Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101548
Name   oriT_LRPF007|unnamed1 in_silico
Organism   Escherichia coli strain LRPF007
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAPVBS010000007 (86498..86621 [-], 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_LRPF007|unnamed1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1371 GenBank   WP_042092642
Name   traI_O2W52_RS23075_LRPF007|unnamed1 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: 191872.54 Da        Isoelectric Point: 5.8496

>WP_042092642.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEEAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRNVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDNVYHRIAGISKDDRLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSEDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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)

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

(633-712)

AAA domain (AAA_30)

(968-1155)


  Protein structure



No available structure.




Auxiliary protein

ID   486 GenBank   WP_001254388
Name   WP_001254388_LRPF007|unnamed1 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

ID   487 GenBank   WP_001151562
Name   WP_001151562_LRPF007|unnamed1 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


T4CP

ID   1001 GenBank   WP_128598795
Name   traD_O2W52_RS23080_LRPF007|unnamed1 insolico UniProt ID   _
Length   777 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 777 a.a.        Molecular weight: 88508.51 Da        Isoelectric Point: 5.1644

>WP_128598795.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVS
VPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGED
VEPGDDF

  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   1002 GenBank   WP_042092645
Name   traC_O2W52_RS23180_LRPF007|unnamed1 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: 99311.04 Da        Isoelectric Point: 6.1912

>WP_042092645.1 type IV secretion system protein TraC [Escherichia coli]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITWAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAEHVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(469-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 58615..84268

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
O2W52_RS23080 (O2W52_23045) 58615..60948 - 2334 WP_128598795 type IV conjugative transfer system coupling protein TraD prgC
O2W52_RS23085 (O2W52_23050) 60999..61736 - 738 WP_000199901 hypothetical protein -
O2W52_RS23090 (O2W52_23055) 61939..62670 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
O2W52_RS23095 (O2W52_23060) 62719..63204 - 486 WP_000605869 hypothetical protein -
O2W52_RS23100 (O2W52_23065) 63220..66042 - 2823 WP_001007080 conjugal transfer mating-pair stabilization protein TraG traG
O2W52_RS23105 (O2W52_23070) 66039..67412 - 1374 WP_269686791 conjugal transfer pilus assembly protein TraH traH
O2W52_RS23110 (O2W52_23075) 67399..67791 - 393 WP_000660700 F-type conjugal transfer protein TrbF -
O2W52_RS23115 (O2W52_23080) 67772..68119 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
O2W52_RS23120 (O2W52_23085) 68049..68594 - 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
O2W52_RS23125 (O2W52_23090) 68581..68865 - 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
O2W52_RS23130 (O2W52_23095) 68946..69281 + 336 WP_000736414 hypothetical protein -
O2W52_RS23135 (O2W52_23100) 69262..69603 - 342 WP_001298557 conjugal transfer protein TrbA -
O2W52_RS23140 (O2W52_23105) 69617..70360 - 744 WP_001030385 type-F conjugative transfer system pilin assembly protein TraF traF
O2W52_RS23145 (O2W52_23110) 70353..70610 - 258 WP_000864314 conjugal transfer protein TrbE -
O2W52_RS23150 (O2W52_23115) 70637..72487 - 1851 WP_000821859 type-F conjugative transfer system mating-pair stabilization protein TraN traN
O2W52_RS23155 (O2W52_23120) 72484..73122 - 639 WP_001080251 type-F conjugative transfer system pilin assembly protein TrbC trbC
O2W52_RS23160 (O2W52_23125) 73131..73436 - 306 WP_000224418 hypothetical protein -
O2W52_RS23165 (O2W52_23130) 73466..74458 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
O2W52_RS23170 (O2W52_23135) 74455..75087 - 633 WP_001203736 type-F conjugative transfer system protein TraW traW
O2W52_RS23175 (O2W52_23140) 75084..75470 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
O2W52_RS23180 (O2W52_23145) 75467..78097 - 2631 WP_042092645 type IV secretion system protein TraC virb4
O2W52_RS25095 78223..78436 - 214 Protein_83 hypothetical protein -
O2W52_RS23185 (O2W52_23150) 78464..78682 - 219 WP_000556746 hypothetical protein -
O2W52_RS23190 (O2W52_23155) 78762..79235 - 474 WP_000549566 hypothetical protein -
O2W52_RS23195 (O2W52_23160) 79228..79449 - 222 WP_001278694 conjugal transfer protein TraR -
O2W52_RS23200 (O2W52_23165) 79584..80099 - 516 WP_000809889 type IV conjugative transfer system lipoprotein TraV traV
O2W52_RS23205 (O2W52_23170) 80096..80347 - 252 WP_001038341 conjugal transfer protein TrbG -
O2W52_RS23210 (O2W52_23175) 80340..80660 - 321 WP_042092647 conjugal transfer protein TrbD virb4
O2W52_RS23215 (O2W52_23180) 80647..81237 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
O2W52_RS23220 (O2W52_23185) 81227..82654 - 1428 WP_000146665 F-type conjugal transfer pilus assembly protein TraB traB
O2W52_RS23225 (O2W52_23190) 82654..83382 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
O2W52_RS23230 (O2W52_23195) 83369..83935 - 567 WP_000399776 type IV conjugative transfer system protein TraE traE
O2W52_RS23235 (O2W52_23200) 83957..84268 - 312 WP_000012100 type IV conjugative transfer system protein TraL traL
O2W52_RS23240 (O2W52_23205) 84283..84642 - 360 WP_001098988 type IV conjugative transfer system pilin TraA -
O2W52_RS23245 (O2W52_23210) 84676..84903 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
O2W52_RS23250 (O2W52_23215) 84997..85683 - 687 WP_000332487 PAS domain-containing protein -
O2W52_RS23255 (O2W52_23220) 85877..86260 - 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
O2W52_RS23260 (O2W52_23225) 86591..86767 + 177 Protein_99 lytic transglycosylase -
O2W52_RS23265 (O2W52_23230) 86940..87761 - 822 WP_001234489 DUF932 domain-containing protein -
O2W52_RS23270 (O2W52_23235) 87880..88167 - 288 WP_000107526 hypothetical protein -
O2W52_RS23275 (O2W52_23240) 88468..88765 + 298 Protein_102 hypothetical protein -
O2W52_RS23280 (O2W52_23245) 89083..89208 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -

Host bacterium

ID   1992 GenBank   NZ_JAPVBS010000007
Plasmid name   LRPF007|unnamed1 Incompatibility group   IncFIB
Plasmid size   111595 bp Coordinate of oriT [Strand]   86498..86621 [-]
Host baterium   Escherichia coli strain LRPF007

Cargo genes

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