Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106954
Name   oriT_pYRW13-125 in_silico
Organism   Yokenella regensburgei strain W13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050812 (78291..78377 [-], 87 nt)
oriT length   87 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 87 nt

>oriT_pYRW13-125
GGGTGTCGGGGCGGAGCCCTGACCAGGTGGCATTTGTGATATCGTGCGTGCGCGGTATTACAAATGCACATCCTGTCCCGTCTTTCG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4595 GenBank   WP_022650008
Name   Relaxase_HEC60_RS24470_pYRW13-125 insolico UniProt ID   A0A4Q2QTK9
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 102314.37 Da        Isoelectric Point: 8.2756

>WP_022650008.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacterales]
MIPVIPPKRQDGKSSFGDLVSYVSVRDEPRDDDLMEAVRASGTKPEMPHSSRFSRLVDYATKLRDESFIS
LVDVMPDGGEWVNFYGVTCFHNCTSIESAAEEMEFSARKTKFAHNKSDPVFHYILSWQSHESPRPEQIYD
SVSHTLSRLGLAGHQFVAAVHTDTDNLHVHIAVNRVHPETGYLNRLAYSQEKLSKACRELELKHGFSPDN
GCYVIAPDNRIVRRTSVERDRQSAWKRGRNQSLREYIADTAIAGLRESPVTDWSSLHQRFAKEGLFLTKE
SGELKVKDGWDSERPGVTLSAFGHAFDTDKLIRKLGEFVPPVQDIFSQVPAVGRYEPDKIIMPSRPERMT
EKESLSDYAIARLRAPLIALDQDPTQRTIQSVHTLLAQSGLYLKEQHDRLVICDGYDSTRTPVRAERVWP
ALTKAILDSYKGGWQPVPKDIFQQVPPAEQFTGGSLEATPVSDREWRKLRTGSGPQGALKREIFSDKESL
WGYAVSHCRQDIESLIGSGEFTWERCHELLARQGLLLMREQQGLVVMDAYNHEQTPVKASHVHPDLTLAR
AEPHAGSFVSVPADIFERVKPASRYNPELAVSDRDIPGMKRDPELRRQRREARAAAREDLKARYAAWRAN
WQRPDLHGRERYQAIHDECRIRKARIRIEHRDPLVRKLHYHIAELQRMQALIALKETMKAERAELIGQGK
WYPPSYRQWVEAEAVKGDKAAISQLRGWDYRDRRGNAVKSTTDNRCVVICEPGGTPMYSGVPGLRASLKK
NGRVQFRDPETGRHICTDYGDRVIFRNSGDYDALKRDMVKVAPVLFSRSPSVAMAPEGNNEQFNTAFAKM
VAWHNVNHRDEGEYQISRPEVDQVRVESEMRFAEMTNQGSNTEAVRNESGPNWKPPSPL

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(51-317)


  Protein structure


Source ID Structure
AlphaFold DB A0A4Q2QTK9


T4CP

ID   4691 GenBank   WP_022650006
Name   trbC_HEC60_RS24485_pYRW13-125 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: 87660.94 Da        Isoelectric Point: 6.8660

>WP_022650006.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacterales]
MNYTPVNQALMKRNAWNSPVLELLRDHLLYAGIMAGSVVAGFIWPLAIPLLLLLAIVASISFGTHRWRMP
MRMPVHLNKVDPSEDRKVRRSLFRRFPSLFQYETTQESKGKGIFYLGYRRMNDIGRELWLTIDDLTRHVM
FFASTGGGKTETIYAWMLNSFCWGRGFTFVDGKAQNDTARTCYYLARRFGREDDVEYINFMNSGMSRSEM
IHNGDKSRPQSHQWNPFCYSTEAFVAETMQSMLPTNVQGGEWQSRAIAMNKALVFGTKFYCVRENKTMSL
QLLREFMPLEKLAELYCRAIDDQWPEEAVSPLYNYLVDVPGFDMATVRQPSAWTEEPRKQHSYLTGQFLE
TFNTFTETFGNIFAEDAGDIDIRDSIHSDRILLVLIPAMNTSQHTTSALGRMFVTQQSMILARDLGHRLE
GLDSEALEITKYKGPFPYMNYLDEVGAYYTERIAVQATQVRSLDFSIVMMSQDQERIESQTSATNVATLM
QNAGTKVAGKIVSDDKTAKTITNAAGQEARANMVSLQRRDGIIGTSWIDGDHINIQMENKINVQDLIKLQ
PGENYTVFQGDPVPGASFYIEPQDKTCNAPVIINRYITINPPNLKQLRKLVPRTAQRRLPAPENVSKIIG
VLTEKPSRRRKAAKAEPWKIIDTFQQRLANRQEAHNLMTEYDTDHRGREENLWEEALEVIRTTTMAERTI
RYITLNKPESEPTQVSAEEIQLAPDAILRTLTLPQPAYIPPSRYRNEPFISPKLPDSPHPDMEWPE

  Protein domains


Predicted by InterproScan.

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

(440-528)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 84500..118907

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HEC60_RS24475 (HEC60_24475) 81516..81719 - 204 WP_123839396 hypothetical protein -
HEC60_RS24480 (HEC60_24480) 81853..82122 - 270 WP_022650007 hypothetical protein -
HEC60_RS24485 (HEC60_24485) 82196..84496 - 2301 WP_022650006 F-type conjugative transfer protein TrbC -
HEC60_RS24490 (HEC60_24490) 84500..85756 - 1257 WP_126530067 hypothetical protein trbB
HEC60_RS24495 (HEC60_24495) 85737..86945 - 1209 WP_022650004 hypothetical protein trbA
HEC60_RS24500 (HEC60_24500) 87266..87898 - 633 WP_022650003 plasmid IncI1-type surface exclusion protein ExcA -
HEC60_RS24505 (HEC60_24505) 87960..90119 - 2160 WP_022650002 DotA/TraY family protein traY
HEC60_RS24510 (HEC60_24510) 90177..90719 - 543 WP_022650001 conjugal transfer protein TraX -
HEC60_RS24515 (HEC60_24515) 90716..91918 - 1203 WP_022650000 conjugal transfer protein TraW traW
HEC60_RS24520 (HEC60_24520) 91931..92503 - 573 WP_154590113 conjugal transfer protein TraV traV
HEC60_RS24525 (HEC60_24525) 92500..94575 - 2076 WP_280823395 hypothetical protein traU
HEC60_RS26005 94572..95516 - 945 WP_280823397 hypothetical protein traU
HEC60_RS24530 (HEC60_24530) 95603..96328 - 726 WP_063864836 hypothetical protein traT
HEC60_RS24535 (HEC60_24535) 96512..96916 - 405 WP_022649996 DUF6750 family protein traR
HEC60_RS24540 (HEC60_24540) 96951..97475 - 525 WP_022649995 conjugal transfer protein TraQ traQ
HEC60_RS24545 (HEC60_24545) 97475..98248 - 774 WP_123839398 conjugal transfer protein TraP traP
HEC60_RS24550 (HEC60_24550) 98229..99536 - 1308 WP_022649993 conjugal transfer protein TraO traO
HEC60_RS24555 (HEC60_24555) 99536..100516 - 981 WP_022649992 DotH/IcmK family type IV secretion protein traN
HEC60_RS24560 (HEC60_24560) 100527..101144 - 618 WP_179297403 DotI/IcmL family type IV secretion protein traM
HEC60_RS24565 (HEC60_24565) 101234..101584 - 351 WP_022649990 hypothetical protein traL
HEC60_RS24570 (HEC60_24570) 101602..105144 - 3543 WP_032635082 LPD7 domain-containing protein -
HEC60_RS24575 (HEC60_24575) 105216..105503 - 288 WP_022649988 hypothetical protein traK
HEC60_RS24580 (HEC60_24580) 105500..106660 - 1161 WP_022649987 plasmid transfer ATPase TraJ virB11
HEC60_RS24585 (HEC60_24585) 106673..107479 - 807 WP_022649986 type IV secretory system conjugative DNA transfer family protein traI
HEC60_RS24590 (HEC60_24590) 107476..107949 - 474 WP_022649985 DotD/TraH family lipoprotein -
HEC60_RS24595 (HEC60_24595) 108020..108436 - 417 WP_123839394 hypothetical protein -
HEC60_RS24600 (HEC60_24600) 108545..109750 - 1206 WP_022649984 conjugal transfer protein TraF -
HEC60_RS24605 (HEC60_24605) 109856..110692 - 837 WP_022649983 hypothetical protein traE
HEC60_RS24610 (HEC60_24610) 110839..111315 - 477 WP_022649982 hypothetical protein -
HEC60_RS24615 (HEC60_24615) 111335..112495 - 1161 WP_022649981 site-specific integrase -
HEC60_RS24620 (HEC60_24620) 113076..114410 - 1335 WP_032627586 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HEC60_RS24625 (HEC60_24625) 114407..115081 - 675 WP_022649979 prepilin peptidase -
HEC60_RS24630 (HEC60_24630) 115066..115548 - 483 WP_045261878 lytic transglycosylase domain-containing protein virB1
HEC60_RS24635 (HEC60_24635) 115633..116247 - 615 WP_022649977 type 4 pilus major pilin -
HEC60_RS24640 (HEC60_24640) 116261..117355 - 1095 WP_032623575 type II secretion system F family protein -
HEC60_RS24645 (HEC60_24645) 117348..118907 - 1560 WP_022649975 ATPase, T2SS/T4P/T4SS family virB11
HEC60_RS24650 (HEC60_24650) 118910..119425 - 516 WP_022649974 type IV pilus biogenesis protein PilP -
HEC60_RS24655 (HEC60_24655) 119409..120713 - 1305 WP_022649973 type 4b pilus protein PilO2 -
HEC60_RS24660 (HEC60_24660) 120715..122391 - 1677 WP_022649972 PilN family type IVB pilus formation outer membrane protein -
HEC60_RS24665 (HEC60_24665) 122406..122843 - 438 WP_022649971 type IV pilus biogenesis protein PilM -
HEC60_RS25820 122843..123535 - 693 WP_245248639 toxin co-regulated pilus biosynthesis Q family protein -

Host bacterium

ID   7391 GenBank   NZ_CP050812
Plasmid name   pYRW13-125 Incompatibility group   -
Plasmid size   125281 bp Coordinate of oriT [Strand]   78291..78377 [-]
Host baterium   Yokenella regensburgei strain W13

Cargo genes

Drug resistance gene   sul2, floR, dfrA14, ant(3'')-Ia, blaOXA-10, cmlA1, ARR-3, tet(A), blaLAP-2, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIC1, AcrIIA7