Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118498
Name   oriT_FDAARGOS_549|unnamed in_silico
Organism   Citrobacter freundii strain FDAARGOS_549
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP033743 (98727..98815 [-], 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_FDAARGOS_549|unnamed
GGGTGTCGGGGCGGAGCCCTGACCAGGTGGTATTTGTAATATCGTGCGTGCGCGGTATTACAAATGCACATCCTGTCCCGCTTTTTCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11743 GenBank   WP_123924681
Name   Relaxase_EGX89_RS00575_FDAARGOS_549|unnamed insolico UniProt ID   _
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 102453.80 Da        Isoelectric Point: 8.9079

>WP_123924681.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Citrobacter]
MIPVIPPKRQDGKSSFGDLVSYVSVRDEPRDDDLMEAVKASGTKPEMPHRSRFSRLVDYATKLRDESFIS
LVDVMPDGSEWVNFYGVTCFHNCTSIESAAEEMEFSARKAKFAHNKSDPVFHYILSWQSHESPRPEQIYD
SVSHTLSRLGLAGHQFVSAVHTDTDNLHVHIAVNRVHPETGYLNRLAYSQEKLSKACRELELKHGFSPDN
GCYVIAPDNRIVRRTSIERDRQSAWKRGRIQSLREYIADTAIAGLREAPVTDWSSLHQRFAKEGLFLSAD
NGELKVKDGWNRERPGVTLSAFGHAFDTDKLIRKMGEFIPPAQDIFAQVPAVGRYEPDKIIVSSRPERMT
EKESLSDYAIARLRAPLIALDQDPSQRTIQSVHTLLAQSGLYLKEQHDRLVICDGYDPARTPVRAERVWP
ALTKAVLNSYKGGWQPVPKDIFQQVPPAEQFTSGGLEPTPVSDREWRKLRTGSGPQGALKREIFSDKESL
WGYAISHCRQEIETLISSKHFSWERCHEQFAKQGLLLVREQQGLVVMDAYNREQTPVKASHVHPDLTLAR
AEPHAGSFVPVPADIFKRIKPVSRYNPELAVSDRDIPGMKRDPELRRQRREARAAAREDLKARYAAWRAN
WQRPDLHGRERYQVIHDECRMRKARIRIEHRDPLVRKLHYHIAELQRMQALITLKEAMKAERAELIGQGK
WYPPSYRQWVEAEAVKGDKAAISQLRGWDYRDRRGNAVKATTDSRCVVICEPGGTPIYSGVPGLQASLKK
NGRVQFRDPETGRHICTDYGDRVIFRNTGDYDALKRDMIKVAPVLFSRSPTVAMAPEGNDEQFNTAFAKM
VAWHNVNHRDEGEYQISRPDVDQVRVESEIRFSETMSQVSNSEPARNEPGSSWKPPSPL

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(53-317)


  Protein structure



No available structure.




T4CP

ID   13754 GenBank   WP_123924683
Name   trbC_EGX89_RS00595_FDAARGOS_549|unnamed 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: 87182.20 Da        Isoelectric Point: 6.5154

>WP_123924683.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Citrobacter]
MNNTPVNQALMTRSAWNSPVLELMRDHLLYAGIMAGSVVAGFIWPLAIPLLLLLAIVASISFGTHRWRMP
MRMPVHLNKTDPSEDRKARRSLFSVFPSLFQYETTQESKGKGIFYIGYKRMNDIGRELWLTLDDLTRHVM
FFASTGGGKTETIYAWMLNSFCWGRGFTFVDGKAQNDTARTCYYLARRFGREDDVEYINFMNSGMSRSEM
IQNGDKSRPQSHQWNPFCYSTEAFVAETMQSMLPTNVQGGEWQSRAIAMNKALVFGTKFYCVRENKTMSL
QLLREFMPLEKLAGLYCRAVDDQWPEEAVSPLYNYLVDVPGFDMATVRQPSAWTEEPRKQHSYLTGQFLE
TFNTFTETFGNIFAEDAGDIDIRDSIHSDRILLVLIPAMNTSQHTTSALGRMFVTQQSMILARDLGHRLE
GLDSDALEITKYKGKFPYMNYLDEVGAYYTERIAVQATQVRSLDFALVMMSQDQERIENQTSAANVATLM
QNAGTKVAGKIVSDDKTARTISNAAGQEARANMVSLQRQDGLIGTSWIDGDHINIQMENKINVQDLIKLQ
PGENYTVFQGDPVPGASFYIEPQDKTCNAPVIINRYITINPPTLKHLRRLVPRTAQRRLPAPENVSRIIG
VLTEKPSRRRKAARTEPWKIIDTFQQRLANRQEAHNLMTEYDMDHRGREENLWAEALEIISTTTMAERTI
RYITLNKPESESAEVNAEDIQLAPDAILRNLTLPQPASVPPTRHRNEPLIPPKQTDSPQPDMEWPE

  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: 2335..15391

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EGX89_RS00010 (EGX89_00010) 1755..2294 - 540 WP_040231190 hypothetical protein -
EGX89_RS00015 (EGX89_00015) 2335..2622 - 288 WP_040231189 hypothetical protein traK
EGX89_RS00020 (EGX89_00020) 2619..3779 - 1161 WP_123924624 plasmid transfer ATPase TraJ virB11
EGX89_RS00025 (EGX89_00025) 3791..4597 - 807 WP_040231187 type IV secretory system conjugative DNA transfer family protein traI
EGX89_RS00030 (EGX89_00030) 4594..5067 - 474 WP_040231184 DotD/TraH family lipoprotein -
EGX89_RS00035 (EGX89_00035) 5200..6408 - 1209 WP_040231181 conjugal transfer protein TraF -
EGX89_RS00040 (EGX89_00040) 6511..7347 - 837 WP_040231179 hypothetical protein traE
EGX89_RS00045 7492..7968 - 477 WP_123924625 hypothetical protein -
EGX89_RS00050 (EGX89_00050) 7988..9148 - 1161 WP_040231242 site-specific integrase -
EGX89_RS00055 (EGX89_00055) 9881..10894 - 1014 Protein_10 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
EGX89_RS00060 (EGX89_00060) 10891..11565 - 675 WP_123924627 prepilin peptidase -
EGX89_RS00065 (EGX89_00065) 11550..12032 - 483 WP_123924696 lytic transglycosylase domain-containing protein virB1
EGX89_RS00070 (EGX89_00070) 12117..12731 - 615 WP_052463753 type 4 pilus major pilin -
EGX89_RS00075 (EGX89_00075) 12745..13839 - 1095 WP_123924697 type II secretion system F family protein -
EGX89_RS00080 (EGX89_00080) 13832..15391 - 1560 WP_040231336 GspE/PulE family protein virB11
EGX89_RS00085 (EGX89_00085) 15394..15894 - 501 WP_052463752 type IV pilus biogenesis protein PilP -
EGX89_RS00090 (EGX89_00090) 15878..17182 - 1305 WP_123924628 type 4b pilus protein PilO2 -
EGX89_RS00095 (EGX89_00095) 17184..18860 - 1677 WP_040231333 PilN family type IVB pilus formation outer membrane protein -
EGX89_RS00100 (EGX89_00100) 18875..19285 - 411 WP_228553291 type IV pilus biogenesis protein PilM -
EGX89_RS00105 (EGX89_00105) 19312..20166 - 855 WP_233609724 toxin co-regulated pilus biosynthesis Q family protein -

Region 2: 105457..124064

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EGX89_RS00580 (EGX89_00580) 101980..102213 + 234 WP_040231217 hypothetical protein -
EGX89_RS00585 (EGX89_00585) 102234..102749 + 516 WP_167335593 type II toxin-antitoxin system YafO family toxin -
EGX89_RS00590 (EGX89_00590) 102811..103080 - 270 WP_123924682 hypothetical protein -
EGX89_RS00595 (EGX89_00595) 103153..105453 - 2301 WP_123924683 F-type conjugative transfer protein TrbC -
EGX89_RS00600 (EGX89_00600) 105457..106644 - 1188 WP_123924684 hypothetical protein trbB
EGX89_RS00605 (EGX89_00605) 106697..107905 - 1209 WP_123924685 conjugal transfer protein TrbA trbA
EGX89_RS00610 (EGX89_00610) 108216..108848 - 633 WP_123924686 plasmid IncI1-type surface exclusion protein ExcA -
EGX89_RS00615 (EGX89_00615) 108910..111072 - 2163 WP_123924687 DotA/TraY family protein traY
EGX89_RS00620 (EGX89_00620) 111130..111672 - 543 WP_072041438 conjugal transfer protein TraX -
EGX89_RS00625 (EGX89_00625) 111669..112871 - 1203 WP_123924689 conjugal transfer protein TraW traW
EGX89_RS24840 112884..113453 - 570 WP_172960221 conjugal transfer protein TraV traV
EGX89_RS00630 (EGX89_00630) 113453..116506 - 3054 WP_040231206 conjugal transfer protein traU
EGX89_RS00635 (EGX89_00635) 116586..117818 + 1233 WP_123924690 hypothetical protein -
EGX89_RS00640 (EGX89_00640) 118117..118797 - 681 WP_233609727 conjugal transfer protein TraT traT
EGX89_RS00645 (EGX89_00645) 118981..119385 - 405 WP_040231201 DUF6750 family protein traR
EGX89_RS00650 (EGX89_00650) 119419..119943 - 525 WP_040231200 conjugal transfer protein TraQ traQ
EGX89_RS00655 (EGX89_00655) 119943..120716 - 774 WP_123924692 conjugal transfer protein TraP traP
EGX89_RS00660 (EGX89_00660) 120697..122013 - 1317 WP_123924693 conjugal transfer protein TraO traO
EGX89_RS00665 (EGX89_00665) 122013..122996 - 984 WP_123924694 DotH/IcmK family type IV secretion protein traN
EGX89_RS00670 (EGX89_00670) 123007..123708 - 702 WP_040231195 DotI/IcmL/TraM family protein traM
EGX89_RS00675 (EGX89_00675) 123714..124064 - 351 WP_040231192 hypothetical protein traL

Host bacterium

ID   18931 GenBank   NZ_CP033743
Plasmid name   FDAARGOS_549|unnamed Incompatibility group   -
Plasmid size   127175 bp Coordinate of oriT [Strand]   98727..98815 [-]
Host baterium   Citrobacter freundii strain FDAARGOS_549

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -