Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119121
Name   oriT_pHDAS3.2 in_silico
Organism   Candidatus Hamiltonella defensa strain AS3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP017612 (34472..34616 [+], 145 nt)
oriT length   145 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 145 nt

>oriT_pHDAS3.2
TGGTCGATGTGAACCCCTTCGACAGGGTTATGAATGCGTTGAAAAGTCGTGGACGCAAGAACGCCCATATCCTGAGCATCCTTCAATTCGACTGGCCTGCATCTGAGATCATCATTGAGAAGCTGAGCTGTTACATCACAGACGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12086 GenBank   WP_100103821
Name   mobH_BJP42_RS11355_pHDAS3.2 insolico UniProt ID   _
Length   833 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 833 a.a.        Molecular weight: 93040.68 Da        Isoelectric Point: 5.5687

>WP_100103821.1 MobH family relaxase [Candidatus Hamiltonella defensa]
MMRALKKLFGGRSGVIETAPSDRVMPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDEFNRLVLPVIYRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWANRHKIDRYFIRWRDKRHKRHEQFSL
LTIDRIIPAESREFLSTSGPSIMEAMLEAISGTRVNQPVTRLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNQPGAKVWHLNQGIFIAWKHLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAIPNTVQEKGERAYYRYWKVLPEMLQETAGSVKILMLRLESNDLVFTTEPPAAVTAEVVGDVEDAEIE
FVDPEEDDDEQEEGEAALNNDMLAAEQEAGKALAGIGFGNAENDNPLFTDAPEQKRPESDLPQTDKLEQK
GKDAKTVLNEILAGYGEASILLEQAIIPVLEGKTTLGEVLCLMKGQAVILYPEGARSLGAPSEVLSKLSH
ANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSSAVVAAIKDAETSMGGYQDAFELVSPPGADASNSQSAQK
KQSQKKPQQQQQKTDVGSGKTAPAQNATGKSSQQPPKEKKVDVDTVVEDKKRKPVEEKQNLARLPKREAQ
PTAVEPKVEREKELGHVEWREREDQEVREFEPPKAKTNPKDIKEEDFLPSGVTPQKAIQMLKDMIQKRSG
RWLVTPVLEEDGCLVTSDKAFDMIAGENTGISKHILCGLLSRAQRRPLLKKRQGKLYLEVDET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   14155 GenBank   WP_100097193
Name   traD_BJP42_RS11360_pHDAS3.2 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: 69452.97 Da        Isoelectric Point: 7.3339

>WP_100097193.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Candidatus Hamiltonella]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLRGRDLEFISIAELQKYIKDRPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTLKKVVRKI
RGKRKALPIGQPWIHGVEPKEEQLMQPLKHTEGHTLIVGTTGSGKTRLFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPAESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNITQGLVITHDRPNLTKLRRFLEGGAAGLVIRAVQTYSERVMSDWETEAAAYLEKVKNGSREKIAFA
LMKFYYEVIQPEHANSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFIATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHEGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILIQ

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(170-327)

TraM recognition site of TraD and TraG (TraG-D_C)

(471-598)

  Protein structure



No available structure.



ID   14156 GenBank   WP_100103811
Name   traC_BJP42_RS11430_pHDAS3.2 insolico UniProt ID   _
Length   814 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 814 a.a.        Molecular weight: 92520.68 Da        Isoelectric Point: 5.9774

>WP_100103811.1 type IV secretion system protein TraC [Candidatus Hamiltonella defensa]
MIVTIKKKLEETVIPEHFRAAGIIPVLAYDEDDHVFLMDDHSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMINLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTDKGIYDNGLIQ
DLKLFVTCKVPISNNNPSEIELQHLAQLRTKVQSSLQTVGLRPRTMKAVNYIRIMSTILNWGPDASWRHD
AVDWEMNKPICEQIFDYSTDVEVSKNGIRLGDYNAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDILYESMKEGAKPVKITYSVVLF
APTKERVEAEAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRHKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVITAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQTSALKQVLSRLWE
EKGKEMKVDDIAEHCLEGEDVRLRDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHLR
QVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLYE
NAVGRAIAENSASMYLLGQTEETVESVKRSGRLSLSEGGFHTLKTVHTLQGVYSEIFIKSKSGMGVGRLI
VGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRQQSA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(21-255)

TraG P-loop domain (P-loop_TraG)

(449-808)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 18862..64431

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BJP42_RS11255 (BJP42_10855) 14732..14950 + 219 WP_100097211 hypothetical protein -
BJP42_RS11925 14968..15141 + 174 WP_157791491 hypothetical protein -
BJP42_RS11260 (BJP42_10860) 15367..16152 + 786 WP_100097210 ParA family protein -
BJP42_RS11265 (BJP42_10865) 16156..17337 + 1182 WP_100103818 ParB/RepB/Spo0J family partition protein -
BJP42_RS11270 (BJP42_10870) 17386..17658 + 273 WP_100097208 helix-turn-helix domain-containing protein -
BJP42_RS11275 (BJP42_10875) 17704..18246 - 543 WP_100097207 FlhC family transcriptional regulator -
BJP42_RS11280 (BJP42_10880) 18243..18851 - 609 WP_100097206 flagellar transcriptional regulator FlhD -
BJP42_RS11285 (BJP42_10885) 18862..19395 - 534 WP_100097205 transglycosylase SLT domain-containing protein virB1
BJP42_RS11290 (BJP42_10890) 19434..19601 - 168 Protein_15 nucleotide excision repair protein -
BJP42_RS11295 (BJP42_10895) 20284..20646 + 363 WP_100141782 permease -
BJP42_RS11300 (BJP42_10900) 20684..21652 - 969 Protein_17 conjugal transfer protein TraG -
BJP42_RS11305 (BJP42_10905) 21696..22073 + 378 WP_012737971 IS630 transposase-related protein -
BJP42_RS12895 22114..22278 + 165 WP_234810885 hypothetical protein -
BJP42_RS12900 22321..22518 + 198 WP_234810886 transposase -
BJP42_RS11315 (BJP42_10915) 22536..25199 - 2664 Protein_21 conjugal transfer protein TraG N-terminal domain-containing protein -
BJP42_RS11320 (BJP42_10920) 25212..26645 - 1434 WP_100103816 conjugal transfer protein TraH traH
BJP42_RS11325 (BJP42_10925) 26647..27108 - 462 Protein_23 conjugal transfer protein TraF -
BJP42_RS12905 27131..27328 - 198 WP_234810886 transposase -
BJP42_RS12910 27371..27535 - 165 WP_234810885 hypothetical protein -
BJP42_RS11335 (BJP42_10935) 27576..27953 - 378 WP_012737971 IS630 transposase-related protein -
BJP42_RS12115 (BJP42_10940) 28199..28477 + 279 Protein_27 hypothetical protein -
BJP42_RS11345 (BJP42_10945) 28479..28898 + 420 WP_100097196 H-NS histone family protein -
BJP42_RS11350 (BJP42_10950) 29275..29889 - 615 WP_100103815 hypothetical protein -
BJP42_RS11355 (BJP42_10955) 30058..32559 + 2502 WP_100103821 MobH family relaxase -
BJP42_RS11360 (BJP42_10960) 32556..34421 + 1866 WP_100097193 conjugative transfer system coupling protein TraD virb4
BJP42_RS11365 (BJP42_10965) 34432..35016 + 585 WP_100097192 hypothetical protein -
BJP42_RS11370 (BJP42_10970) 34973..35602 + 630 WP_100097191 DUF4400 domain-containing protein tfc7
BJP42_RS11375 (BJP42_10975) 35769..36020 + 252 WP_100103814 hypothetical protein -
BJP42_RS11380 (BJP42_10980) 36065..36346 + 282 WP_100097189 type IV conjugative transfer system protein TraL traL
BJP42_RS11385 (BJP42_10985) 36343..36969 + 627 WP_100097188 TraE/TraK family type IV conjugative transfer system protein traE
BJP42_RS11390 (BJP42_10990) 36953..37537 + 585 WP_234813191 hypothetical protein traK
BJP42_RS11395 (BJP42_10995) 37554..37931 + 378 WP_012737971 IS630 transposase-related protein -
BJP42_RS11400 (BJP42_11000) 37855..38376 + 522 WP_320410290 IS630 family transposase -
BJP42_RS11405 (BJP42_11005) 38385..38774 + 390 WP_234813190 type-F conjugative transfer system secretin TraK traK
BJP42_RS11410 (BJP42_11010) 38774..40087 + 1314 WP_193432663 TraB/VirB10 family protein traB
BJP42_RS11415 (BJP42_11015) 40084..40650 + 567 WP_100103813 type IV conjugative transfer system lipoprotein TraV traV
BJP42_RS11420 (BJP42_11020) 40663..41046 + 384 WP_100097184 TraA family conjugative transfer protein -
BJP42_RS11930 41226..41381 + 156 WP_157791490 hypothetical protein -
BJP42_RS11425 (BJP42_11025) 41530..42237 + 708 WP_100103812 DsbC family protein -
BJP42_RS11430 (BJP42_11030) 42234..44678 + 2445 WP_100103811 type IV secretion system protein TraC virb4
BJP42_RS11435 (BJP42_11035) 44692..45009 + 318 WP_100097181 hypothetical protein -
BJP42_RS11440 (BJP42_11040) 45006..45536 + 531 WP_100103810 S26 family signal peptidase -
BJP42_RS11445 (BJP42_11045) 45499..46764 + 1266 WP_100097179 TrbC family F-type conjugative pilus assembly protein traW
BJP42_RS13135 46774..46974 + 201 Protein_50 EAL domain-containing protein -
BJP42_RS11455 (BJP42_11050) 47001..47984 + 984 WP_234811159 TraU family protein traU
BJP42_RS11460 (BJP42_11055) 48100..50892 + 2793 WP_100103809 conjugal transfer mating pair stabilization protein TraN traN
BJP42_RS11465 (BJP42_11060) 50979..51377 + 399 WP_100103805 DUF6750 family protein traR
BJP42_RS11470 (BJP42_11065) 51646..52254 - 609 WP_234813278 hypothetical protein -
BJP42_RS12915 52251..52499 - 249 WP_234813279 lipoprotein -
BJP42_RS11475 (BJP42_11070) 52621..53268 - 648 WP_100103820 hypothetical protein -
BJP42_RS11485 (BJP42_11075) 53872..54186 - 315 WP_100103807 hypothetical protein -
BJP42_RS11490 (BJP42_11080) 54399..55370 + 972 WP_100103808 Rpn family recombination-promoting nuclease/putative transposase -
BJP42_RS11495 (BJP42_11085) 56063..57034 - 972 WP_100103808 Rpn family recombination-promoting nuclease/putative transposase -
BJP42_RS11500 (BJP42_11090) 57247..57561 + 315 WP_100103807 hypothetical protein -
BJP42_RS11510 (BJP42_11095) 58165..58812 + 648 WP_100103820 hypothetical protein -
BJP42_RS11515 (BJP42_11100) 58934..59788 + 855 WP_100103806 hypothetical protein -
BJP42_RS11520 (BJP42_11105) 60057..60455 - 399 WP_100103805 DUF6750 family protein traR
BJP42_RS11525 (BJP42_11110) 60542..63332 - 2791 Protein_64 conjugal transfer mating pair stabilization protein TraN -
BJP42_RS11530 (BJP42_11115) 63448..64431 - 984 WP_234811159 TraU family protein traU
BJP42_RS13140 64458..64658 - 201 Protein_66 EAL domain-containing protein -
BJP42_RS11540 (BJP42_11120) 64668..65931 - 1264 Protein_67 TrbC family F-type conjugative pilus assembly protein -
BJP42_RS12920 65966..66187 - 222 Protein_68 S26 family signal peptidase -
BJP42_RS12120 66192..66422 - 231 WP_193432767 hypothetical protein -
BJP42_RS11550 (BJP42_11130) 66424..66734 - 311 Protein_70 hypothetical protein -
BJP42_RS11555 (BJP42_11140) 66748..67581 - 834 Protein_71 ATP-binding protein -

Host bacterium

ID   19552 GenBank   NZ_CP017612
Plasmid name   pHDAS3.2 Incompatibility group   -
Plasmid size   67631 bp Coordinate of oriT [Strand]   34472..34616 [+]
Host baterium   Candidatus Hamiltonella defensa strain AS3

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -