Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101787
Name   oriT_BX1S46|unnamed3 in_silico
Organism   Escherichia coli strain BX1S46
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SMSZ01000031 (2196..2319 [+], 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_BX1S46|unnamed3
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1500 GenBank   WP_000986934
Name   traI_E1N53_RS20515_BX1S46|unnamed3 insolico UniProt ID   A0A291R9S5
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191764.68 Da        Isoelectric Point: 5.9593

>WP_000986934.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRTEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTEMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(968-1156)

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)


  Protein structure



No available structure.




Auxiliary protein

ID   602 GenBank   WP_001151564
Name   WP_001151564_BX1S46|unnamed3 insolico UniProt ID   A0AA36PD43
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14446.39 Da        Isoelectric Point: 4.7197

>WP_001151564.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   603 GenBank   WP_001254388
Name   WP_001254388_BX1S46|unnamed3 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


T4CP

ID   1178 GenBank   WP_001064239
Name   traC_E1N53_RS20420_BX1S46|unnamed3 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: 99485.47 Da        Isoelectric Point: 6.6265

>WP_001064239.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREGM
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   1179 GenBank   WP_031943252
Name   traD_E1N53_RS20510_BX1S46|unnamed3 insolico UniProt ID   _
Length   726 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 726 a.a.        Molecular weight: 82587.30 Da        Isoelectric Point: 5.1048

>WP_031943252.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGISTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPVSPAINDKKSDSGVNIPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQ
QMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1624..24288

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
E1N53_RS25540 (E1N53_20335) 1..73 + 73 Protein_0 single-stranded DNA-binding protein -
E1N53_RS20340 (E1N53_20340) 98..385 + 288 WP_000107537 hypothetical protein -
E1N53_RS20345 (E1N53_20345) 506..1327 + 822 WP_001234469 DUF932 domain-containing protein -
E1N53_RS20350 (E1N53_20350) 1624..2271 - 648 WP_000614282 transglycosylase SLT domain-containing protein virB1
E1N53_RS20355 (E1N53_20355) 2557..2940 + 384 WP_001151564 conjugal transfer relaxosome DNA-binding protein TraM -
E1N53_RS20360 (E1N53_20360) 3134..3820 + 687 WP_000332487 PAS domain-containing protein -
E1N53_RS20365 (E1N53_20365) 3914..4141 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
E1N53_RS20370 (E1N53_20370) 4175..4537 + 363 WP_001098998 type IV conjugative transfer system pilin TraA -
E1N53_RS20375 (E1N53_20375) 4542..4853 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
E1N53_RS20380 (E1N53_20380) 4875..5441 + 567 WP_000399804 type IV conjugative transfer system protein TraE traE
E1N53_RS20385 (E1N53_20385) 5428..6156 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
E1N53_RS20390 (E1N53_20390) 6156..7583 + 1428 WP_000146638 F-type conjugal transfer pilus assembly protein TraB traB
E1N53_RS20395 (E1N53_20395) 7573..8157 + 585 WP_000002795 conjugal transfer pilus-stabilizing protein TraP -
E1N53_RS20400 (E1N53_20400) 8144..8464 + 321 WP_001057302 conjugal transfer protein TrbD virb4
E1N53_RS20405 (E1N53_20405) 8457..8708 + 252 WP_001038341 conjugal transfer protein TrbG -
E1N53_RS20410 (E1N53_20410) 8705..9220 + 516 WP_000809893 type IV conjugative transfer system lipoprotein TraV traV
E1N53_RS20415 (E1N53_20415) 9355..9576 + 222 WP_001278978 conjugal transfer protein TraR -
E1N53_RS20420 (E1N53_20420) 9736..12363 + 2628 WP_001064239 type IV secretion system protein TraC virb4
E1N53_RS20425 (E1N53_20425) 12360..12746 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
E1N53_RS20430 (E1N53_20430) 12743..13375 + 633 WP_001203717 type-F conjugative transfer system protein TraW traW
E1N53_RS20435 (E1N53_20435) 13372..14364 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
E1N53_RS20440 (E1N53_20440) 14394..14699 + 306 WP_000224411 hypothetical protein -
E1N53_RS20445 (E1N53_20445) 14708..15346 + 639 WP_001080257 type-F conjugative transfer system pilin assembly protein TrbC trbC
E1N53_RS20450 (E1N53_20450) 15343..17151 + 1809 WP_000821863 type-F conjugative transfer system mating-pair stabilization protein TraN traN
E1N53_RS20455 (E1N53_20455) 17178..17435 + 258 WP_000864320 conjugal transfer protein TrbE -
E1N53_RS20460 (E1N53_20460) 17428..18171 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
E1N53_RS20465 (E1N53_20465) 18187..18525 + 339 WP_001287905 conjugal transfer protein TrbA -
E1N53_RS20470 (E1N53_20470) 18652..18936 + 285 WP_001448202 type-F conjugative transfer system pilin chaperone TraQ -
E1N53_RS20475 (E1N53_20475) 18923..19468 + 546 WP_000059824 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
E1N53_RS20480 (E1N53_20480) 19398..19739 + 342 WP_001448115 P-type conjugative transfer protein TrbJ -
E1N53_RS20485 (E1N53_20485) 19720..20112 + 393 WP_000660703 F-type conjugal transfer protein TrbF -
E1N53_RS20490 (E1N53_20490) 20099..21472 + 1374 WP_001137364 conjugal transfer pilus assembly protein TraH traH
E1N53_RS20495 (E1N53_20495) 21469..24288 + 2820 WP_001007057 conjugal transfer mating-pair stabilization protein TraG traG
E1N53_RS20500 (E1N53_20500) 24307..24804 + 498 WP_000605861 hypothetical protein -
E1N53_RS20505 (E1N53_20505) 24836..25567 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
E1N53_RS20510 (E1N53_20510) 25820..28000 + 2181 WP_031943252 type IV conjugative transfer system coupling protein TraD -

Host bacterium

ID   2231 GenBank   NZ_SMSZ01000031
Plasmid name   BX1S46|unnamed3 Incompatibility group   IncFII
Plasmid size   44517 bp Coordinate of oriT [Strand]   2196..2319 [+]
Host baterium   Escherichia coli strain BX1S46

Cargo genes

Drug resistance gene   blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -