Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101330
Name   oriT_pRHB08-C04_3 in_silico
Organism   Escherichia fergusonii strain RHB08-C04
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXUZ010000003 (65203..65291 [-], 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_pRHB08-C04_3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1248 GenBank   WP_001405892
Name   nikB_HVW15_RS23035_pRHB08-C04_3 insolico UniProt ID   A0A3V4WX06
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103883.32 Da        Isoelectric Point: 7.3373

>WP_001405892.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A3V4WX06


Auxiliary protein

ID   437 GenBank   WP_001283947
Name   WP_001283947_pRHB08-C04_3 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   856 GenBank   WP_001289282
Name   trbC_HVW15_RS23040_pRHB08-C04_3 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: 86969.12 Da        Isoelectric Point: 6.7713

>WP_001289282.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMARLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
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: 70669..105766

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVW15_RS23040 (HVW15_23040) 68385..70676 - 2292 WP_001289282 F-type conjugative transfer protein TrbC -
HVW15_RS23045 (HVW15_23045) 70669..71739 - 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
HVW15_RS23050 (HVW15_23050) 71758..72966 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
HVW15_RS23055 (HVW15_23055) 73258..73410 + 153 WP_001303307 Hok/Gef family protein -
HVW15_RS23060 (HVW15_23060) 73482..73733 - 252 WP_001291965 hypothetical protein -
HVW15_RS24190 74236..74331 + 96 WP_275056147 DinQ-like type I toxin DqlB -
HVW15_RS23070 (HVW15_23070) 74396..74572 - 177 WP_001054900 hypothetical protein -
HVW15_RS23075 (HVW15_23075) 74964..75173 + 210 WP_182228692 HEAT repeat domain-containing protein -
HVW15_RS23080 (HVW15_23080) 75245..75895 - 651 WP_182228694 plasmid IncI1-type surface exclusion protein ExcA -
HVW15_RS23085 (HVW15_23085) 75969..78137 - 2169 WP_182228696 DotA/TraY family protein traY
HVW15_RS23090 (HVW15_23090) 78234..78818 - 585 WP_079967443 IncI1-type conjugal transfer protein TraX -
HVW15_RS23095 (HVW15_23095) 78847..80049 - 1203 WP_182228698 IncI1-type conjugal transfer protein TraW traW
HVW15_RS23100 (HVW15_23100) 80016..80630 - 615 WP_001542516 IncI1-type conjugal transfer protein TraV traV
HVW15_RS23105 (HVW15_23105) 80630..83674 - 3045 WP_181464524 IncI1-type conjugal transfer protein TraU traU
HVW15_RS23110 (HVW15_23110) 83764..84564 - 801 WP_181464525 IncI1-type conjugal transfer protein TraT traT
HVW15_RS23115 (HVW15_23115) 84548..84736 - 189 WP_001277255 putative conjugal transfer protein TraS -
HVW15_RS23120 (HVW15_23120) 84800..85204 - 405 WP_077137006 IncI1-type conjugal transfer protein TraR traR
HVW15_RS23125 (HVW15_23125) 85255..85782 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HVW15_RS23130 (HVW15_23130) 85782..86486 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HVW15_RS23135 (HVW15_23135) 86486..87775 - 1290 WP_181464526 conjugal transfer protein TraO traO
HVW15_RS23140 (HVW15_23140) 87778..88761 - 984 WP_181464527 IncI1-type conjugal transfer protein TraN traN
HVW15_RS23145 (HVW15_23145) 88772..89464 - 693 WP_080242525 DotI/IcmL family type IV secretion protein traM
HVW15_RS23150 (HVW15_23150) 89461..89808 - 348 WP_001055900 conjugal transfer protein traL
HVW15_RS23155 (HVW15_23155) 89826..93593 - 3768 WP_080242524 LPD7 domain-containing protein -
HVW15_RS23160 (HVW15_23160) 93683..94234 - 552 WP_000014584 phospholipase D family protein -
HVW15_RS23165 (HVW15_23165) 94249..94539 - 291 WP_001299214 hypothetical protein traK
HVW15_RS23170 (HVW15_23170) 94536..95684 - 1149 WP_181464528 plasmid transfer ATPase TraJ virB11
HVW15_RS23175 (HVW15_23175) 95681..96499 - 819 WP_181464529 IncI1-type conjugal transfer lipoprotein TraI traI
HVW15_RS23180 (HVW15_23180) 96496..96954 - 459 WP_181464530 IncI1-type conjugal transfer lipoprotein TraH -
HVW15_RS23185 (HVW15_23185) 97469..98671 - 1203 WP_181464531 conjugal transfer protein TraF -
HVW15_RS23190 (HVW15_23190) 98757..99580 - 824 Protein_106 conjugal transfer protein TraE -
HVW15_RS24245 99739..99810 - 72 Protein_107 shufflon-specific DNA recombinase -
HVW15_RS23195 (HVW15_23195) 99945..101273 - 1329 WP_181464532 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HVW15_RS23200 (HVW15_23200) 101273..101929 - 657 WP_001193549 A24 family peptidase -
HVW15_RS23205 (HVW15_23205) 101914..102474 - 561 WP_172692750 lytic transglycosylase domain-containing protein virB1
HVW15_RS23210 (HVW15_23210) 102484..103098 - 615 WP_000908227 type 4 pilus major pilin -
HVW15_RS23215 (HVW15_23215) 103115..104200 - 1086 WP_001208802 type II secretion system F family protein -
HVW15_RS23220 (HVW15_23220) 104213..105766 - 1554 WP_001545756 ATPase, T2SS/T4P/T4SS family virB11
HVW15_RS23225 (HVW15_23225) 105777..106229 - 453 WP_001247333 type IV pilus biogenesis protein PilP -
HVW15_RS23230 (HVW15_23230) 106216..107511 - 1296 WP_181464533 type 4b pilus protein PilO2 -
HVW15_RS23235 (HVW15_23235) 107504..109186 - 1683 WP_181464534 PilN family type IVB pilus formation outer membrane protein -
HVW15_RS23240 (HVW15_23240) 109200..109637 - 438 WP_181464535 type IV pilus biogenesis protein PilM -
HVW15_RS23245 (HVW15_23245) 109637..110704 - 1068 WP_181464536 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   1774 GenBank   NZ_JABXUZ010000003
Plasmid name   pRHB08-C04_3 Incompatibility group   IncI1
Plasmid size   116352 bp Coordinate of oriT [Strand]   65203..65291 [-]
Host baterium   Escherichia fergusonii strain RHB08-C04

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -