Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200436
Name   oriT_ICEMsp.SymM4B in_silico
Organism   Mesorhizobium sp. M4B.F.Ca.ET.058.02.1.1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP034450 (481531..481590 [-], 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.SymM4B
AAAACGATGTGCAGACAAAGATTTAACCGCCTCCTGGAGGCGGTACCTTTATCTTGCCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   17022 GenBank   AZO50446
Name   t4cp2_EJ073_24050_ICEMsp.SymM4B 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: 74605.81 Da        Isoelectric Point: 6.6481

>AZO50446.1 conjugal transfer protein TraG [Mesorhizobium sp. M4B.F.Ca.ET.058.02.1.1]
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.



ID   17023 GenBank   AZO50451
Name   t4cp2_EJ073_24075_ICEMsp.SymM4B 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: 90415.89 Da        Isoelectric Point: 5.9950

>AZO50451.1 conjugal transfer protein TrbE [Mesorhizobium sp. M4B.F.Ca.ET.058.02.1.1]
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: 4961746..4970798

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EJ073_24050 4959195..4961219 + 2025 AZO50446 conjugal transfer protein TraG -
EJ073_24055 4961336..4961749 + 414 AZO50447 CopG family transcriptional regulator -
EJ073_24060 4961746..4962714 + 969 AZO50448 P-type conjugative transfer ATPase TrbB virB11
EJ073_24065 4962727..4963035 + 309 AZO50449 conjugal transfer protein TrbC virB2
EJ073_24070 4963035..4963307 + 273 AZO50450 conjugal transfer protein virB3
EJ073_24075 4963301..4965751 + 2451 AZO50451 conjugal transfer protein TrbE virb4
EJ073_24080 4965748..4966473 + 726 AZO50452 P-type conjugative transfer protein TrbJ virB5
EJ073_24085 4966507..4967829 + 1323 AZO50453 P-type conjugative transfer protein TrbL virB6
EJ073_24090 4967830..4969587 + 1758 AZO50454 P-type conjugative transfer protein TrbG virB9
EJ073_24095 4969584..4970798 + 1215 AZO50455 TrbI/VirB10 family protein virB10
EJ073_24100 4970811..4971053 + 243 AZO50456 DUF2274 domain-containing protein -
EJ073_24105 4971289..4972638 - 1350 AZO52033 oxygen-independent coproporphyrinogen III oxidase -
EJ073_24110 4972791..4973534 + 744 AZO50457 Crp/Fnr family transcriptional regulator -
EJ073_24115 4974031..4975650 + 1620 AZO50458 cytochrome-c oxidase, cbb3-type subunit I -

Host bacterium

ID   387 Element type   ICE (Integrative and conjugative element)
Element name   ICEMsp.SymM4B GenBank   CP034450
Element size   6461656 bp Coordinate of oriT [Strand]   481531..481590 [-]
Host bacterium   Mesorhizobium sp. M4B.F.Ca.ET.058.02.1.1 Coordinate of element   4459725..4989466

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, mlr1025, nolV, nolU, nolT, nolB, nolW, nodX, fixN, fixO, fixQ, fixP, fixG, fixH, fixI, fixS
Anti-CRISPR   AcrIIA7