Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   110601
Name   oriT_p59174-171.4 in_silico
Organism   Citrobacter freundii strain 59174
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP098334 (64663..64813 [+], 151 nt)
oriT length   151 nt
IRs (inverted repeats)      93..98, 106..111  (TGGCCT..AGGCCA)
 12..17, 24..29  (AACCCT..AGGGTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT_p59174-171.4
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7046 GenBank   WP_001337757
Name   mobH_NB664_RS26925_p59174-171.4 insolico UniProt ID   A0A709FRI2
Length   992 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 992 a.a.        Molecular weight: 109581.85 Da        Isoelectric Point: 4.8956

>WP_001337757.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREDPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A709FRI2


T4CP

ID   7990 GenBank   WP_000178856
Name   traD_NB664_RS26930_p59174-171.4 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: 69197.66 Da        Isoelectric Point: 6.9403

>WP_000178856.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKAKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  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   7991 GenBank   WP_000637386
Name   traC_NB664_RS27010_p59174-171.4 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: 92590.87 Da        Isoelectric Point: 5.9222

>WP_000637386.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTERIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRQQAA

  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: 62747..87938

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NB664_RS26915 (NB664_26915) 58772..59005 - 234 WP_001191892 hypothetical protein -
NB664_RS26920 (NB664_26920) 58987..59604 - 618 WP_001249396 hypothetical protein -
NB664_RS26925 (NB664_26925) 59772..62750 + 2979 WP_001337757 MobH family relaxase -
NB664_RS26930 (NB664_26930) 62747..64612 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
NB664_RS26935 (NB664_26935) 64662..65207 + 546 WP_000228720 hypothetical protein -
NB664_RS26940 (NB664_26940) 65164..65793 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
NB664_RS26945 (NB664_26945) 65803..66249 + 447 WP_000122506 hypothetical protein -
NB664_RS26950 (NB664_26950) 66259..66636 + 378 WP_000869261 hypothetical protein -
NB664_RS26955 (NB664_26955) 66636..67298 + 663 WP_001231463 hypothetical protein -
NB664_RS26960 (NB664_26960) 67479..67622 + 144 WP_001275801 hypothetical protein -
NB664_RS26965 (NB664_26965) 67634..67999 + 366 WP_001052531 hypothetical protein -
NB664_RS26970 (NB664_26970) 68144..68425 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
NB664_RS26975 (NB664_26975) 68422..69048 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
NB664_RS26980 (NB664_26980) 69032..69949 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
NB664_RS26985 (NB664_26985) 69949..71262 + 1314 WP_024131605 TraB/VirB10 family protein traB
NB664_RS26990 (NB664_26990) 71259..71837 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
NB664_RS26995 (NB664_26995) 71841..72233 + 393 WP_000479535 TraA family conjugative transfer protein -
NB664_RS27000 (NB664_27000) 72434..77965 + 5532 WP_000606833 Ig-like domain-containing protein -
NB664_RS27005 (NB664_27005) 78114..78821 + 708 WP_001259347 DsbC family protein -
NB664_RS27010 (NB664_27010) 78818..81265 + 2448 WP_000637386 type IV secretion system protein TraC virb4
NB664_RS27015 (NB664_27015) 81280..81597 + 318 WP_000351984 hypothetical protein -
NB664_RS27020 (NB664_27020) 81594..82124 + 531 WP_001010738 S26 family signal peptidase -
NB664_RS27025 (NB664_27025) 82087..83352 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
NB664_RS27030 (NB664_27030) 83349..84020 + 672 WP_001337754 EAL domain-containing protein -
NB664_RS27035 (NB664_27035) 84020..85024 + 1005 WP_043940352 TraU family protein traU
NB664_RS27040 (NB664_27040) 85140..87938 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
NB664_RS27045 (NB664_27045) 87977..88837 - 861 WP_000709517 hypothetical protein -
NB664_RS27050 (NB664_27050) 88960..89601 - 642 WP_000796664 hypothetical protein -
NB664_RS27055 (NB664_27055) 89895..90215 + 321 WP_000547566 hypothetical protein -
NB664_RS27060 (NB664_27060) 90519..90704 + 186 WP_001186917 hypothetical protein -
NB664_RS27065 (NB664_27065) 90924..91892 + 969 WP_000085162 AAA family ATPase -
NB664_RS27070 (NB664_27070) 91903..92811 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   11036 GenBank   NZ_CP098334
Plasmid name   p59174-171.4 Incompatibility group   IncA/C2
Plasmid size   171445 bp Coordinate of oriT [Strand]   64663..64813 [+]
Host baterium   Citrobacter freundii strain 59174

Cargo genes

Drug resistance gene   blaFOX-5, ant(2'')-Ia, catB3, qacE, sul1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -