Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106062
Name   oriT_SNU WT2|unnamed1 in_silico
Organism   Citrobacter tructae strain SNU WT2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP038468 (77554..77642 [-], 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_SNU WT2|unnamed1
GGGTGTCGGGGCGGAGCCCTGACCAGGTGGCATTTGTAATATCGTGCGTGCGCGGTATTACAAATGCACATCCTGTCCCGTTTTTTCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4069 GenBank   WP_058687263
Name   Relaxase_E4Z61_RS00505_SNU WT2|unnamed1 insolico UniProt ID   A0A4P7IYD1
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 102463.46 Da        Isoelectric Point: 8.3859

>WP_058687263.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MIAVIPPKRQDGKSSFGDLVSYVSVRDEPRDDDLMEAVKASGTKPEMPHSSRFSRLVDYATKLRDESFIS
LVDVMPDGSEWVNFYGVTCFHNCTSIESAAEEMEFSARKAKFAHNKSDPVFHYILSWQSHESPRPEQIYD
SVSHTLSRLGLAGHQFVSAVHTDTDNLHVHIAVNRVHPETGYLNRLAYSQEKLSKACRELELKHGFSPDN
GCYVIAPDNRIVRRTSIERDRQSAWKRGRIQSLREYIADTAIAGLREAPVTDWSSLHQRFAKEGLFLSAD
NGELKVKDGWDSERPGVTLSAFGHAFDTEKLIRKLGEFTPPAQDIFSQVQAVGRYEPEKITVPSRPERMT
EKDTLTDYATARLRAPLIALDQDPSQRTIQSVHTLLAKSGLYLKEQHDRLVICDGYDPTRTPVRAERVWP
ALTKAVLDSYKGGWKPVPKDIFQQVPPAEQFTGGGLEATPVSDREWRKLRTGSGPQGALKREIFSDKESL
WGYAVSHCRQEIETLISSKHFSWERCHEQFAKQGLLLVREQQGLVVMDAYNREQTPVKASHVHPDLTLAR
AEPHAGSFVPVPADIFERVKPVSRYNPELAVSDRDIPGMKRDPELRRQRREARAAAREDLKARYAAWRAN
WQRPDLRGRERYQAIHDECRMRKARIRIEHRDPLVRKLYYHIVELQRMQALITLKEAMKAERAELIGQGT
WYPPSYRQWVEAEAVKGDKAAISQLRGWDYKDRRGNAVKSTTDSRCVVICEPGGTPMYSGVPGLQASLKK
NGRVQFRDPETGRHICTDYGDRVIFRNTGDYDSLKRDMVKVAPVLFSRSPTVAMAPEGNDEQFNTAFAKM
VAWHNVNHRDEAEYHIARPDVDQVRVEHEQQFTNVLNQSSYAPDAQASHQNTWEPPTPR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(53-317)


  Protein structure


Source ID Structure
AlphaFold DB A0A4P7IYD1


T4CP

ID   4083 GenBank   WP_053389033
Name   trbC_E4Z61_RS00525_SNU WT2|unnamed1 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: 87413.54 Da        Isoelectric Point: 6.8253

>WP_053389033.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MNNTPVNQALMKRNAWNSPVLELMRDHLLYAGIMAGSVVAGFIWPLAIPLFLLLTIVASISFGTHRWRMP
MRMPVHLNKVDPSEDRKVRRSFFRAFPSLFQYETTQESKGKGIFYIGYKRMNDIGRELWLTLDDLTRHVM
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: 2463..17212

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
E4Z61_RS00010 (E4Z61_00010) 2463..2750 - 288 WP_048227635 hypothetical protein traK
E4Z61_RS00015 (E4Z61_00015) 2747..3907 - 1161 WP_053389045 plasmid transfer ATPase TraJ virB11
E4Z61_RS00020 (E4Z61_00020) 3919..4725 - 807 WP_053389046 type IV secretory system conjugative DNA transfer family protein traI
E4Z61_RS00025 (E4Z61_00025) 4722..5195 - 474 WP_053389047 DotD/TraH family lipoprotein -
E4Z61_RS00030 (E4Z61_00030) 5328..6536 - 1209 WP_053389048 conjugal transfer protein TraF -
E4Z61_RS00035 (E4Z61_00035) 6639..7475 - 837 WP_053389049 hypothetical protein traE
E4Z61_RS00040 (E4Z61_00040) 7621..8097 - 477 WP_127341066 hypothetical protein -
E4Z61_RS00045 (E4Z61_00045) 8117..9277 - 1161 WP_053389050 site-specific integrase -
E4Z61_RS00050 (E4Z61_00050) 9334..9714 + 381 Protein_9 phage tail protein -
E4Z61_RS00065 (E4Z61_00065) 10868..11374 - 507 WP_077223963 sugar O-acetyltransferase -
E4Z61_RS00070 (E4Z61_00070) 11429..12715 - 1287 WP_058687259 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
E4Z61_RS00075 (E4Z61_00075) 12712..13386 - 675 WP_053389052 prepilin peptidase -
E4Z61_RS00080 (E4Z61_00080) 13371..13853 - 483 WP_069325157 lytic transglycosylase domain-containing protein virB1
E4Z61_RS00085 (E4Z61_00085) 13938..14552 - 615 WP_052463753 type 4 pilus major pilin -
E4Z61_RS00090 (E4Z61_00090) 14566..15660 - 1095 WP_040231337 type II secretion system F family protein -
E4Z61_RS00095 (E4Z61_00095) 15653..17212 - 1560 WP_048227627 ATPase, T2SS/T4P/T4SS family virB11
E4Z61_RS00100 (E4Z61_00100) 17215..17715 - 501 WP_053069306 type IV pilus biogenesis protein PilP -
E4Z61_RS00105 (E4Z61_00105) 17699..19003 - 1305 WP_048227626 type 4b pilus protein PilO2 -
E4Z61_RS00110 (E4Z61_00110) 19005..20681 - 1677 WP_048227625 PilN family type IVB pilus formation outer membrane protein -
E4Z61_RS00115 (E4Z61_00115) 20696..21136 - 441 WP_224773767 type IV pilus biogenesis protein PilM -

Region 2: 86831..103954

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
E4Z61_RS00515 (E4Z61_00515) 82087..82863 + 777 WP_094935554 hypothetical protein -
E4Z61_RS00520 (E4Z61_00520) 82894..83163 - 270 WP_048227650 hypothetical protein -
E4Z61_RS00525 (E4Z61_00525) 83236..85536 - 2301 WP_053389033 F-type conjugative transfer protein TrbC -
E4Z61_RS00530 (E4Z61_00530) 85645..86775 + 1131 WP_058687261 RNA-guided endonuclease TnpB family protein -
E4Z61_RS00535 (E4Z61_00535) 86831..88030 - 1200 WP_053389035 thioredoxin fold domain-containing protein trbB
E4Z61_RS00540 (E4Z61_00540) 88083..89291 - 1209 WP_053389036 hypothetical protein trbA
E4Z61_RS00545 (E4Z61_00545) 89594..90226 - 633 WP_053069310 plasmid IncI1-type surface exclusion protein ExcA -
E4Z61_RS00550 (E4Z61_00550) 90288..92450 - 2163 WP_053389037 DotA/TraY family protein traY
E4Z61_RS00555 (E4Z61_00555) 92507..93049 - 543 WP_094935555 conjugal transfer protein TraX -
E4Z61_RS00560 (E4Z61_00560) 93046..94248 - 1203 WP_048227644 conjugal transfer protein TraW traW
E4Z61_RS23795 94261..94833 - 573 WP_161556285 conjugal transfer protein TraV traV
E4Z61_RS00565 (E4Z61_00565) 94830..97883 - 3054 WP_053389039 conjugal transfer protein traU
E4Z61_RS00570 (E4Z61_00570) 97955..98686 - 732 WP_069325142 hypothetical protein traT
E4Z61_RS00575 (E4Z61_00575) 98870..99274 - 405 WP_048227642 DUF6750 family protein traR
E4Z61_RS00580 (E4Z61_00580) 99309..99833 - 525 WP_048227641 conjugal transfer protein TraQ traQ
E4Z61_RS00585 (E4Z61_00585) 99833..100603 - 771 WP_048227640 conjugal transfer protein TraP traP
E4Z61_RS00590 (E4Z61_00590) 100587..101903 - 1317 WP_053389040 conjugal transfer protein TraO traO
E4Z61_RS00595 (E4Z61_00595) 101903..102886 - 984 WP_053389041 DotH/IcmK family type IV secretion protein traN
E4Z61_RS00600 (E4Z61_00600) 102897..103514 - 618 WP_227525330 DotI/IcmL/TraM family protein traM
E4Z61_RS00605 (E4Z61_00605) 103604..103954 - 351 WP_053389043 hypothetical protein traL

Host bacterium

ID   6499 GenBank   NZ_CP038468
Plasmid name   SNU WT2|unnamed1 Incompatibility group   -
Plasmid size   106068 bp Coordinate of oriT [Strand]   77554..77642 [-]
Host baterium   Citrobacter tructae strain SNU WT2

Cargo genes

Drug resistance gene   aph(3')-Ia, sul2, aph(3'')-Ib, aph(6)-Id, floR, tet(D)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -