Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113610
Name   oriT_S14BD05406|p4 in_silico
Organism   Shigella sonnei strain S14BD05406
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099782 (38147..38235 [-], 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_S14BD05406|p4
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8719 GenBank   WP_031942444
Name   nikB_NHV81_RS00265_S14BD05406|p4 insolico UniProt ID   A0A075UES7
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104017.50 Da        Isoelectric Point: 7.2816

>WP_031942444.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESCYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A075UES7


Auxiliary protein

ID   5105 GenBank   WP_001283947
Name   WP_001283947_S14BD05406|p4 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   10096 GenBank   WP_012783931
Name   trbC_NHV81_RS00270_S14BD05406|p4 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: 86911.02 Da        Isoelectric Point: 6.7713

>WP_012783931.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 43613..83115

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV81_RS00270 41329..43620 - 2292 WP_012783931 F-type conjugative transfer protein TrbC -
NHV81_RS00275 43613..44683 - 1071 WP_031942445 IncI1-type conjugal transfer protein TrbB trbB
NHV81_RS00280 44702..45910 - 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
NHV81_RS00285 46216..46995 - 780 WP_275542888 protein FinQ -
NHV81_RS00290 47622..47774 + 153 WP_001331364 Hok/Gef family protein -
NHV81_RS00295 47846..48097 - 252 WP_001291964 hypothetical protein -
NHV81_RS00550 48598..48693 + 96 WP_000609148 DinQ-like type I toxin DqlB -
NHV81_RS00305 48758..48934 - 177 WP_001054898 hypothetical protein -
NHV81_RS00310 49117..49326 - 210 WP_001140543 hemolysin expression modulator Hha -
NHV81_RS00315 49424..50038 - 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
NHV81_RS00320 50114..52282 - 2169 WP_031942447 IncI1-type conjugal transfer membrane protein TraY traY
NHV81_RS00325 52379..52963 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
NHV81_RS00330 52992..54194 - 1203 WP_031942448 IncI1-type conjugal transfer protein TraW traW
NHV81_RS00335 54161..54775 - 615 WP_031942449 IncI1-type conjugal transfer protein TraV traV
NHV81_RS00340 54775..57819 - 3045 WP_001024789 IncI1-type conjugal transfer protein TraU traU
NHV81_RS00345 57909..58709 - 801 WP_001164783 IncI1-type conjugal transfer protein TraT traT
NHV81_RS00350 58693..58881 - 189 WP_001277253 putative conjugal transfer protein TraS -
NHV81_RS00355 58945..59349 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
NHV81_RS00360 59400..59927 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NHV81_RS00365 59927..60631 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
NHV81_RS00370 60631..61920 - 1290 WP_001271994 conjugal transfer protein TraO traO
NHV81_RS00375 61923..62906 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
NHV81_RS00380 62917..63609 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NHV81_RS00385 63606..63953 - 348 WP_001055900 conjugal transfer protein traL
NHV81_RS00390 63971..67735 - 3765 WP_001141540 LPD7 domain-containing protein -
NHV81_RS00395 67825..68376 - 552 WP_000014586 phospholipase D family protein -
NHV81_RS00400 68391..68681 - 291 WP_001314267 hypothetical protein traK
NHV81_RS00405 68678..69826 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
NHV81_RS00410 69823..70641 - 819 WP_031942450 IncI1-type conjugal transfer lipoprotein TraI traI
NHV81_RS00415 70638..71096 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NHV81_RS00420 71491..72075 - 585 WP_000977522 histidine phosphatase family protein -
NHV81_RS00425 72135..73337 - 1203 WP_000976351 conjugal transfer protein TraF -
NHV81_RS00430 73422..74246 - 825 WP_001238939 conjugal transfer protein TraE traE
NHV81_RS00435 74397..75551 - 1155 WP_001139957 tyrosine-type recombinase/integrase -
NHV81_RS00440 75535..75861 + 327 WP_001213803 hypothetical protein -
NHV81_RS00445 76179..76436 + 258 WP_001302706 hypothetical protein -
NHV81_RS00450 76726..76881 - 156 WP_001302705 hypothetical protein -
NHV81_RS00455 77072..77320 + 249 WP_001349157 hypothetical protein -
NHV81_RS00460 77317..78609 - 1293 WP_001417545 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV81_RS00465 78609..79265 - 657 WP_001193553 prepilin peptidase -
NHV81_RS00470 79250..79810 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
NHV81_RS00475 79820..80434 - 615 WP_000959785 type 4 pilus major pilin -
NHV81_RS00480 80452..81549 - 1098 WP_001208805 type II secretion system F family protein -
NHV81_RS00485 81562..83115 - 1554 WP_000362202 GspE/PulE family protein virB11
NHV81_RS00490 83126..83578 - 453 WP_001247336 type IV pilus biogenesis protein PilP -
NHV81_RS00495 83565..84860 - 1296 WP_021560540 type 4b pilus protein PilO2 -
NHV81_RS00500 84853..86535 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
NHV81_RS00505 86549..86986 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
NHV81_RS00510 86986..88053 - 1068 WP_031942452 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   14045 GenBank   NZ_CP099782
Plasmid name   S14BD05406|p4 Incompatibility group   IncI1
Plasmid size   93713 bp Coordinate of oriT [Strand]   38147..38235 [-]
Host baterium   Shigella sonnei strain S14BD05406

Cargo genes

Drug resistance gene   blaCTX-M-15, aac(3)-IId, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2