Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100772
Name   oriT_pJJ1887-4 in_silico
Organism   Escherichia coli JJ1887
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014321 (28313..28762 [+], 450 nt)
oriT length   450 nt
IRs (inverted repeats)      IR1: 201..215, 222..236  (ATTCATTGGTGAATC..GATTCACCAATGAAT)
 IR2: 308..315, 318..325  (GCAAAAAC..GTTTTTGC)
Location of nic site      334..335
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 450 nt

>oriT_pJJ1887-4
ATATGTATACCTCTTTATTTTCTTATCGCATCAAATTTATTTCACATATAAAAAAATGACAATTCATCGATGAATCGAATCGTGACGCAAGTTACGAAAATTACGATTCATGCAGCAAATCACATCACGAATTGAATCTAGAGTCAATTCGCTTTAACTCGTTGTTTTATTATTACTGATTCATCTATGAGTTGCGTTAAATTCATTGGTGAATCATATGCGATTCACCAATGAATCCTTTTTATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGTTAATGATTCAAATAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   844 GenBank   WP_074159540
Name   TraI_pJJ1887-4 insolico UniProt ID   _
Length   1370 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1370 a.a.        Molecular weight: 149289.00 Da        Isoelectric Point: 6.2108

>WP_074159540.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MRQKAASSLTLQQCQQNRVTVHPEKSVPRTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMA
REQGREVQIIAADRRSQMNLKQDERLSGELITGRRQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAA
RHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRWQGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEE
SVAQVSGVREQAILTQAIRSELKTQGVLGHPEVTMTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSH
DRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQ
VASVSEDAMTVVVPGRAEPASLPVSDSPFTALKLENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLA
RSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQIKARAGETLLETAISLQKAGLHTPAQQAIHLALPVLE
SKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRH
ILEGKEAVTPLMERVPGELMETLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASE
RPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNTEMARAYAL
IAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAADVVIMKEIVRQTPELREAVYSLINRDVERALSGLE
SVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEAQQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQ
TLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVMVPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHR
IAGISKDDGLITLQDAEGNTRLISPREAVAEGVTLYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTA
VSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAYVAL
SRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVLEPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGL
AGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAGIWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQG
SRNGESLLADNMQDGVRIARDNPDSGVVVRIAGEGRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAE
VLAQRQAEEAIRRETERRADEIVRKMAENKPDLPDGKTELAVRDIAGQERDRSAISERETALPESVLRES
QREREAVREVARENLLQERLQQMERDMVRDLQKEKTLGGD

  Protein domains


Predicted by InterproScan.

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

(189-240)

AAA domain (AAA_30)

(582-770)

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

(247-326)

DNA helicase TraI (TraI_C)

(1048-1171)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11403..29247

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AX202_RS26365 (AX202_26360) 9195..9899 - 705 WP_001067855 IS6-like element IS26 family transposase -
AX202_RS26370 (AX202_26365) 9963..10772 - 810 Protein_12 conjugal transfer protein TraH -
AX202_RS26375 (AX202_26370) 10759..11151 - 393 WP_000660703 F-type conjugal transfer protein TrbF -
AX202_RS26380 (AX202_26375) 11132..11473 - 342 WP_001448115 P-type conjugative transfer protein TrbJ -
AX202_RS26385 (AX202_26380) 11403..11948 - 546 WP_000059824 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AX202_RS26390 (AX202_26385) 11935..12219 - 285 WP_001448202 type-F conjugative transfer system pilin chaperone TraQ -
AX202_RS26395 (AX202_26390) 12346..12684 - 339 WP_001287905 conjugal transfer protein TrbA -
AX202_RS26400 (AX202_26395) 12700..13443 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
AX202_RS26405 (AX202_26400) 13436..13693 - 258 WP_000864320 conjugal transfer protein TrbE -
AX202_RS26410 (AX202_26405) 13720..15528 - 1809 WP_000821863 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AX202_RS26415 (AX202_26410) 15525..16163 - 639 WP_001080257 type-F conjugative transfer system pilin assembly protein TrbC trbC
AX202_RS26420 (AX202_26415) 16172..16477 - 306 WP_000224411 hypothetical protein -
AX202_RS26425 (AX202_26420) 16507..17499 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
AX202_RS26430 (AX202_26425) 17496..18128 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
AX202_RS26435 (AX202_26430) 18125..18511 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
AX202_RS26440 (AX202_26435) 18508..21135 - 2628 WP_001064239 type IV secretion system protein TraC virb4
AX202_RS28890 21295..21516 - 222 WP_001278978 conjugal transfer protein TraR -
AX202_RS26445 (AX202_26440) 21651..22166 - 516 WP_000809893 type IV conjugative transfer system lipoprotein TraV traV
AX202_RS26450 (AX202_26445) 22163..22414 - 252 WP_001038341 conjugal transfer protein TrbG -
AX202_RS26455 (AX202_26450) 22407..22727 - 321 WP_001057302 conjugal transfer protein TrbD virb4
AX202_RS26460 (AX202_26455) 22714..23298 - 585 WP_000002795 conjugal transfer pilus-stabilizing protein TraP -
AX202_RS26465 (AX202_26460) 23288..24715 - 1428 WP_000146638 F-type conjugal transfer pilus assembly protein TraB traB
AX202_RS26470 (AX202_26465) 24715..25443 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
AX202_RS26475 (AX202_26470) 25430..25996 - 567 WP_000399804 type IV conjugative transfer system protein TraE traE
AX202_RS26480 (AX202_26475) 26018..26329 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
AX202_RS26485 (AX202_26480) 26334..26696 - 363 WP_001098998 type IV conjugative transfer system pilin TraA -
AX202_RS26490 (AX202_26485) 26730..26957 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
AX202_RS26495 (AX202_26490) 27051..27737 - 687 WP_000332487 PAS domain-containing protein -
AX202_RS26500 (AX202_26495) 27931..28314 - 384 WP_001151564 conjugal transfer relaxosome DNA-binding protein TraM -
AX202_RS26505 (AX202_26500) 28600..29247 + 648 WP_000614282 transglycosylase SLT domain-containing protein virB1
AX202_RS26510 (AX202_26505) 29544..30365 - 822 WP_001234469 DUF932 domain-containing protein -
AX202_RS26515 (AX202_26510) 30485..30772 - 288 WP_000107537 hypothetical protein -
AX202_RS31115 31070..31243 + 174 Protein_43 hypothetical protein -
AX202_RS26520 (AX202_26515) 31464..32168 - 705 WP_001067855 IS6-like element IS26 family transposase -
AX202_RS26525 (AX202_26520) 32448..33209 + 762 WP_001225378 Na(+)-translocating NADH-quinone reductase subunit C -

Host bacterium

ID   1232 GenBank   NZ_CP014321
Plasmid name   pJJ1887-4 Incompatibility group   IncFII
Plasmid size   107507 bp Coordinate of oriT [Strand]   28313..28762 [+]
Host baterium   Escherichia coli JJ1887

Cargo genes

Drug resistance gene   blaOXA-1, aac(6')-Ib-cr, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -