Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101677
Name   oriT_p2018n8250667_3 in_silico
Organism   Escherichia coli strain COL3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JACYGB010000005 (8468..8568 [-], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      80..85, 91..96  (AAAAAA..TTTTTT)
 20..26, 38..44  (TAAATCA..TGATTTA)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 101 nt

>oriT_p2018n8250667_3
TATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1451 GenBank   WP_011407157
Name   mobF_IYX22_RS24445_p2018n8250667_3 insolico UniProt ID   A0A740S2B6
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120179.41 Da        Isoelectric Point: 6.5766

>WP_011407157.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
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 A0A740S2B6


Auxiliary protein

ID   578 GenBank   WP_000706094
Name   WP_000706094_p2018n8250667_3 insolico UniProt ID   B6UZ32
Length   96 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 96 a.a.        Molecular weight: 10829.54 Da        Isoelectric Point: 8.5040

>WP_000706094.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MKIVADRLSDVNRKLDYLFDRASDADFGPLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIA
EPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB B6UZ32


T4CP

ID   1126 GenBank   WP_000342688
Name   t4cp2_IYX22_RS24440_p2018n8250667_3 insolico UniProt ID   _
Length   509 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57762.87 Da        Isoelectric Point: 9.6551

>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(113-489)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9135..25558

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IYX22_RS24400 4158..4667 + 510 WP_000129958 antirestriction protein ArdA -
IYX22_RS24405 5499..5678 + 180 WP_000214483 protein CcgAI -
IYX22_RS24410 5733..6053 + 321 WP_000211833 protein CcgAII -
IYX22_RS24415 6164..6508 - 345 WP_000999874 hypothetical protein -
IYX22_RS24420 6690..7058 - 369 WP_000414913 plasmid stabilization protein StbC -
IYX22_RS24425 7060..7776 - 717 WP_000861577 StbB family protein -
IYX22_RS24965 7785..8204 - 420 WP_000802909 plasmid stabilization protein StbA -
IYX22_RS24435 8843..9133 + 291 WP_000706094 hypothetical protein -
IYX22_RS24440 9135..10664 + 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
IYX22_RS24445 10664..13900 + 3237 WP_011407157 MobF family relaxase -
IYX22_RS24450 13900..14526 + 627 WP_000434930 DUF6710 family protein -
IYX22_RS24455 14700..15233 - 534 WP_000731968 phospholipase D family protein -
IYX22_RS24460 15233..16228 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
IYX22_RS24465 16270..17430 - 1161 WP_000101711 type IV secretion system protein VirB10 virB10
IYX22_RS24470 17430..18314 - 885 WP_000735067 TrbG/VirB9 family P-type conjugative transfer protein virB9
IYX22_RS24475 18325..19023 - 699 WP_000646594 type IV secretion system protein virB8
IYX22_RS24480 19013..19159 - 147 WP_001257173 conjugal transfer protein TraN -
IYX22_RS24485 19242..20282 - 1041 WP_000886022 type IV secretion system protein virB6
IYX22_RS24490 20298..20525 - 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
IYX22_RS24495 20533..21246 - 714 WP_000749362 type IV secretion system protein virB5
IYX22_RS24500 21264..23864 - 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
IYX22_RS24505 23864..24181 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
IYX22_RS24510 24231..24524 - 294 WP_000209137 TrbC/VirB2 family protein virB2
IYX22_RS24515 24534..24815 - 282 WP_000440698 transcriptional repressor KorA -
IYX22_RS24520 24824..25558 - 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
IYX22_RS24525 25667..25972 + 306 WP_000960954 H-NS family nucleoid-associated regulatory protein -
IYX22_RS24530 25988..26365 + 378 WP_000504251 hypothetical protein -
IYX22_RS24535 26328..26642 + 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
IYX22_RS24540 26678..26989 + 312 WP_001452736 hypothetical protein -
IYX22_RS24545 27177..27686 + 510 WP_000893479 restriction endonuclease -
IYX22_RS24550 27691..27888 + 198 WP_000844102 hypothetical protein -
IYX22_RS24555 27950..28654 - 705 WP_001067855 IS6-like element IS26 family transposase -
IYX22_RS24560 28807..29628 - 822 WP_000939727 lincosamide nucleotidyltransferase Lnu(F) -
IYX22_RS24565 29713..30551 - 839 Protein_40 AadA family aminoglycoside 3''-O-nucleotidyltransferase -

Host bacterium

ID   2121 GenBank   NZ_JACYGB010000005
Plasmid name   p2018n8250667_3 Incompatibility group   IncN
Plasmid size   41881 bp Coordinate of oriT [Strand]   8468..8568 [-]
Host baterium   Escherichia coli strain COL3

Cargo genes

Drug resistance gene   lnu(F), ant(3'')-Ia
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -