Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113611
Name   oriT_S15BD06969|p9 in_silico
Organism   Shigella sonnei strain S15BD06969
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099780 (54545..54633 [-], 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_S15BD06969|p9
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8720 GenBank   WP_024143648
Name   nikB_NHV79_RS00345_S15BD06969|p9 insolico UniProt ID   A0A023JAU0
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104010.41 Da        Isoelectric Point: 7.4265

>WP_024143648.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNNDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A023JAU0


Auxiliary protein

ID   5106 GenBank   WP_001283947
Name   WP_001283947_S15BD06969|p9 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   10097 GenBank   WP_001289276
Name   trbC_NHV79_RS00350_S15BD06969|p9 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: 60011..102066

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV79_RS00350 57727..60018 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
NHV79_RS00355 60011..61081 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
NHV79_RS00360 61100..62308 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
NHV79_RS00365 62600..62752 + 153 WP_001331364 Hok/Gef family protein -
NHV79_RS00370 62824..63075 - 252 WP_001291964 hypothetical protein -
NHV79_RS00640 63574..63669 + 96 WP_001303310 DinQ-like type I toxin DqlB -
NHV79_RS00380 63734..63910 - 177 WP_001054904 hypothetical protein -
NHV79_RS00385 64302..64511 + 210 WP_000062603 HEAT repeat domain-containing protein -
NHV79_RS00390 64583..65257 - 675 WP_223866377 plasmid IncI1-type surface exclusion protein ExcA -
NHV79_RS00395 65307..67475 - 2169 WP_021537350 DotA/TraY family protein traY
NHV79_RS00400 67572..68156 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
NHV79_RS00405 68185..69387 - 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
NHV79_RS00410 69354..69968 - 615 WP_000337398 IncI1-type conjugal transfer protein TraV traV
NHV79_RS00415 69968..73012 - 3045 WP_021265678 IncI1-type conjugal transfer protein TraU traU
NHV79_RS00420 73102..73902 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
NHV79_RS00425 73886..74074 - 189 WP_001277255 putative conjugal transfer protein TraS -
NHV79_RS00430 74138..74542 - 405 WP_000086958 IncI1-type conjugal transfer protein TraR traR
NHV79_RS00435 74593..75120 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NHV79_RS00440 75120..75824 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
NHV79_RS00445 75824..77113 - 1290 WP_001272003 conjugal transfer protein TraO traO
NHV79_RS00450 77116..78099 - 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
NHV79_RS00455 78110..78802 - 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
NHV79_RS00460 78799..79146 - 348 WP_001055900 conjugal transfer protein traL
NHV79_RS00465 79164..82931 - 3768 WP_001141527 LPD7 domain-containing protein -
NHV79_RS00470 83020..83571 - 552 WP_000014583 phospholipase D family protein -
NHV79_RS00475 83586..83876 - 291 WP_001299214 hypothetical protein traK
NHV79_RS00480 83873..85021 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
NHV79_RS00485 85018..85836 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
NHV79_RS00490 85833..86291 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NHV79_RS00495 86686..87270 - 585 WP_000977522 histidine phosphatase family protein -
NHV79_RS00500 87330..88532 - 1203 WP_000976351 conjugal transfer protein TraF -
NHV79_RS00505 88617..89441 - 825 WP_001238939 conjugal transfer protein TraE traE
NHV79_RS00510 89592..90746 - 1155 WP_001139957 tyrosine-type recombinase/integrase -
NHV79_RS00515 90730..91029 + 300 WP_223873359 pilus assembly protein PilV -
NHV79_RS00520 91540..92802 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
NHV79_RS00525 93009..93866 - 858 WP_247153114 IS5 family transposase -
NHV79_RS00530 94167..95042 + 876 WP_013188473 extended-spectrum class A beta-lactamase CTX-M-1 -
NHV79_RS00535 95089..95433 - 345 Protein_107 WbuC family cupin fold metalloprotein -
NHV79_RS00540 95433..95642 + 210 Protein_108 hypothetical protein -
NHV79_RS00545 96023..96271 + 249 WP_001349157 hypothetical protein -
NHV79_RS00550 96268..97560 - 1293 WP_001417545 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV79_RS00555 97560..98216 - 657 WP_001193553 prepilin peptidase -
NHV79_RS00560 98201..98761 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
NHV79_RS00565 98771..99385 - 615 WP_000959785 type 4 pilus major pilin -
NHV79_RS00570 99403..100500 - 1098 WP_001208805 type II secretion system F family protein -
NHV79_RS00575 100513..102066 - 1554 WP_000362202 GspE/PulE family protein virB11
NHV79_RS00580 102077..102529 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
NHV79_RS00585 102516..103811 - 1296 WP_000752772 type 4b pilus protein PilO2 -
NHV79_RS00590 103804..105486 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
NHV79_RS00595 105500..105937 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
NHV79_RS00600 105937..107004 - 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   14046 GenBank   NZ_CP099780
Plasmid name   S15BD06969|p9 Incompatibility group   IncI1
Plasmid size   112547 bp Coordinate of oriT [Strand]   54545..54633 [-]
Host baterium   Shigella sonnei strain S15BD06969

Cargo genes

Drug resistance gene   aadA5, sul2, blaCTX-M-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -