Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104622
Name   oriT_YL6-1|p2 in_silico
Organism   Klebsiella michiganensis strain YL6-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084417 (116840..116990 [+], 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_YL6-1|p2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3322 GenBank   WP_001337757
Name   mobH_LDP80_RS30390_YL6-1|p2 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   3260 GenBank   WP_000178856
Name   traD_LDP80_RS30395_YL6-1|p2 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   3261 GenBank   WP_000637386
Name   traC_LDP80_RS30470_YL6-1|p2 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: 114924..140115

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDP80_RS30380 (LDP80_30420) 110949..111182 - 234 WP_001191892 hypothetical protein -
LDP80_RS30385 (LDP80_30425) 111164..111781 - 618 WP_001249396 hypothetical protein -
LDP80_RS30390 (LDP80_30430) 111949..114927 + 2979 WP_001337757 MobH family relaxase -
LDP80_RS30395 (LDP80_30435) 114924..116789 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
LDP80_RS30400 (LDP80_30440) 116839..117384 + 546 WP_000228720 hypothetical protein -
LDP80_RS30405 (LDP80_30445) 117341..117970 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
LDP80_RS30410 (LDP80_30450) 117980..118426 + 447 WP_000122506 hypothetical protein -
LDP80_RS30415 (LDP80_30455) 118436..118813 + 378 WP_000869261 hypothetical protein -
LDP80_RS30420 (LDP80_30460) 118813..119475 + 663 WP_001231463 hypothetical protein -
LDP80_RS30425 (LDP80_30465) 119811..120176 + 366 WP_001052531 hypothetical protein -
LDP80_RS30430 (LDP80_30470) 120321..120602 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
LDP80_RS30435 (LDP80_30475) 120599..121225 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
LDP80_RS30440 (LDP80_30480) 121209..122126 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
LDP80_RS30445 (LDP80_30485) 122126..123439 + 1314 WP_024131605 TraB/VirB10 family protein traB
LDP80_RS30450 (LDP80_30490) 123436..124014 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
LDP80_RS30455 (LDP80_30495) 124018..124410 + 393 WP_000479535 TraA family conjugative transfer protein -
LDP80_RS30460 (LDP80_30500) 124611..130142 + 5532 WP_000606833 Ig-like domain-containing protein -
LDP80_RS30465 (LDP80_30505) 130291..130998 + 708 WP_001259347 DsbC family protein -
LDP80_RS30470 (LDP80_30510) 130995..133442 + 2448 WP_000637386 type IV secretion system protein TraC virb4
LDP80_RS30475 (LDP80_30515) 133457..133774 + 318 WP_000351984 hypothetical protein -
LDP80_RS30480 (LDP80_30520) 133771..134301 + 531 WP_001010738 S26 family signal peptidase -
LDP80_RS30485 (LDP80_30525) 134264..135529 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
LDP80_RS30490 (LDP80_30530) 135526..136197 + 672 WP_001337754 EAL domain-containing protein -
LDP80_RS30495 (LDP80_30535) 136197..137201 + 1005 WP_043940352 TraU family protein traU
LDP80_RS30500 (LDP80_30540) 137317..140115 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
LDP80_RS30505 (LDP80_30545) 140154..141014 - 861 WP_000709517 hypothetical protein -
LDP80_RS30510 (LDP80_30550) 141137..141778 - 642 WP_000796664 hypothetical protein -
LDP80_RS30515 (LDP80_30555) 142072..142392 + 321 WP_000547566 hypothetical protein -
LDP80_RS30520 (LDP80_30560) 142696..142881 + 186 WP_001186917 hypothetical protein -
LDP80_RS30525 (LDP80_30565) 143101..144069 + 969 WP_000085162 AAA family ATPase -
LDP80_RS30530 (LDP80_30570) 144080..144988 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   5061 GenBank   NZ_CP084417
Plasmid name   YL6-1|p2 Incompatibility group   IncA/C2
Plasmid size   145051 bp Coordinate of oriT [Strand]   116840..116990 [+]
Host baterium   Klebsiella michiganensis strain YL6-1

Cargo genes

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