Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102415
Name   oriT_SMG003F3|unnamed1 in_silico
Organism   Escherichia coli strain SMG003F3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKVSU010000021 (30226..30349 [+], 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_SMG003F3|unnamed1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1808 GenBank   WP_000948348
Name   traI_ML376_RS21940_SMG003F3|unnamed1 insolico UniProt ID   A0A7I0KNL8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191759.33 Da        Isoelectric Point: 5.7433

>WP_000948348.1 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
EPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
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)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   726 GenBank   WP_001151562
Name   WP_001151562_SMG003F3|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

ID   727 GenBank   WP_001254388
Name   WP_001254388_SMG003F3|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


T4CP

ID   1391 GenBank   WP_000069778
Name   traC_ML376_RS21835_SMG003F3|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: 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   1392 GenBank   WP_032164615
Name   traD_ML376_RS21935_SMG003F3|unnamed1 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: 85681.49 Da        Isoelectric Point: 5.1644

>WP_032164615.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPP
GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 29662..58161

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ML376_RS21720 (ML376_21715) 25639..26073 + 435 WP_000845910 conjugation system SOS inhibitor PsiB -
ML376_RS21725 (ML376_21720) 26070..26833 + 764 Protein_33 plasmid SOS inhibition protein A -
ML376_RS21730 (ML376_21725) 27007..27156 + 150 Protein_34 DUF5431 family protein -
ML376_RS21735 (ML376_21730) 27098..27223 + 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
ML376_RS21740 (ML376_21735) 27541..27838 - 298 Protein_36 hypothetical protein -
ML376_RS21745 (ML376_21740) 28139..28426 + 288 WP_000107526 hypothetical protein -
ML376_RS21750 (ML376_21745) 28545..29366 + 822 WP_001234489 DUF932 domain-containing protein -
ML376_RS21755 (ML376_21750) 29662..30171 - 510 WP_000759167 transglycosylase SLT domain-containing protein virB1
ML376_RS21760 (ML376_21755) 30587..30970 + 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
ML376_RS21765 (ML376_21760) 31164..31850 + 687 WP_000332487 PAS domain-containing protein -
ML376_RS21770 (ML376_21765) 31944..32171 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
ML376_RS21775 (ML376_21770) 32205..32564 + 360 WP_001098988 type IV conjugative transfer system pilin TraA -
ML376_RS21780 (ML376_21775) 32579..32890 + 312 WP_000012100 type IV conjugative transfer system protein TraL traL
ML376_RS21785 (ML376_21780) 32912..33478 + 567 WP_000399776 type IV conjugative transfer system protein TraE traE
ML376_RS21790 (ML376_21785) 33465..34193 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ML376_RS21795 (ML376_21790) 34193..35620 + 1428 WP_000146665 F-type conjugal transfer pilus assembly protein TraB traB
ML376_RS21800 (ML376_21795) 35610..36200 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
ML376_RS21805 (ML376_21800) 36187..36507 + 321 WP_001057275 conjugal transfer protein TrbD virb4
ML376_RS21810 (ML376_21805) 36500..36752 + 253 Protein_50 conjugal transfer protein TrbG -
ML376_RS21815 (ML376_21810) 36749..37264 + 516 WP_000809888 type IV conjugative transfer system lipoprotein TraV traV
ML376_RS21820 (ML376_21815) 37399..37620 + 222 WP_001278694 conjugal transfer protein TraR -
ML376_RS21825 (ML376_21820) 37613..38086 + 474 WP_000549566 hypothetical protein -
ML376_RS21830 (ML376_21825) 38166..38384 + 219 WP_000556746 hypothetical protein -
ML376_RS25975 38412..38625 + 214 Protein_55 hypothetical protein -
ML376_RS21835 (ML376_21830) 38751..41381 + 2631 WP_000069778 type IV secretion system protein TraC virb4
ML376_RS21840 (ML376_21835) 41378..41764 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
ML376_RS21845 (ML376_21840) 41761..42393 + 633 WP_001203736 type-F conjugative transfer system protein TraW traW
ML376_RS21850 (ML376_21845) 42390..43382 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
ML376_RS21855 (ML376_21850) 43412..43717 + 306 WP_000224418 hypothetical protein -
ML376_RS21860 (ML376_21855) 43726..44364 + 639 WP_001080251 type-F conjugative transfer system pilin assembly protein TrbC trbC
ML376_RS21865 (ML376_21860) 44361..46211 + 1851 WP_000821859 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ML376_RS21870 (ML376_21865) 46238..46495 + 258 WP_000864314 conjugal transfer protein TrbE -
ML376_RS21875 (ML376_21870) 46488..47231 + 744 WP_001030385 type-F conjugative transfer system pilin assembly protein TraF traF
ML376_RS21880 (ML376_21875) 47245..47586 + 342 WP_001298557 conjugal transfer protein TrbA -
ML376_RS21885 (ML376_21880) 47567..47902 - 336 WP_000736414 hypothetical protein -
ML376_RS21890 (ML376_21885) 47983..48267 + 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
ML376_RS21895 (ML376_21890) 48254..48799 + 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ML376_RS21900 (ML376_21895) 48729..49076 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
ML376_RS21905 (ML376_21900) 49057..49449 + 393 WP_000660700 F-type conjugal transfer protein TrbF -
ML376_RS21910 (ML376_21905) 49436..50809 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
ML376_RS21915 (ML376_21910) 50806..53628 + 2823 WP_001007080 conjugal transfer mating-pair stabilization protein TraG traG
ML376_RS21920 (ML376_21915) 53644..54129 + 486 WP_000605869 hypothetical protein -
ML376_RS21925 (ML376_21920) 54178..54909 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
ML376_RS21930 (ML376_21925) 55112..55849 + 738 WP_000199901 hypothetical protein -
ML376_RS21935 (ML376_21930) 55900..58161 + 2262 WP_032164615 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2859 GenBank   NZ_JAKVSU010000021
Plasmid name   SMG003F3|unnamed1 Incompatibility group   IncFII
Plasmid size   86343 bp Coordinate of oriT [Strand]   30226..30349 [+]
Host baterium   Escherichia coli strain SMG003F3

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -