Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117990
Name   oriT_pHDA2C.2 in_silico
Organism   Candidatus Hamiltonella defensa strain A2C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP017608 (32389..32533 [-], 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_pHDA2C.2
TGGTCGATGTGAACCCCTTCGACAGGGTTATGAATGCGTTGAAAAGTCGTGGACGCAAGAACGCCCATATCCTGAGCATCCTTCAATTCGACTGGCCTGCATCTGAGATCATCATTGAGAAGCTGAGCTGTTACATCACAGACGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11411 GenBank   WP_100103821
Name   mobH_BJP41_RS10745_pHDA2C.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   13335 GenBank   WP_100103811
Name   traC_BJP41_RS10670_pHDA2C.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.



ID   13336 GenBank   WP_100097193
Name   traD_BJP41_RS10740_pHDA2C.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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1129..48143

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BJP41_RS10545 51..251 + 201 WP_234811153 hypothetical protein -
BJP41_RS10550 (BJP41_10180) 265..582 + 318 WP_100097181 hypothetical protein -
BJP41_RS10555 (BJP41_10185) 579..1067 + 489 WP_100103803 S26 family signal peptidase -
BJP41_RS10560 (BJP41_10190) 1129..2277 + 1149 WP_100103804 TrbC family F-type conjugative pilus assembly protein traW
BJP41_RS12590 2347..2547 + 201 Protein_4 EAL domain-containing protein -
BJP41_RS10570 (BJP41_10195) 2550..3555 + 1006 Protein_5 TraU family protein -
BJP41_RS10575 (BJP41_10200) 3671..6462 + 2792 Protein_6 conjugal transfer mating pair stabilization protein TraN -
BJP41_RS10580 (BJP41_10205) 6549..6947 + 399 WP_100103805 DUF6750 family protein traR
BJP41_RS10585 (BJP41_10210) 7216..8070 - 855 WP_100103806 hypothetical protein -
BJP41_RS10590 (BJP41_10215) 8192..8839 - 648 WP_100103820 hypothetical protein -
BJP41_RS10600 (BJP41_10220) 9443..9730 - 288 WP_157791489 hypothetical protein -
BJP41_RS10605 (BJP41_10225) 9970..10941 + 972 WP_100103808 Rpn family recombination-promoting nuclease/putative transposase -
BJP41_RS10610 (BJP41_10230) 11634..12605 - 972 WP_100103808 Rpn family recombination-promoting nuclease/putative transposase -
BJP41_RS10615 (BJP41_10235) 12845..13132 + 288 WP_157791489 hypothetical protein -
BJP41_RS10625 (BJP41_10240) 13736..14383 + 648 WP_100103820 hypothetical protein -
BJP41_RS10630 (BJP41_10245) 14505..15359 + 855 WP_100103806 hypothetical protein -
BJP41_RS10635 (BJP41_10250) 15628..16026 - 399 WP_100103805 DUF6750 family protein traR
BJP41_RS10640 (BJP41_10255) 16113..18905 - 2793 WP_100103809 conjugal transfer mating pair stabilization protein TraN traN
BJP41_RS10645 (BJP41_10260) 19021..20004 - 984 WP_234811159 TraU family protein traU
BJP41_RS12595 20031..20231 - 201 Protein_19 EAL domain-containing protein -
BJP41_RS10655 (BJP41_10265) 20241..21506 - 1266 WP_100097179 TrbC family F-type conjugative pilus assembly protein traW
BJP41_RS10660 (BJP41_10270) 21469..21999 - 531 WP_100103810 S26 family signal peptidase -
BJP41_RS10665 (BJP41_10275) 21996..22313 - 318 WP_100097181 hypothetical protein -
BJP41_RS10670 (BJP41_10280) 22327..24771 - 2445 WP_100103811 type IV secretion system protein TraC virb4
BJP41_RS10675 (BJP41_10285) 24768..25475 - 708 WP_100103812 DsbC family protein -
BJP41_RS11565 25624..25779 - 156 WP_157791490 hypothetical protein -
BJP41_RS10680 (BJP41_10290) 25959..26342 - 384 WP_100097184 TraA family conjugative transfer protein -
BJP41_RS10685 (BJP41_10295) 26355..26921 - 567 WP_100103813 type IV conjugative transfer system lipoprotein TraV traV
BJP41_RS10690 (BJP41_10300) 26918..28231 - 1314 WP_193432663 TraB/VirB10 family protein traB
BJP41_RS10695 (BJP41_10305) 28231..28668 - 438 WP_320410296 type-F conjugative transfer system secretin TraK traK
BJP41_RS10700 (BJP41_10310) 28629..29162 - 534 WP_320410289 IS630 family transposase -
BJP41_RS10705 (BJP41_10315) 29074..29451 - 378 WP_012737971 IS630 transposase-related protein -
BJP41_RS10710 (BJP41_10320) 29468..30013 - 546 WP_234811157 hypothetical protein traK
BJP41_RS10715 (BJP41_10325) 30036..30662 - 627 WP_100097188 TraE/TraK family type IV conjugative transfer system protein traE
BJP41_RS10720 (BJP41_10330) 30659..30940 - 282 WP_100097189 type IV conjugative transfer system protein TraL traL
BJP41_RS10725 (BJP41_10335) 30985..31302 - 318 WP_158530228 hypothetical protein -
BJP41_RS10730 (BJP41_10340) 31403..32032 - 630 WP_100097191 DUF4400 domain-containing protein tfc7
BJP41_RS10735 (BJP41_10345) 31989..32573 - 585 WP_100097192 hypothetical protein -
BJP41_RS10740 (BJP41_10350) 32584..34449 - 1866 WP_100097193 conjugative transfer system coupling protein TraD virb4
BJP41_RS10745 (BJP41_10355) 34446..36947 - 2502 WP_100103821 MobH family relaxase -
BJP41_RS10750 (BJP41_10360) 37116..37730 + 615 WP_100103815 hypothetical protein -
BJP41_RS10755 (BJP41_10365) 38107..38526 - 420 WP_100097196 H-NS histone family protein -
BJP41_RS11725 38528..38806 - 279 Protein_42 hypothetical protein -
BJP41_RS10765 (BJP41_10375) 39052..39429 + 378 WP_012737971 IS630 transposase-related protein -
BJP41_RS10770 (BJP41_10380) 39353..39874 + 522 WP_302476659 IS630 family transposase -
BJP41_RS10775 (BJP41_10385) 39897..40358 + 462 Protein_45 conjugal transfer protein TraF -
BJP41_RS10780 (BJP41_10390) 40360..41793 + 1434 WP_100103816 conjugal transfer protein TraH traH
BJP41_RS10785 (BJP41_10395) 41806..44469 + 2664 Protein_47 conjugal transfer protein TraG N-terminal domain-containing protein -
BJP41_RS10790 (BJP41_10400) 44487..45020 - 534 WP_086934965 IS630 family transposase -
BJP41_RS10795 (BJP41_10405) 44932..45309 - 378 WP_012737971 IS630 transposase-related protein -
BJP41_RS10800 (BJP41_10410) 45353..46321 + 969 Protein_50 conjugal transfer protein TraG -
BJP41_RS10805 (BJP41_10415) 46359..46721 - 363 WP_100103817 permease -
BJP41_RS11730 (BJP41_10420) 47404..47571 + 168 Protein_52 nucleotide excision repair protein -
BJP41_RS10815 (BJP41_10425) 47610..48143 + 534 WP_100097205 transglycosylase SLT domain-containing protein virB1
BJP41_RS10820 (BJP41_10430) 48154..48762 + 609 WP_100097206 flagellar transcriptional regulator FlhD -
BJP41_RS10825 (BJP41_10435) 48759..49301 + 543 WP_100097207 FlhC family transcriptional regulator -
BJP41_RS10830 (BJP41_10440) 49347..49619 - 273 WP_100097208 helix-turn-helix domain-containing protein -
BJP41_RS10835 (BJP41_10445) 49668..50849 - 1182 WP_100103818 ParB/RepB/Spo0J family partition protein -
BJP41_RS10840 (BJP41_10450) 50853..51638 - 786 WP_100097210 ParA family protein -
BJP41_RS11570 51864..52037 - 174 WP_157791491 hypothetical protein -
BJP41_RS10845 (BJP41_10455) 52055..52273 - 219 WP_100097211 hypothetical protein -

Host bacterium

ID   18423 GenBank   NZ_CP017608
Plasmid name   pHDA2C.2 Incompatibility group   -
Plasmid size   72453 bp Coordinate of oriT [Strand]   32389..32533 [-]
Host baterium   Candidatus Hamiltonella defensa strain A2C

Cargo genes

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