Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100736
Name   oriT_pCFSAN004180G in_silico
Organism   Escherichia coli strain 09-00049
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP012500 (76651..77100 [+], 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_pCFSAN004180G
ATATGTATACCTCTTTATTTTCTTATCGCATCAAATTTATTTCACATATAAAAAAATGACAATTCATCGATGAATCGAATCGTGACGCAAGTTACGATAATTACGATTCATGCAGCAAATCACATCACGATTTGAATCTAGAGTCAATTCGCTTTAACTCGTTGTTTTATTATTACTGATTCATCTATGAGTTGTGTTAAATTCATTGGTGAATCATATGTGATTCACCAATGAATCCTTTTTATAATGTAAAATAAATTAAAATACATTATTTAAGACATAAGTTAATGATTCAAATAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACAGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   808 GenBank   WP_000986971
Name   TraI_pCFSAN004180G insolico UniProt ID   A0A193MHV9
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192129.86 Da        Isoelectric Point: 5.8508

>WP_000986971.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Escherichia]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMPGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIRAAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAESRMQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTTGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLISDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKIPVAEGERLRVTGKIPGLRISGGDRLQVASVSEDAMTVVVPGRAEPASLPVGYSPFTALKL
ESGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTSFTDLGREINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETIDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDAIVLVDNVYHRIAGISRDDGLITLQDTDGNSRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVMAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIALGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSEDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAEEKPDQP
DDKTEQAVRDIAGQERDRAVTSEREAVLPESVLREPQRVQDAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

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

(575-626)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 48560..77585

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GJ12_RS00280 (GJ12_p00305) 47926..48153 + 228 WP_000450526 toxin-antitoxin system antitoxin VapB -
GJ12_RS00285 (GJ12_p00310) 48153..48551 + 399 WP_000911316 type II toxin-antitoxin system VapC family toxin -
GJ12_RS00290 (GJ12_p00315) 48560..50704 - 2145 WP_000009375 type IV conjugative transfer system coupling protein TraD virb4
GJ12_RS30160 50760..51490 - 731 Protein_55 hypothetical protein -
GJ12_RS00300 (GJ12_p00325) 51725..52204 - 480 WP_001355324 hypothetical protein -
GJ12_RS00305 (GJ12_p00330) 52408..53139 - 732 WP_001364068 conjugal transfer complement resistance protein TraT -
GJ12_RS00310 (GJ12_p00335) 53171..53674 - 504 WP_000605506 hypothetical protein -
GJ12_RS00315 (GJ12_p00340) 53690..56533 - 2844 WP_001006995 conjugal transfer mating-pair stabilization protein TraG traG
GJ12_RS00320 (GJ12_p00345) 56530..57903 - 1374 WP_001137366 conjugal transfer pilus assembly protein TraH traH
GJ12_RS00325 (GJ12_p00350) 57890..58282 - 393 WP_000138366 F-type conjugal transfer protein TrbF -
GJ12_RS00330 (GJ12_p00355) 58236..58550 - 315 WP_001244895 P-type conjugative transfer protein TrbJ -
GJ12_RS00335 (GJ12_p00360) 58540..59076 - 537 WP_000059854 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
GJ12_RS00340 (GJ12_p00365) 59063..59347 - 285 WP_000624195 type-F conjugative transfer system pilin chaperone TraQ -
GJ12_RS00345 (GJ12_p00370) 59428..59763 + 336 WP_000415768 hypothetical protein -
GJ12_RS28190 (GJ12_p00375) 59744..60049 - 306 WP_236922840 conjugal transfer protein TrbA -
GJ12_RS00350 (GJ12_p00380) 60094..60837 - 744 WP_001030399 type-F conjugative transfer system pilin assembly protein TraF traF
GJ12_RS00355 (GJ12_p00385) 60830..61087 - 258 WP_000864356 conjugal transfer protein TrbE -
GJ12_RS00360 (GJ12_p00390) 61101..63005 - 1905 WP_000662057 type-F conjugative transfer system mating-pair stabilization protein TraN traN
GJ12_RS30925 63033..63251 + 219 WP_001364024 hypothetical protein -
GJ12_RS00365 (GJ12_p00395) 63240..63620 - 381 WP_000009645 hypothetical protein -
GJ12_RS00370 (GJ12_p00400) 63617..64255 - 639 WP_000087541 type-F conjugative transfer system pilin assembly protein TrbC trbC
GJ12_RS32275 (GJ12_p00405) 64282..64801 - 520 Protein_73 hypothetical protein -
GJ12_RS00380 (GJ12_p00415) 65077..66069 - 993 WP_001355328 conjugal transfer pilus assembly protein TraU traU
GJ12_RS00385 (GJ12_p00420) 66066..66698 - 633 WP_000650119 type-F conjugative transfer system protein TraW traW
GJ12_RS00390 (GJ12_p00425) 66695..67081 - 387 WP_000214089 type-F conjugative transfer system protein TrbI -
GJ12_RS00395 (GJ12_p00430) 67078..69705 - 2628 WP_001064271 type IV secretion system protein TraC virb4
GJ12_RS28195 (GJ12_p00440) 69865..70086 - 222 WP_001278688 conjugal transfer protein TraR -
GJ12_RS00400 (GJ12_p00445) 70221..70736 - 516 WP_000802746 type IV conjugative transfer system lipoprotein TraV traV
GJ12_RS00405 (GJ12_p00450) 70733..71053 - 321 WP_001057269 DUF2689 domain-containing protein -
GJ12_RS00410 (GJ12_p00455) 71040..71627 - 588 WP_000002892 conjugal transfer pilus-stabilizing protein TraP -
GJ12_RS00415 (GJ12_p00460) 71617..73047 - 1431 WP_000146619 F-type conjugal transfer pilus assembly protein TraB traB
GJ12_RS00420 (GJ12_p00465) 73047..73775 - 729 WP_001355329 type-F conjugative transfer system secretin TraK traK
GJ12_RS00425 (GJ12_p00470) 73762..74328 - 567 WP_000399757 type IV conjugative transfer system protein TraE traE
GJ12_RS00430 (GJ12_p00475) 74350..74661 - 312 WP_000012121 type IV conjugative transfer system protein TraL traL
GJ12_RS00435 (GJ12_p00480) 74676..75035 - 360 WP_000340277 type IV conjugative transfer system pilin TraA -
GJ12_RS00440 (GJ12_p00485) 75069..75296 - 228 WP_001254381 conjugal transfer relaxosome protein TraY -
GJ12_RS00445 (GJ12_p00490) 75389..76075 - 687 WP_000332479 PAS domain-containing protein -
GJ12_RS00450 (GJ12_p00495) 76269..76652 - 384 WP_001151555 conjugal transfer relaxosome DNA-binding protein TraM -
GJ12_RS00455 (GJ12_p00500) 76938..77585 + 648 WP_000614283 transglycosylase SLT domain-containing protein virB1
GJ12_RS00460 (GJ12_p00510) 77882..78703 - 822 Protein_91 DUF932 domain-containing protein -
GJ12_RS00465 (GJ12_p00515) 78822..79109 - 288 WP_000107535 hypothetical protein -
GJ12_RS00470 (GJ12_p00520) 79360..80364 + 1005 WP_024166184 IS110 family transposase -
GJ12_RS31765 (GJ12_p00525) 80458..80718 - 261 WP_000547943 hypothetical protein -
GJ12_RS31770 80788..80960 + 173 Protein_95 hypothetical protein -

Host bacterium

ID   1196 GenBank   NZ_CP012500
Plasmid name   pCFSAN004180G Incompatibility group   IncFIB
Plasmid size   225292 bp Coordinate of oriT [Strand]   76651..77100 [+]
Host baterium   Escherichia coli strain 09-00049

Cargo genes

Drug resistance gene   -
Virulence gene   hlyD, hlyB, hlyA, hlyC, estIa, faeJ, faeI, faeH, faeF, faeE, faeD, faeC
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11