Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104507
Name   oriT_SWHIN_104|unnamed2 in_silico
Organism   Shigella flexneri strain SWHIN_104
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055111 (30284..30372 [-], 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_104|unnamed2
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3262 GenBank   WP_021513956
Name   nikB_HUZ82_RS24370_SWHIN_104|unnamed2 insolico UniProt ID   A0A6Y5CJU6
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104040.45 Da        Isoelectric Point: 7.3526

>WP_021513956.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSMHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCTEKLMKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETE
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 A0A6Y5CJU6


Auxiliary protein

ID   1449 GenBank   WP_024175674
Name   WP_024175674_SWHIN_104|unnamed2 insolico UniProt ID   A0A6Y5CHR0
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12643.59 Da        Isoelectric Point: 10.7463

>WP_024175674.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMES

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A6Y5CHR0


T4CP

ID   3190 GenBank   WP_001289269
Name   trbC_HUZ82_RS24375_SWHIN_104|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: 86899.11 Da        Isoelectric Point: 6.7712

>WP_001289269.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTAKTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 35750..75460

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ82_RS24375 (HUZ82_24165) 33466..35757 - 2292 WP_001289269 F-type conjugative transfer protein TrbC -
HUZ82_RS24380 (HUZ82_24170) 35750..36820 - 1071 WP_000151579 IncI1-type conjugal transfer protein TrbB trbB
HUZ82_RS24385 (HUZ82_24175) 36839..38047 - 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
HUZ82_RS24390 (HUZ82_24180) 38265..39251 - 987 WP_001257838 hypothetical protein -
HUZ82_RS24395 (HUZ82_24185) 39820..39972 + 153 WP_023156060 Hok/Gef family protein -
HUZ82_RS24400 (HUZ82_24190) 40044..40295 - 252 WP_021513960 hypothetical protein -
HUZ82_RS24740 40793..40888 + 96 WP_001303310 DinQ-like type I toxin DqlB -
HUZ82_RS24410 (HUZ82_24195) 40953..41129 - 177 WP_001054900 hypothetical protein -
HUZ82_RS24415 (HUZ82_24200) 41461..41670 + 210 WP_000062602 HEAT repeat domain-containing protein -
HUZ82_RS24420 (HUZ82_24205) 41742..42404 - 663 WP_000644792 plasmid IncI1-type surface exclusion protein ExcA -
HUZ82_RS24425 (HUZ82_24210) 42469..44637 - 2169 WP_000698366 DotA/TraY family protein traY
HUZ82_RS24430 (HUZ82_24215) 44734..45318 - 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
HUZ82_RS24435 (HUZ82_24220) 45347..46549 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
HUZ82_RS24440 (HUZ82_24225) 46516..47130 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
HUZ82_RS24445 (HUZ82_24230) 47130..50174 - 3045 WP_001024776 IncI1-type conjugal transfer protein TraU traU
HUZ82_RS24450 (HUZ82_24235) 50264..51064 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HUZ82_RS24455 (HUZ82_24240) 51048..51236 - 189 WP_001277255 putative conjugal transfer protein TraS -
HUZ82_RS24460 (HUZ82_24245) 51300..51704 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
HUZ82_RS24465 (HUZ82_24250) 51755..52282 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HUZ82_RS24470 (HUZ82_24255) 52282..52986 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HUZ82_RS24475 (HUZ82_24260) 52986..54275 - 1290 WP_001271994 conjugal transfer protein TraO traO
HUZ82_RS24480 (HUZ82_24265) 54278..55261 - 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
HUZ82_RS24485 (HUZ82_24270) 55272..55964 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HUZ82_RS24490 (HUZ82_24275) 55961..56308 - 348 WP_001055900 conjugal transfer protein traL
HUZ82_RS24495 (HUZ82_24280) 56326..60093 - 3768 WP_021513964 LPD7 domain-containing protein -
HUZ82_RS24500 (HUZ82_24285) 60183..60734 - 552 WP_000014584 phospholipase D family protein -
HUZ82_RS24505 (HUZ82_24290) 60749..61039 - 291 WP_001299214 hypothetical protein traK
HUZ82_RS24510 (HUZ82_24295) 61036..62184 - 1149 WP_001024975 plasmid transfer ATPase TraJ virB11
HUZ82_RS24515 (HUZ82_24300) 62181..62999 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
HUZ82_RS24520 (HUZ82_24305) 62996..63454 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HUZ82_RS24525 (HUZ82_24310) 63849..64433 - 585 WP_000977520 histidine phosphatase family protein -
HUZ82_RS24530 (HUZ82_24315) 64493..65695 - 1203 WP_000976357 conjugal transfer protein TraF -
HUZ82_RS24535 (HUZ82_24320) 65781..66605 - 825 WP_015058912 conjugal transfer protein TraE traE
HUZ82_RS24540 (HUZ82_24325) 66756..67910 - 1155 WP_001139955 site-specific integrase -
HUZ82_RS24545 (HUZ82_24330) 69430..69678 + 249 WP_001349157 hypothetical protein -
HUZ82_RS24550 (HUZ82_24335) 69675..70967 - 1293 WP_039719938 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HUZ82_RS24555 (HUZ82_24340) 70967..71623 - 657 WP_001193551 A24 family peptidase -
HUZ82_RS24560 (HUZ82_24345) 71608..72168 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
HUZ82_RS24565 (HUZ82_24350) 72178..72792 - 615 WP_000908228 type 4 pilus major pilin -
HUZ82_RS24570 (HUZ82_24355) 72809..73894 - 1086 WP_001208803 type II secretion system F family protein -
HUZ82_RS24575 (HUZ82_24360) 73907..75460 - 1554 WP_000362204 ATPase, T2SS/T4P/T4SS family virB11
HUZ82_RS24580 (HUZ82_24365) 75471..75923 - 453 WP_001247333 type IV pilus biogenesis protein PilP -
HUZ82_RS24585 (HUZ82_24370) 75910..77205 - 1296 WP_021513967 type 4b pilus protein PilO2 -
HUZ82_RS24590 (HUZ82_24375) 77198..78880 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HUZ82_RS24595 (HUZ82_24380) 78894..79331 - 438 WP_000539811 type IV pilus biogenesis protein PilM -
HUZ82_RS24600 (HUZ82_24385) 79331..80398 - 1068 WP_021513968 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   4946 GenBank   NZ_CP055111
Plasmid name   SWHIN_104|unnamed2 Incompatibility group   IncI1
Plasmid size   84883 bp Coordinate of oriT [Strand]   30284..30372 [-]
Host baterium   Shigella flexneri strain SWHIN_104

Cargo genes

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