Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113609
Name   oriT_S17BD00672|p31 in_silico
Organism   Shigella flexneri strain S17BD00672
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099777 (31022..31110 [-], 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_S17BD00672|p31
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8718 GenBank   WP_011264053
Name   nikB_NHV85_RS00230_S17BD00672|p31 insolico UniProt ID   A0A767TAZ8
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103882.34 Da        Isoelectric Point: 7.4198

>WP_011264053.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
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 A0A767TAZ8


Auxiliary protein

ID   5104 GenBank   WP_063119516
Name   WP_063119516_S17BD00672|p31 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: 12585.55 Da        Isoelectric Point: 10.6897

>WP_063119516.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVKKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   10095 GenBank   WP_011264051
Name   trbC_NHV85_RS00235_S17BD00672|p31 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: 86954.10 Da        Isoelectric Point: 6.7713

>WP_011264051.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36488..76472

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV85_RS00235 34204..36495 - 2292 WP_011264051 F-type conjugative transfer protein TrbC -
NHV85_RS00240 36488..37558 - 1071 WP_000151590 IncI1-type conjugal transfer protein TrbB trbB
NHV85_RS00245 37577..38785 - 1209 WP_107372241 IncI1-type conjugal transfer protein TrbA trbA
NHV85_RS00250 39092..39871 - 780 WP_275450201 protein FinQ -
NHV85_RS00255 40498..40650 + 153 WP_001387489 Hok/Gef family protein -
NHV85_RS00260 40722..40973 - 252 WP_001291964 hypothetical protein -
NHV85_RS00510 41474..41569 + 96 WP_000609148 DinQ-like type I toxin DqlB -
NHV85_RS00270 41634..41810 - 177 WP_001054898 hypothetical protein -
NHV85_RS00275 42176..42385 + 210 WP_000062603 HEAT repeat domain-containing protein -
NHV85_RS00280 42457..43131 - 675 WP_223866377 plasmid IncI1-type surface exclusion protein ExcA -
NHV85_RS00285 43181..45349 - 2169 WP_001774191 DotA/TraY family protein traY
NHV85_RS00290 45446..46030 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
NHV85_RS00295 46059..47261 - 1203 WP_107372242 IncI1-type conjugal transfer protein TraW traW
NHV85_RS00300 47228..47842 - 615 WP_000337395 IncI1-type conjugal transfer protein TraV traV
NHV85_RS00305 47842..50886 - 3045 WP_107372243 IncI1-type conjugal transfer protein TraU traU
NHV85_RS00310 50976..51776 - 801 WP_107372244 IncI1-type conjugal transfer protein TraT traT
NHV85_RS00315 51760..51948 - 189 WP_001277253 putative conjugal transfer protein TraS -
NHV85_RS00320 52012..52416 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
NHV85_RS00325 52467..52994 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NHV85_RS00330 52994..53698 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
NHV85_RS00335 53698..54987 - 1290 WP_001271994 conjugal transfer protein TraO traO
NHV85_RS00340 54990..55973 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
NHV85_RS00345 55984..56676 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NHV85_RS00350 56673..57020 - 348 WP_001055900 conjugal transfer protein traL
NHV85_RS00355 57038..60802 - 3765 WP_001141540 LPD7 domain-containing protein -
NHV85_RS00360 60892..61443 - 552 WP_000014586 phospholipase D family protein -
NHV85_RS00365 61458..61748 - 291 WP_001314267 hypothetical protein traK
NHV85_RS00370 61745..62893 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
NHV85_RS00375 62890..63708 - 819 WP_097763371 IncI1-type conjugal transfer lipoprotein TraI traI
NHV85_RS00380 63705..64163 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NHV85_RS00385 64558..65142 - 585 WP_000977522 histidine phosphatase family protein -
NHV85_RS00390 65202..66404 - 1203 WP_000976353 conjugal transfer protein TraF -
NHV85_RS00395 66490..67314 - 825 WP_001545755 conjugal transfer protein TraE traE
NHV85_RS00400 67465..68619 - 1155 WP_001139958 tyrosine-type recombinase/integrase -
NHV85_RS00405 68603..68971 + 369 WP_015059923 hypothetical protein -
NHV85_RS00410 69106..69354 + 249 WP_001349157 hypothetical protein -
NHV85_RS00415 69351..70643 - 1293 WP_001390622 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV85_RS00420 70643..71299 - 657 WP_001193549 A24 family peptidase -
NHV85_RS00425 71284..71511 - 228 Protein_85 lytic transglycosylase domain-containing protein -
NHV85_RS00430 71604..72832 + 1229 WP_088895425 IS3-like element IS2 family transposase -
NHV85_RS00435 72845..73180 - 336 Protein_87 lytic transglycosylase domain-containing protein -
NHV85_RS00440 73190..73804 - 615 WP_000908227 type 4 pilus major pilin -
NHV85_RS00445 73821..74906 - 1086 WP_001208802 type II secretion system F family protein -
NHV85_RS00450 74919..76472 - 1554 WP_001545756 GspE/PulE family protein virB11
NHV85_RS00455 76483..76935 - 453 WP_001247333 type IV pilus biogenesis protein PilP -
NHV85_RS00460 76922..78217 - 1296 WP_016245572 type 4b pilus protein PilO2 -
NHV85_RS00465 78210..79892 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
NHV85_RS00470 79906..80343 - 438 WP_001545758 type IV pilus biogenesis protein PilM -
NHV85_RS00475 80343..81410 - 1068 WP_001545759 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   14044 GenBank   NZ_CP099777
Plasmid name   S17BD00672|p31 Incompatibility group   IncI1
Plasmid size   86642 bp Coordinate of oriT [Strand]   31022..31110 [-]
Host baterium   Shigella flexneri strain S17BD00672

Cargo genes

Drug resistance gene   blaCTX-M-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2