Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106776
Name   oriT_pCF1807-4 in_silico
Organism   Citrobacter freundii strain CF1807
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP110890 (11379..11468 [-], 90 nt)
oriT length   90 nt
IRs (inverted repeats)      34..41, 44..51  (AGTGCGAT..ATCGCACT)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 90 nt

>oriT_pCF1807-4
TATTTCATTTTTTGTTTTTTTAATCAGTTAGTTAGTGCGATTCATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4467 GenBank   WP_024561907
Name   mobF_OQW59_RS00110_pCF1807-4 insolico UniProt ID   H1ZMV6
Length   1072 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1072 a.a.        Molecular weight: 118896.59 Da        Isoelectric Point: 6.4636

>WP_024561907.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDHDKEGYGL

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-288)

AAA domain (AAA_30)

(480-656)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(855-899)


  Protein structure


Source ID Structure
AlphaFold DB H1ZMV6


T4CP

ID   4514 GenBank   WP_032493179
Name   t4cp2_OQW59_RS00105_pCF1807-4 insolico UniProt ID   _
Length   510 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 510 a.a.        Molecular weight: 57912.96 Da        Isoelectric Point: 9.5127

>WP_032493179.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERDHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGTDKRIVLDPNGEYVETFYRPGDVILSPYDKRSPGWSMFNEIRDDFDYDLYAVSIIQ
ESKERSAEEWYRYGRLIYREVSKKLLTLKRSPTMEEVMHWCTIVENEKLKEFVKGTPAEALFIKGAERAT
GSARFVLGDKLAPHLKMPAGDFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTYSQLIERYGINIAETLLGSMRSGIVMGSSRL
GKETLEQMSRALGEIEGEVEHKQGNPFQAGIGNRPRIETRTVRAVTPTEISELKNLTGYVYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(113-492)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12039..29539

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OQW59_RS00055 (OQW59_00055) 7154..7354 + 201 WP_015060066 hypothetical protein -
OQW59_RS00060 (OQW59_00060) 7409..7906 + 498 WP_040115102 MucR family transcriptional regulator -
OQW59_RS00065 (OQW59_00065) 8279..8536 - 258 WP_157676234 hypothetical protein -
OQW59_RS00070 (OQW59_00070) 8686..8892 + 207 WP_032493183 DUF905 family protein -
OQW59_RS00075 (OQW59_00075) 8967..9149 + 183 WP_032493182 hypothetical protein -
OQW59_RS00080 (OQW59_00080) 9208..9558 - 351 WP_014014961 hypothetical protein -
OQW59_RS00085 (OQW59_00085) 9620..9988 - 369 WP_000360828 plasmid stabilization protein StbC -
OQW59_RS00090 (OQW59_00090) 9991..10707 - 717 WP_000861579 StbB family protein -
OQW59_RS00095 (OQW59_00095) 10716..11147 - 432 WP_029697170 plasmid stabilization protein StbA -
OQW59_RS00100 (OQW59_00100) 11614..12039 + 426 WP_225247941 traK protein -
OQW59_RS00105 (OQW59_00105) 12039..13571 + 1533 WP_032493179 type IV secretion system DNA-binding domain-containing protein virb4
OQW59_RS00110 (OQW59_00110) 13576..16794 + 3219 WP_024561907 MobF family relaxase -
OQW59_RS00115 (OQW59_00115) 16791..17456 + 666 WP_000971716 DUF6710 family protein -
OQW59_RS00120 (OQW59_00120) 17449..17811 + 363 WP_024561906 hypothetical protein -
OQW59_RS00125 (OQW59_00125) 18739..19251 - 513 WP_029697418 phospholipase D family protein -
OQW59_RS00130 (OQW59_00130) 19263..20264 - 1002 WP_001076634 ATPase, T2SS/T4P/T4SS family virB11
OQW59_RS00135 (OQW59_00135) 20315..21448 - 1134 WP_000101920 type IV secretion system protein VirB10 virB10
OQW59_RS00140 (OQW59_00140) 21448..22335 - 888 WP_000758230 TrbG/VirB9 family P-type conjugative transfer protein virB9
OQW59_RS00145 (OQW59_00145) 22346..23041 - 696 WP_001208352 type IV secretion system protein virB8
OQW59_RS28915 23052..23183 - 132 WP_032493177 hypothetical protein -
OQW59_RS00150 (OQW59_00150) 23260..24297 - 1038 WP_014014948 type IV secretion system protein virB6
OQW59_RS00155 (OQW59_00155) 24314..24556 - 243 WP_000858958 EexN family lipoprotein -
OQW59_RS00160 (OQW59_00160) 24566..25267 - 702 WP_014014949 type IV secretion system protein virB5
OQW59_RS00165 (OQW59_00165) 25283..27856 - 2574 WP_032493176 VirB4 family type IV secretion/conjugal transfer ATPase virb4
OQW59_RS00170 (OQW59_00170) 27857..28174 - 318 WP_000462629 VirB3 family type IV secretion system protein virB3
OQW59_RS00175 (OQW59_00175) 28214..28510 - 297 WP_015060075 TrbC/VirB2 family protein virB2
OQW59_RS00185 (OQW59_00180) 28757..29539 - 783 WP_024562119 lytic transglycosylase domain-containing protein virB1
OQW59_RS00190 (OQW59_00185) 29639..29956 + 318 WP_000960955 H-NS family nucleoid-associated regulatory protein -
OQW59_RS00195 (OQW59_00190) 29960..30310 + 351 WP_024562120 hypothetical protein -
OQW59_RS00200 (OQW59_00195) 30307..30645 + 339 WP_032493175 hypothetical protein -
OQW59_RS00205 (OQW59_00200) 30649..30957 + 309 WP_000733764 hypothetical protein -
OQW59_RS00210 (OQW59_00205) 31242..31427 + 186 WP_024562121 ribbon-helix-helix domain-containing protein -
OQW59_RS00215 (OQW59_00210) 31424..32032 - 609 WP_000275218 recombinase family protein -
OQW59_RS00220 (OQW59_00215) 32219..32551 - 333 WP_045723726 hypothetical protein -
OQW59_RS00225 (OQW59_00220) 32623..32817 - 195 WP_050136673 hypothetical protein -
OQW59_RS00230 (OQW59_00225) 32904..33533 - 630 WP_064754415 hypothetical protein -

Host bacterium

ID   7213 GenBank   NZ_CP110890
Plasmid name   pCF1807-4 Incompatibility group   IncN3
Plasmid size   33719 bp Coordinate of oriT [Strand]   11379..11468 [-]
Host baterium   Citrobacter freundii strain CF1807

Cargo genes

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