Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101465
Name   oriT_pRHBSTW-00509_4 in_silico
Organism   Citrobacter sp. RHBSTW-00509
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXPU010000004 (12435..12517 [-], 83 nt)
oriT length   83 nt
IRs (inverted repeats)      27..34, 37..44  (AGTGCGAT..ATCGCACT)
 13..18, 32..37  (TAAATC..GATTTA)
Location of nic site      55..56
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 83 nt

>oriT_pRHBSTW-00509_4
TTTTTTATTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1319 GenBank   WP_050136475
Name   mobF_HV224_RS27205_pRHBSTW-00509_4 insolico UniProt ID   _
Length   1072 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1072 a.a.        Molecular weight: 118873.51 Da        Isoelectric Point: 6.4635

>WP_050136475.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGDIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDVEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNDSQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGYNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNSKG
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



No available structure.




T4CP

ID   937 GenBank   WP_202048443
Name   t4cp2_HV224_RS27200_pRHBSTW-00509_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: 57947.12 Da        Isoelectric Point: 9.6871

>WP_202048443.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Citrobacter]
MTEQERGLIFLCSLLGPIPFVWFITAKFTYGINSETAHYLVPYLLKNTFNLWPLWTAIIAGVVIGLCGFI
GFIIYDKGRVYKGPRFKRILRGTKLARASTLAEKTKERGKKQLMIAGVPVPTEYETLHFSIGGATGTGKS
TVIKEAIYSSLKRGTDKRIVLDPNGEYVETFYRPGDVILSPYDKRSPGWSMFNEIRDDFDYDLYAVSIIQ
ESKERSAEEWYRYGRLIYREVSKKLLTLKRNPTMEEVMHWCTIVENDKLKEFVKGTPAEALFIKGAERAT
GSARFVLGDKLAPHLKMPAGDFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTYSQLIERYGINIAETLLGSMRSGIVMGSSRL
GKETLEQMSRALGEIEGEVEHKQGNPFQAGIGNRPRIETRTVRAVTPTEISELKNLTGYVYFPGDLPVGK
FKTKYVKYTRKNPVPGIIMR

  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: 58887..69172

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV224_RS27360 (HV224_27340) 54435..55439 - 1005 WP_000427614 IS110-like element IS5075 family transposase -
HV224_RS27365 (HV224_27345) 55705..56304 + 600 WP_032736817 GNAT family N-acetyltransferase -
HV224_RS27370 (HV224_27350) 56484..57506 + 1023 WP_132967450 IS110-like element IS5708 family transposase -
HV224_RS27375 (HV224_27355) 57795..58052 + 258 Protein_56 Tn3 family transposase -
HV224_RS27380 (HV224_27360) 58093..58332 + 240 Protein_57 Tn3 family transposase -
HV224_RS27385 (HV224_27365) 58366..58830 - 465 Protein_58 phospholipase D family protein -
HV224_RS27390 (HV224_27370) 58887..59888 - 1002 WP_048918087 ATPase, T2SS/T4P/T4SS family virB11
HV224_RS27395 (HV224_27375) 59939..61072 - 1134 WP_058687582 type IV secretion system protein VirB10 virB10
HV224_RS27400 (HV224_27380) 61072..61959 - 888 WP_000758230 TrbG/VirB9 family P-type conjugative transfer protein virB9
HV224_RS27405 (HV224_27385) 61970..62665 - 696 WP_001208352 type IV secretion system protein virB8
HV224_RS29020 62676..62807 - 132 WP_032493177 hypothetical protein -
HV224_RS27410 (HV224_27390) 62884..63921 - 1038 WP_117246091 type IV secretion system protein virB6
HV224_RS27415 (HV224_27395) 63938..64180 - 243 WP_040223412 EexN family lipoprotein -
HV224_RS27420 (HV224_27400) 64190..64900 - 711 WP_040223411 type IV secretion system protein virB5
HV224_RS27425 (HV224_27405) 64916..67489 - 2574 WP_040223410 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HV224_RS27430 (HV224_27410) 67490..67807 - 318 WP_040223409 VirB3 family type IV secretion system protein virB3
HV224_RS27435 (HV224_27415) 67847..68143 - 297 WP_015060075 TrbC/VirB2 family protein virB2
HV224_RS27440 (HV224_27420) 68390..69172 - 783 WP_014014952 lytic transglycosylase domain-containing protein virB1
HV224_RS27445 (HV224_27425) 69272..69589 + 318 WP_000960955 H-NS family nucleoid-associated regulatory protein -
HV224_RS27450 (HV224_27430) 69593..69943 + 351 WP_014014953 hypothetical protein -
HV224_RS27455 (HV224_27435) 69940..70278 + 339 WP_000040982 hypothetical protein -
HV224_RS27460 (HV224_27440) 70282..70590 + 309 WP_117242105 hypothetical protein -
HV224_RS27465 (HV224_27445) 70875..71060 + 186 WP_024562121 ribbon-helix-helix domain-containing protein -
HV224_RS27470 (HV224_27450) 71057..71665 - 609 WP_040223437 recombinase family protein -
HV224_RS27475 (HV224_27455) 71831..72163 - 333 WP_202048434 hypothetical protein -

Host bacterium

ID   1909 GenBank   NZ_JABXPU010000004
Plasmid name   pRHBSTW-00509_4 Incompatibility group   IncN2
Plasmid size   72302 bp Coordinate of oriT [Strand]   12435..12517 [-]
Host baterium   Citrobacter sp. RHBSTW-00509

Cargo genes

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