Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100572
Name   oriT_pL2-43 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_024974 (12067..12715 [-], 649 nt)
oriT length   649 nt
IRs (inverted repeats)      IR1: 198..207, 211..220  (ATTAGGTGTT..AATACCTAAT)
 IR2:319..324, 330..335  (AAAAAA..TTTTTT)
  IR3: 393..402, 405..414  (GTATTCATGC..GCATGAATAC)
Location of nic site      301..302
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 649 nt

>oriT_pL2-43
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAACAAAAGATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTAGGTGTTTTTAATACCTAATTATTACCGAATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGATCTACGTAGGTTAAGGACTAACTGACTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACACTATTACAACAAAAGTACATCAAAATTACATCAAAAGTACATCACTTGAAGGTTGACAGTACAACAGAATTACATCATTATCTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   644 GenBank   YP_009061037
Name   TraI_pL2-43 insolico UniProt ID   I7EM40
Length   1078 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120126.36 Da        Isoelectric Point: 6.5223

>YP_009061037.1 TraI (plasmid) [Escherichia coli]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAACALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB I7EM40


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 13043..29467

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTD13_RS00055 (D616_p124014) 8066..8575 + 510 WP_000129958 antirestriction protein ArdA -
HTD13_RS00060 (D616_p124016) 9407..9586 + 180 WP_000214483 protein CcgAI -
HTD13_RS00065 (D616_p124017) 9641..9961 + 321 WP_000211833 protein CcgAII -
HTD13_RS00070 (D616_p124019) 10072..10416 - 345 WP_015059326 hypothetical protein -
HTD13_RS00075 (D616_p124020) 10598..10966 - 369 WP_000414913 plasmid stabilization protein StbC -
HTD13_RS00080 (D616_p124021) 10968..11684 - 717 WP_000861577 StbB family protein -
HTD13_RS00270 11693..12112 - 420 WP_000802909 plasmid stabilization protein StbA -
HTD13_RS00090 (D616_p124023) 12625..13041 + 417 WP_001532083 hypothetical protein -
HTD13_RS00095 (D616_p124024) 13043..14572 + 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
HTD13_RS00100 (D616_p124025) 14572..17808 + 3237 WP_015059325 MobF family relaxase -
HTD13_RS00105 (D616_p124026) 17808..18434 + 627 WP_000434930 DUF6710 family protein -
HTD13_RS00110 (D616_p124027) 18608..19141 - 534 WP_000731968 phospholipase D family protein -
HTD13_RS00115 (D616_p124028) 19141..20136 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTD13_RS00120 (D616_p124029) 20178..21338 - 1161 WP_000101711 type IV secretion system protein VirB10 virB10
HTD13_RS00125 (D616_p124030) 21338..22222 - 885 WP_000735067 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTD13_RS00130 (D616_p124031) 22233..22931 - 699 WP_000646594 type IV secretion system protein virB8
HTD13_RS00135 (D616_p124032) 22921..23079 - 159 WP_012561180 hypothetical protein -
HTD13_RS00140 (D616_p124033) 23150..24190 - 1041 WP_000886022 type IV secretion system protein virB6
HTD13_RS00145 (D616_p124034) 24206..24433 - 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
HTD13_RS00150 (D616_p124035) 24441..25154 - 714 WP_000749362 type IV secretion system protein virB5
HTD13_RS00155 (D616_p124036) 25172..27658 - 2487 WP_031942423 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTD13_RS00160 (D616_p124037) 27773..28090 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTD13_RS00165 (D616_p124038) 28140..28433 - 294 WP_000209137 TrbC/VirB2 family protein virB2
HTD13_RS00170 (D616_p124039) 28443..28724 - 282 WP_000440698 transcriptional repressor KorA -
HTD13_RS00175 (D616_p124040) 28733..29467 - 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
HTD13_RS00180 (D616_p124041) 29510..29881 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTD13_RS00185 (D616_p124042) 29897..30274 + 378 WP_000504251 hypothetical protein -
HTD13_RS00190 (D616_p124043) 30237..30551 + 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
HTD13_RS00195 (D616_p124044) 30665..30898 + 234 WP_001191790 hypothetical protein -
HTD13_RS00200 (D616_p124046) 30954..31595 + 642 WP_001694850 restriction endonuclease -
HTD13_RS00205 (D616_p124047) 31600..31797 + 198 WP_000844102 hypothetical protein -
HTD13_RS00210 (D616_p124048) 31859..32563 - 705 WP_001067855 IS6-like element IS26 family transposase -
HTD13_RS00215 (D616_p124050) 32921..33796 + 876 WP_013188473 extended-spectrum class A beta-lactamase CTX-M-1 -
HTD13_RS00220 33843..34247 - 405 WP_223951531 WbuC family cupin fold metalloprotein -
HTD13_RS00275 34186..34428 - 243 Protein_44 MFS transporter -

Host bacterium

ID   1032 GenBank   NC_024974
Plasmid name   pL2-43 Incompatibility group   IncN
Plasmid size   43265 bp Coordinate of oriT [Strand]   12067..12715 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   blaCTX-M-1, mph(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -