Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107837
Name   oriT_pJD053-124K in_silico
Organism   Escherichia fergusonii strain EF21JD053
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP095789 (97606..97729 [-], 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_pJD053-124K
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5261 GenBank   WP_247859139
Name   traI_MYB88_RS23575_pJD053-124K insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191945.85 Da        Isoelectric Point: 6.0918

>WP_247859139.1 conjugative transfer relaxase/helicase TraI [Escherichia fergusonii]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT
LKETGFDIRAYRDAAEQRAYTRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
AGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFAAVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KAHAGETSLETSISLQKAGLHTPAQQAIHLALPVLESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESMRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   2410 GenBank   WP_001254386
Name   WP_001254386_pJD053-124K 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

ID   2411 GenBank   WP_000124981
Name   WP_000124981_pJD053-124K 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


T4CP

ID   5504 GenBank   WP_247859140
Name   traD_MYB88_RS23580_pJD053-124K insolico UniProt ID   _
Length   723 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 723 a.a.        Molecular weight: 82181.76 Da        Isoelectric Point: 5.1083

>WP_247859140.1 type IV conjugative transfer system coupling protein TraD [Escherichia fergusonii]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDTQQQMQ
RREEVNINVHRERGEDVEPGDDF

  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   5505 GenBank   WP_001064268
Name   traC_MYB88_RS23670_pJD053-124K 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: 99248.97 Da        Isoelectric Point: 6.0801

>WP_001064268.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNKARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 71620..98301

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MYB88_RS23580 (MYB88_23575) 71620..73791 - 2172 WP_247859140 type IV conjugative transfer system coupling protein TraD virb4
MYB88_RS23585 (MYB88_23580) 74044..74775 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
MYB88_RS23590 (MYB88_23585) 74807..75310 - 504 WP_000605510 hypothetical protein -
MYB88_RS23595 (MYB88_23590) 75325..78147 - 2823 WP_001007026 conjugal transfer mating-pair stabilization protein TraG traG
MYB88_RS23600 (MYB88_23595) 78144..79517 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
MYB88_RS23605 (MYB88_23600) 79517..79879 - 363 WP_001443292 P-type conjugative transfer protein TrbJ -
MYB88_RS23610 (MYB88_23605) 79809..80354 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MYB88_RS23615 (MYB88_23610) 80341..80625 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
MYB88_RS23620 (MYB88_23615) 80744..81091 - 348 WP_072834356 conjugal transfer protein TrbA -
MYB88_RS23625 (MYB88_23620) 81107..81850 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
MYB88_RS23630 (MYB88_23625) 81843..82100 - 258 WP_000864325 conjugal transfer protein TrbE -
MYB88_RS23635 (MYB88_23630) 82127..83935 - 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MYB88_RS23640 (MYB88_23635) 83932..84570 - 639 WP_001104248 type-F conjugative transfer system pilin assembly protein TrbC trbC
MYB88_RS23645 (MYB88_23640) 84598..85050 - 453 WP_000069427 hypothetical protein -
MYB88_RS23650 (MYB88_23645) 85080..85541 - 462 WP_000277845 hypothetical protein -
MYB88_RS23655 (MYB88_23650) 85567..86559 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
MYB88_RS23660 (MYB88_23655) 86556..87188 - 633 WP_001203745 type-F conjugative transfer system protein TraW traW
MYB88_RS23665 (MYB88_23660) 87185..87571 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
MYB88_RS23670 (MYB88_23665) 87568..90195 - 2628 WP_001064268 type IV secretion system protein TraC virb4
MYB88_RS23675 (MYB88_23670) 90355..90576 - 222 WP_001278689 conjugal transfer protein TraR -
MYB88_RS23680 (MYB88_23675) 90711..91226 - 516 WP_000809906 type IV conjugative transfer system lipoprotein TraV traV
MYB88_RS23685 (MYB88_23680) 91223..91474 - 252 WP_001038341 conjugal transfer protein TrbG -
MYB88_RS23690 (MYB88_23685) 91471..91788 - 318 WP_001057292 conjugal transfer protein TrbD virb4
MYB88_RS23695 (MYB88_23690) 91785..92357 - 573 WP_000002780 conjugal transfer pilus-stabilizing protein TraP -
MYB88_RS23700 (MYB88_23695) 92347..93774 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
MYB88_RS23705 (MYB88_23700) 93774..94502 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
MYB88_RS23710 (MYB88_23705) 94489..95055 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
MYB88_RS23715 (MYB88_23710) 95077..95388 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
MYB88_RS23720 (MYB88_23715) 95403..95762 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
MYB88_RS23725 (MYB88_23720) 95796..96023 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
MYB88_RS23730 (MYB88_23725) 96117..96803 - 687 WP_000332484 PAS domain-containing protein -
MYB88_RS23735 (MYB88_23730) 96994..97377 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
MYB88_RS23740 (MYB88_23735) 97654..98301 + 648 WP_000614936 transglycosylase SLT domain-containing protein virB1
MYB88_RS23745 (MYB88_23740) 98598..99419 - 822 WP_001234469 DUF932 domain-containing protein -
MYB88_RS23750 (MYB88_23745) 99541..99828 - 288 WP_000107535 hypothetical protein -
MYB88_RS23755 (MYB88_23750) 99853..100059 - 207 WP_000547939 hypothetical protein -
MYB88_RS23760 (MYB88_23755) 100129..100302 + 174 Protein_119 hypothetical protein -
MYB88_RS23765 (MYB88_23760) 101031..102698 + 1668 WP_001762494 group II intron reverse transcriptase/maturase -
MYB88_RS23770 (MYB88_23765) 102811..102987 + 177 Protein_121 pilus protein -

Host bacterium

ID   8272 GenBank   NZ_CP095789
Plasmid name   pJD053-124K Incompatibility group   IncFIB
Plasmid size   124926 bp Coordinate of oriT [Strand]   97606..97729 [-]
Host baterium   Escherichia fergusonii strain EF21JD053

Cargo genes

Drug resistance gene   aph(3')-Ia, sul3, dfrA14, floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaTEM-1B, aac(3)-IId, sitABCD
Virulence gene   -
Metal resistance gene   merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -