Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   112892
Name   oriT_MSB1_9C|2 in_silico
Organism   Serratia marcescens strain MSB1_9C isolate MSB1_9C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LR890658 (52022..52172 [+], 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_MSB1_9C|2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8295 GenBank   WP_001337757
Name   mobH_JMX15_RS26860_MSB1_9C|2 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   9617 GenBank   WP_000178856
Name   traD_JMX15_RS26865_MSB1_9C|2 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   9618 GenBank   WP_024945386
Name   traC_JMX15_RS26955_MSB1_9C|2 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: 92618.93 Da        Isoelectric Point: 5.9222

>WP_024945386.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTERIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQVAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRQQAA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraG P-loop domain (P-loop_TraG)

(449-809)

TraC protein (TraC_F_IV)

(21-255)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 50106..77607

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JMX15_RS26850 46131..46364 - 234 WP_001191892 hypothetical protein -
JMX15_RS26855 46346..46963 - 618 WP_001249396 hypothetical protein -
JMX15_RS26860 47131..50109 + 2979 WP_001337757 MobH family relaxase -
JMX15_RS26865 50106..51971 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
JMX15_RS26870 52021..52566 + 546 WP_000228720 hypothetical protein -
JMX15_RS26875 52523..53152 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
JMX15_RS26880 53162..53608 + 447 WP_000122506 hypothetical protein -
JMX15_RS26885 53618..53995 + 378 WP_000869261 hypothetical protein -
JMX15_RS26890 53995..54657 + 663 WP_001231463 hypothetical protein -
JMX15_RS26895 54838..54981 + 144 WP_001275801 hypothetical protein -
JMX15_RS26900 54993..55358 + 366 WP_001052531 hypothetical protein -
JMX15_RS26905 55503..55784 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
JMX15_RS26910 55781..56407 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
JMX15_RS26915 56391..57308 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
JMX15_RS26920 57308..58621 + 1314 WP_024131605 TraB/VirB10 family protein traB
JMX15_RS26925 58618..59196 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
JMX15_RS26930 59200..59592 + 393 WP_000479535 TraA family conjugative transfer protein -
JMX15_RS26935 59793..65324 + 5532 WP_000606833 Ig-like domain-containing protein -
JMX15_RS26940 65473..65844 + 372 WP_236582499 disulfide isomerase DsbC N-terminal domain-containing protein -
JMX15_RS26945 65941..66972 + 1032 WP_001395480 IS630-like element ISEc33 family transposase -
JMX15_RS26950 67018..67335 + 318 WP_236582500 hypothetical protein -
JMX15_RS26955 67332..69779 + 2448 WP_024945386 type IV secretion system protein TraC virb4
JMX15_RS26960 69794..70111 + 318 WP_000351984 hypothetical protein -
JMX15_RS26965 70108..70638 + 531 WP_001010738 S26 family signal peptidase -
JMX15_RS26970 70601..71866 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
JMX15_RS26975 71863..72534 + 672 WP_001337754 EAL domain-containing protein -
JMX15_RS26980 72534..73538 + 1005 WP_043940352 TraU family protein traU
JMX15_RS26985 73654..76185 + 2532 Protein_100 conjugal transfer mating pair stabilization protein TraN -
JMX15_RS26990 76203..77234 - 1032 WP_001395480 IS630-like element ISEc33 family transposase -
JMX15_RS26995 77374..77607 + 234 WP_236582501 hypothetical protein traN
JMX15_RS27000 77646..78506 - 861 WP_000709517 hypothetical protein -
JMX15_RS27005 78629..79270 - 642 WP_000796664 hypothetical protein -
JMX15_RS27010 79564..79884 + 321 WP_000547566 hypothetical protein -
JMX15_RS27015 80188..80373 + 186 WP_001186917 hypothetical protein -
JMX15_RS27020 80593..81561 + 969 WP_000085162 AAA family ATPase -
JMX15_RS27025 81572..82480 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   13327 GenBank   NZ_LR890658
Plasmid name   MSB1_9C|2 Incompatibility group   IncA/C2
Plasmid size   184703 bp Coordinate of oriT [Strand]   52022..52172 [+]
Host baterium   Serratia marcescens strain MSB1_9C isolate MSB1_9C

Cargo genes

Drug resistance gene   blaIMP-4, catB3, qacE, sul1, tet(A), blaTEM-1B
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR, merB
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -