Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120586
Name   oriT_2022CK-00369|unnamed2 in_silico
Organism   Citrobacter freundii strain 2022CK-00369
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP115616 (143257..143407 [-], 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_2022CK-00369|unnamed2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12966 GenBank   WP_261588778
Name   mobH_PF691_RS27060_2022CK-00369|unnamed2 insolico UniProt ID   _
Length   992 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 992 a.a.        Molecular weight: 109567.83 Da        Isoelectric Point: 4.8944

>WP_261588778.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMDMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREDPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   15225 GenBank   WP_104457263
Name   t4cp2_PF691_RS26445_2022CK-00369|unnamed2 insolico UniProt ID   _
Length   701 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 701 a.a.        Molecular weight: 77343.46 Da        Isoelectric Point: 10.0162

>WP_104457263.1 MULTISPECIES: conjugal transfer protein TraG [Enterobacterales]
MRGGRILWGQIAVVITIVLVMTWAATQWVAFRLGFQPQLGAPWFDLAGLPVYYPPAFFWWWFSFDAYAPA
IFVEGGIIAVSGGFIAIAAAILMSIIRAREARNIATYGSARWAEDKEIRAAGLLGPDGVVLGRHTQDYLR
HDGPEHVLCFAPTRSGKGVGLVVPTLLTWPASAIVHDIKGENWTLTAGFRAKHGRVLLFDPTNAGSSAYN
PLLEVRRGEWEVRDVQNIADILVDPEGSLDKRNHWEKTSHSLLVGAILHVLYAERDKTLAGVANFLSDPR
RPVEATLRAMMDTPHLGEAGVHPVIASSARELLNKSENERSGVLSTAMSFLGLYRDPVVARVTARCDWRI
ADLVGSRRPVTLYLVVPPSDINRTKPLIRLILNQIGRRLTEELTTSGKRHRLLLMLDEFPALGRLDFFES
ALAFMAGYGIKGFLIAQSLNQIERAYGPNNAILDNCHVRVSFATNDERTAKRVSDALGAATELRDSTNYA
GHRLAPWLGHLMVSRQETARPLLTPGEIMQLPPTDEIVMVAGTPPIRATKARYFEDARFQERILTPPKLV
AAPLTSSPLDFIARLAALVPKPRVNLTRFHGVFAPNSRHRALVTPAKRGRGNKVRVADEPATPAQRRASM
TWAQRLKRVFNIDIETCSGCGGAMKVIACIEDPIVIKQILDHLKHKAETSGTRALPESRAPPAELLLGLF
D

  Protein domains


Predicted by InterproScan.

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

(111-557)

Putative transposase (Y2_Tnp)

(561-597)

  Protein structure



No available structure.



ID   15226 GenBank   WP_000637386
Name   traC_PF691_RS26975_2022CK-00369|unnamed2 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.



ID   15227 GenBank   WP_000178856
Name   traD_PF691_RS27055_2022CK-00369|unnamed2 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 120132..145323

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PF691_RS26915 (PF691_26910) 115259..116167 - 909 WP_000739139 hypothetical protein -
PF691_RS26920 (PF691_26915) 116178..117146 - 969 WP_000085162 AAA family ATPase -
PF691_RS26925 (PF691_26920) 117366..117551 - 186 WP_001186917 hypothetical protein -
PF691_RS26930 (PF691_26925) 117855..118175 - 321 WP_000547566 hypothetical protein -
PF691_RS26935 (PF691_26930) 118469..119110 + 642 WP_000796664 hypothetical protein -
PF691_RS26940 (PF691_26935) 119233..120093 + 861 WP_000709517 hypothetical protein -
PF691_RS26945 (PF691_26940) 120132..122930 - 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
PF691_RS26950 (PF691_26945) 123046..124050 - 1005 WP_043940352 TraU family protein traU
PF691_RS26955 (PF691_26950) 124050..124721 - 672 WP_001337754 EAL domain-containing protein -
PF691_RS26960 (PF691_26955) 124718..125983 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
PF691_RS26965 (PF691_26960) 125946..126476 - 531 WP_001010738 S26 family signal peptidase -
PF691_RS26970 (PF691_26965) 126473..126790 - 318 WP_000351984 hypothetical protein -
PF691_RS26975 (PF691_26970) 126805..129252 - 2448 WP_000637386 type IV secretion system protein TraC virb4
PF691_RS26980 (PF691_26975) 129249..129956 - 708 WP_001259347 DsbC family protein -
PF691_RS26985 (PF691_26980) 130105..135636 - 5532 WP_000606833 Ig-like domain-containing protein -
PF691_RS26990 (PF691_26985) 135837..136229 - 393 WP_000479535 TraA family conjugative transfer protein -
PF691_RS26995 (PF691_26990) 136233..136811 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
PF691_RS27000 (PF691_26995) 136808..138121 - 1314 WP_024131605 TraB/VirB10 family protein traB
PF691_RS27005 (PF691_27000) 138121..139038 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
PF691_RS27010 (PF691_27005) 139022..139648 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
PF691_RS27015 (PF691_27010) 139645..139926 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
PF691_RS27020 (PF691_27015) 140071..140436 - 366 WP_001052531 hypothetical protein -
PF691_RS27025 (PF691_27020) 140448..140591 - 144 WP_001275801 hypothetical protein -
PF691_RS27030 (PF691_27025) 140772..141434 - 663 WP_001231463 hypothetical protein -
PF691_RS27035 (PF691_27030) 141434..141811 - 378 WP_000869261 hypothetical protein -
PF691_RS27040 (PF691_27035) 141821..142267 - 447 WP_000122506 hypothetical protein -
PF691_RS27045 (PF691_27040) 142277..142906 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
PF691_RS27050 (PF691_27045) 142863..143408 - 546 WP_000228720 hypothetical protein -
PF691_RS27055 (PF691_27050) 143458..145323 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
PF691_RS27060 (PF691_27055) 145320..148298 - 2979 WP_261588778 MobH family relaxase -
PF691_RS27065 (PF691_27060) 148466..149083 + 618 WP_001249396 hypothetical protein -
PF691_RS27070 (PF691_27065) 149065..149298 + 234 WP_001191892 hypothetical protein -

Host bacterium

ID   21015 GenBank   NZ_CP115616
Plasmid name   2022CK-00369|unnamed2 Incompatibility group   IncA/C2
Plasmid size   210045 bp Coordinate of oriT [Strand]   143257..143407 [-]
Host baterium   Citrobacter freundii strain 2022CK-00369

Cargo genes

Drug resistance gene   floR, sul2, blaKPC-2, sul1, qacE, aac(6')-33, ant(2'')-Ia, blaTEM-1D
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE, merC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -