Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100277
Name   oriT_NR1 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_009133 (50352..50901 [-], 550 nt)
oriT length   550 nt
IRs (inverted repeats)      243..255, 257..269  (TATTTAATAATTC..GAATTATTAAATA)
 311..318, 321..328  (GCAAAAAC..GTTTTTGC)
Location of nic site      337..338
Conserved sequence flanking the
  nic site    		  GTAGTGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 550 nt

>oriT_NR1
TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAATGAACTTTTCACTATAAATATGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTATAAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCATGAAAATTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTCTCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCAATCTGCCTGATGTTTATAAATGGGATCTGCGAAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTGAGAGCGATATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   348 GenBank   YP_001096501
Name   Nickase_NR1 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>YP_001096501.1 conjugal transfer nickase/helicase (plasmid) [Escherichia coli]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 49964..78474

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS396_RS00275 (D616_p81058) 45281..45868 + 588 Protein_54 hypothetical protein -
HS396_RS00280 (D616_p81059) 45937..46370 + 434 Protein_55 conjugation system SOS inhibitor PsiB -
HS396_RS00285 (D616_p81060) 46367..47129 + 763 Protein_56 plasmid SOS inhibition protein A -
HS396_RS00580 47308..47457 + 150 Protein_57 plasmid maintenance protein Mok -
HS396_RS00290 (D616_p81064) 47399..47524 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HS396_RS00295 (D616_p81063) 47843..48139 - 297 Protein_59 hypothetical protein -
HS396_RS00300 (D616_p81065) 48439..48735 + 297 WP_001272251 hypothetical protein -
HS396_RS00305 (D616_p81066) 48846..49667 + 822 WP_001234445 DUF932 domain-containing protein -
HS396_RS00310 (D616_p81069) 49964..50566 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
HS396_RS00315 (D616_p81068) 50889..51272 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HS396_RS00320 (D616_p81070) 51466..52137 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HS396_RS00325 (D616_p81071) 52274..52501 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HS396_RS00330 (D616_p81072) 52534..52893 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HS396_RS00335 (D616_p81073) 52908..53219 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HS396_RS00340 (D616_p81075) 53241..53807 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HS396_RS00345 (D616_p81074) 53794..54522 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HS396_RS00350 (D616_p81076) 54522..55973 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HS396_RS00355 (D616_p81078) 55963..56529 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HS396_RS00360 (D616_p81077) 56516..56836 + 321 WP_001057307 conjugal transfer protein TrbD -
HS396_RS00365 (D616_p81079) 56833..57348 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HS396_RS00370 (D616_p81080) 57483..57704 + 222 WP_001278683 conjugal transfer protein TraR -
HS396_RS00375 (D616_p81081) 57697..58110 + 414 WP_000549589 hypothetical protein -
HS396_RS00380 (D616_p81082) 58103..58576 + 474 WP_000549568 hypothetical protein -
HS396_RS00385 (D616_p81083) 58656..58874 + 219 WP_000556745 hypothetical protein -
HS396_RS00390 (D616_p81084) 58902..59249 + 348 WP_000836682 hypothetical protein -
HS396_RS00395 (D616_p81085) 59375..62005 + 2631 WP_000069777 type IV secretion system protein TraC virb4
HS396_RS00400 (D616_p81086) 62002..62388 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HS396_RS00405 (D616_p81087) 62385..63017 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HS396_RS00410 (D616_p81088) 63014..64006 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HS396_RS00415 (D616_p81089) 64036..64341 + 306 WP_000224416 hypothetical protein -
HS396_RS00420 (D616_p81090) 64350..64988 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS396_RS00425 (D616_p81091) 64985..66835 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS396_RS00430 (D616_p81092) 66862..67119 + 258 WP_000864353 conjugal transfer protein TrbE -
HS396_RS00435 (D616_p81093) 67112..67855 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HS396_RS00440 (D616_p81094) 67869..68213 + 345 WP_000556796 conjugal transfer protein TrbA -
HS396_RS00445 (D616_p81095) 68332..68616 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HS396_RS00450 (D616_p81096) 68603..69148 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS396_RS00455 (D616_p81097) 69078..69425 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HS396_RS00460 (D616_p81098) 69406..69798 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HS396_RS00465 (D616_p81099) 69785..71158 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HS396_RS00470 (D616_p81100) 71155..73977 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HS396_RS00475 (D616_p81101) 73993..74478 + 486 WP_000605870 hypothetical protein -
HS396_RS00480 (D616_p81102) 74527..75258 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HS396_RS00485 (D616_p81104) 75461..76198 + 738 WP_000199905 hypothetical protein -
HS396_RS00490 (D616_p81103) 76249..78474 + 2226 WP_011867779 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   739 GenBank   NC_009133
Plasmid name   NR1 Incompatibility group   IncFII
Plasmid size   94289 bp Coordinate of oriT [Strand]   50352..50901 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   sul1, qacE, ant(3'')-Ia, catA1, tet(B)
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -