Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120453
Name   oriT_BIDMC108|unnamed2 in_silico
Organism   Citrobacter sp. BIDMC108
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP073009 (80618..80706 [-], 89 nt)
oriT length   89 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 89 nt

>oriT_BIDMC108|unnamed2
GGGTGTCGGGGCGGAGCCCTGACCAGGTGGCATTTGTAATATCGTGCGTGCGCGGTATTACAAATGCACATCCTGTCCCGTTTTTTCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12880 GenBank   WP_048227654
Name   Relaxase_SK40_RS26695_BIDMC108|unnamed2 insolico UniProt ID   A0A8H9UN45
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 102477.49 Da        Isoelectric Point: 8.3859

>WP_048227654.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MIAVIPPKRQDGKSSFGDLVSYVSVRDEPRDDDLMEAVKASGTKPEMPHSSRFSRLVDYATKLRDESFIS
LVDVMPDGSEWVNFYGVTCFHNCTSIESAAEEMEFSARKAKFAHNKSDPVFHYILSWQSHESPRPEQIYD
SVSHTLSRLGLAGHQFVSAVHTDTDNLHVHIAVNRVHPETGYLNRLAYSQEKLSKACRELELKHGFSPDN
GCYVIAPDNRIVRRTSIERDRQSAWKRGRIQSLREYIADTAIAGLREAPVTDWSSLHQRFAKEGLFLSAD
NGELKVKDGWDSERPGVTLSAFGHAFDTEKLIRKLGEFTPPAQDIFSQVQAVGRYEPEKITVPSRPERMT
EKDTLTDYATARLRAPLIALDQDPSQRTIQSVHTLLAKSGLYLKEQHDRLVICDGYDPTRTPVRAERVWP
ALTKAVLDSYKGGWKPVPKDIFQQVPPAEQFTGGGLEATPVSDREWRKLRTGSGPQGALKREIFSDKESL
WGYAVSHCRQEIETLISSKHFSWERCHEQFAKQGLLLVREQQGLVVMDAYNREQTPVKASHVHPDLTLAR
AEPHAGSFVPVPADIFERVKPVSRYNPELAVSDRDIPGMKRDPELRRQRREARAAAREDLKARYAAWRAN
WQRPDLRGRERYQAIHDECRMRKARIRIEHRDPLVRKLYYHIVELQRMQALITLKEAMKAERAELIGQGT
WYPPSYRQWVEAEAVKGDKAAISQLRGWDYKDRRGNAVKSTTDSRCVVICEPGGTPMYSGVPGLQASLKK
NGRVQFRDPETGRHICTDYGDRVIFRNTGDYDSLKRDMVKVAPVLFSRSPTVAMAPEGNDEQFNTAFAKM
VAWHNVNHRDEAEYHIARPDVDQLRVEHEQQFTNVLNQSSYAPDAQASHQNTWEPPTPR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(53-317)


  Protein structure



No available structure.




T4CP

ID   15129 GenBank   WP_048227649
Name   trbC_SK40_RS26755_BIDMC108|unnamed2 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 87397.54 Da        Isoelectric Point: 6.8253

>WP_048227649.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Citrobacter freundii complex]
MNNTPVNQALMKRNAWNSPVLELMRDHLLYAGIMAGSVVAGFIWPLAIPLFLLLAIVASISFGTHRWRMP
MRMPVHLNKIDPSEDRKVRRSFFRAFPSLFQYETTQESKGKGIFYIGYKRMNDIGRELWLTLDDLTRHVM
FFASTGGGKTETIYAWMLNSFCWGRGFTFVDGKAQNDTARTCYYLARRFGREDDVEYINFMNSGMSRSEM
IQNGDKSRPQSHQWNPFCYSTEAFVAETMQSMLPTNVQGGEWQSRAIAMNKALVFGTKFYCVRENKTMSL
QLLREFMPLEKLAGLYCRAVDDQWPEEAVSPLYNYLVDVPGFDMATVRQPSAWTEEPRKQHSYLTGQFLE
TFNTFTETFGNIFAEDAGDIDIRDSIHSDRILLVLIPAMNTSQHTTSALGRMFVTQQSMILARDLGHKLE
GLDSEALEITKYKGKFPYMNYLDEVGAYYTERIAVQATQVRSLEFALVMMSQDQERIENQTSAANVATLM
QNAGTKVAGKIVSDDKTARTISNAAGQEARANMVSLQRQDGLIGTSWIDGDHINIQMENKINVQDLIKLQ
PGENYTVFQGDPVPGASFYIEPQDKTCNAPVIINRYITINPPNLKQLRKLVPRTAQRRLPAAENVSKIIG
VLTEKPSRRRKAARTEPWKIIDTFQQRLANRQEAHNLMTEYDMDHGGREENLWAEALEIIRTTTMAERTI
RYITLNKPESESTEVNAEEIQLAPDAILRNLTLPQPAYVPPARHRNEPFFSPKQTSSPQPDMEWPE

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(440-527)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 96957..133417

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SK40_RS26740 92000..92557 + 558 WP_003100847 recombinase family protein -
SK40_RS26745 92636..93640 + 1005 WP_000427614 IS110-like element IS5075 family transposase -
SK40_RS26750 94311..94580 - 270 WP_048227650 hypothetical protein -
SK40_RS26755 94653..96953 - 2301 WP_048227649 F-type conjugative transfer protein TrbC -
SK40_RS26760 96957..98156 - 1200 WP_053069311 hypothetical protein trbB
SK40_RS26765 98209..99417 - 1209 WP_048227648 hypothetical protein trbA
SK40_RS26770 99720..100352 - 633 WP_053069310 plasmid IncI1-type surface exclusion protein ExcA -
SK40_RS26775 100414..102576 - 2163 WP_048227646 DotA/TraY family protein traY
SK40_RS26780 102633..103175 - 543 WP_048227645 conjugal transfer protein TraX -
SK40_RS26785 103172..104374 - 1203 WP_048227644 conjugal transfer protein TraW traW
SK40_RS26790 104387..104959 - 573 WP_156174666 conjugal transfer protein TraV traV
SK40_RS26795 104956..108009 - 3054 WP_048227643 conjugal transfer protein traU
SK40_RS26800 108081..108812 - 732 WP_069325142 hypothetical protein traT
SK40_RS26805 108996..109400 - 405 WP_048227642 DUF6750 family protein traR
SK40_RS26810 109435..109959 - 525 WP_048227641 conjugal transfer protein TraQ traQ
SK40_RS26815 109959..110732 - 774 WP_129719564 conjugal transfer protein TraP traP
SK40_RS26820 110713..112029 - 1317 WP_048227639 conjugal transfer protein TraO traO
SK40_RS26825 112029..113012 - 984 WP_048227638 DotH/IcmK family type IV secretion protein traN
SK40_RS26830 113023..113724 - 702 WP_048227637 DotI/IcmL/TraM family protein traM
SK40_RS26835 113730..114080 - 351 WP_048227636 hypothetical protein traL
SK40_RS26840 115382..118597 - 3216 Protein_116 LPD7 domain-containing protein -
SK40_RS26845 118669..118956 - 288 WP_048227635 hypothetical protein traK
SK40_RS26850 118953..120113 - 1161 WP_048227634 plasmid transfer ATPase TraJ virB11
SK40_RS26855 120125..120931 - 807 WP_048227633 type IV secretory system conjugative DNA transfer family protein traI
SK40_RS26860 120928..121401 - 474 WP_048227632 DotD/TraH family lipoprotein -
SK40_RS26865 121534..122742 - 1209 WP_048227631 conjugal transfer protein TraF -
SK40_RS26870 122845..123681 - 837 WP_048227630 hypothetical protein traE
SK40_RS26875 123827..124303 - 477 WP_127674287 hypothetical protein -
SK40_RS26880 124323..125483 - 1161 WP_048227629 site-specific integrase -
SK40_RS26885 126080..126463 + 384 Protein_125 phage tail protein -
SK40_RS26890 127073..127579 - 507 WP_077223963 sugar O-acetyltransferase -
SK40_RS26895 127634..128920 - 1287 WP_053069307 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
SK40_RS26900 128917..129591 - 675 WP_048227628 prepilin peptidase -
SK40_RS26905 129576..130058 - 483 WP_069325157 lytic transglycosylase domain-containing protein virB1
SK40_RS26910 130143..130757 - 615 WP_052463753 type 4 pilus major pilin -
SK40_RS26915 130771..131865 - 1095 WP_040231337 type II secretion system F family protein -
SK40_RS26920 131858..133417 - 1560 WP_048227627 GspE/PulE family protein virB11
SK40_RS26925 133420..133920 - 501 WP_053069306 type IV pilus biogenesis protein PilP -
SK40_RS26930 133904..135208 - 1305 WP_048227626 type 4b pilus protein PilO2 -
SK40_RS26935 135210..136886 - 1677 WP_048227625 PilN family type IVB pilus formation outer membrane protein -
SK40_RS26940 136901..137341 - 441 WP_224773767 type IV pilus biogenesis protein PilM -

Host bacterium

ID   20882 GenBank   NZ_CP073009
Plasmid name   BIDMC108|unnamed2 Incompatibility group   -
Plasmid size   142355 bp Coordinate of oriT [Strand]   80618..80706 [-]
Host baterium   Citrobacter sp. BIDMC108

Cargo genes

Drug resistance gene   blaKPC-3, aac(6')-Ib, ant(3'')-Ia, blaOXA-9, blaTEM-1A
Virulence gene   -
Metal resistance gene   arsH, merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -