Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116100
Name   oriT_pCf.1-1 in_silico
Organism   Citrobacter freundii strain Cf.1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OM506550 (98026..98114 [+], 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_pCf.1-1
GGGTGTCGGGGCGGAGCCCTGACCAGGTGGCATTTGTAATATCGTGCGTGCGCGGTATTACAAATGCACATCCTGTCCCGTTTTTTCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10294 GenBank   WP_048227654
Name   Relaxase_OCH92_RS00475_pCf.1-1 insolico UniProt ID   A0A8H9UN45
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 102477.49 Da        Isoelectric Point: 8.3859

>WP_048227654.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MIAVIPPKRQDGKSSFGDLVSYVSVRDEPRDDDLMEAVKASGTKPEMPHSSRFSRLVDYATKLRDESFIS
LVDVMPDGSEWVNFYGVTCFHNCTSIESAAEEMEFSARKAKFAHNKSDPVFHYILSWQSHESPRPEQIYD
SVSHTLSRLGLAGHQFVSAVHTDTDNLHVHIAVNRVHPETGYLNRLAYSQEKLSKACRELELKHGFSPDN
GCYVIAPDNRIVRRTSIERDRQSAWKRGRIQSLREYIADTAIAGLREAPVTDWSSLHQRFAKEGLFLSAD
NGELKVKDGWDSERPGVTLSAFGHAFDTEKLIRKLGEFTPPAQDIFSQVQAVGRYEPEKITVPSRPERMT
EKDTLTDYATARLRAPLIALDQDPSQRTIQSVHTLLAKSGLYLKEQHDRLVICDGYDPTRTPVRAERVWP
ALTKAVLDSYKGGWKPVPKDIFQQVPPAEQFTGGGLEATPVSDREWRKLRTGSGPQGALKREIFSDKESL
WGYAVSHCRQEIETLISSKHFSWERCHEQFAKQGLLLVREQQGLVVMDAYNREQTPVKASHVHPDLTLAR
AEPHAGSFVPVPADIFERVKPVSRYNPELAVSDRDIPGMKRDPELRRQRREARAAAREDLKARYAAWRAN
WQRPDLRGRERYQAIHDECRMRKARIRIEHRDPLVRKLYYHIVELQRMQALITLKEAMKAERAELIGQGT
WYPPSYRQWVEAEAVKGDKAAISQLRGWDYKDRRGNAVKSTTDSRCVVICEPGGTPMYSGVPGLQASLKK
NGRVQFRDPETGRHICTDYGDRVIFRNTGDYDSLKRDMVKVAPVLFSRSPTVAMAPEGNDEQFNTAFAKM
VAWHNVNHRDEAEYHIARPDVDQLRVEHEQQFTNVLNQSSYAPDAQASHQNTWEPPTPR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(53-317)


  Protein structure



No available structure.




T4CP

ID   12036 GenBank   WP_053389033
Name   trbC_OCH92_RS00455_pCf.1-1 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: 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: 52388..88837

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OCH92_RS00260 48464..48904 + 441 WP_224773767 type IV pilus biogenesis protein PilM -
OCH92_RS00265 48919..50595 + 1677 WP_048227625 PilN family type IVB pilus formation outer membrane protein -
OCH92_RS00270 50597..51901 + 1305 WP_048227626 type 4b pilus protein PilO2 -
OCH92_RS00275 51885..52385 + 501 WP_053069306 type IV pilus biogenesis protein PilP -
OCH92_RS00280 52388..53947 + 1560 WP_048227627 GspE/PulE family protein virB11
OCH92_RS00285 53940..55034 + 1095 WP_040231337 type II secretion system F family protein -
OCH92_RS00290 55048..55662 + 615 WP_052463753 type 4 pilus major pilin -
OCH92_RS00295 55747..56229 + 483 WP_069325157 lytic transglycosylase domain-containing protein virB1
OCH92_RS00300 56214..56888 + 675 WP_053389052 prepilin peptidase -
OCH92_RS00305 56885..58171 + 1287 WP_058687259 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
OCH92_RS00310 58226..58732 + 507 WP_077223963 sugar O-acetyltransferase -
OCH92_RS00315 59109..59318 - 210 WP_259408540 hypothetical protein -
OCH92_RS00320 59337..59723 - 387 Protein_63 phage tail protein -
OCH92_RS00325 60323..61483 + 1161 WP_053389050 site-specific integrase -
OCH92_RS00330 61503..61979 + 477 WP_127341066 hypothetical protein -
OCH92_RS00335 62125..62961 + 837 WP_053389049 hypothetical protein traE
OCH92_RS00340 63064..64272 + 1209 WP_053389048 conjugal transfer protein TraF -
OCH92_RS00345 64405..64878 + 474 WP_053389047 DotD/TraH family lipoprotein -
OCH92_RS00350 64875..65681 + 807 WP_053389046 type IV secretory system conjugative DNA transfer family protein traI
OCH92_RS00355 65693..66853 + 1161 WP_053389045 plasmid transfer ATPase TraJ virB11
OCH92_RS00360 66850..67137 + 288 WP_048227635 hypothetical protein traK
OCH92_RS00685 67209..70373 + 3165 Protein_72 DUF5710 domain-containing protein -
OCH92_RS00375 71714..72064 + 351 WP_053389043 hypothetical protein traL
OCH92_RS00380 72070..72771 + 702 WP_053389042 DotI/IcmL/TraM family protein traM
OCH92_RS00385 72782..73765 + 984 WP_053389041 DotH/IcmK family type IV secretion protein traN
OCH92_RS00390 73765..75081 + 1317 WP_053389040 conjugal transfer protein TraO traO
OCH92_RS00395 75065..75835 + 771 WP_048227640 conjugal transfer protein TraP traP
OCH92_RS00400 75835..76359 + 525 WP_048227641 conjugal transfer protein TraQ traQ
OCH92_RS00405 76394..76798 + 405 WP_048227642 DUF6750 family protein traR
OCH92_RS00410 76982..77713 + 732 WP_069325142 hypothetical protein traT
OCH92_RS00415 77785..80838 + 3054 WP_261452497 ATP-binding protein traU
OCH92_RS00420 81420..82622 + 1203 WP_048227644 conjugal transfer protein TraW traW
OCH92_RS00425 82619..83161 + 543 WP_094935555 conjugal transfer protein TraX -
OCH92_RS00430 83218..85380 + 2163 WP_053389037 DotA/TraY family protein traY
OCH92_RS00435 85442..86074 + 633 WP_053069310 plasmid IncI1-type surface exclusion protein ExcA -
OCH92_RS00440 86377..87585 + 1209 WP_053389036 hypothetical protein trbA
OCH92_RS00445 87638..88837 + 1200 WP_053389035 thioredoxin fold domain-containing protein trbB
OCH92_RS00450 88893..90023 - 1131 WP_053389034 RNA-guided endonuclease TnpB family protein -
OCH92_RS00455 90132..92432 + 2301 WP_053389033 F-type conjugative transfer protein TrbC -
OCH92_RS00460 92505..92774 + 270 WP_048227650 hypothetical protein -
OCH92_RS00465 92805..93599 - 795 WP_058687262 hypothetical protein -

Host bacterium

ID   16533 GenBank   NZ_OM506550
Plasmid name   pCf.1-1 Incompatibility group   IncFIB
Plasmid size   128344 bp Coordinate of oriT [Strand]   98026..98114 [+]
Host baterium   Citrobacter freundii strain Cf.1

Cargo genes

Drug resistance gene   tet(D), blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -