Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105228
Name   oriT_pRHB02-C22_2 in_silico
Organism   Escherichia fergusonii strain RHB02-C22
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058058 (61594..61680 [-], 87 nt)
oriT length   87 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 87 nt

>oriT_pRHB02-C22_2
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3593 GenBank   WP_001354015
Name   nikB_HVV54_RS23100_pRHB02-C22_2 insolico UniProt ID   E8XLT1
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104018.47 Da        Isoelectric Point: 7.3526

>WP_001354015.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCLAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB E8XLT1


Auxiliary protein

ID   1608 GenBank   WP_001281051
Name   WP_001281051_pRHB02-C22_2 insolico UniProt ID   A0A3U8I0C6
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12646.44 Da        Isoelectric Point: 10.4030

>WP_001281051.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSDKRQRSGSERRQKTILRAVRFSPDEDETICKNAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A3U8I0C6


T4CP

ID   3553 GenBank   WP_001289276
Name   trbC_HVV54_RS23105_pRHB02-C22_2 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: 86941.11 Da        Isoelectric Point: 6.7713

>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 67059..106206

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVV54_RS23105 (HVV54_23105) 64775..67066 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
HVV54_RS23110 (HVV54_23110) 67059..68129 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
HVV54_RS23115 (HVV54_23115) 68148..69356 - 1209 WP_181465534 IncI1-type conjugal transfer protein TrbA trbA
HVV54_RS23120 (HVV54_23120) 69648..69800 + 153 WP_001331364 Hok/Gef family protein -
HVV54_RS23125 (HVV54_23125) 69872..70123 - 252 WP_001291965 hypothetical protein -
HVV54_RS24285 70624..70719 + 96 WP_000609148 DinQ-like type I toxin DqlB -
HVV54_RS23135 (HVV54_23135) 70784..70960 - 177 WP_001054904 hypothetical protein -
HVV54_RS23140 (HVV54_23140) 71352..71561 + 210 WP_000062603 HEAT repeat domain-containing protein -
HVV54_RS23145 (HVV54_23145) 71633..72295 - 663 WP_000653334 plasmid IncI1-type surface exclusion protein ExcA -
HVV54_RS23150 (HVV54_23150) 72360..74522 - 2163 WP_000698351 DotA/TraY family protein traY
HVV54_RS23155 (HVV54_23155) 74619..75203 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
HVV54_RS23160 (HVV54_23160) 75232..76434 - 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
HVV54_RS23165 (HVV54_23165) 76401..77015 - 615 WP_000337398 IncI1-type conjugal transfer protein TraV traV
HVV54_RS23170 (HVV54_23170) 77015..80059 - 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
HVV54_RS23175 (HVV54_23175) 80149..80949 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HVV54_RS23180 (HVV54_23180) 80933..81121 - 189 WP_001277255 putative conjugal transfer protein TraS -
HVV54_RS23185 (HVV54_23185) 81185..81589 - 405 WP_000086957 IncI1-type conjugal transfer protein TraR traR
HVV54_RS23190 (HVV54_23190) 81640..82167 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HVV54_RS23195 (HVV54_23195) 82167..82871 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HVV54_RS23200 (HVV54_23200) 82871..84160 - 1290 WP_001272005 conjugal transfer protein TraO traO
HVV54_RS23205 (HVV54_23205) 84163..85146 - 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
HVV54_RS23210 (HVV54_23210) 85157..85849 - 693 WP_000138548 DotI/IcmL family type IV secretion protein traM
HVV54_RS23215 (HVV54_23215) 85846..86193 - 348 WP_001055900 conjugal transfer protein traL
HVV54_RS23220 (HVV54_23220) 86211..89978 - 3768 WP_001141529 LPD7 domain-containing protein -
HVV54_RS23225 (HVV54_23225) 90068..90619 - 552 WP_000014583 phospholipase D family protein -
HVV54_RS23230 (HVV54_23230) 90634..90924 - 291 WP_001299214 hypothetical protein traK
HVV54_RS23235 (HVV54_23235) 90921..92069 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HVV54_RS23240 (HVV54_23240) 92066..92884 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
HVV54_RS23245 (HVV54_23245) 92881..93339 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HVV54_RS23250 (HVV54_23250) 93734..94066 - 333 Protein_111 lipopolysaccharide core heptose(II)-phosphate phosphatase -
HVV54_RS23255 (HVV54_23255) 94158..95386 + 1229 WP_164473239 IS3-like element IS2 family transposase -
HVV54_RS24200 95379..95654 - 276 Protein_113 histidine phosphatase family protein -
HVV54_RS23260 (HVV54_23260) 95714..96916 - 1203 WP_000976351 conjugal transfer protein TraF -
HVV54_RS23265 (HVV54_23265) 97001..97825 - 825 WP_001238939 conjugal transfer protein TraE traE
HVV54_RS23270 (HVV54_23270) 97976..99130 - 1155 WP_001139957 site-specific integrase -
HVV54_RS23275 (HVV54_23275) 99966..100172 - 207 WP_000008649 hypothetical protein -
HVV54_RS23280 (HVV54_23280) 100322..100570 + 249 WP_001349157 hypothetical protein -
HVV54_RS23285 (HVV54_23285) 100567..101859 - 1293 WP_001417545 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HVV54_RS23290 (HVV54_23290) 101859..102515 - 657 WP_001193553 prepilin peptidase -
HVV54_RS23295 (HVV54_23295) 102500..103060 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HVV54_RS23300 (HVV54_23300) 103070..103684 - 615 WP_000959785 type 4 pilus major pilin -
HVV54_RS23305 (HVV54_23305) 103702..104799 - 1098 WP_001208805 type II secretion system F family protein -
HVV54_RS23310 (HVV54_23310) 104812..106365 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family -
HVV54_RS23315 (HVV54_23315) 106376..106828 - 453 WP_001247336 type IV pilus biogenesis protein PilP -
HVV54_RS23320 (HVV54_23320) 106815..108110 - 1296 WP_000752774 type 4b pilus protein PilO2 -
HVV54_RS23325 (HVV54_23325) 108103..109785 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HVV54_RS23330 (HVV54_23330) 109799..110236 - 438 WP_000539807 type IV pilus biogenesis protein PilM -

Host bacterium

ID   5666 GenBank   NZ_CP058058
Plasmid name   pRHB02-C22_2 Incompatibility group   IncI1
Plasmid size   116881 bp Coordinate of oriT [Strand]   61594..61680 [-]
Host baterium   Escherichia fergusonii strain RHB02-C22

Cargo genes

Drug resistance gene   tet(A), aadA2, cmlA1, ant(3'')-Ia, sul3
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -