Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100355
Name   oriT_pEG356 in_silico
Organism   Shigella sonnei
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_013727 (32602..33151 [-], 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_pEG356
TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAATGAACTTTTCACTATAAATATGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTATAAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCATGAAAATTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTCTCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGTAATCTGCCTGATGTTTATAAATGGGATCTGCGAAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTGAGAGCGATATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   426 GenBank   YP_003377786
Name   Nickase/helicase_pEG356 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_003377786.1 conjugal transfer nickase/helicase (plasmid) [Shigella sonnei]
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: 32214..60724

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXG12_RS00180 (EG356c_047) 27546..27860 + 315 WP_000872086 hypothetical protein -
HXG12_RS00455 28050..28163 + 114 Protein_40 DUF5431 family protein -
HXG12_RS00185 28108..28230 + 123 WP_223412041 Hok/Gef family protein -
HXG12_RS00190 28531..28780 - 250 Protein_42 hypothetical protein -
HXG12_RS00195 (EG356c_051) 29076..29399 + 324 WP_000533253 hypothetical protein -
HXG12_RS00200 (EG356c_052) 29458..29700 + 243 WP_000540588 hypothetical protein -
HXG12_RS00460 29966..30220 + 255 WP_072254791 hypothetical protein -
HXG12_RS00205 (EG356c_056) 30691..30987 + 297 WP_001272251 hypothetical protein -
HXG12_RS00210 (EG356c_057) 31097..31918 + 822 WP_001234437 DUF932 domain-containing protein -
HXG12_RS00215 (EG356c_058) 32214..32816 - 603 WP_000243715 transglycosylase SLT domain-containing protein virB1
HXG12_RS00220 (EG356c_059) 33139..33522 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HXG12_RS00225 (EG356c_060) 33716..34387 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HXG12_RS00230 (EG356c_061) 34524..34751 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HXG12_RS00235 (EG356c_062) 34784..35143 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HXG12_RS00240 (EG356c_063) 35158..35469 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HXG12_RS00245 (EG356c_064) 35491..36057 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HXG12_RS00250 (EG356c_065) 36044..36772 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HXG12_RS00255 (EG356c_066) 36772..38223 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HXG12_RS00260 (EG356c_067) 38213..38779 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HXG12_RS00265 (EG356c_068) 38766..39086 + 321 WP_001057307 conjugal transfer protein TrbD -
HXG12_RS00270 (EG356c_069) 39083..39598 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HXG12_RS00275 (EG356c_070) 39733..39954 + 222 WP_001278683 conjugal transfer protein TraR -
HXG12_RS00280 (EG356c_071) 39947..40360 + 414 WP_000549589 hypothetical protein -
HXG12_RS00285 (EG356c_072) 40353..40826 + 474 WP_000549568 hypothetical protein -
HXG12_RS00290 (EG356c_073) 40906..41124 + 219 WP_000556745 hypothetical protein -
HXG12_RS00295 (EG356c_074) 41152..41499 + 348 WP_000836682 hypothetical protein -
HXG12_RS00300 (EG356c_075) 41625..44255 + 2631 WP_012917677 type IV secretion system protein TraC virb4
HXG12_RS00305 (EG356c_076) 44252..44638 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HXG12_RS00310 (EG356c_078) 44635..45267 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HXG12_RS00315 (EG356c_079) 45264..46256 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HXG12_RS00320 (EG356c_080) 46286..46591 + 306 WP_000224416 hypothetical protein -
HXG12_RS00325 (EG356c_081) 46600..47238 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HXG12_RS00330 (EG356c_082) 47235..49085 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HXG12_RS00335 (EG356c_083) 49112..49369 + 258 WP_000864353 conjugal transfer protein TrbE -
HXG12_RS00340 (EG356c_084) 49362..50105 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HXG12_RS00345 (EG356c_085) 50119..50463 + 345 WP_000556796 conjugal transfer protein TrbA -
HXG12_RS00350 (EG356c_086) 50582..50866 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HXG12_RS00355 (EG356c_087) 50853..51398 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HXG12_RS00360 (EG356c_088) 51328..51675 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HXG12_RS00365 (EG356c_089) 51656..52048 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HXG12_RS00370 (EG356c_090) 52035..53408 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HXG12_RS00375 (EG356c_091) 53405..56227 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HXG12_RS00380 (EG356c_092) 56243..56728 + 486 WP_000605870 hypothetical protein -
HXG12_RS00385 (EG356c_093) 56777..57508 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HXG12_RS00390 (EG356c_094) 57711..58448 + 738 WP_000199905 hypothetical protein -
HXG12_RS00395 (EG356c_095) 58499..60724 + 2226 WP_011867779 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   816 GenBank   NC_013727
Plasmid name   pEG356 Incompatibility group   IncFII
Plasmid size   70275 bp Coordinate of oriT [Strand]   32602..33151 [-]
Host baterium   Shigella sonnei

Cargo genes

Drug resistance gene   blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7