Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107845
Name   oriT_pZY-1 in_silico
Organism   Citrobacter freundii strain ZY198
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055248 (52379..52502 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 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_pZY-1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5266 GenBank   WP_061093447
Name   traI_GTH18_RS24440_pZY-1 insolico UniProt ID   A0A2Z4I1F4
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192119.90 Da        Isoelectric Point: 6.0788

>WP_061093447.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

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

(633-712)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   2414 GenBank   WP_000124981
Name   WP_000124981_pZY-1 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   2415 GenBank   WP_001254386
Name   WP_001254386_pZY-1 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   5510 GenBank   WP_112929298
Name   traC_GTH18_RS24330_pZY-1 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: 99397.23 Da        Isoelectric Point: 6.3465

>WP_112929298.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREGM
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.



ID   5511 GenBank   WP_072646483
Name   traD_GTH18_RS24435_pZY-1 insolico UniProt ID   _
Length   747 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 747 a.a.        Molecular weight: 84966.71 Da        Isoelectric Point: 5.0504

>WP_072646483.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESG
EVVDMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 51807..80013

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GTH18_RS24235 (GTH18_24235) 47797..48231 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
GTH18_RS24240 (GTH18_24240) 48228..48947 + 720 WP_001276217 plasmid SOS inhibition protein A -
GTH18_RS25980 49169..49318 + 150 Protein_62 plasmid maintenance protein Mok -
GTH18_RS24245 (GTH18_24245) 49260..49385 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
GTH18_RS25755 49686..49982 - 297 Protein_64 hypothetical protein -
GTH18_RS24250 (GTH18_24250) 50282..50578 + 297 WP_001272251 hypothetical protein -
GTH18_RS24255 (GTH18_24255) 50689..51510 + 822 WP_001234445 DUF932 domain-containing protein -
GTH18_RS24260 (GTH18_24260) 51807..52454 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
GTH18_RS24265 (GTH18_24265) 52731..53114 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
GTH18_RS24270 (GTH18_24270) 53305..53991 + 687 WP_015059009 PAS domain-containing protein -
GTH18_RS24275 (GTH18_24275) 54085..54312 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
GTH18_RS24280 (GTH18_24280) 54346..54711 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
GTH18_RS24285 (GTH18_24285) 54726..55037 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
GTH18_RS24290 (GTH18_24290) 55059..55625 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
GTH18_RS24295 (GTH18_24295) 55612..56340 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
GTH18_RS24300 (GTH18_24300) 56340..57767 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
GTH18_RS24305 (GTH18_24305) 57757..58347 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
GTH18_RS24310 (GTH18_24310) 58334..58531 + 198 WP_001324648 conjugal transfer protein TrbD -
GTH18_RS24315 (GTH18_24315) 58543..58794 + 252 WP_001038341 conjugal transfer protein TrbG -
GTH18_RS24320 (GTH18_24320) 58791..59306 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
GTH18_RS24325 (GTH18_24325) 59441..59662 + 222 WP_001278692 conjugal transfer protein TraR -
GTH18_RS24330 (GTH18_24330) 59822..62449 + 2628 WP_112929298 type IV secretion system protein TraC virb4
GTH18_RS24335 (GTH18_24335) 62446..62832 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
GTH18_RS24340 (GTH18_24340) 62829..63461 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
GTH18_RS24345 (GTH18_24345) 63458..64450 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
GTH18_RS24350 (GTH18_24350) 64477..64785 + 309 WP_000412447 hypothetical protein -
GTH18_RS24355 (GTH18_24355) 64848..65369 + 522 WP_015059014 hypothetical protein -
GTH18_RS24360 (GTH18_24360) 65396..66034 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
GTH18_RS24365 (GTH18_24365) 66031..66402 + 372 WP_000056336 hypothetical protein -
GTH18_RS24370 (GTH18_24370) 66428..66850 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
GTH18_RS24375 (GTH18_24375) 66847..68697 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
GTH18_RS24380 (GTH18_24380) 68724..68981 + 258 WP_000864320 conjugal transfer protein TrbE -
GTH18_RS24385 (GTH18_24385) 68974..69717 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
GTH18_RS24390 (GTH18_24390) 69878..70114 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
GTH18_RS24395 (GTH18_24395) 70101..70646 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
GTH18_RS24400 (GTH18_24400) 70636..70950 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
GTH18_RS24405 (GTH18_24405) 70904..71296 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
GTH18_RS24410 (GTH18_24410) 71283..72656 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
GTH18_RS24415 (GTH18_24415) 72653..75469 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
GTH18_RS24420 (GTH18_24420) 75502..76023 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
GTH18_RS24425 (GTH18_24425) 76048..76779 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
GTH18_RS24430 (GTH18_24430) 76982..77719 + 738 WP_015059020 hypothetical protein -
GTH18_RS24435 (GTH18_24435) 77770..80013 + 2244 WP_072646483 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   8280 GenBank   NZ_CP055248
Plasmid name   pZY-1 Incompatibility group   ColE10
Plasmid size   89672 bp Coordinate of oriT [Strand]   52379..52502 [+]
Host baterium   Citrobacter freundii strain ZY198

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, fosA3, blaTEM-1B, blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -