Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100408
Name   oriT_pUMNK88_Ent in_silico
Organism   Escherichia coli UMNK88
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_017640 (57013..57476 [+], 464 nt)
oriT length   464 nt
IRs (inverted repeats)      142..151, 154..163  (ATAGGGTCGT..ACGACCCTAT)
 231..237, 243..249  (GCAAAAA..TTTTTGC)
Location of nic site      258..259
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 464 nt

>oriT_pUMNK88_Ent
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGTCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATAAAATTTGTCAGTACTGACCCTAACAAGGGTCGCCATAGGGTCGCCATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGCTAATGATTCAAAAAGCAAATCAGCAAAAACTTGTTTTTTGCGTGGGGTGTGGTGCTTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGCCAGGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   479 GenBank   WP_000986925
Name   TraI_pUMNK88_Ent insolico UniProt ID   A0A0E0U825
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192096.85 Da        Isoelectric Point: 5.7912

>WP_000986925.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYSDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGRNRHRSGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAARQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGPASPDGPDVQQAMTQAIAGLSERKVQFTYTDMLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQERPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRRELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRQEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVGDSPFTALKL
ESGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRML
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGAGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTMSDRERGYVANSVWTVTAVSGDSVTLSDGLQTRVIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDERQGWTDAINNAVQKGTAHDVL
EPKADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSWDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(11-283)

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

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: 34648..57872

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
UMNK88_RS27690 30911..33106 - 2196 Protein_36 type IV conjugative transfer system coupling protein TraD -
UMNK88_RS27695 (UMNK88_pEnt45) 33427..34119 - 693 WP_000351852 hypothetical protein -
UMNK88_RS27700 (UMNK88_pEnt46) 34334..34645 + 312 WP_000522221 heavy metal-binding domain-containing protein -
UMNK88_RS27705 (UMNK88_pEnt47) 34648..37467 - 2820 WP_001007033 conjugal transfer mating-pair stabilization protein TraG traG
UMNK88_RS27710 (UMNK88_pEnt48) 37464..38838 - 1375 Protein_40 conjugal transfer pilus assembly protein TraH -
UMNK88_RS27715 (UMNK88_pEnt49) 38825..39217 - 393 WP_000126336 F-type conjugal transfer protein TrbF -
UMNK88_RS35090 39171..39485 - 315 WP_236432668 P-type conjugative transfer protein TrbJ -
UMNK88_RS35095 39486..40019 - 534 Protein_43 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB -
UMNK88_RS27725 (UMNK88_pEnt51) 40006..40290 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
UMNK88_RS27730 (UMNK88_pEnt52) 40409..40756 - 348 WP_001287893 conjugal transfer protein TrbA -
UMNK88_RS27735 (UMNK88_pEnt53) 40772..41515 - 744 WP_001030376 type-F conjugative transfer system pilin assembly protein TraF traF
UMNK88_RS27740 41508..41765 - 258 WP_000864325 conjugal transfer protein TrbE -
UMNK88_RS27745 (UMNK88_pEnt54) 41792..43600 - 1809 WP_000821823 type-F conjugative transfer system mating-pair stabilization protein TraN traN
UMNK88_RS27750 (UMNK88_pEnt55) 43597..44235 - 639 WP_001104248 type-F conjugative transfer system pilin assembly protein TrbC trbC
UMNK88_RS27755 (UMNK88_pEnt56) 44263..44715 - 453 WP_000069427 hypothetical protein -
UMNK88_RS27760 (UMNK88_pEnt57) 44745..45206 - 462 WP_000277845 hypothetical protein -
UMNK88_RS27765 (UMNK88_pEnt58) 45232..46224 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
UMNK88_RS27770 (UMNK88_pEnt59) 46221..46853 - 633 WP_001203747 type-F conjugative transfer system protein TraW traW
UMNK88_RS27775 46850..47236 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
UMNK88_RS27780 (UMNK88_pEnt60) 47233..49859 - 2627 Protein_55 type IV secretion system protein TraC -
UMNK88_RS31875 50021..50242 - 222 WP_001278692 conjugal transfer protein TraR -
UMNK88_RS27785 (UMNK88_pEnt61) 50377..50892 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
UMNK88_RS27790 50889..51141 - 253 Protein_58 conjugal transfer protein TrbG -
UMNK88_RS27795 51153..51350 - 198 WP_001423674 conjugal transfer protein TrbD -
UMNK88_RS33565 51337..51927 - 591 Protein_60 conjugal transfer pilus-stabilizing protein TraP -
UMNK88_RS27805 (UMNK88_pEnt64) 51917..53344 - 1428 WP_000146630 F-type conjugal transfer pilus assembly protein TraB traB
UMNK88_RS27810 (UMNK88_pEnt65) 53344..54072 - 729 WP_001230789 type-F conjugative transfer system secretin TraK traK
UMNK88_RS27815 (UMNK88_pEnt66) 54059..54625 - 567 WP_000399785 type IV conjugative transfer system protein TraE traE
UMNK88_RS27820 (UMNK88_pEnt67) 54647..54958 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
UMNK88_RS27825 (UMNK88_pEnt68) 54973..55332 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
UMNK88_RS27830 55366..55593 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
UMNK88_RS27835 (UMNK88_pEnt69) 55687..56373 - 687 WP_000332484 PAS domain-containing protein -
UMNK88_RS27840 (UMNK88_pEnt70) 56560..56946 - 387 WP_000124984 conjugal transfer relaxosome DNA-binding protein TraM -
UMNK88_RS27845 (UMNK88_pEnt71) 57282..57872 + 591 WP_000252680 transglycosylase SLT domain-containing protein -
UMNK88_RS27850 (UMNK88_pEnt72) 58169..58990 - 822 WP_001234469 DUF932 domain-containing protein -
UMNK88_RS27855 (UMNK88_pEnt73) 59110..59397 - 288 WP_000107537 hypothetical protein -
UMNK88_RS35100 59695..59868 + 174 Protein_72 hypothetical protein -
UMNK88_RS35105 59866..60096 - 231 WP_071587244 hypothetical protein -
UMNK88_RS27865 60316..60441 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
UMNK88_RS35110 60383..60532 - 150 Protein_75 plasmid maintenance protein Mok -
UMNK88_RS27875 (UMNK88_pEnt74) 60711..61473 - 763 Protein_76 plasmid SOS inhibition protein A -
UMNK88_RS31890 61470..61903 - 434 Protein_77 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   869 GenBank   NC_017640
Plasmid name   pUMNK88_Ent Incompatibility group   IncFIB
Plasmid size   81475 bp Coordinate of oriT [Strand]   57013..57476 [+]
Host baterium   Escherichia coli UMNK88

Cargo genes

Drug resistance gene   -
Virulence gene   eltA, eltB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -