Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108348
Name   oriT_pS1330-110kb in_silico
Organism   Salmonella enterica subsp. enterica serovar Derby strain S1330
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OM048933 (53613..53701 [-], 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_pS1330-110kb
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5583 GenBank   WP_001405892
Name   nikB_M5D68_RS00360_pS1330-110kb 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   2679 GenBank   WP_001283947
Name   WP_001283947_pS1330-110kb 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   5959 GenBank   WP_198869309
Name   trbC_M5D68_RS00365_pS1330-110kb 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: 86957.15 Da        Isoelectric Point: 6.7713

>WP_198869309.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRILSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 59079..100210

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
M5D68_RS00365 (JJFKNCNO_00072) 56795..59086 - 2292 WP_198869309 F-type conjugative transfer protein TrbC -
M5D68_RS00370 (JJFKNCNO_00073) 59079..60149 - 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
M5D68_RS00375 (JJFKNCNO_00074) 60168..61376 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
M5D68_RS00380 (JJFKNCNO_00075) 61683..62456 - 774 WP_248782104 protein FinQ -
M5D68_RS00385 (JJFKNCNO_00077) 62520..63748 + 1229 WP_088895425 IS3-like element IS2 family transposase -
M5D68_RS00390 (JJFKNCNO_00078) 63673..64110 - 438 WP_248782105 hypothetical protein -
M5D68_RS00395 64425..64577 + 153 WP_001303307 Hok/Gef family protein -
M5D68_RS00400 (JJFKNCNO_00079) 64649..64900 - 252 WP_001291968 hypothetical protein -
M5D68_RS00405 (JJFKNCNO_00080) 65824..66000 - 177 WP_001054900 hypothetical protein -
M5D68_RS00410 (JJFKNCNO_00081) 66209..66418 - 210 WP_001140545 hemolysin expression modulator Hha -
M5D68_RS00415 (JJFKNCNO_00082) 66516..67130 - 615 WP_000578649 plasmid IncI1-type surface exclusion protein ExcA -
M5D68_RS00420 (JJFKNCNO_00083) 67206..69374 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
M5D68_RS00425 (JJFKNCNO_00084) 69471..70055 - 585 WP_001579774 IncI1-type conjugal transfer protein TraX -
M5D68_RS00430 (JJFKNCNO_00085) 70084..71286 - 1203 WP_001189159 IncI1-type conjugal transfer protein TraW traW
M5D68_RS00435 (JJFKNCNO_00086) 71253..71867 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
M5D68_RS00440 (JJFKNCNO_00087) 71867..74911 - 3045 WP_001024752 IncI1-type conjugal transfer protein TraU traU
M5D68_RS00445 (JJFKNCNO_00088) 75001..75801 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
M5D68_RS00450 (JJFKNCNO_00089) 75785..75973 - 189 WP_001277255 putative conjugal transfer protein TraS -
M5D68_RS00455 (JJFKNCNO_00090) 76037..76441 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
M5D68_RS00460 (JJFKNCNO_00091) 76492..77019 - 528 WP_001055569 conjugal transfer protein TraQ traQ
M5D68_RS00465 (JJFKNCNO_00092) 77019..77723 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
M5D68_RS00470 (JJFKNCNO_00093) 77723..79012 - 1290 WP_063074922 conjugal transfer protein TraO traO
M5D68_RS00475 (JJFKNCNO_00094) 79015..79998 - 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
M5D68_RS00480 (JJFKNCNO_00095) 80009..80701 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
M5D68_RS00485 (JJFKNCNO_00096) 80698..81045 - 348 WP_001055900 conjugal transfer protein traL
M5D68_RS00490 (JJFKNCNO_00097) 81063..84830 - 3768 WP_001579768 LPD7 domain-containing protein -
M5D68_RS00495 (JJFKNCNO_00098) 84920..85471 - 552 WP_000014584 phospholipase D family protein -
M5D68_RS00500 (JJFKNCNO_00099) 85486..85776 - 291 WP_001372180 hypothetical protein traK
M5D68_RS00505 (JJFKNCNO_00100) 85773..86921 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
M5D68_RS00510 (JJFKNCNO_00101) 86918..87736 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
M5D68_RS00515 (JJFKNCNO_00102) 87733..88191 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
M5D68_RS00520 (JJFKNCNO_00103) 88586..89170 - 585 WP_000977522 histidine phosphatase family protein -
M5D68_RS00525 (JJFKNCNO_00104) 89230..90432 - 1203 WP_000976353 conjugal transfer protein TraF -
M5D68_RS00530 (JJFKNCNO_00105) 90518..91342 - 825 WP_001238929 conjugal transfer protein TraE traE
M5D68_RS00535 (JJFKNCNO_00106) 91493..92647 - 1155 WP_001139958 site-specific integrase -
M5D68_RS00540 92631..92930 + 300 WP_223873359 pilus assembly protein PilV -
M5D68_RS00545 93752..94099 - 348 WP_072205986 shufflon protein D' -
M5D68_RS00550 94167..94415 + 249 WP_001349157 hypothetical protein -
M5D68_RS00555 (JJFKNCNO_00109) 94412..95704 - 1293 WP_001417545 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
M5D68_RS00560 (JJFKNCNO_00110) 95704..96360 - 657 WP_001193553 prepilin peptidase -
M5D68_RS00565 (JJFKNCNO_00111) 96345..96905 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
M5D68_RS00570 (JJFKNCNO_00112) 96915..97529 - 615 WP_000959786 type 4 pilus major pilin -
M5D68_RS00575 (JJFKNCNO_00113) 97547..98644 - 1098 WP_001208805 type II secretion system F family protein -
M5D68_RS00580 (JJFKNCNO_00114) 98657..100210 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
M5D68_RS00585 (JJFKNCNO_00115) 100221..100673 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
M5D68_RS00590 (JJFKNCNO_00116) 100660..101955 - 1296 WP_000752772 type 4b pilus protein PilO2 -
M5D68_RS00595 (JJFKNCNO_00117) 101948..103630 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
M5D68_RS00600 (JJFKNCNO_00118) 103644..104081 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
M5D68_RS00605 (JJFKNCNO_00119) 104081..105148 - 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   8783 GenBank   NZ_OM048933
Plasmid name   pS1330-110kb Incompatibility group   IncI1
Plasmid size   110440 bp Coordinate of oriT [Strand]   53613..53701 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Derby strain S1330

Cargo genes

Drug resistance gene   ant(3'')-Ia, aac(3)-IId, mph(A), erm(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2