Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103040
Name   oriT_pHNRD174 in_silico
Organism   Escherichia coli strain RD174
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX246268 (31447..31535 [-], 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_pHNRD174
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2272 GenBank   WP_012783930
Name   nikB_HTJ38_RS00220_pHNRD174 insolico UniProt ID   N0GUP8
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104070.55 Da        Isoelectric Point: 7.3623

>WP_012783930.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB N0GUP8


Auxiliary protein

ID   933 GenBank   WP_001283947
Name   WP_001283947_pHNRD174 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   1973 GenBank   WP_012783931
Name   trbC_HTJ38_RS00225_pHNRD174 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: 86911.02 Da        Isoelectric Point: 6.7713

>WP_012783931.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36913..76144

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTJ38_RS00225 34629..36920 - 2292 WP_012783931 F-type conjugative transfer protein TrbC -
HTJ38_RS00230 36913..37983 - 1071 WP_012783932 IncI1-type conjugal transfer protein TrbB trbB
HTJ38_RS00235 38002..39210 - 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
HTJ38_RS00240 39517..40296 - 780 WP_275450201 protein FinQ -
HTJ38_RS00245 40923..41075 + 153 WP_001387489 Hok/Gef family protein -
HTJ38_RS00250 41147..41398 - 252 WP_001291964 hypothetical protein -
HTJ38_RS00510 41899..41994 + 96 WP_000609148 DinQ-like type I toxin DqlB -
HTJ38_RS00260 42059..42343 - 285 WP_014640317 hypothetical protein -
HTJ38_RS00265 42627..42836 + 210 WP_000062603 HEAT repeat domain-containing protein -
HTJ38_RS00270 42908..43570 - 663 WP_012783935 plasmid IncI1-type surface exclusion protein ExcA -
HTJ38_RS00275 43641..45809 - 2169 WP_015508354 DotA/TraY family protein traY
HTJ38_RS00280 45906..46490 - 585 WP_012783937 conjugal transfer protein TraX -
HTJ38_RS00285 46519..47721 - 1203 WP_012783938 IncI1-type conjugal transfer protein TraW traW
HTJ38_RS00290 47688..48302 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
HTJ38_RS00295 48302..51346 - 3045 WP_012783939 IncI1-type conjugal transfer protein TraU traU
HTJ38_RS00300 51436..52236 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HTJ38_RS00305 52220..52408 - 189 WP_001277255 putative conjugal transfer protein TraS -
HTJ38_RS00310 52472..52876 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
HTJ38_RS00315 52927..53454 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HTJ38_RS00320 53454..54158 - 705 WP_001493811 IncI1-type conjugal transfer protein TraP traP
HTJ38_RS00325 54158..55447 - 1290 WP_011264042 conjugal transfer protein TraO traO
HTJ38_RS00330 55450..56433 - 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
HTJ38_RS00335 56444..57136 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HTJ38_RS00340 57133..57480 - 348 WP_001055900 conjugal transfer protein traL
HTJ38_RS00345 57498..61265 - 3768 WP_012783940 LPD7 domain-containing protein -
HTJ38_RS00350 61355..61906 - 552 WP_012783942 phospholipase D family protein -
HTJ38_RS00355 61921..62211 - 291 WP_001314267 hypothetical protein traK
HTJ38_RS00360 62208..63356 - 1149 WP_001024971 plasmid transfer ATPase TraJ virB11
HTJ38_RS00365 63353..64171 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
HTJ38_RS00370 64168..64626 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HTJ38_RS00375 65020..65604 - 585 WP_000977522 histidine phosphatase family protein -
HTJ38_RS00380 65664..66866 - 1203 WP_000976353 conjugal transfer protein TraF -
HTJ38_RS00385 66952..67776 - 825 WP_001238932 conjugal transfer protein TraE traE
HTJ38_RS00390 67927..69081 - 1155 WP_172688961 site-specific integrase -
HTJ38_RS00395 69065..69391 + 327 WP_001213803 hypothetical protein -
HTJ38_RS00400 69709..69966 + 258 WP_236919519 shufflon protein D' -
HTJ38_RS00515 69996..70217 + 222 Protein_79 prepilin -
HTJ38_RS00410 70214..71638 - 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HTJ38_RS00415 71638..72294 - 657 WP_001193553 prepilin peptidase -
HTJ38_RS00420 72279..72839 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HTJ38_RS00425 72849..73463 - 615 WP_001542527 type 4 pilus major pilin -
HTJ38_RS00430 73481..74578 - 1098 WP_001492931 type II secretion system F family protein -
HTJ38_RS00435 74591..76144 - 1554 WP_001492932 ATPase, T2SS/T4P/T4SS family virB11
HTJ38_RS00440 76155..76607 - 453 WP_012783945 type IV pilus biogenesis protein PilP -
HTJ38_RS00445 76594..77889 - 1296 WP_012783946 type 4b pilus protein PilO2 -
HTJ38_RS00450 77882..79564 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HTJ38_RS00455 79578..80015 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
HTJ38_RS00460 80015..81082 - 1068 WP_012783947 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   3483 GenBank   NZ_KX246268
Plasmid name   pHNRD174 Incompatibility group   IncI1
Plasmid size   86207 bp Coordinate of oriT [Strand]   31447..31535 [-]
Host baterium   Escherichia coli strain RD174

Cargo genes

Drug resistance gene   blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2