Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100737
Name   oriT_pSF-468-1 in_silico
Organism   Escherichia coli strain SF-468
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP012626 (56253..56714 [-], 462 nt)
oriT length   462 nt
IRs (inverted repeats)      142..151, 154..163  (ATAGGGTCGT..ACGACCCTAT)
 231..238, 241..248  (GCAAAAAC..GTTTTTGC)
Location of nic site      257..258
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 462 nt

>oriT_pSF-468-1
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGGCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATGAAAATTGTCAGCACTGACCCTAACAAGGGTCGTCATAGGGTCGCTATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAGAACATAAACTAATGATTTAAAAAACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGAGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGTCTGGCCACTGATTGCTTTGATCTTGCAGGCAGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   809 GenBank   WP_060710372
Name   TraI_pSF-468-1 insolico UniProt ID   A0A1V2SSV8
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192173.07 Da        Isoelectric Point: 5.8420

>WP_060710372.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHTVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKDTGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTLGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYAQLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KVRAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGIGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESTYVALSRMKQHVQVYTDDRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGCVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAWQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-282)

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

(575-626)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 55857..81503

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AN206_RS26320 (AN206_26405) 51848..52282 + 435 WP_000845922 conjugation system SOS inhibitor PsiB -
AN206_RS26325 (AN206_26410) 52279..53065 + 787 Protein_58 plasmid SOS inhibition protein A -
AN206_RS31545 53255..53368 + 114 Protein_59 DUF5431 family protein -
AN206_RS26335 (AN206_26420) 53313..53435 + 123 WP_223195199 Hok/Gef family protein -
AN206_RS31065 (AN206_26425) 53736..54033 - 298 Protein_61 hypothetical protein -
AN206_RS26350 (AN206_26435) 54334..54621 + 288 WP_000107520 hypothetical protein -
AN206_RS26355 (AN206_26440) 54740..55561 + 822 WP_001234468 DUF932 domain-containing protein -
AN206_RS26360 (AN206_26445) 55857..56366 - 510 WP_060710371 transglycosylase SLT domain-containing protein virB1
AN206_RS26365 (AN206_26450) 56781..57164 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
AN206_RS26370 (AN206_26455) 57354..58040 + 687 WP_000332490 PAS domain-containing protein -
AN206_RS26375 (AN206_26460) 58134..58361 + 228 WP_001442099 conjugal transfer relaxosome protein TraY -
AN206_RS26380 (AN206_26465) 58395..58760 + 366 WP_000340270 type IV conjugative transfer system pilin TraA -
AN206_RS26385 (AN206_26470) 58775..59086 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
AN206_RS26390 (AN206_26475) 59108..59674 + 567 WP_001563715 type IV conjugative transfer system protein TraE traE
AN206_RS26395 (AN206_26480) 59661..60389 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
AN206_RS26400 (AN206_26485) 60389..61816 + 1428 WP_025670721 F-type conjugal transfer pilus assembly protein TraB traB
AN206_RS26405 (AN206_26490) 61806..62396 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
AN206_RS26410 (AN206_26495) 62383..62580 + 198 WP_001324648 conjugal transfer protein TrbD -
AN206_RS26415 (AN206_26500) 62592..62843 + 252 WP_001038351 conjugal transfer protein TrbG -
AN206_RS26420 (AN206_26505) 62840..63355 + 516 WP_000809834 type IV conjugative transfer system lipoprotein TraV traV
AN206_RS29210 (AN206_26510) 63490..63711 + 222 WP_032330955 conjugal transfer protein TraR -
AN206_RS26425 (AN206_26515) 63871..66498 + 2628 WP_001064245 type IV secretion system protein TraC virb4
AN206_RS26430 (AN206_26520) 66495..66881 + 387 WP_000099688 type-F conjugative transfer system protein TrbI -
AN206_RS26435 (AN206_26525) 66878..67510 + 633 WP_025670720 type-F conjugative transfer system protein TraW traW
AN206_RS26440 (AN206_26530) 67507..68499 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
AN206_RS26445 (AN206_26535) 68508..69146 + 639 WP_000777703 type-F conjugative transfer system pilin assembly protein TrbC trbC
AN206_RS26450 (AN206_26540) 69143..70951 + 1809 WP_025670719 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AN206_RS26455 (AN206_26545) 70978..71235 + 258 WP_000864318 conjugal transfer protein TrbE -
AN206_RS26460 (AN206_26550) 71228..71971 + 744 WP_025670718 type-F conjugative transfer system pilin assembly protein TraF traF
AN206_RS26465 (AN206_26555) 71987..72334 + 348 WP_001287893 conjugal transfer protein TrbA -
AN206_RS26470 (AN206_26560) 72453..72737 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
AN206_RS26475 (AN206_26565) 72724..73269 + 546 WP_000052614 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AN206_RS26480 (AN206_26570) 73199..73561 + 363 WP_023181029 P-type conjugative transfer protein TrbJ -
AN206_RS26485 (AN206_26575) 73561..74934 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
AN206_RS26490 (AN206_26580) 74931..77756 + 2826 WP_001007030 conjugal transfer mating-pair stabilization protein TraG traG
AN206_RS26495 (AN206_26585) 77753..78262 + 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
AN206_RS26500 (AN206_26590) 78276..79007 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
AN206_RS26505 (AN206_26595) 79260..81503 + 2244 WP_001697871 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1197 GenBank   NZ_CP012626
Plasmid name   pSF-468-1 Incompatibility group   IncFIB
Plasmid size   110808 bp Coordinate of oriT [Strand]   56253..56714 [-]
Host baterium   Escherichia coli strain SF-468

Cargo genes

Drug resistance gene   aph(3'')-Ib, aph(6)-Id, sitABCD, dfrA17, aac(3)-IId, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -