Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104511
Name   oriT_STEFF_3|unnamed3 in_silico
Organism   Shigella flexneri strain STEFF_3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055202 (39390..39478 [-], 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_STEFF_3|unnamed3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3265 GenBank   WP_001306778
Name   nikB_HUZ39_RS25640_STEFF_3|unnamed3 insolico UniProt ID   Q79VV7
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_001306778.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
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 Q79VV7


Auxiliary protein

ID   1452 GenBank   WP_001283947
Name   WP_001283947_STEFF_3|unnamed3 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   3194 GenBank   WP_021497839
Name   trbC_HUZ39_RS25645_STEFF_3|unnamed3 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: 86967.19 Da        Isoelectric Point: 7.0662

>WP_021497839.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLKCADPSQDRMIKRSLFSFWPTLFQYEVILESPANGIFYVGYQRVRDIGRELWLSMDDLTRHIM
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: 44856..82268

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ39_RS25645 (HUZ39_25480) 42572..44863 - 2292 WP_021497839 F-type conjugative transfer protein TrbC -
HUZ39_RS25650 (HUZ39_25485) 44856..45926 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
HUZ39_RS25655 (HUZ39_25490) 45945..47153 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
HUZ39_RS25660 (HUZ39_25495) 47445..47597 + 153 WP_001387489 Hok/Gef family protein -
HUZ39_RS25665 (HUZ39_25500) 47669..47920 - 252 WP_001291964 hypothetical protein -
HUZ39_RS26135 48419..48514 + 96 WP_001303310 DinQ-like type I toxin DqlB -
HUZ39_RS25675 (HUZ39_25505) 48579..48755 - 177 WP_001054900 hypothetical protein -
HUZ39_RS25680 (HUZ39_25510) 49087..49296 + 210 WP_000062602 HEAT repeat domain-containing protein -
HUZ39_RS25685 (HUZ39_25515) 49368..50030 - 663 WP_000644792 plasmid IncI1-type surface exclusion protein ExcA -
HUZ39_RS25690 (HUZ39_25520) 50095..52263 - 2169 WP_077250315 DotA/TraY family protein traY
HUZ39_RS25695 (HUZ39_25525) 52360..52944 - 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
HUZ39_RS25700 (HUZ39_25530) 52973..54175 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
HUZ39_RS25705 (HUZ39_25535) 54142..54756 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
HUZ39_RS25710 (HUZ39_25540) 54756..57800 - 3045 WP_001024776 IncI1-type conjugal transfer protein TraU traU
HUZ39_RS25715 (HUZ39_25545) 57890..58690 - 801 WP_001164792 IncI1-type conjugal transfer protein TraT traT
HUZ39_RS25720 (HUZ39_25550) 58674..58862 - 189 WP_001277255 putative conjugal transfer protein TraS -
HUZ39_RS25725 (HUZ39_25555) 58926..59330 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
HUZ39_RS25730 (HUZ39_25560) 59381..59908 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HUZ39_RS25735 (HUZ39_25565) 59908..60612 - 705 WP_023155244 IncI1-type conjugal transfer protein TraP traP
HUZ39_RS25740 (HUZ39_25570) 60612..61901 - 1290 WP_001271994 conjugal transfer protein TraO traO
HUZ39_RS25745 (HUZ39_25575) 61904..62887 - 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
HUZ39_RS25750 (HUZ39_25580) 62898..63590 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HUZ39_RS25755 (HUZ39_25585) 63587..63934 - 348 WP_001055900 conjugal transfer protein traL
HUZ39_RS25760 (HUZ39_25590) 63952..67719 - 3768 WP_006855639 LPD7 domain-containing protein -
HUZ39_RS25765 (HUZ39_25595) 67809..68360 - 552 WP_000014584 phospholipase D family protein -
HUZ39_RS25770 (HUZ39_25600) 68375..68665 - 291 WP_001299214 hypothetical protein traK
HUZ39_RS25775 (HUZ39_25605) 68662..69810 - 1149 WP_001024976 plasmid transfer ATPase TraJ virB11
HUZ39_RS25780 (HUZ39_25610) 69807..70625 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
HUZ39_RS25785 (HUZ39_25615) 70622..71080 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HUZ39_RS25790 (HUZ39_25620) 71475..72059 - 585 WP_124770274 histidine phosphatase family protein -
HUZ39_RS25795 (HUZ39_25625) 72119..73321 - 1203 WP_000976357 conjugal transfer protein TraF -
HUZ39_RS25800 (HUZ39_25630) 73407..74231 - 825 WP_015058912 conjugal transfer protein TraE traE
HUZ39_RS25805 (HUZ39_25635) 74382..75536 - 1155 WP_001139955 site-specific integrase -
HUZ39_RS25810 (HUZ39_25640) 76450..77775 - 1326 WP_239637985 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HUZ39_RS25815 (HUZ39_25645) 77775..78431 - 657 WP_001193551 A24 family peptidase -
HUZ39_RS25820 (HUZ39_25650) 78416..78976 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
HUZ39_RS25825 (HUZ39_25655) 78986..79600 - 615 WP_000908228 type 4 pilus major pilin -
HUZ39_RS25830 (HUZ39_25660) 79617..80702 - 1086 WP_001208803 type II secretion system F family protein -
HUZ39_RS25835 (HUZ39_25665) 80715..82268 - 1554 WP_000362204 ATPase, T2SS/T4P/T4SS family virB11
HUZ39_RS25840 (HUZ39_25670) 82279..82731 - 453 WP_001247333 type IV pilus biogenesis protein PilP -
HUZ39_RS25845 (HUZ39_25675) 82718..84013 - 1296 WP_000752776 type 4b pilus protein PilO2 -
HUZ39_RS25850 (HUZ39_25680) 84006..85688 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HUZ39_RS25855 (HUZ39_25685) 85702..86139 - 438 WP_000539811 type IV pilus biogenesis protein PilM -
HUZ39_RS25860 (HUZ39_25690) 86139..87206 - 1068 WP_021513968 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   4950 GenBank   NZ_CP055202
Plasmid name   STEFF_3|unnamed3 Incompatibility group   IncI1
Plasmid size   91691 bp Coordinate of oriT [Strand]   39390..39478 [-]
Host baterium   Shigella flexneri strain STEFF_3

Cargo genes

Drug resistance gene   blaCTX-M-24
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -