Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122449
Name   oriT1_pHDZA17.1 in_silico
Organism   Candidatus Hamiltonella defensa strain ZA17
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP017614 (36698..36842 [-], 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

>oriT1_pHDZA17.1
TGGTCGATGTGAACCCCTTCGACAGGGTTATGAATGCGTTGAAAAGTCGTGGACGCAAGAACGCCCATATCCTGAGCATCCTTCAATTCGACTGGCCTGCATCTGAGATCATCATTGAGAAGCTGAGCTGTTACATCACAGACGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14153 GenBank   WP_100097194
Name   mobH_BJP43_RS10610_pHDZA17.1 insolico UniProt ID   _
Length   834 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 834 a.a.        Molecular weight: 93246.88 Da        Isoelectric Point: 5.4207

>WP_100097194.1 MobH family relaxase [Candidatus Hamiltonella defensa]
MMRALKKLFGGRSGVIETAPSDRVMPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDEFNRLVLPVIYRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWANRHKIDRYFIRWRDKRHKRHEQFSL
LTIDRIIPAESREFLSTSGPSIMEAMLEAISGTRVNQPVTRLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNQPGAKVWHLNQGIFIAWKHLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAIPNTVQEKGERAYYRYWKVLPEMLQETAGSVKILMLRLESNDLVFTTEPPAAVTAEVVGDVEDAEIE
FVDPEEDDDEQEEGEAALNNDMLAAEQEAGKALAGIGFGNAENDNPLFTDAPEQKRPESDLPQTDKLEQK
GKDAKTVLNEILAGYGEASILLEQAIIPVLEGKTTLGEVLCLMKGQAVILYPEGARSLGAPSEVLSKLSH
ANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSSAVVAAIKDAETSMGGYQDAFELVSPPGADASKSQSAQK
KQSQKKPQQQQQKTDVGSGETAPAQNATGKSSQQPPKEKKVDVDTVVEDKKRKPVEEKQNLARLPKREAQ
PTAVEPKFEREKELGHVEWREREEDQEVREFEPPKAKTNPKDIKEEDFLPSGVTPQKAIQMLKDMIQKRS
GRWLVTPVLEEDGCLVTSDKAFEMIAGENTGISKHILCGLLSRAQRRPLLKKRQGKLYLEVDET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   16454 GenBank   WP_100097182
Name   traC_BJP43_RS10550_pHDZA17.1 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: 92517.64 Da        Isoelectric Point: 6.0486

>WP_100097182.1 MULTISPECIES: type IV secretion system protein TraC [Candidatus Hamiltonella]
MIVTIKKKLEETVIPEHFRAAGIIPVLAYDEDDHVFLMDDHSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMINLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTDKGIYDNGLIQ
DLKLFVTCKVPISNNNPSESELQHLAQLRTKVQSSLQTVGLRPRTMKAVNYIRIMSTILNWGPDASWRHD
AVDWEMNKPICEQIFDYSTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
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   16455 GenBank   WP_100097193
Name   traD_BJP43_RS10605_pHDZA17.1 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: 21326..55377

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BJP43_RS11705 16821..17036 + 216 WP_158531014 Tn3 family transposase -
BJP43_RS11710 18100..18261 + 162 WP_158531013 hypothetical protein -
BJP43_RS12965 18314..18445 + 132 WP_267892432 hypothetical protein -
BJP43_RS10505 (BJP43_10240) 18534..19703 - 1170 WP_100097175 YopJ family acetyltransferase -
BJP43_RS10510 (BJP43_10245) 19738..20625 - 888 WP_100097176 IS982 family transposase -
BJP43_RS13075 21011..21056 + 46 Protein_23 hypothetical protein -
BJP43_RS13080 21085..21240 - 156 Protein_24 DUF6750 family protein -
BJP43_RS10520 (BJP43_10255) 21326..24118 - 2793 WP_100097177 conjugal transfer mating pair stabilization protein TraN traN
BJP43_RS10525 (BJP43_10260) 24234..25217 - 984 WP_234811159 TraU family protein traU
BJP43_RS13085 25244..25444 - 201 Protein_27 EAL domain-containing protein -
BJP43_RS10535 (BJP43_10265) 25454..26719 - 1266 WP_100097179 TrbC family F-type conjugative pilus assembly protein traW
BJP43_RS10540 (BJP43_10270) 26682..27212 - 531 WP_100097180 signal peptidase I -
BJP43_RS10545 (BJP43_10275) 27209..27526 - 318 WP_100097181 hypothetical protein -
BJP43_RS10550 (BJP43_10280) 27540..29984 - 2445 WP_100097182 type IV secretion system protein TraC virb4
BJP43_RS10555 (BJP43_10285) 29981..30688 - 708 WP_100097183 DsbC family protein -
BJP43_RS10560 (BJP43_10290) 31172..31555 - 384 WP_100097184 TraA family conjugative transfer protein -
BJP43_RS10565 (BJP43_10295) 31568..32134 - 567 WP_100097185 type IV conjugative transfer system lipoprotein TraV traV
BJP43_RS10570 (BJP43_10300) 32131..33444 - 1314 WP_193432663 TraB/VirB10 family protein traB
BJP43_RS10575 (BJP43_10305) 33444..34361 - 918 WP_100097187 type-F conjugative transfer system secretin TraK traK
BJP43_RS10580 (BJP43_10310) 34345..34971 - 627 WP_100097188 TraE/TraK family type IV conjugative transfer system protein traE
BJP43_RS10585 (BJP43_10315) 34968..35249 - 282 WP_100097189 type IV conjugative transfer system protein TraL traL
BJP43_RS10590 (BJP43_10320) 35294..35545 - 252 WP_100097190 hypothetical protein -
BJP43_RS10595 (BJP43_10325) 35712..36341 - 630 WP_100097191 DUF4400 domain-containing protein tfc7
BJP43_RS10600 (BJP43_10330) 36298..36843 - 546 WP_234817548 hypothetical protein -
BJP43_RS10605 (BJP43_10335) 36893..38758 - 1866 WP_100097193 conjugative transfer system coupling protein TraD virb4
BJP43_RS10610 (BJP43_10340) 38755..41259 - 2505 WP_100097194 MobH family relaxase -
BJP43_RS10615 (BJP43_10345) 41428..42042 + 615 WP_100097195 hypothetical protein -
BJP43_RS10620 (BJP43_10350) 42419..42838 - 420 WP_100097196 H-NS histone family protein -
BJP43_RS12005 (BJP43_10355) 42840..43118 - 279 Protein_46 hypothetical protein -
BJP43_RS10630 (BJP43_10360) 43655..44194 + 540 WP_193432662 conjugative transfer protein MobI(A/C) -
BJP43_RS12730 44199..44285 + 87 Protein_48 hypothetical protein -
BJP43_RS12735 44303..44430 + 128 Protein_49 hypothetical protein -
BJP43_RS10635 (BJP43_10370) 44511..44699 + 189 Protein_50 zinc ribbon domain-containing protein -
BJP43_RS10640 (BJP43_10375) 44761..45627 + 867 WP_100097198 DsbA family protein -
BJP43_RS10645 (BJP43_10380) 45729..46773 + 1045 Protein_52 conjugal transfer protein TraF -
BJP43_RS10650 (BJP43_10385) 46775..48208 + 1434 WP_100097200 conjugal transfer protein TraH traH
BJP43_RS10655 (BJP43_10390) 48221..51793 + 3573 WP_100097201 conjugal transfer protein TraG N-terminal domain-containing protein traG
BJP43_RS10660 (BJP43_10395) 51898..53106 - 1209 WP_100097202 RNA-guided endonuclease TnpB family protein -
BJP43_RS10665 (BJP43_10400) 53129..53545 + 417 WP_193432661 IS200/IS605 family transposase -
BJP43_RS10670 (BJP43_10405) 53560..53953 - 394 Protein_57 permease -
BJP43_RS10675 (BJP43_10410) 54638..54805 + 168 Protein_58 nucleotide excision repair protein -
BJP43_RS10680 (BJP43_10415) 54844..55377 + 534 WP_100097205 transglycosylase SLT domain-containing protein virB1
BJP43_RS10685 (BJP43_10420) 55388..55996 + 609 WP_100097206 flagellar transcriptional regulator FlhD -
BJP43_RS10690 (BJP43_10425) 55993..56535 + 543 WP_100097207 FlhC family transcriptional regulator -
BJP43_RS10695 (BJP43_10430) 56581..56853 - 273 WP_100097208 helix-turn-helix domain-containing protein -
BJP43_RS10700 (BJP43_10435) 56902..58083 - 1182 WP_100097209 ParB/RepB/Spo0J family partition protein -
BJP43_RS10705 (BJP43_10440) 58087..58872 - 786 WP_100097210 ParA family protein -
BJP43_RS11720 59098..59271 - 174 WP_157791491 hypothetical protein -
BJP43_RS12015 (BJP43_10445) 59289..59507 - 219 WP_100097211 hypothetical protein -

Host bacterium

ID   22875 GenBank   NZ_CP017614
Plasmid name   pHDZA17.1 Incompatibility group   -
Plasmid size   98627 bp Coordinate of oriT [Strand]   36698..36842 [-]; 43526..43629 [+]
Host baterium   Candidatus Hamiltonella defensa strain ZA17

Cargo genes

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