Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103715
Name   oriT_pTMTA97342 in_silico
Organism   Phytobacter diazotrophicus strain TA9734
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP025336 (88584..88734 [+], 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_pTMTA97342
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2753 GenBank   WP_143474952
Name   mobH_L6445_RS28850_pTMTA97342 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: 109639.89 Da        Isoelectric Point: 4.8747

>WP_143474952.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEESALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREDPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   2591 GenBank   WP_000178856
Name   traD_L6445_RS28855_pTMTA97342 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   2592 GenBank   WP_000637386
Name   traC_L6445_RS28930_pTMTA97342 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: 86668..111859

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L6445_RS28840 82693..82926 - 234 WP_143474954 hypothetical protein -
L6445_RS28845 (PDTA9734_57070) 82908..83525 - 618 WP_143474953 hypothetical protein -
L6445_RS28850 (PDTA9734_57080) 83693..86671 + 2979 WP_143474952 MobH family relaxase -
L6445_RS28855 (PDTA9734_57090) 86668..88533 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
L6445_RS28860 (PDTA9734_57100) 88583..89128 + 546 WP_000228720 hypothetical protein -
L6445_RS28865 (PDTA9734_57110) 89085..89714 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
L6445_RS28870 (PDTA9734_57120) 89724..90170 + 447 WP_000122506 hypothetical protein -
L6445_RS28875 (PDTA9734_57130) 90180..90557 + 378 WP_000869261 hypothetical protein -
L6445_RS28880 (PDTA9734_57140) 90557..91219 + 663 WP_001231463 hypothetical protein -
L6445_RS28885 (PDTA9734_57160) 91555..91920 + 366 WP_001052531 hypothetical protein -
L6445_RS28890 (PDTA9734_57170) 92065..92346 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
L6445_RS28895 (PDTA9734_57180) 92343..92969 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
L6445_RS28900 (PDTA9734_57190) 92953..93870 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
L6445_RS28905 (PDTA9734_57200) 93870..95183 + 1314 WP_024131605 TraB/VirB10 family protein traB
L6445_RS28910 (PDTA9734_57210) 95180..95758 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
L6445_RS28915 (PDTA9734_57220) 95762..96154 + 393 WP_000479535 TraA family conjugative transfer protein -
L6445_RS28920 (PDTA9734_57230) 96355..101886 + 5532 WP_000606833 Ig-like domain-containing protein -
L6445_RS28925 (PDTA9734_57240) 102035..102742 + 708 WP_001259347 DsbC family protein -
L6445_RS28930 (PDTA9734_57250) 102739..105186 + 2448 WP_000637386 type IV secretion system protein TraC virb4
L6445_RS28935 (PDTA9734_57260) 105201..105518 + 318 WP_000351984 hypothetical protein -
L6445_RS28940 (PDTA9734_57270) 105515..106045 + 531 WP_001010738 S26 family signal peptidase -
L6445_RS28945 (PDTA9734_57280) 106008..107273 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
L6445_RS28950 (PDTA9734_57290) 107270..107941 + 672 WP_001337754 EAL domain-containing protein -
L6445_RS28955 (PDTA9734_57300) 107941..108945 + 1005 WP_043940352 TraU family protein traU
L6445_RS28960 (PDTA9734_57310) 109061..111859 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
L6445_RS28965 (PDTA9734_57320) 111898..112758 - 861 WP_000709517 hypothetical protein -
L6445_RS28970 (PDTA9734_57330) 112881..113522 - 642 WP_000796664 hypothetical protein -
L6445_RS28975 (PDTA9734_57340) 113816..114136 + 321 WP_000547566 hypothetical protein -
L6445_RS28980 (PDTA9734_57350) 114440..114625 + 186 WP_001186917 hypothetical protein -
L6445_RS28985 (PDTA9734_57360) 114845..115813 + 969 WP_000085162 AAA family ATPase -
L6445_RS28990 (PDTA9734_57370) 115824..116732 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   4158 GenBank   NZ_AP025336
Plasmid name   pTMTA97342 Incompatibility group   IncA/C2
Plasmid size   174343 bp Coordinate of oriT [Strand]   88584..88734 [+]
Host baterium   Phytobacter diazotrophicus strain TA9734

Cargo genes

Drug resistance gene   fosA3, aac(6')-IIa, dfrA1, aadA2, qacE, sul1, blaNDM-1, catB3, ARR-3, armA, msr(E), mph(E), sul2, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -