Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111000
Name   oriT_pCf-VIM in_silico
Organism   Citrobacter freundii strain Cf-Emp
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP110776 (34344..34494 [+], 151 nt)
oriT length   151 nt
IRs (inverted repeats)      12..17, 24..29  (AACCCG..CGGGTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT_pCf-VIM
TGGTCGATGTGAACCCGTTTGACCGGGTTATGAATGAGTTGAAAAGTCGTGGCCGCAAGAACGCTCATATCCTGAGCATCCTTCAATTCGACTGGCCCGCATCGGAGGTCATCATCGAGAAGCTGAGCTGTTACATCACAGATGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7237 GenBank   WP_058662807
Name   mobH_OPR78_RS25505_pCf-VIM insolico UniProt ID   A0A221KLA3
Length   987 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 987 a.a.        Molecular weight: 109306.91 Da        Isoelectric Point: 4.9372

>WP_058662807.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALHKLFGGRSGAIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAYRHGIDRYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVNEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGPVKILMLRLESNDLVFTTEPPAAVTGEVVGDVEDAEIE
FVDPEEADEDQAEGDAGLNNDMLAAELEAEKALAGLGFGDAMAMLKSTSDIAEEKPEQEDTESTELPKPD
ASKKGKQQSKPGKARAEKQPQKPEVKEDLSPQDIAKNAPPLANDDPLQALKDVGGGLGDIDFPFDVFNAS
AETACTDATNLAIPDITEPVKQEEQPKPDFVPQEQNSLQNGDFPIFSDSDEPPSWAIEPLPMLTDTPEQT
IPAPDMQHAGKPKELEKDAKTLLSEMLAGYGEASTLLEQAIMPVLEGKTTLGEVLCLMKGQAVILYPEGA
RSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLVDQLSDAVVAAIKDAEASMGGYQEAFELV
SPPGSGVSKNKSAPKQQSRKKTQQQKPEVDAGAGSEQKTKDKSLQQQPKEKQGNVASLVEEQKRKPVQDQ
EKQNVARLPKREAQPVASKPKVEHERELGHVEVRERDEPEVREFEPPKAKTNPKDINEEDFLPSGVTPEK
ALLMLKDMIQKRSGRWLVTPVLEEDGCLVTSVKAFDMIAGENVGISKHILYGLLSRAQRRPLLKKRQGKL
YLEVDKA

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A221KLA3


T4CP

ID   8240 GenBank   WP_000178858
Name   traD_OPR78_RS25510_pCf-VIM insolico UniProt ID   _
Length   621 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 621 a.a.        Molecular weight: 69248.76 Da        Isoelectric Point: 7.1093

>WP_000178858.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWMAASCAALAVEQVSTMPSEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGKESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVLTHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVKPDWEAEAAAYLEKAKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNTDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

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

(471-598)

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

(170-297)

  Protein structure



No available structure.



ID   8241 GenBank   WP_051479468
Name   traC_OPR78_RS25590_pCf-VIM insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 92523.78 Da        Isoelectric Point: 5.9204

>WP_051479468.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIITIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDQSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTSLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTSKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQHLAQIRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYDDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSQKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSDGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRKQAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(449-809)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 32428..57532

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OPR78_RS25495 (OPR78_25485) 28468..28701 - 234 WP_039272424 hypothetical protein -
OPR78_RS25500 (OPR78_25490) 28683..29300 - 618 WP_012766323 hypothetical protein -
OPR78_RS25505 (OPR78_25495) 29468..32431 + 2964 WP_058662807 MobH family relaxase -
OPR78_RS25510 (OPR78_25500) 32428..34293 + 1866 WP_000178858 conjugative transfer system coupling protein TraD virb4
OPR78_RS25515 (OPR78_25505) 34343..34888 + 546 WP_023356350 hypothetical protein -
OPR78_RS25520 (OPR78_25510) 34845..35474 + 630 WP_000743448 DUF4400 domain-containing protein tfc7
OPR78_RS25525 (OPR78_25515) 35485..35931 + 447 WP_039272421 hypothetical protein -
OPR78_RS25530 (OPR78_25520) 35941..36318 + 378 WP_000869260 hypothetical protein -
OPR78_RS25535 (OPR78_25525) 36318..36980 + 663 WP_039272419 hypothetical protein -
OPR78_RS25540 (OPR78_25530) 37159..37302 + 144 WP_168199038 hypothetical protein -
OPR78_RS25545 (OPR78_25535) 37315..37662 + 348 WP_039272417 hypothetical protein -
OPR78_RS25550 (OPR78_25540) 37805..38086 + 282 WP_000805626 type IV conjugative transfer system protein TraL traL
OPR78_RS25555 (OPR78_25545) 38083..38709 + 627 WP_039272415 TraE/TraK family type IV conjugative transfer system protein traE
OPR78_RS25560 (OPR78_25550) 38693..39610 + 918 WP_012766326 type-F conjugative transfer system secretin TraK traK
OPR78_RS25565 (OPR78_25555) 39607..40923 + 1317 WP_039272412 TraB/VirB10 family protein traB
OPR78_RS25570 (OPR78_25560) 40920..41498 + 579 WP_039272410 type IV conjugative transfer system lipoprotein TraV traV
OPR78_RS25575 (OPR78_25565) 41502..41894 + 393 WP_012766327 TraA family conjugative transfer protein -
OPR78_RS25580 (OPR78_25570) 42095..47581 + 5487 WP_039272407 Ig-like domain-containing protein -
OPR78_RS25585 (OPR78_25575) 47730..48437 + 708 WP_001259344 DsbC family protein -
OPR78_RS25590 (OPR78_25580) 48434..50881 + 2448 WP_051479468 type IV secretion system protein TraC virb4
OPR78_RS25595 (OPR78_25585) 50896..51213 + 318 WP_000364398 hypothetical protein -
OPR78_RS25600 (OPR78_25590) 51210..51740 + 531 WP_000672456 S26 family signal peptidase -
OPR78_RS25605 (OPR78_25595) 51703..52971 + 1269 WP_039272404 TrbC family F-type conjugative pilus assembly protein traW
OPR78_RS25610 (OPR78_25600) 52968..53645 + 678 WP_039272402 EAL domain-containing protein -
OPR78_RS25615 (OPR78_25605) 53639..54643 + 1005 WP_000911304 TraU family protein traU
OPR78_RS25620 (OPR78_25610) 54794..57532 + 2739 WP_058662805 conjugal transfer mating pair stabilization protein TraN traN
OPR78_RS25625 (OPR78_25615) 57571..58431 - 861 WP_000679674 hypothetical protein -
OPR78_RS25630 (OPR78_25620) 58543..59193 - 651 WP_000796641 hypothetical protein -
OPR78_RS25635 (OPR78_25625) 59485..59805 + 321 WP_012766334 hypothetical protein -
OPR78_RS25640 (OPR78_25630) 60050..60301 + 252 WP_226453752 hypothetical protein -
OPR78_RS25645 (OPR78_25635) 60522..61490 + 969 WP_001553257 AAA family ATPase -
OPR78_RS25650 (OPR78_25640) 61502..62407 + 906 WP_058662804 hypothetical protein -

Host bacterium

ID   11435 GenBank   NZ_CP110776
Plasmid name   pCf-VIM Incompatibility group   IncA/C
Plasmid size   151674 bp Coordinate of oriT [Strand]   34344..34494 [+]
Host baterium   Citrobacter freundii strain Cf-Emp

Cargo genes

Drug resistance gene   dfrA14, mph(A), blaSHV-12, blaVIM-1, aph(3')-XV, ant(3'')-Ia, catB2, qacE, sul1
Virulence gene   -
Metal resistance gene   merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -