Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113991
Name   oriT_pHNTS45-1 in_silico
Organism   Citrobacter freundii strain TS45CTX
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK167988 (57440..57524 [+], 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_pHNTS45-1
GGGTGTCGGGGCGGAGCCCTGACCAGGTGGTGTTTGTAATATCGTGCGCGCGCGGTATTACAAACACACATCCTGTCCCGTCTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8986 GenBank   WP_153754027
Name   Relaxase_HTV38_RS00260_pHNTS45-1 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   10422 GenBank   WP_115490298
Name   trbC_HTV38_RS00240_pHNTS45-1 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: 13970..50797

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTV38_RS00055 10046..10486 + 441 WP_233609726 type IV pilus biogenesis protein PilM -
HTV38_RS00060 10501..12177 + 1677 WP_040231333 PilN family type IVB pilus formation outer membrane protein -
HTV38_RS00065 12179..13483 + 1305 WP_153754047 type 4b pilus protein PilO2 -
HTV38_RS00070 13467..13967 + 501 WP_153754046 type IV pilus biogenesis protein PilP -
HTV38_RS00075 13970..15529 + 1560 WP_153754045 GspE/PulE family protein virB11
HTV38_RS00080 15522..16616 + 1095 WP_040231337 type II secretion system F family protein -
HTV38_RS00085 16630..17244 + 615 WP_052463753 type 4 pilus major pilin -
HTV38_RS00090 17329..17811 + 483 WP_123924696 lytic transglycosylase domain-containing protein virB1
HTV38_RS00095 17796..18470 + 675 WP_040231341 prepilin peptidase -
HTV38_RS00100 18467..19690 + 1224 WP_153754044 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HTV38_RS00105 20299..20595 - 297 WP_153754043 hypothetical protein -
HTV38_RS00110 20845..21162 - 318 WP_172694112 hypothetical protein -
HTV38_RS00115 21409..22569 + 1161 WP_228553303 site-specific integrase -
HTV38_RS00120 22589..23065 + 477 WP_123924625 hypothetical protein -
HTV38_RS00125 23210..24046 + 837 WP_040231179 hypothetical protein traE
HTV38_RS00130 24149..25357 + 1209 WP_153754042 conjugal transfer protein TraF -
HTV38_RS00135 25490..25963 + 474 WP_172694113 DotD/TraH family lipoprotein -
HTV38_RS00140 25960..26766 + 807 WP_153754041 type IV secretory system conjugative DNA transfer family protein traI
HTV38_RS00145 26778..27938 + 1161 WP_153754040 plasmid transfer ATPase TraJ virB11
HTV38_RS00150 27935..28222 + 288 WP_040231189 hypothetical protein traK
HTV38_RS00155 28251..28802 + 552 WP_172694114 hypothetical protein -
HTV38_RS00610 29164..32379 + 3216 Protein_30 LPD7 domain-containing protein -
HTV38_RS00165 33669..34028 + 360 WP_228553289 conjugal transfer protein traL
HTV38_RS00170 34025..34726 + 702 WP_040231195 DotI/IcmL/TraM family protein traM
HTV38_RS00175 34737..35720 + 984 WP_123924694 DotH/IcmK family type IV secretion protein traN
HTV38_RS00180 35720..37036 + 1317 WP_153754037 conjugal transfer protein TraO traO
HTV38_RS00185 37020..37790 + 771 WP_052463736 conjugal transfer protein TraP traP
HTV38_RS00190 37790..38314 + 525 WP_040231200 conjugal transfer protein TraQ traQ
HTV38_RS00195 38348..38752 + 405 WP_040231201 DUF6750 family protein traR
HTV38_RS00200 38936..39667 + 732 WP_228553287 conjugal transfer protein TraT traT
HTV38_RS00205 39739..42792 + 3054 WP_153754035 ATP-binding protein traU
HTV38_RS00210 43374..44576 + 1203 WP_153754033 conjugal transfer protein TraW traW
HTV38_RS00215 44573..45115 + 543 WP_153754032 conjugal transfer protein TraX -
HTV38_RS00220 45173..47332 + 2160 WP_172694115 DotA/TraY family protein traY
HTV38_RS00225 47394..48026 + 633 WP_153754030 plasmid IncI1-type surface exclusion protein ExcA -
HTV38_RS00230 48337..49545 + 1209 WP_153754029 conjugal transfer protein TrbA trbA
HTV38_RS00235 49598..50797 + 1200 WP_153754028 thioredoxin fold domain-containing protein trbB
HTV38_RS00240 50801..53101 + 2301 WP_115490298 F-type conjugative transfer protein TrbC -
HTV38_RS00245 53174..53443 + 270 WP_115490299 hypothetical protein -
HTV38_RS00250 53506..54015 - 510 WP_172694116 type II toxin-antitoxin system YafO family toxin -
HTV38_RS00255 54042..54275 - 234 WP_040231217 hypothetical protein -

Host bacterium

ID   14426 GenBank   NZ_MK167988
Plasmid name   pHNTS45-1 Incompatibility group   -
Plasmid size   114632 bp Coordinate of oriT [Strand]   57440..57524 [+]
Host baterium   Citrobacter freundii strain TS45CTX

Cargo genes

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