Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114427
Name   oriT_pS40-1 in_silico
Organism   Citrobacter sp. S40-1-2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP045841 (57652..57736 [-], 85 nt)
oriT length   85 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 85 nt

>oriT_pS40-1
GGGTGTCGGGGCGGAGCCCTGACCAGGTGGTGTTTGTAATATCGTGCGCGCGCGGTATTACAAACACACATCCTGTCCCGTCTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9248 GenBank   WP_153754027
Name   Relaxase_GHC23_RS23820_pS40-1 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: 102404.56 Da        Isoelectric Point: 8.8125

>WP_153754027.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Citrobacter]
MIPVIPPKRQDGKSSFGDLVSYVSVRDEPRDDDLMDAVKASGTRPEMPHSSRFSRLVDYATKLRDESFIS
LVDVMPDGGEWVNFYGVTCFHNCTSIETAAEEMEFTARQAKHSRSNSDPVFHYLLSWQSHESPRPEQVYD
SVRHSLKRLGMGDHQFVAAIHTDTDNLHVHVAVNRVHPGTGYLNWLSYSQEKLHKACRELELKHGFAPDN
GCYVIAPDNRIVRRTSVERDRQSAWTRGRNQSLKEYVADTAIASLRESPVTGWSSLHQRFAKEGLFLSAD
NGELKVKDGWNRERPGVTLSAFGHAFDTDKLIRKMGEFIPPAQDIFAQVPAVGRYEPDKIIVSSRPERMT
EKESLSDYAIARLRAPLIALDQDPSQRTIQSVHTLLAQSGLYLKEQHDRLVICDGYDPTRTPVRAERVWP
ALTKAVLNSYKGGWQPVPKDIFQQVPPAEQFTGGGLEPTPVSDREWRKLRTGSGPQGALKREIFSDKESL
WGYAISHCRQEIETLISSKHFSWERCHEQFAKQGLLLVREQQGLVVMDAYNREQTPVKASHVHPDLTLAR
AEPHAGSFVPVPADIFKRIKPVSRYNPELAVSDRDIPGMKRDPELRRQRREARAAAREDLKARYAAWRAN
WQRPDLHGRERYQVIHDECRIRKARIRIEHRDPLVRKLHYHIAELQRMQALITLKEAMKAERAELIGQGK
WYPPSYRQWVEAEAVKGDKAAISQLRGWDYRDRRGNAVKATTDSRCVVICEPGGTPIYSGVPGLQASLKK
NGRVQFRDPETGRHICTDYGDRVIFRNTGDYDALKRDMIKVAPVLFSRSPTVAMAPEGNDEQFNTAFAKM
VAWHNVNHRDEGEYQISRPDVDQVRVESEIRFSETMSQVSNSEPARNEPGSSWKPPSPL

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(51-317)


  Protein structure



No available structure.




T4CP

ID   10717 GenBank   WP_115490298
Name   trbC_GHC23_RS23840_pS40-1 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: 87341.52 Da        Isoelectric Point: 6.7428

>WP_115490298.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Citrobacter]
MNNTPVNQALMKRNAWNSPVLELMRDHLLYAGIMAGSVVAGFIWPLAIPLFLLLAIVASISFGTHRWRMP
MRMPVHLNKVDPSEDRKVRRSFFRAFPSLFQYETTQESKGKGIFYIGYKRMNDIGRELWLTLDDLTRHVM
FFASTGGGKTETIYAWMLNSFCWGRGFTFVDGKAQNDTARTCYYLARRFGREDDVEYINFMNSGMSRSEM
IQNGDKSRPQSHQWNPFCYSTEAFVAETMQSMLPTNVQGGEWQSRAIAMNKALVFGTKFYCVRENKTMSL
QLLREFMPLEKLAGLYCRAVDDQWPEEAVSPLYNYLVDVPGFDMATVRQPSAWTEEPRKQHSYLTGQFLE
TFNTFTETFGNIFAEDAGDIDIRDSIHSDRILLVLIPAMNTSQHTTSALGRMFVTQQSMILARDLGHKLE
GLDSEALEITKYKGKFPYMNYLDEVGAYYTERIAVQATQVRSLEFALVMMSQDQERIENQTSAANVATLM
QNAGTKIAGKIVSDDKTAKTISNAAGQEARANMVSLQRQEGIIGTSWIDGDHINIQMENKINVQDLIKLQ
PGENYTVFQGDPVPGASFYIEPQDKTCNAPVIINRYITINPPTLKHLRRLVPRTAQRRLPAPENVSRIIG
VLTEKPSRRRKAARTEPWKIIDTFQQRLANRQEAHNLMTEYDMDHRGREENLWAEALEIISTTTMAERTI
RYITLNKPESESAEVNAEDIQLAPDAILRNLTLPQPASVPPARHRNEPLIPPKQTDSPQPDMEWPE

  Protein domains


Predicted by InterproScan.

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

(440-525)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 64379..101206

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GHC23_RS23825 60901..61134 + 234 WP_040231217 hypothetical protein -
GHC23_RS23830 61155..61670 + 516 WP_167335593 type II toxin-antitoxin system YafO family toxin -
GHC23_RS23835 61733..62002 - 270 WP_115490299 hypothetical protein -
GHC23_RS23840 62075..64375 - 2301 WP_115490298 F-type conjugative transfer protein TrbC -
GHC23_RS23845 64379..65578 - 1200 WP_153754028 thioredoxin fold domain-containing protein trbB
GHC23_RS23850 65631..66839 - 1209 WP_153754029 conjugal transfer protein TrbA trbA
GHC23_RS23855 67150..67782 - 633 WP_153754030 plasmid IncI1-type surface exclusion protein ExcA -
GHC23_RS23860 67844..70003 - 2160 WP_153754031 DotA/TraY family protein traY
GHC23_RS23865 70061..70603 - 543 WP_153754032 conjugal transfer protein TraX -
GHC23_RS23870 70600..71802 - 1203 WP_153754033 conjugal transfer protein TraW traW
GHC23_RS23875 71815..72387 - 573 WP_153754034 conjugal transfer protein TraV traV
GHC23_RS23880 72384..75437 - 3054 WP_153754035 ATP-binding protein traU
GHC23_RS23885 75509..76240 - 732 WP_228553287 conjugal transfer protein TraT traT
GHC23_RS23890 76424..76828 - 405 WP_040231201 DUF6750 family protein traR
GHC23_RS23895 76862..77386 - 525 WP_040231200 conjugal transfer protein TraQ traQ
GHC23_RS23900 77386..78159 - 774 WP_153754036 conjugal transfer protein TraP traP
GHC23_RS23905 78140..79456 - 1317 WP_153754037 conjugal transfer protein TraO traO
GHC23_RS23910 79456..80439 - 984 WP_123924694 DotH/IcmK family type IV secretion protein traN
GHC23_RS23915 80450..81151 - 702 WP_040231195 DotI/IcmL/TraM family protein traM
GHC23_RS23920 81148..81507 - 360 WP_228553289 conjugal transfer protein traL
GHC23_RS24780 81525..83402 - 1878 WP_228553301 LPD7 domain-containing protein -
GHC23_RS24785 84780..86012 - 1233 Protein_90 DUF5710 domain-containing protein -
GHC23_RS23930 86374..86913 - 540 WP_153754039 hypothetical protein -
GHC23_RS23935 86954..87241 - 288 WP_040231189 hypothetical protein traK
GHC23_RS23940 87238..88398 - 1161 WP_153754040 plasmid transfer ATPase TraJ virB11
GHC23_RS23945 88410..89216 - 807 WP_153754041 type IV secretory system conjugative DNA transfer family protein traI
GHC23_RS23950 89213..89686 - 474 WP_040231184 DotD/TraH family lipoprotein -
GHC23_RS23955 89819..91027 - 1209 WP_153754042 conjugal transfer protein TraF -
GHC23_RS23960 91130..91966 - 837 WP_040231179 hypothetical protein traE
GHC23_RS23965 92111..92587 - 477 WP_123924625 hypothetical protein -
GHC23_RS23970 92607..93767 - 1161 WP_228553303 site-specific integrase -
GHC23_RS23975 94352..94648 + 297 WP_153754043 hypothetical protein -
GHC23_RS23980 95486..96709 - 1224 WP_153754044 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
GHC23_RS23985 96706..97380 - 675 WP_040231341 prepilin peptidase -
GHC23_RS23990 97365..97847 - 483 WP_123924696 lytic transglycosylase domain-containing protein virB1
GHC23_RS23995 97932..98546 - 615 WP_052463753 type 4 pilus major pilin -
GHC23_RS24000 98560..99654 - 1095 WP_040231337 type II secretion system F family protein -
GHC23_RS24005 99647..101206 - 1560 WP_153754045 GspE/PulE family protein virB11
GHC23_RS24010 101209..101709 - 501 WP_153754046 type IV pilus biogenesis protein PilP -
GHC23_RS24015 101693..102997 - 1305 WP_153754047 type 4b pilus protein PilO2 -
GHC23_RS24020 102999..104675 - 1677 WP_040231333 PilN family type IVB pilus formation outer membrane protein -
GHC23_RS24025 104690..105100 - 411 WP_228553291 type IV pilus biogenesis protein PilM -

Host bacterium

ID   14862 GenBank   NZ_CP045841
Plasmid name   pS40-1 Incompatibility group   -
Plasmid size   110138 bp Coordinate of oriT [Strand]   57652..57736 [-]
Host baterium   Citrobacter sp. S40-1-2

Cargo genes

Drug resistance gene   blaCTX-M-14, fosA3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -