Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105150
Name   oriT_pRHB41-C23_3 in_silico
Organism   Escherichia fergusonii strain RHB41-C23
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055601 (58824..58912 [-], 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_pRHB41-C23_3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3562 GenBank   WP_024143648
Name   nikB_HV014_RS22910_pRHB41-C23_3 insolico UniProt ID   A0A023JAU0
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104010.41 Da        Isoelectric Point: 7.4265

>WP_024143648.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNNDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A023JAU0


Auxiliary protein

ID   1590 GenBank   WP_001283947
Name   WP_001283947_pRHB41-C23_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   3527 GenBank   WP_001289276
Name   trbC_HV014_RS22915_pRHB41-C23_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: 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: 64290..102957

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV014_RS22915 (HV014_22925) 62006..64297 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
HV014_RS22920 (HV014_22930) 64290..65360 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
HV014_RS22925 (HV014_22935) 65379..66587 - 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
HV014_RS22930 (HV014_22940) 66805..67791 - 987 WP_001257838 hypothetical protein -
HV014_RS22935 (HV014_22945) 68360..68512 + 153 WP_001331364 Hok/Gef family protein -
HV014_RS22940 (HV014_22950) 68584..68835 - 252 WP_001291965 hypothetical protein -
HV014_RS24225 69334..69429 + 96 WP_001303310 DinQ-like type I toxin DqlB -
HV014_RS22945 (HV014_22955) 69494..69670 - 177 WP_001054897 hypothetical protein -
HV014_RS22950 (HV014_22960) 69879..70088 - 210 WP_052939150 hemolysin expression modulator Hha -
HV014_RS22955 (HV014_22965) 70186..70800 - 615 WP_000578649 plasmid IncI1-type surface exclusion protein ExcA -
HV014_RS22960 (HV014_22970) 70876..73044 - 2169 WP_063267537 IncI1-type conjugal transfer membrane protein TraY traY
HV014_RS22965 (HV014_22975) 73141..73725 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
HV014_RS22970 (HV014_22980) 73754..74956 - 1203 WP_001385654 IncI1-type conjugal transfer protein TraW traW
HV014_RS22975 (HV014_22985) 74923..75537 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
HV014_RS22980 (HV014_22990) 75537..78581 - 3045 WP_129753780 IncI1-type conjugal transfer protein TraU traU
HV014_RS22985 (HV014_22995) 78671..79471 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HV014_RS22990 (HV014_23000) 79455..79643 - 189 WP_001277255 putative conjugal transfer protein TraS -
HV014_RS22995 (HV014_23005) 79707..80111 - 405 WP_000086959 IncI1-type conjugal transfer protein TraR traR
HV014_RS23000 (HV014_23010) 80162..80689 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HV014_RS23005 (HV014_23015) 80689..81393 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HV014_RS23010 (HV014_23020) 81393..82682 - 1290 WP_001774189 conjugal transfer protein TraO traO
HV014_RS23015 (HV014_23025) 82685..83668 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
HV014_RS23020 (HV014_23030) 83679..84371 - 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
HV014_RS23025 (HV014_23035) 84368..84715 - 348 WP_001055900 conjugal transfer protein traL
HV014_RS23030 (HV014_23040) 84733..88500 - 3768 WP_001141534 LPD7 domain-containing protein -
HV014_RS23035 (HV014_23045) 88590..89141 - 552 WP_000014584 phospholipase D family protein -
HV014_RS23040 (HV014_23050) 89156..89446 - 291 WP_001299214 hypothetical protein traK
HV014_RS23045 (HV014_23055) 89443..90591 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HV014_RS23050 (HV014_23060) 90588..91406 - 819 WP_052962236 IncI1-type conjugal transfer lipoprotein TraI traI
HV014_RS23055 (HV014_23065) 91403..91861 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HV014_RS23060 (HV014_23070) 92256..92840 - 585 WP_000977522 histidine phosphatase family protein -
HV014_RS23065 (HV014_23075) 92900..94102 - 1203 WP_000976353 conjugal transfer protein TraF -
HV014_RS23070 (HV014_23080) 94188..95012 - 825 WP_001545755 conjugal transfer protein TraE traE
HV014_RS23075 (HV014_23085) 95163..96317 - 1155 WP_001139958 site-specific integrase -
HV014_RS24125 96316..96600 + 285 WP_187642572 pilus assembly protein PilV -
HV014_RS23085 (HV014_23095) 97136..98464 - 1329 WP_069057437 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HV014_RS23090 (HV014_23100) 98464..99120 - 657 WP_001193549 A24 family peptidase -
HV014_RS23095 (HV014_23105) 99105..99665 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
HV014_RS23100 (HV014_23110) 99675..100289 - 615 WP_000908228 type 4 pilus major pilin -
HV014_RS23105 (HV014_23115) 100306..101391 - 1086 WP_129753666 type II secretion system F family protein -
HV014_RS23110 (HV014_23120) 101404..102957 - 1554 WP_000362204 ATPase, T2SS/T4P/T4SS family virB11
HV014_RS23115 (HV014_23125) 102968..103420 - 453 WP_001247333 type IV pilus biogenesis protein PilP -
HV014_RS23120 (HV014_23130) 103407..104702 - 1296 WP_000752776 type 4b pilus protein PilO2 -
HV014_RS23125 (HV014_23135) 104695..106377 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HV014_RS23130 (HV014_23140) 106391..106828 - 438 WP_000539811 type IV pilus biogenesis protein PilM -
HV014_RS23135 (HV014_23145) 106828..107895 - 1068 WP_021513968 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   5588 GenBank   NZ_CP055601
Plasmid name   pRHB41-C23_3 Incompatibility group   IncI1
Plasmid size   112380 bp Coordinate of oriT [Strand]   58824..58912 [-]
Host baterium   Escherichia fergusonii strain RHB41-C23

Cargo genes

Drug resistance gene   dfrA1, blaTEM-1B, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -