Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100619
Name   oriT_p1ColV5155 in_silico
Organism   Escherichia coli APEC IMT5155
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP005931 (134759..135220 [-], 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_p1ColV5155
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGGCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATGAAAATTGTCAGCACTGACCCTAACAAGGGTCGTCATAGGGTCGCTATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAGAACATAAACTAATGATTTAAAAAACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTACTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAATGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGCCATGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   691 GenBank   WP_040111974
Name   TraI_p1ColV5155 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192071.95 Da        Isoelectric Point: 6.0832

>WP_040111974.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPESVLREPQREREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

AAA domain (AAA_30)

(969-1156)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 134363..154025

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L282_RS25490 (L282_24984) 130632..131066 + 435 WP_000845935 conjugation system SOS inhibitor PsiB -
L282_RS25495 (L282_24989) 131063..131782 + 720 WP_001276275 plasmid SOS inhibition protein A -
L282_RS30045 132038..132151 + 114 Protein_132 DUF5431 family protein -
L282_RS25505 132096..132218 + 123 WP_223195199 Hok/Gef family protein -
L282_RS30050 (L282_24999) 132519..132840 - 322 Protein_134 hypothetical protein -
L282_RS30055 132842..133127 + 286 Protein_135 hypothetical protein -
L282_RS25520 (L282_25009) 133246..134067 + 822 WP_001234485 DUF932 domain-containing protein -
L282_RS25525 (L282_25014) 134363..134965 - 603 WP_023145258 transglycosylase SLT domain-containing protein virB1
L282_RS25530 (L282_25019) 135287..135670 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
L282_RS25535 (L282_25024) 135860..136546 + 687 WP_000332490 PAS domain-containing protein -
L282_RS25540 (L282_25029) 136640..136867 + 228 WP_001442099 conjugal transfer relaxosome protein TraY -
L282_RS25545 (L282_25034) 136901..137266 + 366 WP_000340276 type IV conjugative transfer system pilin TraA -
L282_RS25550 (L282_25039) 137281..137592 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
L282_RS25555 (L282_25044) 137614..138180 + 567 WP_000399774 type IV conjugative transfer system protein TraE traE
L282_RS25560 (L282_25049) 138167..138895 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
L282_RS25565 (L282_25054) 138895..140322 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
L282_RS25570 (L282_25059) 140312..140902 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
L282_RS25575 (L282_25064) 140889..141086 + 198 WP_001324648 conjugal transfer protein TrbD -
L282_RS25580 (L282_25069) 141098..141349 + 252 WP_001038351 conjugal transfer protein TrbG -
L282_RS25585 (L282_25074) 141346..141861 + 516 WP_000809834 type IV conjugative transfer system lipoprotein TraV traV
L282_RS27965 (L282_25079) 141996..142217 + 222 WP_001278690 conjugal transfer protein TraR -
L282_RS25595 (L282_25084) 142377..145004 + 2628 WP_001064245 type IV secretion system protein TraC virb4
L282_RS25600 (L282_25089) 145001..145387 + 387 WP_000099688 type-F conjugative transfer system protein TrbI -
L282_RS25605 (L282_25094) 145384..146016 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
L282_RS25610 (L282_25099) 146013..147005 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
L282_RS25615 (L282_25104) 147014..147652 + 639 WP_000777703 type-F conjugative transfer system pilin assembly protein TrbC trbC
L282_RS25620 (L282_25109) 147649..149457 + 1809 WP_000821867 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L282_RS25625 (L282_25114) 149484..149741 + 258 WP_000864318 conjugal transfer protein TrbE -
L282_RS25630 (L282_25119) 149734..150477 + 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
L282_RS29545 150493..150840 + 348 Protein_159 conjugal transfer protein TrbA -
L282_RS27970 150842..151117 - 276 WP_001513501 hypothetical protein -
L282_RS25640 (L282_25129) 151198..151483 + 286 Protein_161 type-F conjugative transfer system pilin chaperone TraQ -
L282_RS25645 (L282_25134) 151470..152015 + 546 WP_021512271 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L282_RS27975 (L282_25139) 151945..152286 + 342 WP_071833523 P-type conjugative transfer protein TrbJ -
L282_RS30060 152273..152665 + 393 Protein_164 F-type conjugal transfer protein TrbF -
L282_RS25660 (L282_25149) 152652..154025 + 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
L282_RS25665 154022..156847 + 2826 Protein_166 conjugal transfer mating-pair stabilization protein TraG -
L282_RS25670 (L282_25164) 156844..157353 + 510 WP_040111998 conjugal transfer entry exclusion protein TraS -
L282_RS25675 (L282_25169) 157367..158098 + 732 WP_000850416 conjugal transfer complement resistance protein TraT -

Host bacterium

ID   1079 GenBank   NZ_CP005931
Plasmid name   p1ColV5155 Incompatibility group   IncFIC
Plasmid size   194170 bp Coordinate of oriT [Strand]   134759..135220 [-]
Host baterium   Escherichia coli APEC IMT5155

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   iroN, iroE, iroD, iroC, iroB, iucA, iucB, iucC, iutA, vat
Metal resistance gene   copper resistance
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -