 4242077..4244527 - 2451 AMX95308 conjugal transfer protein TrbE virb4
A4R28_20770 4244521..4244793 - 273 AMX95309 conjugal transfer protein virB3
A4R28_20775 4244793..4245101 - 309 AMX95310 conjugal transfer protein TrbC virB2
A4R28_20780 4245114..4246082 - 969 AMX95311 P-type conjugative transfer ATPase TrbB virB11
A4R28_20785 4246079..4246492 - 414 AMX97330 CopG family transcriptional regulator -
A4R28_20790 4246609..4248633 - 2025 AMX95312 conjugal transfer protein TraG -

Host bacterium

ID   315 Element type   ICE (Integrative and conjugative element)
Element name   ICEMcSym1192 GenBank   CP015062
Element size   6295397 bp Coordinate of oriT [Strand]   52001..52060 [+]
Host bacterium   Mesorhizobium ciceri strain CC1192 Coordinate of element   4216410..4635338

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixI, fixH, fixG, fixP, fixQ, fixO, fixN, nolX, nolW, nolB, nolT, nolV, nopC, mlr6097, nifX, nifN, nifE, nifK, nifD, nifH, nifQ, nifS, nifW, fixA, fixB, fixC, fixX, nifB, nifZ, fixU, nodE, nodF, nodD, nodH, nodJ, nodI, nodC, nodB, nodA, mlr1025
Anti-CRISPR   AcrIIA8