Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103222
Name   oriT_pEC006 in_silico
Organism   Escherichia coli strain EC006
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY748188 (51859..51947 [-], 89 nt)
oriT length   89 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 89 nt

>oriT_pEC006
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2410 GenBank   WP_001493820
Name   nikB_HTR38_RS00320_pEC006 insolico UniProt ID   A0A229B7S1
Length   900 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 900 a.a.        Molecular weight: 104037.65 Da        Isoelectric Point: 7.3321

>WP_001493820.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVDFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHCTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLNGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRIVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
YNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKLWEPPSPMR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A229B7S1


Auxiliary protein

ID   1027 GenBank   WP_001283947
Name   WP_001283947_pEC006 insolico UniProt ID   A0A142CMC2
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12613.57 Da        Isoelectric Point: 10.7463

>WP_001283947.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A142CMC2


T4CP

ID   2176 GenBank   WP_001289272
Name   trbC_HTR38_RS00330_pEC006 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86924.04 Da        Isoelectric Point: 6.6402

>WP_001289272.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPIVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETNEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 58305..96720

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTR38_RS00325 (pEC006_00060) 55130..55948 + 819 WP_000106196 DUF2971 domain-containing protein -
HTR38_RS00330 (pEC006_00061) 56021..58312 - 2292 WP_001289272 F-type conjugative transfer protein TrbC -
HTR38_RS00335 (pEC006_00062) 58305..59375 - 1071 WP_001535705 IncI1-type conjugal transfer protein TrbB trbB
HTR38_RS00340 (pEC006_00063) 59394..60602 - 1209 WP_001535704 IncI1-type conjugal transfer protein TrbA trbA
HTR38_RS00345 (pEC006_00064) 60894..61046 + 153 WP_001331364 Hok/Gef family protein -
HTR38_RS00350 (pEC006_00065) 61118..61369 - 252 WP_001535703 hypothetical protein -
HTR38_RS00610 61870..61965 + 96 WP_000609148 DinQ-like type I toxin DqlB -
HTR38_RS00360 (pEC006_00067) 62030..62314 - 285 WP_024129996 hypothetical protein -
HTR38_RS00365 (pEC006_00068) 62415..62624 - 210 WP_001140545 hemolysin expression modulator Hha -
HTR38_RS00370 (pEC006_00069) 62722..63336 - 615 WP_000578649 plasmid IncI1-type surface exclusion protein ExcA -
HTR38_RS00375 (pEC006_00070) 63412..65580 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
HTR38_RS00380 (pEC006_00071) 65677..66261 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
HTR38_RS00385 (pEC006_00072) 66290..67492 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
HTR38_RS00390 (pEC006_00073) 67459..68073 - 615 WP_000337400 IncI1-type conjugal transfer protein TraV traV
HTR38_RS00395 (pEC006_00074) 68073..71117 - 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
HTR38_RS00400 (pEC006_00075) 71207..72007 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HTR38_RS00405 (pEC006_00076) 71991..72179 - 189 WP_001277255 putative conjugal transfer protein TraS -
HTR38_RS00410 (pEC006_00077) 72243..72647 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
HTR38_RS00415 (pEC006_00078) 72698..73225 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HTR38_RS00420 (pEC006_00079) 73225..73929 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HTR38_RS00425 (pEC006_00080) 73929..75218 - 1290 WP_001535701 conjugal transfer protein TraO traO
HTR38_RS00430 (pEC006_00081) 75221..76204 - 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
HTR38_RS00435 (pEC006_00082) 76215..76907 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HTR38_RS00440 (pEC006_00083) 76904..77251 - 348 WP_001055900 conjugal transfer protein traL
HTR38_RS00445 (pEC006_00084) 77269..81036 - 3768 WP_001141542 LPD7 domain-containing protein -
HTR38_RS00450 (pEC006_00085) 81126..81677 - 552 WP_000014584 phospholipase D family protein -
HTR38_RS00455 (pEC006_00086) 81692..81982 - 291 WP_001372180 hypothetical protein traK
HTR38_RS00460 (pEC006_00087) 81979..83127 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HTR38_RS00465 (pEC006_00088) 83124..83681 - 558 Protein_90 IncI1-type conjugal transfer lipoprotein TraI -
HTR38_RS00470 (pEC006_00089) 83697..84905 - 1209 WP_001352368 IS4-like element ISVsa5 family transposase -
HTR38_RS00475 (pEC006_00090) 85011..85280 - 270 Protein_92 IncI1-type conjugal transfer lipoprotein TraI -
HTR38_RS00480 (pEC006_00091) 85277..85735 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HTR38_RS00485 (pEC006_00092) 86130..86714 - 585 WP_000977522 histidine phosphatase family protein -
HTR38_RS00490 (pEC006_00093) 86774..87976 - 1203 WP_000976351 conjugal transfer protein TraF -
HTR38_RS00495 (pEC006_00094) 88061..88885 - 825 WP_001238939 conjugal transfer protein TraE traE
HTR38_RS00500 (pEC006_00095) 89036..90190 - 1155 WP_001139957 site-specific integrase -
HTR38_RS00605 90189..90542 + 354 WP_001393368 hypothetical protein -
HTR38_RS00620 90572..90793 + 222 Protein_99 prepilin -
HTR38_RS00520 (pEC006_00097) 90790..92214 - 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HTR38_RS00525 (pEC006_00098) 92214..92870 - 657 WP_001193553 prepilin peptidase -
HTR38_RS00530 (pEC006_00099) 92855..93415 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HTR38_RS00535 (pEC006_00100) 93425..94039 - 615 WP_000959785 type 4 pilus major pilin -
HTR38_RS00540 (pEC006_00101) 94057..95154 - 1098 WP_001208805 type II secretion system F family protein -
HTR38_RS00545 (pEC006_00102) 95167..96720 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
HTR38_RS00550 (pEC006_00103) 96731..97183 - 453 WP_001247336 type IV pilus biogenesis protein PilP -
HTR38_RS00555 (pEC006_00104) 97170..98465 - 1296 WP_000752774 type 4b pilus protein PilO2 -
HTR38_RS00560 (pEC006_00105) 98458..100140 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HTR38_RS00565 (pEC006_00106) 100154..100591 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
HTR38_RS00570 (pEC006_00107) 100591..101658 - 1068 WP_000742600 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   3665 GenBank   NZ_KY748188
Plasmid name   pEC006 Incompatibility group   IncI1
Plasmid size   106128 bp Coordinate of oriT [Strand]   51859..51947 [-]
Host baterium   Escherichia coli strain EC006

Cargo genes

Drug resistance gene   blaTEM-1B, rmtB, sul1, qacE, aadA2, dfrA12
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -