Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100763
Name   oriT_pCD306 in_silico
Organism   Escherichia coli strain CD306
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP013832 (117156..117605 [+], 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_pCD306
ATATGTATACCTCTTTATTTTCTTATCGCATCAAATTTATTTCACATATAAAAAAATGACAATTCATCGATGAATCGAATCGTGACGCAAGTTACGAAAATTACGATTCATGCAGCAAATCACATCACGAATTGAATCTAGAGTCAATTCGCTTTAACTCGTTGTTTTATTATTACTGATTCATCTATGAGTTGCGTTAAATTCATTGGTGAATCATATGCGATTCACCAATGAATCCTTTTTATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGTTAATGATTCAAATAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   835 GenBank   WP_059218026
Name   TraI_pCD306 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191778.70 Da        Isoelectric Point: 5.9596

>WP_059218026.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRTEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTEMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPEREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(968-1156)

TrwC relaxase (TrwC)

(10-283)

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: 92886..118090

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AVR67_RS25940 (AVR67_25890) 89156..91354 - 2199 WP_000009360 type IV conjugative transfer system coupling protein TraD -
AVR67_RS25945 (AVR67_25895) 91607..92338 - 732 WP_000850422 conjugal transfer complement resistance protein TraT -
AVR67_RS25950 (AVR67_25900) 92370..92867 - 498 WP_000605861 hypothetical protein -
AVR67_RS25955 (AVR67_25905) 92886..95705 - 2820 WP_001007057 conjugal transfer mating-pair stabilization protein TraG traG
AVR67_RS25960 (AVR67_25910) 95702..97075 - 1374 WP_001137364 conjugal transfer pilus assembly protein TraH traH
AVR67_RS30020 (AVR67_25915) 97062..97241 - 180 Protein_101 conjugal transfer protein TrbF -
AVR67_RS25970 (AVR67_25920) 97328..97753 + 426 WP_000422741 transposase -
AVR67_RS25975 (AVR67_25925) 97750..98100 + 351 WP_000624722 IS66 family insertion sequence element accessory protein TnpB -
AVR67_RS25980 (AVR67_25930) 98131..99744 + 1614 WP_000080195 IS66-like element ISEc23 family transposase -
AVR67_RS25985 (AVR67_25935) 99776..99994 - 219 Protein_105 conjugal transfer protein TrbF -
AVR67_RS28155 99975..100316 - 342 WP_001448115 P-type conjugative transfer protein TrbJ -
AVR67_RS25990 (AVR67_25940) 100246..100791 - 546 WP_000059824 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AVR67_RS25995 (AVR67_25945) 100778..101062 - 285 WP_001448202 type-F conjugative transfer system pilin chaperone TraQ -
AVR67_RS26000 (AVR67_25950) 101189..101527 - 339 WP_001287905 conjugal transfer protein TrbA -
AVR67_RS26005 (AVR67_25955) 101543..102286 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
AVR67_RS26010 (AVR67_25960) 102279..102536 - 258 WP_000864320 conjugal transfer protein TrbE -
AVR67_RS26015 (AVR67_25965) 102563..104371 - 1809 WP_000821863 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AVR67_RS26020 (AVR67_25970) 104368..105006 - 639 WP_001080257 type-F conjugative transfer system pilin assembly protein TrbC trbC
AVR67_RS26025 (AVR67_25975) 105015..105320 - 306 WP_000224411 hypothetical protein -
AVR67_RS26030 (AVR67_25980) 105350..106342 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
AVR67_RS26035 (AVR67_25985) 106339..106971 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
AVR67_RS26040 (AVR67_25990) 106968..107354 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
AVR67_RS26045 (AVR67_25995) 107351..109978 - 2628 WP_001064239 type IV secretion system protein TraC virb4
AVR67_RS28160 110138..110359 - 222 WP_001278978 conjugal transfer protein TraR -
AVR67_RS26050 (AVR67_26000) 110494..111009 - 516 WP_000809893 type IV conjugative transfer system lipoprotein TraV traV
AVR67_RS26055 (AVR67_26005) 111006..111256 - 251 Protein_121 conjugal transfer protein TrbG -
AVR67_RS26060 (AVR67_26010) 111249..111569 - 321 WP_001057302 conjugal transfer protein TrbD virb4
AVR67_RS26065 (AVR67_26015) 111556..112140 - 585 WP_000002795 conjugal transfer pilus-stabilizing protein TraP -
AVR67_RS26070 (AVR67_26020) 112130..113557 - 1428 WP_000146638 F-type conjugal transfer pilus assembly protein TraB traB
AVR67_RS26075 (AVR67_26025) 113557..114285 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
AVR67_RS26080 (AVR67_26030) 114272..114838 - 567 WP_000399804 type IV conjugative transfer system protein TraE traE
AVR67_RS26085 (AVR67_26035) 114860..115171 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
AVR67_RS26090 (AVR67_26040) 115176..115538 - 363 WP_001098998 type IV conjugative transfer system pilin TraA -
AVR67_RS26095 (AVR67_26045) 115572..115799 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
AVR67_RS26100 (AVR67_26050) 115894..116580 - 687 WP_000332487 PAS domain-containing protein -
AVR67_RS26105 (AVR67_26055) 116774..117157 - 384 WP_001151564 conjugal transfer relaxosome DNA-binding protein TraM -
AVR67_RS26110 (AVR67_26060) 117443..118090 + 648 WP_000614282 transglycosylase SLT domain-containing protein virB1
AVR67_RS26115 (AVR67_26065) 118387..119208 - 822 WP_001234469 DUF932 domain-containing protein -
AVR67_RS26120 (AVR67_26070) 119328..119615 - 288 WP_000107537 hypothetical protein -
AVR67_RS30025 119913..120086 + 174 Protein_135 hypothetical protein -
AVR67_RS30030 120084..120314 - 231 WP_071587244 hypothetical protein -
AVR67_RS26140 (AVR67_26090) 120534..120659 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
AVR67_RS30035 120601..120750 - 150 Protein_138 plasmid maintenance protein Mok -
AVR67_RS29580 (AVR67_26095) 120772..120960 + 189 WP_001299721 hypothetical protein -
AVR67_RS26150 (AVR67_26100) 120929..121691 - 763 Protein_140 plasmid SOS inhibition protein A -
AVR67_RS26155 (AVR67_26105) 121688..122122 - 435 WP_000845901 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   1223 GenBank   NZ_CP013832
Plasmid name   pCD306 Incompatibility group   IncFIB
Plasmid size   145221 bp Coordinate of oriT [Strand]   117156..117605 [+]
Host baterium   Escherichia coli strain CD306

Cargo genes

Drug resistance gene   sul1, qacE, aadA5, sitABCD, blaTEM-1B
Virulence gene   iucA, iucC, iutA
Metal resistance gene   merR, merT, merP, merD, merE, yfeC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -