Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100688
Name   oriT_pAPEC-O78-ColV in_silico
Organism   Escherichia coli strain 789
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP010316 (84497..84789 [-], 293 nt)
oriT length   293 nt
IRs (inverted repeats)      228..235, 238..245 n  (GCAAAAAC..GTTTTTGC)
Location of nic site      254..255
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 293 nt

>oriT_pAPEC-O78-ColV
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCCCCCCCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   760 GenBank   WP_000986993
Name   TraI_pAPEC-O78-ColV insolico UniProt ID   A0A0D8W3C5
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191812.64 Da        Isoelectric Point: 6.0533

>WP_000986993.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQVILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ESGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESGRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSGGQQTRVIRPAQVRAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGSRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDTPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DSKTEQAVREIAGQERDRSAISEREAALPESVLRESQREREAVREVARENLLQERLQQMEQDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

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

(633-712)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 83935..109727

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AC789_RS25195 (AC789_145pl00930) 79926..80360 + 435 WP_044502442 conjugation system SOS inhibitor PsiB -
AC789_RS25200 (AC789_145pl00940) 80357..81143 + 787 Protein_77 plasmid SOS inhibition protein A -
AC789_RS30525 81333..81446 + 114 Protein_78 DUF5431 family protein -
AC789_RS25210 (AC789_145pl00950) 81391..81513 + 123 WP_223195199 Hok/Gef family protein -
AC789_RS30105 (AC789_145pl00960) 81814..82111 - 298 Protein_80 hypothetical protein -
AC789_RS25225 (AC789_145pl00980) 82412..82699 + 288 WP_000107520 hypothetical protein -
AC789_RS25230 (AC789_145pl00990) 82818..83639 + 822 WP_001234468 DUF932 domain-containing protein -
AC789_RS25235 (AC789_145pl01010) 83935..84444 - 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
AC789_RS25240 (AC789_145pl01020) 84861..85244 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
AC789_RS25245 (AC789_145pl01030) 85431..86120 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
AC789_RS25250 (AC789_145pl01040) 86219..86614 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
AC789_RS25255 (AC789_145pl01050) 86647..87012 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
AC789_RS25260 (AC789_145pl01060) 87027..87338 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
AC789_RS25265 (AC789_145pl01070) 87360..87926 + 567 WP_000399785 type IV conjugative transfer system protein TraE traE
AC789_RS25270 (AC789_145pl01080) 87913..88641 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
AC789_RS25275 (AC789_145pl01090) 88641..90068 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
AC789_RS25280 (AC789_145pl01100) 90058..90648 + 591 WP_000002796 conjugal transfer pilus-stabilizing protein TraP -
AC789_RS25285 (AC789_145pl01110) 90635..90832 + 198 WP_001324648 conjugal transfer protein TrbD -
AC789_RS25290 (AC789_145pl01120) 90844..91095 + 252 WP_001038342 conjugal transfer protein TrbG -
AC789_RS25295 (AC789_145pl01130) 91092..91607 + 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
AC789_RS28350 (AC789_145pl01140) 91742..91963 + 222 WP_001278689 conjugal transfer protein TraR -
AC789_RS25305 (AC789_145pl01150) 92123..94750 + 2628 WP_001064252 type IV secretion system protein TraC virb4
AC789_RS25310 (AC789_145pl01160) 94747..95133 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
AC789_RS25315 (AC789_145pl01170) 95130..95762 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
AC789_RS25320 (AC789_145pl01180) 95759..96751 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
AC789_RS25325 (AC789_145pl01190) 96760..97398 + 639 WP_000777693 type-F conjugative transfer system pilin assembly protein TrbC trbC
AC789_RS25330 (AC789_145pl01200) 97395..99203 + 1809 WP_044502452 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AC789_RS25335 (AC789_145pl01210) 99230..99487 + 258 WP_000864325 conjugal transfer protein TrbE -
AC789_RS25340 (AC789_145pl01220) 99480..100223 + 744 WP_001030389 type-F conjugative transfer system pilin assembly protein TraF traF
AC789_RS25345 (AC789_145pl01230) 100239..100586 + 348 WP_001287676 conjugal transfer protein TrbA -
AC789_RS25350 (AC789_145pl01240) 100705..100989 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
AC789_RS25355 (AC789_145pl01250) 100976..101521 + 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AC789_RS25360 (AC789_145pl01260) 101451..101813 + 363 WP_071779407 P-type conjugative transfer protein TrbJ -
AC789_RS25365 (AC789_145pl01270) 101813..103186 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
AC789_RS25370 (AC789_145pl01280) 103183..106005 + 2823 WP_001007012 conjugal transfer mating-pair stabilization protein TraG traG
AC789_RS25375 (AC789_145pl01290) 106020..106523 + 504 WP_000605510 hypothetical protein -
AC789_RS25380 (AC789_145pl01300) 106555..107286 + 732 WP_001447147 conjugal transfer complement resistance protein TraT -
AC789_RS25385 (AC789_145pl01310) 107538..109727 + 2190 WP_044502453 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1148 GenBank   NZ_CP010316
Plasmid name   pAPEC-O78-ColV Incompatibility group   IncFIB
Plasmid size   144859 bp Coordinate of oriT [Strand]   84497..84789 [-]
Host baterium   Escherichia coli strain 789

Cargo genes

Drug resistance gene   sitABCD, tet(A)
Virulence gene   iroN, iroE, iroD, iroC, iroB, iucA, iucB, iucC, iutA
Metal resistance gene   merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -