Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101886
Name   oriT_LBV045/18_urine|unnamed in_silico
Organism   Escherichia coli strain LBV045/18_urine
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAPQMD010000103 (2444..2567 [+], 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_LBV045/18_urine|unnamed
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure



Relaxase

ID   1547 GenBank   WP_000948349
Name   traI_OH695_RS25420_LBV045/18_urine|unnamed insolico UniProt ID   C8CGS7
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191729.35 Da        Isoelectric Point: 5.7956

>WP_000948349.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

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

(575-626)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   623 GenBank   WP_001151562
Name   WP_001151562_LBV045/18_urine|unnamed insolico UniProt ID   A0A7I0KNG1
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14420.36 Da        Isoelectric Point: 4.8624

>WP_001151562.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVHEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0KNG1

ID   624 GenBank   WP_001254388
Name   WP_001254388_LBV045/18_urine|unnamed 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   1219 GenBank   WP_000069778
Name   traC_OH695_RS25315_LBV045/18_urine|unnamed 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: 99300.06 Da        Isoelectric Point: 6.3461

>WP_000069778.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.



ID   1220 GenBank   WP_277561984
Name   traD_OH695_RS25415_LBV045/18_urine|unnamed insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83842.53 Da        Isoelectric Point: 5.2308

>WP_277561984.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYGIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 1872..30334

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OH695_RS25225 (OH695_25170) 349..636 + 288 WP_000107526 hypothetical protein -
OH695_RS25230 (OH695_25175) 755..1576 + 822 WP_001234489 DUF932 domain-containing protein -
OH695_RS25235 (OH695_25180) 1872..2462 - 591 WP_000252681 transglycosylase SLT domain-containing protein -
OH695_RS25240 (OH695_25185) 2805..3188 + 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
OH695_RS25245 (OH695_25190) 3382..4068 + 687 WP_000332487 PAS domain-containing protein -
OH695_RS25250 (OH695_25195) 4162..4389 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
OH695_RS25255 (OH695_25200) 4423..4782 + 360 WP_001098988 type IV conjugative transfer system pilin TraA -
OH695_RS25260 (OH695_25205) 4797..5108 + 312 WP_000012100 type IV conjugative transfer system protein TraL traL
OH695_RS25265 (OH695_25210) 5130..5696 + 567 WP_000399776 type IV conjugative transfer system protein TraE traE
OH695_RS25270 (OH695_25215) 5683..6411 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
OH695_RS25275 (OH695_25220) 6411..7838 + 1428 WP_000146665 F-type conjugal transfer pilus assembly protein TraB traB
OH695_RS25280 (OH695_25225) 7828..8418 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
OH695_RS25285 (OH695_25230) 8405..8725 + 321 WP_001057275 conjugal transfer protein TrbD virb4
OH695_RS25290 (OH695_25235) 8718..8970 + 253 Protein_13 conjugal transfer protein TrbG -
OH695_RS25295 (OH695_25240) 8967..9482 + 516 WP_000809889 type IV conjugative transfer system lipoprotein TraV traV
OH695_RS25300 (OH695_25245) 9617..9838 + 222 WP_001278694 conjugal transfer protein TraR -
OH695_RS25305 (OH695_25250) 9831..10304 + 474 WP_000549566 hypothetical protein -
OH695_RS25310 (OH695_25255) 10384..10602 + 219 WP_000556746 hypothetical protein -
OH695_RS26060 10630..10843 + 214 Protein_18 hypothetical protein -
OH695_RS25315 (OH695_25260) 10969..13599 + 2631 WP_000069778 type IV secretion system protein TraC virb4
OH695_RS25320 (OH695_25265) 13596..13982 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
OH695_RS25325 (OH695_25270) 13979..14611 + 633 WP_001203736 type-F conjugative transfer system protein TraW traW
OH695_RS25330 (OH695_25275) 14608..15600 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
OH695_RS25335 (OH695_25280) 15630..15935 + 306 WP_021537841 hypothetical protein -
OH695_RS25340 (OH695_25285) 15944..16582 + 639 WP_001080251 type-F conjugative transfer system pilin assembly protein TrbC trbC
OH695_RS25345 (OH695_25290) 16579..18429 + 1851 WP_000821859 type-F conjugative transfer system mating-pair stabilization protein TraN traN
OH695_RS25350 (OH695_25295) 18456..18713 + 258 WP_000864320 conjugal transfer protein TrbE -
OH695_RS25355 (OH695_25300) 18706..19449 + 744 WP_001462109 type-F conjugative transfer system pilin assembly protein TraF traF
OH695_RS25360 (OH695_25305) 19463..19804 + 342 WP_001298557 conjugal transfer protein TrbA -
OH695_RS25365 (OH695_25310) 19785..20120 - 336 WP_000736414 hypothetical protein -
OH695_RS25370 (OH695_25315) 20201..20485 + 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
OH695_RS25375 (OH695_25320) 20472..21017 + 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
OH695_RS25380 (OH695_25325) 20947..21294 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
OH695_RS25385 (OH695_25330) 21275..21667 + 393 WP_021537840 F-type conjugal transfer protein TrbF -
OH695_RS25390 (OH695_25335) 21654..23027 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
OH695_RS25395 (OH695_25340) 23024..25846 + 2823 WP_231837307 conjugal transfer mating-pair stabilization protein TraG traG
OH695_RS25400 (OH695_25345) 25862..26347 + 486 WP_000605869 hypothetical protein -
OH695_RS25405 (OH695_25350) 26396..27127 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
OH695_RS25410 (OH695_25355) 27330..28067 + 738 WP_000199901 hypothetical protein -
OH695_RS25415 (OH695_25360) 28118..30334 + 2217 WP_277561984 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2330 GenBank   NZ_JAPQMD010000103
Plasmid name   LBV045/18_urine|unnamed Incompatibility group   IncFII
Plasmid size   44371 bp Coordinate of oriT [Strand]   2444..2567 [+]
Host baterium   Escherichia coli strain LBV045/18_urine

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -