Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113600
Name   oriT_S13BD04362|p3 in_silico
Organism   Shigella sonnei strain S13BD04362
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099783 (38523..38611 [-], 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_S13BD04362|p3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8709 GenBank   WP_059278894
Name   nikB_NHV76_RS00260_S13BD04362|p3 insolico UniProt ID   _
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103987.37 Da        Isoelectric Point: 7.2858

>WP_059278894.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSEHYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure



No available structure.




Auxiliary protein

ID   5093 GenBank   WP_059278893
Name   WP_059278893_S13BD04362|p3 insolico UniProt ID   _
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12585.51 Da        Isoelectric Point: 10.6123

>WP_059278893.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKQINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   10084 GenBank   WP_001289271
Name   trbC_NHV76_RS00265_S13BD04362|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: 86927.12 Da        Isoelectric Point: 6.7713

>WP_001289271.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56329..89399

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV76_RS00315 51754..53016 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
NHV76_RS00320 53679..53831 + 153 WP_001331364 Hok/Gef family protein -
NHV76_RS00325 53903..54154 - 252 WP_001291964 hypothetical protein -
NHV76_RS00560 54653..54748 + 96 WP_001303310 DinQ-like type I toxin DqlB -
NHV76_RS00335 54813..55097 - 285 WP_014640317 hypothetical protein -
NHV76_RS00340 55321..55530 + 210 WP_000062602 HEAT repeat domain-containing protein -
NHV76_RS00345 55602..56264 - 663 WP_000644792 plasmid IncI1-type surface exclusion protein ExcA -
NHV76_RS00350 56329..58497 - 2169 WP_000698366 DotA/TraY family protein traY
NHV76_RS00355 58594..59178 - 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
NHV76_RS00360 59207..60409 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
NHV76_RS00365 60376..60990 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
NHV76_RS00370 60990..64034 - 3045 WP_001024776 IncI1-type conjugal transfer protein TraU traU
NHV76_RS00375 64124..64924 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
NHV76_RS00380 64908..65096 - 189 WP_001277255 putative conjugal transfer protein TraS -
NHV76_RS00385 65160..65564 - 405 WP_001422824 IncI1-type conjugal transfer protein TraR traR
NHV76_RS00390 65615..66142 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NHV76_RS00395 66142..66846 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
NHV76_RS00400 66846..68135 - 1290 WP_001271994 conjugal transfer protein TraO traO
NHV76_RS00405 68138..69121 - 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
NHV76_RS00410 69132..69824 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NHV76_RS00415 69821..70168 - 348 WP_001055900 conjugal transfer protein traL
NHV76_RS00420 70186..73953 - 3768 WP_021513964 LPD7 domain-containing protein -
NHV76_RS00425 74042..74593 - 552 WP_000014584 phospholipase D family protein -
NHV76_RS00430 74608..74898 - 291 WP_001299214 hypothetical protein traK
NHV76_RS00435 74895..76043 - 1149 WP_001024975 plasmid transfer ATPase TraJ virB11
NHV76_RS00440 76040..76858 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
NHV76_RS00445 76855..77313 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NHV76_RS00450 77708..78292 - 585 WP_000977520 histidine phosphatase family protein -
NHV76_RS00455 78352..79554 - 1203 WP_000976357 conjugal transfer protein TraF -
NHV76_RS00460 79640..80464 - 825 WP_015058912 conjugal transfer protein TraE traE
NHV76_RS00465 80615..81769 - 1155 WP_001139955 tyrosine-type recombinase/integrase -
NHV76_RS00470 82977..83234 + 258 WP_001302706 hypothetical protein -
NHV76_RS00475 83369..83617 + 249 WP_001349157 hypothetical protein -
NHV76_RS00480 83614..84906 - 1293 WP_039719938 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV76_RS00485 84906..85562 - 657 WP_001193551 A24 family peptidase -
NHV76_RS00490 85547..86107 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
NHV76_RS00495 86117..86731 - 615 WP_000908228 type 4 pilus major pilin -
NHV76_RS00500 86748..87833 - 1086 WP_001208803 type II secretion system F family protein -
NHV76_RS00505 87846..89399 - 1554 WP_000362204 GspE/PulE family protein virB11
NHV76_RS00510 89410..89862 - 453 WP_001247333 type IV pilus biogenesis protein PilP -
NHV76_RS00515 89849..91144 - 1296 WP_021513967 type 4b pilus protein PilO2 -
NHV76_RS00520 91137..92819 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
NHV76_RS00525 92833..93270 - 438 WP_000539811 type IV pilus biogenesis protein PilM -
NHV76_RS00530 93270..94337 - 1068 WP_113488342 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   14035 GenBank   NZ_CP099783
Plasmid name   S13BD04362|p3 Incompatibility group   IncI1
Plasmid size   98822 bp Coordinate of oriT [Strand]   38523..38611 [-]
Host baterium   Shigella sonnei strain S13BD04362

Cargo genes

Drug resistance gene   blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -