Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104623
Name   oriT_YL9|p1 in_silico
Organism   Klebsiella michiganensis strain YL9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084543 (19055..19205 [+], 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_YL9|p1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3323 GenBank   WP_001337757
Name   mobH_LD277_RS29130_YL9|p1 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   3262 GenBank   WP_000178856
Name   traD_LD277_RS29135_YL9|p1 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   3263 GenBank   WP_000637386
Name   traC_LD277_RS29215_YL9|p1 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: 17139..42330

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LD277_RS29120 (LD277_29155) 13164..13397 - 234 WP_001191892 hypothetical protein -
LD277_RS29125 (LD277_29160) 13379..13996 - 618 WP_001249396 hypothetical protein -
LD277_RS29130 (LD277_29165) 14164..17142 + 2979 WP_001337757 MobH family relaxase -
LD277_RS29135 (LD277_29170) 17139..19004 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
LD277_RS29140 (LD277_29175) 19054..19599 + 546 WP_000228720 hypothetical protein -
LD277_RS29145 (LD277_29180) 19556..20185 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
LD277_RS29150 (LD277_29185) 20195..20641 + 447 WP_000122506 hypothetical protein -
LD277_RS29155 (LD277_29190) 20651..21028 + 378 WP_000869261 hypothetical protein -
LD277_RS29160 (LD277_29195) 21028..21690 + 663 WP_001231463 hypothetical protein -
LD277_RS29165 (LD277_29200) 21871..22014 + 144 WP_001275801 hypothetical protein -
LD277_RS29170 (LD277_29205) 22026..22391 + 366 WP_001052531 hypothetical protein -
LD277_RS29175 (LD277_29210) 22536..22817 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
LD277_RS29180 (LD277_29215) 22814..23440 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
LD277_RS29185 (LD277_29220) 23424..24341 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
LD277_RS29190 (LD277_29225) 24341..25654 + 1314 WP_024131605 TraB/VirB10 family protein traB
LD277_RS29195 (LD277_29230) 25651..26229 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
LD277_RS29200 (LD277_29235) 26233..26625 + 393 WP_000479535 TraA family conjugative transfer protein -
LD277_RS29205 (LD277_29240) 26826..32357 + 5532 WP_000606833 Ig-like domain-containing protein -
LD277_RS29210 (LD277_29245) 32506..33213 + 708 WP_001259347 DsbC family protein -
LD277_RS29215 (LD277_29250) 33210..35657 + 2448 WP_000637386 type IV secretion system protein TraC virb4
LD277_RS29220 (LD277_29255) 35672..35989 + 318 WP_000351984 hypothetical protein -
LD277_RS29225 (LD277_29260) 35986..36516 + 531 WP_001010738 S26 family signal peptidase -
LD277_RS29230 (LD277_29265) 36479..37744 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
LD277_RS29235 (LD277_29270) 37741..38412 + 672 WP_001337754 EAL domain-containing protein -
LD277_RS29240 (LD277_29275) 38412..39416 + 1005 WP_043940352 TraU family protein traU
LD277_RS29245 (LD277_29280) 39532..42330 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
LD277_RS29250 (LD277_29285) 42369..43229 - 861 WP_000709517 hypothetical protein -
LD277_RS29255 (LD277_29290) 43352..43993 - 642 WP_000796664 hypothetical protein -
LD277_RS29260 (LD277_29295) 44287..44607 + 321 WP_000547566 hypothetical protein -
LD277_RS29265 (LD277_29300) 44911..45096 + 186 WP_001186917 hypothetical protein -
LD277_RS29270 (LD277_29305) 45316..46284 + 969 WP_000085162 AAA family ATPase -
LD277_RS29275 (LD277_29310) 46295..47203 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   5062 GenBank   NZ_CP084543
Plasmid name   YL9|p1 Incompatibility group   IncA/C2
Plasmid size   145051 bp Coordinate of oriT [Strand]   19055..19205 [+]
Host baterium   Klebsiella michiganensis strain YL9

Cargo genes

Drug resistance gene   blaVEB-3, qacE, sul1, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -