Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104528
Name   oriT_SWHIN_107|unnamed2 in_silico
Organism   Shigella flexneri strain SWHIN_107
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055101 (34665..34753 [-], 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_SWHIN_107|unnamed2
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3274 GenBank   WP_006855641
Name   nikB_HUZ84_RS24550_SWHIN_107|unnamed2 insolico UniProt ID   A0A620WL05
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104006.42 Da        Isoelectric Point: 7.3526

>WP_006855641.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A620WL05


Auxiliary protein

ID   1465 GenBank   WP_001283947
Name   WP_001283947_SWHIN_107|unnamed2 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   3205 GenBank   WP_001289275
Name   trbC_HUZ84_RS24555_SWHIN_107|unnamed2 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: 86957.15 Da        Isoelectric Point: 6.7713

>WP_001289275.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40131..79546

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ84_RS24555 (HUZ84_24350) 37847..40138 - 2292 WP_001289275 F-type conjugative transfer protein TrbC -
HUZ84_RS24560 (HUZ84_24355) 40131..41201 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
HUZ84_RS24565 (HUZ84_24360) 41220..42428 - 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
HUZ84_RS24570 (HUZ84_24365) 42646..43632 - 987 WP_001257838 hypothetical protein -
HUZ84_RS24575 (HUZ84_24370) 43905..44057 + 153 WP_001331364 Hok/Gef family protein -
HUZ84_RS24580 (HUZ84_24375) 44129..44380 - 252 WP_001291964 hypothetical protein -
HUZ84_RS25515 44879..44974 + 96 WP_001303310 DinQ-like type I toxin DqlB -
HUZ84_RS24590 (HUZ84_24380) 45039..45215 - 177 WP_001054900 hypothetical protein -
HUZ84_RS24595 (HUZ84_24385) 45547..45756 + 210 WP_000062602 HEAT repeat domain-containing protein -
HUZ84_RS24600 (HUZ84_24390) 45828..46490 - 663 WP_000644792 plasmid IncI1-type surface exclusion protein ExcA -
HUZ84_RS24605 (HUZ84_24395) 46555..48723 - 2169 WP_077250315 DotA/TraY family protein traY
HUZ84_RS24610 (HUZ84_24400) 48820..49404 - 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
HUZ84_RS24615 (HUZ84_24405) 49433..50635 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
HUZ84_RS24620 (HUZ84_24410) 50602..51216 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
HUZ84_RS24625 (HUZ84_24415) 51216..54260 - 3045 WP_106108247 IncI1-type conjugal transfer protein TraU traU
HUZ84_RS24630 (HUZ84_24420) 54350..55150 - 801 WP_001164792 IncI1-type conjugal transfer protein TraT traT
HUZ84_RS24635 (HUZ84_24425) 55134..55322 - 189 WP_001277255 putative conjugal transfer protein TraS -
HUZ84_RS24640 (HUZ84_24430) 55386..55790 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
HUZ84_RS24645 (HUZ84_24435) 55841..56368 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HUZ84_RS24650 (HUZ84_24440) 56368..57072 - 705 WP_106108248 IncI1-type conjugal transfer protein TraP traP
HUZ84_RS24655 (HUZ84_24445) 57072..58361 - 1290 WP_001271994 conjugal transfer protein TraO traO
HUZ84_RS24660 (HUZ84_24450) 58364..59347 - 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
HUZ84_RS24665 (HUZ84_24455) 59358..60050 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HUZ84_RS24670 (HUZ84_24460) 60047..60394 - 348 WP_001055900 conjugal transfer protein traL
HUZ84_RS24675 (HUZ84_24465) 60412..64179 - 3768 WP_058649948 LPD7 domain-containing protein -
HUZ84_RS24680 (HUZ84_24470) 64269..64820 - 552 WP_000014584 phospholipase D family protein -
HUZ84_RS24685 (HUZ84_24475) 64835..65125 - 291 WP_001299214 hypothetical protein traK
HUZ84_RS24690 (HUZ84_24480) 65122..66270 - 1149 WP_001024976 plasmid transfer ATPase TraJ virB11
HUZ84_RS24695 (HUZ84_24485) 66267..67085 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
HUZ84_RS24700 (HUZ84_24490) 67082..67540 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HUZ84_RS24705 (HUZ84_24495) 67935..68519 - 585 WP_000977520 histidine phosphatase family protein -
HUZ84_RS24710 (HUZ84_24500) 68579..69781 - 1203 WP_000976357 conjugal transfer protein TraF -
HUZ84_RS24715 (HUZ84_24505) 69867..70691 - 825 WP_015058912 conjugal transfer protein TraE traE
HUZ84_RS24720 (HUZ84_24510) 70842..71996 - 1155 WP_001139955 site-specific integrase -
HUZ84_RS25580 72036..72305 + 270 Protein_83 hypothetical protein -
HUZ84_RS25585 (HUZ84_24515) 73408..73632 + 225 Protein_84 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HUZ84_RS24725 (HUZ84_24520) 73629..75065 - 1437 WP_015058913 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HUZ84_RS24730 (HUZ84_24525) 75053..75709 - 657 WP_001193551 A24 family peptidase -
HUZ84_RS24735 (HUZ84_24530) 75694..76254 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
HUZ84_RS24740 (HUZ84_24535) 76264..76878 - 615 WP_000908228 type 4 pilus major pilin -
HUZ84_RS24745 (HUZ84_24540) 76895..77980 - 1086 WP_001208803 type II secretion system F family protein -
HUZ84_RS24750 (HUZ84_24545) 77993..79546 - 1554 WP_000362204 ATPase, T2SS/T4P/T4SS family virB11
HUZ84_RS24755 (HUZ84_24550) 79557..80009 - 453 WP_058649963 type IV pilus biogenesis protein PilP -
HUZ84_RS24760 (HUZ84_24555) 79996..81291 - 1296 WP_058649964 type 4b pilus protein PilO2 -
HUZ84_RS24765 (HUZ84_24560) 81284..82966 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HUZ84_RS24770 (HUZ84_24565) 82980..83417 - 438 WP_000539811 type IV pilus biogenesis protein PilM -
HUZ84_RS24775 (HUZ84_24570) 83417..84484 - 1068 WP_021513968 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   4967 GenBank   NZ_CP055101
Plasmid name   SWHIN_107|unnamed2 Incompatibility group   IncI1
Plasmid size   88969 bp Coordinate of oriT [Strand]   34665..34753 [-]
Host baterium   Shigella flexneri strain SWHIN_107

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -