Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113092
Name   oriT_pTMTA97302 in_silico
Organism   Phytobacter diazotrophicus strain TA9730
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP028043 (86252..86402 [+], 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_pTMTA97302
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8403 GenBank   WP_143474952
Name   mobH_QUE90_RS28385_pTMTA97302 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   9680 GenBank   WP_000178856
Name   traD_QUE90_RS28390_pTMTA97302 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   9681 GenBank   WP_000637386
Name   traC_QUE90_RS28465_pTMTA97302 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: 84336..109527

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QUE90_RS28375 80361..80594 - 234 WP_143474954 hypothetical protein -
QUE90_RS28380 (PDTA9730_56050) 80576..81193 - 618 WP_143474953 hypothetical protein -
QUE90_RS28385 (PDTA9730_56060) 81361..84339 + 2979 WP_143474952 MobH family relaxase -
QUE90_RS28390 (PDTA9730_56070) 84336..86201 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
QUE90_RS28395 (PDTA9730_56080) 86251..86796 + 546 WP_000228720 hypothetical protein -
QUE90_RS28400 (PDTA9730_56090) 86753..87382 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
QUE90_RS28405 (PDTA9730_56100) 87392..87838 + 447 WP_000122506 hypothetical protein -
QUE90_RS28410 (PDTA9730_56110) 87848..88225 + 378 WP_000869261 hypothetical protein -
QUE90_RS28415 (PDTA9730_56120) 88225..88887 + 663 WP_001231463 hypothetical protein -
QUE90_RS28420 (PDTA9730_56140) 89223..89588 + 366 WP_001052531 hypothetical protein -
QUE90_RS28425 (PDTA9730_56150) 89733..90014 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
QUE90_RS28430 (PDTA9730_56160) 90011..90637 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
QUE90_RS28435 (PDTA9730_56170) 90621..91538 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
QUE90_RS28440 (PDTA9730_56180) 91538..92851 + 1314 WP_024131605 TraB/VirB10 family protein traB
QUE90_RS28445 (PDTA9730_56190) 92848..93426 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
QUE90_RS28450 (PDTA9730_56200) 93430..93822 + 393 WP_000479535 TraA family conjugative transfer protein -
QUE90_RS28455 (PDTA9730_56210) 94023..99554 + 5532 WP_000606833 Ig-like domain-containing protein -
QUE90_RS28460 (PDTA9730_56220) 99703..100410 + 708 WP_001259347 DsbC family protein -
QUE90_RS28465 (PDTA9730_56230) 100407..102854 + 2448 WP_000637386 type IV secretion system protein TraC virb4
QUE90_RS28470 (PDTA9730_56240) 102869..103186 + 318 WP_000351984 hypothetical protein -
QUE90_RS28475 (PDTA9730_56250) 103183..103713 + 531 WP_001010738 S26 family signal peptidase -
QUE90_RS28480 (PDTA9730_56260) 103676..104941 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
QUE90_RS28485 (PDTA9730_56270) 104938..105609 + 672 WP_001337754 EAL domain-containing protein -
QUE90_RS28490 (PDTA9730_56280) 105609..106613 + 1005 WP_043940352 TraU family protein traU
QUE90_RS28495 (PDTA9730_56290) 106729..109527 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
QUE90_RS28500 (PDTA9730_56300) 109566..110426 - 861 WP_000709517 hypothetical protein -
QUE90_RS28505 (PDTA9730_56310) 110549..111190 - 642 WP_000796664 hypothetical protein -
QUE90_RS28510 (PDTA9730_56320) 111484..111804 + 321 WP_000547566 hypothetical protein -
QUE90_RS28515 (PDTA9730_56330) 112108..112293 + 186 WP_001186917 hypothetical protein -
QUE90_RS28520 (PDTA9730_56340) 112513..113481 + 969 WP_000085162 AAA family ATPase -
QUE90_RS28525 (PDTA9730_56350) 113492..114400 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   13527 GenBank   NZ_AP028043
Plasmid name   pTMTA97302 Incompatibility group   IncA/C2
Plasmid size   172011 bp Coordinate of oriT [Strand]   86252..86402 [+]
Host baterium   Phytobacter diazotrophicus strain TA9730

Cargo genes

Drug resistance gene   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   -