Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103345
Name   oriT_pZM3 in_silico
Organism   Salmonella enterica subsp. enterica serovar Wien strain ZM3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK797990 (110913..111036 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pZM3
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTACTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2503 GenBank   WP_001617867
Name   traI_HTW79_RS00470_pZM3 insolico UniProt ID   A0A2Z5WSA2
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191679.38 Da        Isoelectric Point: 5.8498

>WP_001617867.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFPPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTEAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDEPRTAEKLARHPSFTVVSDQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGTSETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGRGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRTASSERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   1069 GenBank   WP_001254388
Name   WP_001254388_pZM3 insolico UniProt ID   W9A0Z2
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB W9A0Z2

ID   1070 GenBank   WP_172694660
Name   WP_172694660_pZM3 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14476.46 Da        Isoelectric Point: 4.8498

>WP_172694660.1 conjugal transfer relaxosome DNA-binding protein TraM [Salmonella enterica]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYETQMERKESAFNQTEFNKLI
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPENDEG

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.




T4CP

ID   2275 GenBank   WP_023356304
Name   traD_HTW79_RS00475_pZM3 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83847.55 Da        Isoelectric Point: 5.1657

>WP_023356304.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   2276 GenBank   WP_001064258
Name   traC_HTW79_RS00580_pZM3 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99195.72 Da        Isoelectric Point: 5.8689

>WP_001064258.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLKSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNYKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFQPLQRDMIGKFGAARDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-763)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 82765..111608

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTW79_RS00475 (NCLADELE_00093) 82765..84981 - 2217 WP_023356304 type IV conjugative transfer system coupling protein TraD virb4
HTW79_RS00480 (NCLADELE_00094) 84978..85757 - 780 WP_000199914 hypothetical protein -
HTW79_RS00485 (NCLADELE_00095) 85960..86691 - 732 WP_000850429 conjugal transfer complement resistance protein TraT -
HTW79_RS00490 (NCLADELE_00096) 86723..87220 - 498 WP_000605862 entry exclusion protein -
HTW79_RS00495 (NCLADELE_00097) 87239..90058 - 2820 WP_001007062 conjugal transfer mating-pair stabilization protein TraG traG
HTW79_RS00500 (NCLADELE_00098) 90055..91428 - 1374 WP_000944328 conjugal transfer pilus assembly protein TraH traH
HTW79_RS00505 91415..91807 - 393 WP_000659962 F-type conjugal transfer protein TrbF -
HTW79_RS00510 91788..92135 - 348 WP_071571857 P-type conjugative transfer protein TrbJ -
HTW79_RS00515 92065..92610 - 546 WP_000059829 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTW79_RS00520 92597..92881 - 285 WP_001617873 type-F conjugative transfer system pilin chaperone TraQ -
HTW79_RS00525 (NCLADELE_00099) 93008..93328 - 321 WP_001348757 conjugal transfer protein TrbA -
HTW79_RS00535 (NCLADELE_00104) 94228..95208 - 981 WP_000019450 IS5-like element ISKpn26 family transposase -
HTW79_RS00540 (NCLADELE_00105) 95338..96081 - 744 WP_001030401 type-F conjugative transfer system pilin assembly protein TraF traF
HTW79_RS00545 (NCLADELE_00106) 96074..96331 - 258 WP_000864347 conjugal transfer protein TrbE -
HTW79_RS00550 (NCLADELE_00107) 96358..98208 - 1851 WP_000821866 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTW79_RS00555 (NCLADELE_00108) 98205..98843 - 639 WP_001080259 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTW79_RS00560 (NCLADELE_00109) 98852..99157 - 306 WP_000224413 hypothetical protein -
HTW79_RS00565 (NCLADELE_00110) 99187..100179 - 993 WP_000830190 conjugal transfer pilus assembly protein TraU traU
HTW79_RS00570 (NCLADELE_00111) 100176..100808 - 633 WP_001203727 type-F conjugative transfer system protein TraW traW
HTW79_RS00575 (NCLADELE_00112) 100805..101191 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTW79_RS00580 (NCLADELE_00113) 101188..103815 - 2628 WP_001064258 type IV secretion system protein TraC virb4
HTW79_RS00585 (NCLADELE_00115) 103975..104196 - 222 WP_001278694 conjugal transfer protein TraR -
HTW79_RS00590 (NCLADELE_00116) 104331..104846 - 516 WP_000809886 type IV conjugative transfer system lipoprotein TraV traV
HTW79_RS00595 (NCLADELE_00100) 104846..105157 - 312 WP_001057272 conjugal transfer protein TrbD -
HTW79_RS00600 (NCLADELE_00118) 105144..105710 - 567 WP_000896601 conjugal transfer pilus-stabilizing protein TraP -
HTW79_RS00605 (NCLADELE_00119) 105700..107151 - 1452 WP_000146687 F-type conjugal transfer pilus assembly protein TraB traB
HTW79_RS00610 (NCLADELE_00120) 107151..107879 - 729 WP_001230808 type-F conjugative transfer system secretin TraK traK
HTW79_RS00615 (NCLADELE_00121) 107866..108432 - 567 WP_000399791 type IV conjugative transfer system protein TraE traE
HTW79_RS00620 (NCLADELE_00122) 108454..108765 - 312 WP_000012107 type IV conjugative transfer system protein TraL traL
HTW79_RS00625 (NCLADELE_00123) 108770..109132 - 363 WP_000338606 type IV conjugative transfer system pilin TraA -
HTW79_RS00630 (NCLADELE_00124) 109166..109393 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
HTW79_RS00635 (NCLADELE_00125) 109481..110158 - 678 WP_001348626 PAS domain-containing protein -
HTW79_RS00640 (NCLADELE_00126) 110292..110675 - 384 WP_172694660 conjugal transfer relaxosome DNA-binding protein TraM -
HTW79_RS00645 (NCLADELE_00127) 111006..111608 + 603 WP_000243712 transglycosylase SLT domain-containing protein virB1
HTW79_RS00650 (NCLADELE_00128) 111905..112726 - 822 WP_001234469 DUF932 domain-containing protein -
HTW79_RS00655 (NCLADELE_00129) 112845..113132 - 288 WP_000107535 hypothetical protein -
HTW79_RS00660 113157..113363 - 207 WP_000275859 hypothetical protein -
HTW79_RS00960 113433..113606 + 174 Protein_134 hypothetical protein -
HTW79_RS00965 113604..113834 - 231 WP_001426396 hypothetical protein -
HTW79_RS00670 (NCLADELE_00130) 114054..114179 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTW79_RS00970 (NCLADELE_00130) 114121..114270 - 150 Protein_137 plasmid maintenance protein Mok -

Host bacterium

ID   3788 GenBank   NZ_MK797990
Plasmid name   pZM3 Incompatibility group   IncFIB
Plasmid size   166767 bp Coordinate of oriT [Strand]   110913..111036 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Wien strain ZM3

Cargo genes

Drug resistance gene   tet(B), catA1, blaOXA-1, ant(3'')-Ia, qacE, sul1, aph(3')-Ia, blaTEM-1A, sitABCD
Virulence gene   iucA, iucB, iucC, iutA
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -