Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101706
Name   oriT_pRHBSTW-00231_3 in_silico
Organism   Citrobacter freundii strain RHBSTW-00231
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXQP010000003 (30686..31300 [-], 615 nt)
oriT length   615 nt
IRs (inverted repeats)      589..594, 599..604  (ATGCCC..GGGCAT)
 517..524, 528..535  (CCTCCCGT..ACGGGAGG)
 275..280, 283..288  (ACGTCA..TGACGT)
 32..37, 46..51  (TGATAA..TTATCA)
Location of nic site      314..315
Conserved sequence flanking the
  nic site    		  TCCTGCATCG
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 615 nt

>oriT_pRHBSTW-00231_3
CTTTGCTTAGCTGTTAAATATAGCGTTGTTTTGATAAAATCATCATTATCATCATTGATGTTTTCTTCTGTTTCTTTACTCTTACTTTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGACATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAACTTTTTTCATAATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCAAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTTAACCATGCCACAACCGAAATTGTGCTTCAGGTTGAACTGAAATGCAAAATCGTAAGGGCTTTGCTGCTGAAAGATTGATAGTATTCGACCGTTAACAAATGAATTGCTATAAGCTCTGTGCGGGGCTGTTCGCTTCGCGAATGGGTCTAGCAGGGGGCGCAAGCGCTGTCCTGCGCTATATGCAAGTAAGCGCCTCCCGTAAAACGGGAGGGCTTCGGCGAATCAACTACAATGATCTATTTTCCCGGCTGATTGTCGCCTTCCATGCCCTCGCGGGCATCATGCAACCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   1134 GenBank   WP_182280086
Name   t4cp2_HV136_RS26670_pRHBSTW-00231_3 insolico UniProt ID   _
Length   919 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 919 a.a.        Molecular weight: 104591.64 Da        Isoelectric Point: 6.0514

>WP_182280086.1 VirB3 family type IV secretion system protein [Citrobacter freundii]
MSTVFKGLTRPALIRGLGVPLYPFLAMCVLVVLLGVWIDDLMYFLILPGWFAIKRVTKIEERFFDLLYLR
AVVKGHPLANKRFSAVHYAGSQYDEVDISNVDNFMKLKDQASIEALIPYSSHITDDLIVTKNRDLLATWQ
VDGAYFECVDDEDLTLLTDQLNTLIRSFEGRAVTFYTHRVRVRKGVKVDFNSKIPFVNRVMNDYYSSLSQ
PEYFENKLYLTICYKPFNIEDKVSQFISKNKKDKNIFDEPINDMNEICGRLDTYLSRFHAHRLGLVEDNG
RVFSDQLSLFQYLLSGKWQKVRVTNSPFYTYLGGKDLFFGNDAGQITASQNARYFRSIEIKDYFQETDAG
IFDALMYLPVEYVFTSSFTSMDKQAAVKALDDQIDKLEMTDDAAKSLLADLCVGVDMVSSGYNSFGKCHQ
TLIVFADTPERLVKDTNIVTTTLEDLGLVVTYSILSLGAAFFSQLPGNYNLRPRLSMLSSLNFAEMESFH
NFFHGKATGNTWGNSLMALRGSGNDVYHLNYHMTTENINFFGKNPTLGHCEILGTSNVGKTVLMMTMSYA
AQQFGTPESFPANRKVRKLTTVFFDKDRAGEVGIRAMGGAYFRVKGGEPTGWNPAALPPTKRNIAFLKDI
IRLICKLNGNTVDDYQNSLISSAVERLMEREDRSYPISKLIPLIMEPDDVETKRHGIKARLRAWKQGGEY
GWLLDNASDSFDVAHLDVFGIDGTEFLDDKVVAPVASFYLIYRVTMLADGRRLLIYMDEFWQWINNDAFK
DFVYNKLKTGRKLDMVLVPATQSPDELIKSPIAAAVREQCATHIYLANPKAKRNEYVDELQVRDLYFDKI
KAIDPLSRQFLVVKNPQRQGERDDFAAFAKLDLGKAAYYLPILSASAEQLELFDEIWSEGMAPEEWIDTY
LERANRGVK

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(272-474)

TraG P-loop domain (P-loop_TraG)

(689-817)

Type IV secretory pathway, VirB3-like protein (VirB3)

(2-83)

  Protein structure



No available structure.



ID   1135 GenBank   WP_182280089
Name   t4cp2_HV136_RS26710_pRHBSTW-00231_3 insolico UniProt ID   _
Length   611 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 611 a.a.        Molecular weight: 69291.13 Da        Isoelectric Point: 7.2867

>WP_182280089.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWVFIILVMCLLTYYIGSVAIYFFNHKTPIYIWKHYDSFLLWQVIIDSSIKTEIRLTAIPS
LLSGVLSSLAAPAFIIWKLNQNDAPLFGDAKFASDSDLKKSKLLKWERENDTDILVGRYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNMLVKKHSIIALDPKQELWKITSKVREVILGNKVYLLDPFNAKTHQCNPLF
YVDLKSESGAKDLLKLVEILFPSFGLTGAEAHFNNLAGQYWTGLAKLLHFFINFAPEWIDEFRVKPVFSI
GTVVDLYSNIDREQVLSNRETFEELAQGNETALFNLKDALTKIREYHETEDEQRSSVDGSFRKKMSLFYL
PTVRKCTDGNHFDLRQMRREDITVYVGVNAEDMILAYDFLNLFFNLVVEVTLRENPDFDPTLKHDCLLFL
DEFPSIGYMPIIKKGSGYIAGYKLKLLTIYQNISQLNEIYGTEGAKTLMSAHPCRVIYAVSEEDDAKKIS
EKLGYITTKSKGSSKTSGKATSRSNSESEAQRALVLPQELGTLDFSEEMIILKGEHPVKAEKALYYLDHY
FMDRLMLVSPKLTALTASINKINNIFGVKGIKYPSKEKMLSVGELESEVLL

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(102-572)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 33861..43750

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV136_RS26620 (HV136_26625) 29326..29592 + 267 WP_069730080 hypothetical protein -
HV136_RS26625 (HV136_26630) 29582..29800 + 219 WP_097472872 hypothetical protein -
HV136_RS26630 (HV136_26635) 29898..30242 + 345 WP_069730081 hypothetical protein -
HV136_RS26635 (HV136_26640) 30319..30468 + 150 WP_170936284 hypothetical protein -
HV136_RS26640 (HV136_26645) 30483..30740 + 258 WP_094169121 hypothetical protein -
HV136_RS26645 (HV136_26650) 31080..31625 + 546 WP_094169120 DNA distortion polypeptide 1 -
HV136_RS26650 (HV136_26655) 31628..32785 + 1158 WP_182280084 MobP1 family relaxase -
HV136_RS26655 (HV136_26660) 33146..33637 + 492 WP_094169118 transcription termination/antitermination NusG family protein -
HV136_RS26660 (HV136_26665) 33861..34505 + 645 WP_182280085 lytic transglycosylase domain-containing protein virB1
HV136_RS26665 (HV136_26670) 34489..34779 + 291 WP_094169115 TrbC/VirB2 family protein virB2
HV136_RS26670 (HV136_26675) 34804..37563 + 2760 WP_182280086 VirB3 family type IV secretion system protein virb4
HV136_RS26675 (HV136_26680) 37565..38302 + 738 WP_182280087 type IV secretion system protein -
HV136_RS26680 (HV136_26685) 38312..38572 + 261 WP_094169112 EexN family lipoprotein -
HV136_RS26685 (HV136_26690) 38585..39640 + 1056 WP_094169111 type IV secretion system protein virB6
HV136_RS26690 (HV136_26695) 39830..40552 + 723 WP_181499693 type IV secretion system protein virB8
HV136_RS26695 (HV136_26700) 40558..41487 + 930 WP_094169109 TrbG/VirB9 family P-type conjugative transfer protein virB9
HV136_RS26700 (HV136_26705) 41484..42695 + 1212 WP_094169108 VirB10/TraB/TrbI family type IV secretion system protein virB10
HV136_RS26705 (HV136_26710) 42713..43750 + 1038 WP_182280088 P-type DNA transfer ATPase VirB11 virB11
HV136_RS26710 (HV136_26715) 43755..45590 + 1836 WP_182280089 type IV secretory system conjugative DNA transfer family protein -
HV136_RS26715 (HV136_26720) 45587..45982 + 396 WP_094169105 cag pathogenicity island Cag12 family protein -
HV136_RS26720 (HV136_26725) 46401..46871 + 471 WP_181499698 thermonuclease family protein -
HV136_RS27405 46884..47318 + 435 WP_247753629 hypothetical protein -
HV136_RS26730 (HV136_26735) 47402..47989 + 588 WP_094169103 DUF6012 family protein -

Host bacterium

ID   2150 GenBank   NZ_JABXQP010000003
Plasmid name   pRHBSTW-00231_3 Incompatibility group   IncX2
Plasmid size   48574 bp Coordinate of oriT [Strand]   30686..31300 [-]
Host baterium   Citrobacter freundii strain RHBSTW-00231

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7