Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105970
Name   oriT_pRHB32-C16_2 in_silico
Organism   Escherichia fergusonii strain RHB32-C16
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP057230 (109980..110237 [-], 258 nt)
oriT length   258 nt
IRs (inverted repeats)      233..238, 241..246  (CGCCCC..GGGGCG)
 172..177, 185..190  (ATAAAA..TTTTAT)
 118..126, 136..144  (GCGGTGTTG..CAACACCGC)
 19..25, 30..36  (GCAAAAA..TTTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 258 nt

>oriT_pRHB32-C16_2
AAAAGCACCACACCCCACGCAAAAACAATTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGACAAATTAGTTCTTCTTGCTCTCTTTGTGATATTTAAAAAAGCGGTGTCGGCGCGGTGTTGTAGCTGCGCCAACACCGCTTTTTAGGGGTGGTACTGACTATTTTCATAAAAAACATCATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTACAGGACGCCCCTGGGGGCGCTGCTAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4019 GenBank   WP_181669070
Name   traI_HVZ03_RS22615_pRHB32-C16_2 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: 192278.17 Da        Isoelectric Point: 5.9889

>WP_181669070.1 conjugative transfer relaxase/helicase TraI [Escherichia fergusonii]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQT
LKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGR
RQLLEGMTFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLIIDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAVSVKAGEESVAQVSGVREQAMLTQTIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGEIPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTEQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRMIRPAQERVEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVQAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRTAITEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-626)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   1777 GenBank   WP_001369361
Name   WP_001369361_pRHB32-C16_2 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   1778 GenBank   WP_001151524
Name   WP_001151524_pRHB32-C16_2 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   4029 GenBank   WP_181669071
Name   traD_HVZ03_RS22630_pRHB32-C16_2 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82884.49 Da        Isoelectric Point: 5.1662

>WP_181669071.1 type IV conjugative transfer system coupling protein TraD [Escherichia fergusonii]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPHVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
IQQQMQRREEVNINVHRERGEDVEPGDDF

  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   4030 GenBank   WP_181669072
Name   traC_HVZ03_RS22720_pRHB32-C16_2 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: 99233.91 Da        Isoelectric Point: 6.0805

>WP_181669072.1 type IV secretion system protein TraC [Escherichia fergusonii]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
KMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFQPLQRDMIGKFGAARDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-763)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 84337..110829

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVZ03_RS22620 (HVZ03_22615) 83703..83930 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
HVZ03_RS22625 (HVZ03_22620) 83930..84328 + 399 WP_000911314 type II toxin-antitoxin system VapC family toxin -
HVZ03_RS22630 (HVZ03_22625) 84337..86526 - 2190 WP_181669071 type IV conjugative transfer system coupling protein TraD virb4
HVZ03_RS22635 (HVZ03_22630) 86779..87510 - 732 WP_000850423 conjugal transfer complement resistance protein TraT -
HVZ03_RS22640 (HVZ03_22635) 87524..88033 - 510 WP_112042696 conjugal transfer entry exclusion protein TraS -
HVZ03_RS22645 (HVZ03_22640) 88030..90855 - 2826 WP_098030591 conjugal transfer mating-pair stabilization protein TraG traG
HVZ03_RS22650 (HVZ03_22645) 90852..92225 - 1374 WP_057781204 conjugal transfer pilus assembly protein TraH traH
HVZ03_RS22655 (HVZ03_22650) 92225..92605 - 381 WP_249418446 F-type conjugal transfer protein TrbF -
HVZ03_RS22660 (HVZ03_22655) 92592..92933 - 342 WP_012477176 P-type conjugative transfer protein TrbJ -
HVZ03_RS22665 (HVZ03_22660) 92863..93408 - 546 WP_000059835 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HVZ03_RS22670 (HVZ03_22665) 93395..93679 - 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
HVZ03_RS22675 (HVZ03_22670) 93760..94074 + 315 WP_000415570 hypothetical protein -
HVZ03_RS22680 (HVZ03_22675) 94076..94423 - 348 WP_001287910 conjugal transfer protein TrbA -
HVZ03_RS22685 (HVZ03_22680) 94439..95182 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
HVZ03_RS22690 (HVZ03_22685) 95175..95432 - 258 WP_000864318 conjugal transfer protein TrbE -
HVZ03_RS22695 (HVZ03_22690) 95460..97268 - 1809 WP_000821840 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HVZ03_RS22700 (HVZ03_22695) 97265..97903 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
HVZ03_RS22705 (HVZ03_22700) 97912..98904 - 993 WP_039587809 conjugal transfer pilus assembly protein TraU traU
HVZ03_RS22710 (HVZ03_22705) 98901..99533 - 633 WP_001203749 type-F conjugative transfer system protein TraW traW
HVZ03_RS22715 (HVZ03_22710) 99530..99916 - 387 WP_000214079 type-F conjugative transfer system protein TrbI -
HVZ03_RS22720 (HVZ03_22715) 99913..102540 - 2628 WP_181669072 type IV secretion system protein TraC virb4
HVZ03_RS22725 (HVZ03_22720) 102700..102921 - 222 WP_001278692 conjugal transfer protein TraR -
HVZ03_RS22730 (HVZ03_22725) 103056..103571 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HVZ03_RS22735 (HVZ03_22730) 103568..103819 - 252 WP_105450581 conjugal transfer protein TrbG -
HVZ03_RS22740 (HVZ03_22735) 103812..104132 - 321 WP_249418447 conjugal transfer protein TrbD virb4
HVZ03_RS22745 (HVZ03_22740) 104119..104709 - 591 WP_163397183 conjugal transfer pilus-stabilizing protein TraP -
HVZ03_RS22750 (HVZ03_22745) 104699..106126 - 1428 WP_181669073 F-type conjugal transfer pilus assembly protein TraB traB
HVZ03_RS22755 (HVZ03_22750) 106126..106854 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HVZ03_RS22760 (HVZ03_22755) 106841..107407 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HVZ03_RS22765 (HVZ03_22760) 107429..107740 - 312 WP_000012126 type IV conjugative transfer system protein TraL traL
HVZ03_RS22770 (HVZ03_22765) 107755..108120 - 366 WP_000994782 type IV conjugative transfer system pilin TraA -
HVZ03_RS22775 (HVZ03_22770) 108153..108548 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HVZ03_RS22780 (HVZ03_22775) 108647..109336 - 690 WP_021532962 conjugal transfer transcriptional regulator TraJ -
HVZ03_RS22785 (HVZ03_22780) 109523..109906 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HVZ03_RS22790 (HVZ03_22785) 110320..110829 + 510 WP_032248719 transglycosylase SLT domain-containing protein -
HVZ03_RS22795 (HVZ03_22790) 111125..111946 - 822 Protein_116 DUF932 domain-containing protein -
HVZ03_RS22800 (HVZ03_22795) 112065..112352 - 288 WP_000107535 hypothetical protein -
HVZ03_RS22805 (HVZ03_22800) 112377..112583 - 207 WP_032248717 hypothetical protein -
HVZ03_RS23550 112653..112825 + 173 Protein_119 hypothetical protein -
HVZ03_RS22810 (HVZ03_22805) 113554..115221 + 1668 WP_052991863 group II intron reverse transcriptase/maturase -
HVZ03_RS22815 (HVZ03_22810) 115362..115529 - 168 WP_001422689 hypothetical protein -
HVZ03_RS22820 (HVZ03_22815) 115622..115744 - 123 WP_223200913 Hok/Gef family protein -

Host bacterium

ID   6407 GenBank   NZ_CP057230
Plasmid name   pRHB32-C16_2 Incompatibility group   IncFIB
Plasmid size   145940 bp Coordinate of oriT [Strand]   109980..110237 [-]
Host baterium   Escherichia fergusonii strain RHB32-C16

Cargo genes

Drug resistance gene   -
Virulence gene   hlyD, hlyB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -