Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101560
Name   oriT_EC-28|unnamed3 in_silico
Organism   Escherichia coli strain EC-28
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAWLTU010000004 (35668..35753 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_EC-28|unnamed3
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1383 GenBank   WP_015059148
Name   traI_V6E60_RS25915_EC-28|unnamed3 insolico UniProt ID   I1YB51
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191713.24 Da        Isoelectric Point: 5.6912

>WP_015059148.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVTLSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

AAA domain (AAA_30)

(968-1156)

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

(575-626)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   502 GenBank   WP_001354030
Name   WP_001354030_EC-28|unnamed3 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3

ID   503 GenBank   WP_000089263
Name   WP_000089263_EC-28|unnamed3 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9


T4CP

ID   1015 GenBank   WP_000069777
Name   traC_V6E60_RS25815_EC-28|unnamed3 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   1016 GenBank   WP_046072940
Name   traD_V6E60_RS25910_EC-28|unnamed3 insolico UniProt ID   _
Length   753 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 753 a.a.        Molecular weight: 85667.46 Da        Isoelectric Point: 5.1644

>WP_046072940.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPP
GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 35100..63243

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6E60_RS25695 31072..31506 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
V6E60_RS25700 31503..32265 + 763 Protein_44 plasmid SOS inhibition protein A -
V6E60_RS25705 32243..32422 - 180 WP_001309233 hypothetical protein -
V6E60_RS25710 32444..32593 + 150 Protein_46 plasmid maintenance protein Mok -
V6E60_RS25715 32535..32660 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6E60_RS25720 32979..33275 - 297 Protein_48 hypothetical protein -
V6E60_RS25725 33575..33871 + 297 WP_001272251 hypothetical protein -
V6E60_RS25730 33982..34803 + 822 WP_001234445 DUF932 domain-containing protein -
V6E60_RS25735 35100..35702 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
V6E60_RS25740 36025..36408 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
V6E60_RS25745 36602..37273 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
V6E60_RS25750 37410..37637 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
V6E60_RS25755 37670..38029 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
V6E60_RS25760 38044..38355 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
V6E60_RS25765 38377..38943 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
V6E60_RS25770 38930..39658 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
V6E60_RS25775 39658..41109 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
V6E60_RS25780 41099..41665 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
V6E60_RS25785 41652..41972 + 321 WP_001057307 conjugal transfer protein TrbD -
V6E60_RS25790 41969..42484 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
V6E60_RS25795 42619..42840 + 222 WP_001278683 conjugal transfer protein TraR -
V6E60_RS25800 42833..43309 + 477 WP_000549587 hypothetical protein -
V6E60_RS25805 43389..43607 + 219 WP_000556745 hypothetical protein -
V6E60_RS25810 43635..43982 + 348 WP_000836682 hypothetical protein -
V6E60_RS25815 44108..46738 + 2631 WP_000069777 type IV secretion system protein TraC virb4
V6E60_RS25820 46735..47121 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
V6E60_RS25825 47118..47750 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
V6E60_RS25830 47747..48739 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
V6E60_RS25835 48769..49074 + 306 WP_000224416 hypothetical protein -
V6E60_RS25840 49083..49721 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6E60_RS25845 49718..51568 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6E60_RS25850 51595..51852 + 258 WP_000864353 conjugal transfer protein TrbE -
V6E60_RS25855 51845..52588 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
V6E60_RS25860 52602..52946 + 345 WP_000556796 conjugal transfer protein TrbA -
V6E60_RS25865 53065..53349 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
V6E60_RS25870 53336..53881 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6E60_RS25875 53811..54158 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
V6E60_RS25880 54139..54531 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
V6E60_RS25885 54518..55891 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
V6E60_RS25890 55888..58710 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
V6E60_RS25895 58726..59211 + 486 WP_000605870 hypothetical protein -
V6E60_RS25900 59260..59991 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
V6E60_RS25905 60194..60931 + 738 WP_000199905 hypothetical protein -
V6E60_RS25910 60982..63243 + 2262 WP_046072940 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2004 GenBank   NZ_JAWLTU010000004
Plasmid name   EC-28|unnamed3 Incompatibility group   IncFII
Plasmid size   73589 bp Coordinate of oriT [Strand]   35668..35753 [-]
Host baterium   Escherichia coli strain EC-28

Cargo genes

Drug resistance gene   fosA3, blaTEM-1B, blaCTX-M-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -