Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105769
Name   oriT_AR_0030|unnamed1 in_silico
Organism   Shigella sonnei strain AR_0030
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032524 (31972..32060 [-], 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_AR_0030|unnamed1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3906 GenBank   WP_024260454
Name   nikB_AM357_RS26290_AR_0030|unnamed1 insolico UniProt ID   A0A5F0RK03
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103933.39 Da        Isoelectric Point: 7.3474

>WP_024260454.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
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 A0A5F0RK03


Auxiliary protein

ID   1760 GenBank   WP_001283947
Name   WP_001283947_AR_0030|unnamed1 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   3917 GenBank   WP_001289278
Name   trbC_AM357_RS26295_AR_0030|unnamed1 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: 86924.02 Da        Isoelectric Point: 6.7713

>WP_001289278.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 37438..69340

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AM357_RS26295 (AM357_28005) 35154..37445 - 2292 WP_001289278 F-type conjugative transfer protein TrbC -
AM357_RS26300 (AM357_28010) 37438..38508 - 1071 WP_000151588 IncI1-type conjugal transfer protein TrbB trbB
AM357_RS26305 (AM357_28015) 38527..39735 - 1209 WP_000121263 IncI1-type conjugal transfer protein TrbA trbA
AM357_RS26310 (AM357_28020) 40042..40821 - 780 WP_275450201 protein FinQ -
AM357_RS26315 (AM357_28025) 41448..41600 + 153 WP_001387489 Hok/Gef family protein -
AM357_RS26320 (AM357_28030) 41672..41923 - 252 WP_001291964 hypothetical protein -
AM357_RS27695 42424..42519 + 96 WP_000609148 DinQ-like type I toxin DqlB -
AM357_RS27020 42584..42760 - 177 WP_001054898 hypothetical protein -
AM357_RS27025 42757..42900 - 144 WP_001032823 hypothetical protein -
AM357_RS26330 (AM357_28040) 42943..43152 - 210 WP_001140543 hemolysin expression modulator Hha -
AM357_RS26335 (AM357_28045) 43250..43864 - 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
AM357_RS26340 (AM357_28050) 43940..46108 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
AM357_RS26345 (AM357_28055) 46205..46789 - 585 WP_001037983 IncI1-type conjugal transfer protein TraX -
AM357_RS26350 (AM357_28060) 46818..48020 - 1203 WP_042004725 IncI1-type conjugal transfer protein TraW traW
AM357_RS26355 (AM357_28065) 47987..48601 - 615 WP_000337395 IncI1-type conjugal transfer protein TraV traV
AM357_RS26360 (AM357_28070) 48601..51645 - 3045 WP_001024789 IncI1-type conjugal transfer protein TraU traU
AM357_RS26365 (AM357_28075) 51735..52535 - 801 WP_001164783 IncI1-type conjugal transfer protein TraT traT
AM357_RS26370 (AM357_28080) 52519..52707 - 189 WP_001277253 putative conjugal transfer protein TraS -
AM357_RS26375 (AM357_28085) 52771..53175 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
AM357_RS26380 (AM357_28090) 53226..53753 - 528 WP_001055569 conjugal transfer protein TraQ traQ
AM357_RS26385 (AM357_28095) 53753..54457 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
AM357_RS26390 (AM357_28100) 54457..55746 - 1290 WP_001271994 conjugal transfer protein TraO traO
AM357_RS26395 (AM357_28105) 55749..56732 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
AM357_RS26400 (AM357_28110) 56743..57435 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
AM357_RS26405 (AM357_28115) 57432..57779 - 348 WP_001055900 conjugal transfer protein traL
AM357_RS26410 (AM357_28120) 57797..61561 - 3765 WP_134812221 LPD7 domain-containing protein -
AM357_RS26415 (AM357_28125) 61651..62202 - 552 WP_000014586 phospholipase D family protein -
AM357_RS26420 (AM357_28130) 62217..62507 - 291 WP_001314267 hypothetical protein traK
AM357_RS26425 (AM357_28135) 62504..63211 - 708 Protein_72 plasmid transfer ATPase TraJ -
AM357_RS26430 (AM357_28140) 63276..64432 + 1157 WP_087879964 IS3-like element IS600 family transposase -
AM357_RS26435 (AM357_28145) 64476..64919 - 444 Protein_74 plasmid transfer ATPase TraJ -
AM357_RS26440 (AM357_28150) 64916..65734 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
AM357_RS26445 (AM357_28155) 65731..66189 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
AM357_RS26450 (AM357_28160) 66584..67168 - 585 WP_000977522 histidine phosphatase family protein -
AM357_RS26455 (AM357_28165) 67228..68430 - 1203 WP_134812223 conjugal transfer protein TraF -
AM357_RS26460 (AM357_28170) 68516..69340 - 825 WP_134812224 conjugal transfer protein TraE traE
AM357_RS26465 (AM357_28175) 69491..70318 - 828 Protein_80 site-specific integrase -
AM357_RS26470 (AM357_28180) 70385..71334 + 950 Protein_81 IS3-like element IS600 family transposase -
AM357_RS26480 (AM357_28190) 72599..72808 + 210 Protein_83 IS3 family transposase -
AM357_RS26485 (AM357_28195) 72847..73179 - 333 Protein_84 integrase -
AM357_RS27030 73178..73585 + 408 WP_003552681 hypothetical protein -
AM357_RS27770 (AM357_28205) 73582..73803 - 222 Protein_86 prepilin -

Host bacterium

ID   6206 GenBank   NZ_CP032524
Plasmid name   AR_0030|unnamed1 Incompatibility group   IncI1
Plasmid size   94537 bp Coordinate of oriT [Strand]   31972..32060 [-]
Host baterium   Shigella sonnei strain AR_0030

Cargo genes

Drug resistance gene   blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2