Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106815
Name   oriT_2008079-SE|p3 in_silico
Organism   Salmonella enterica strain 2008079-SE
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP090532 (43555..43643 [+], 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_2008079-SE|p3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4492 GenBank   WP_070749981
Name   nikB_L0F60_RS25795_2008079-SE|p3 insolico UniProt ID   A0A2K9V0U3
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103913.35 Da        Isoelectric Point: 7.3373

>WP_070749981.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARTEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A2K9V0U3


Auxiliary protein

ID   1995 GenBank   WP_001283947
Name   WP_001283947_2008079-SE|p3 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   4546 GenBank   WP_001289276
Name   trbC_L0F60_RS25790_2008079-SE|p3 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: 1666..38177

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L0F60_RS25610 (L0F60_25610) 1042..1656 + 615 WP_000959786 type 4 pilus major pilin -
L0F60_RS25615 (L0F60_25615) 1666..2226 + 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
L0F60_RS25620 (L0F60_25620) 2211..2867 + 657 WP_001193553 prepilin peptidase -
L0F60_RS25625 (L0F60_25625) 2867..4201 + 1335 WP_001496527 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
L0F60_RS26255 4969..5193 + 225 Protein_5 hypothetical protein -
L0F60_RS25630 (L0F60_25635) 5945..7099 + 1155 WP_001139958 site-specific integrase -
L0F60_RS25635 (L0F60_25640) 7250..8074 + 825 WP_001238929 conjugal transfer protein TraE traE
L0F60_RS25640 (L0F60_25645) 8160..9362 + 1203 WP_000976353 conjugal transfer protein TraF -
L0F60_RS25645 (L0F60_25650) 9422..10006 + 585 WP_001579766 histidine phosphatase family protein -
L0F60_RS25650 (L0F60_25655) 10401..10859 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
L0F60_RS25655 (L0F60_25660) 10856..11674 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
L0F60_RS25660 (L0F60_25665) 11671..12819 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
L0F60_RS25665 (L0F60_25670) 12816..13106 + 291 WP_001372180 hypothetical protein traK
L0F60_RS25670 (L0F60_25675) 13121..13672 + 552 WP_000014584 phospholipase D family protein -
L0F60_RS25675 (L0F60_25680) 13762..17529 + 3768 WP_001579768 LPD7 domain-containing protein -
L0F60_RS25680 (L0F60_25685) 17547..17894 + 348 WP_001055900 conjugal transfer protein traL
L0F60_RS25685 (L0F60_25690) 17891..18583 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
L0F60_RS25690 (L0F60_25695) 18594..19577 + 984 WP_001579769 IncI1-type conjugal transfer protein TraN traN
L0F60_RS25695 (L0F60_25700) 19580..20869 + 1290 WP_001271997 conjugal transfer protein TraO traO
L0F60_RS25700 (L0F60_25705) 20869..21573 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
L0F60_RS25705 (L0F60_25710) 21573..22100 + 528 WP_001055569 conjugal transfer protein TraQ traQ
L0F60_RS25710 (L0F60_25715) 22151..22555 + 405 WP_001579770 DUF6750 family protein traR
L0F60_RS25715 (L0F60_25720) 22619..22807 + 189 WP_001277255 putative conjugal transfer protein TraS -
L0F60_RS25720 (L0F60_25725) 22791..23591 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
L0F60_RS25725 (L0F60_25730) 23681..26725 + 3045 WP_001024752 IncI1-type conjugal transfer protein TraU traU
L0F60_RS25730 (L0F60_25735) 26725..27339 + 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
L0F60_RS25735 (L0F60_25740) 27306..28508 + 1203 WP_001579773 IncI1-type conjugal transfer protein TraW traW
L0F60_RS25740 (L0F60_25745) 28537..29121 + 585 WP_001579774 IncI1-type conjugal transfer protein TraX -
L0F60_RS25745 (L0F60_25750) 29218..31386 + 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
L0F60_RS25750 (L0F60_25755) 31462..32076 + 615 WP_000578649 plasmid IncI1-type surface exclusion protein ExcA -
L0F60_RS25755 (L0F60_25760) 32174..32383 + 210 WP_001140545 hemolysin expression modulator Hha -
L0F60_RS25760 (L0F60_25765) 32592..32768 + 177 WP_001054900 hypothetical protein -
L0F60_RS25765 (L0F60_25770) 33692..33943 + 252 WP_001291968 hypothetical protein -
L0F60_RS25770 (L0F60_25775) 34015..34167 - 153 WP_001303307 Hok/Gef family protein -
L0F60_RS25775 (L0F60_25780) 34794..35573 + 780 WP_275450201 protein FinQ -
L0F60_RS25780 (L0F60_25785) 35880..37088 + 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
L0F60_RS25785 (L0F60_25790) 37107..38177 + 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
L0F60_RS25790 (L0F60_25795) 38170..40461 + 2292 WP_001289276 F-type conjugative transfer protein TrbC -

Host bacterium

ID   7252 GenBank   NZ_CP090532
Plasmid name   2008079-SE|p3 Incompatibility group   IncI1
Plasmid size   93407 bp Coordinate of oriT [Strand]   43555..43643 [+]
Host baterium   Salmonella enterica strain 2008079-SE

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2