Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106889
Name   oriT_pS3160_2 in_silico
Organism   Shigella flexneri strain 3160_NCHU22
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP094989 (47771..47859 [-], 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_pS3160_2
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4555 GenBank   WP_024143648
Name   nikB_MT485_RS24940_pS3160_2 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   2054 GenBank   WP_001283947
Name   WP_001283947_pS3160_2 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   4639 GenBank   WP_001289276
Name   trbC_MT485_RS24945_pS3160_2 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: 53237..90712

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MT485_RS24945 (MT485_24945) 50953..53244 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
MT485_RS24950 (MT485_24950) 53237..54307 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
MT485_RS24955 (MT485_24955) 54326..55534 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
MT485_RS24960 (MT485_24960) 55826..55978 + 153 WP_001331364 Hok/Gef family protein -
MT485_RS24965 (MT485_24965) 56050..56301 - 252 WP_001291964 hypothetical protein -
MT485_RS25335 56800..56895 + 96 WP_001303310 DinQ-like type I toxin DqlB -
MT485_RS24975 (MT485_24975) 56960..57136 - 177 WP_001054904 hypothetical protein -
MT485_RS24980 (MT485_24980) 57528..57737 + 210 WP_244758396 HEAT repeat domain-containing protein -
MT485_RS24985 (MT485_24985) 57809..58459 - 651 WP_001178506 plasmid IncI1-type surface exclusion protein ExcA -
MT485_RS24990 (MT485_24990) 58533..60701 - 2169 WP_021537350 DotA/TraY family protein traY
MT485_RS24995 (MT485_24995) 60798..61382 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
MT485_RS25000 (MT485_25000) 61411..62613 - 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
MT485_RS25005 (MT485_25005) 62580..63194 - 615 WP_000337398 IncI1-type conjugal transfer protein TraV traV
MT485_RS25010 (MT485_25010) 63194..66238 - 3045 WP_021265678 IncI1-type conjugal transfer protein TraU traU
MT485_RS25015 (MT485_25015) 66328..67128 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
MT485_RS25020 (MT485_25020) 67112..67300 - 189 WP_001277255 putative conjugal transfer protein TraS -
MT485_RS25025 (MT485_25025) 67364..67768 - 405 WP_000086958 IncI1-type conjugal transfer protein TraR traR
MT485_RS25030 (MT485_25030) 67819..68346 - 528 WP_001055569 conjugal transfer protein TraQ traQ
MT485_RS25035 (MT485_25035) 68346..69050 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
MT485_RS25040 (MT485_25040) 69050..70339 - 1290 WP_001272003 conjugal transfer protein TraO traO
MT485_RS25045 (MT485_25045) 70342..71325 - 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
MT485_RS25050 (MT485_25050) 71336..72028 - 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
MT485_RS25055 (MT485_25055) 72025..72372 - 348 WP_001055900 conjugal transfer protein traL
MT485_RS25060 (MT485_25060) 72390..76157 - 3768 WP_001141527 LPD7 domain-containing protein -
MT485_RS25065 (MT485_25065) 76246..76797 - 552 WP_000014583 phospholipase D family protein -
MT485_RS25070 (MT485_25070) 76812..77102 - 291 WP_001299214 hypothetical protein traK
MT485_RS25075 (MT485_25075) 77099..78247 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
MT485_RS25080 (MT485_25080) 78244..79062 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
MT485_RS25085 (MT485_25085) 79059..79517 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
MT485_RS25090 (MT485_25090) 79912..80496 - 585 WP_000977522 histidine phosphatase family protein -
MT485_RS25095 (MT485_25095) 80556..81758 - 1203 WP_000976351 conjugal transfer protein TraF -
MT485_RS25100 (MT485_25100) 81843..82667 - 825 WP_001238939 conjugal transfer protein TraE traE
MT485_RS25105 (MT485_25105) 82818..83972 - 1155 WP_001139957 site-specific integrase -
MT485_RS25110 (MT485_25110) 85001..86206 - 1206 WP_244758397 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
MT485_RS25115 (MT485_25115) 86206..86862 - 657 WP_001193553 prepilin peptidase -
MT485_RS25120 (MT485_25120) 86847..87407 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
MT485_RS25125 (MT485_25125) 87417..88031 - 615 WP_000959785 type 4 pilus major pilin -
MT485_RS25130 (MT485_25130) 88049..89146 - 1098 WP_001208805 type II secretion system F family protein -
MT485_RS25135 (MT485_25135) 89159..90712 - 1554 WP_244758398 ATPase, T2SS/T4P/T4SS family virB11
MT485_RS25140 (MT485_25140) 90723..91175 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
MT485_RS25145 (MT485_25145) 91162..92457 - 1296 WP_000752772 type 4b pilus protein PilO2 -
MT485_RS25150 (MT485_25150) 92450..94132 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
MT485_RS25155 (MT485_25155) 94146..94583 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
MT485_RS25160 (MT485_25160) 94583..95650 - 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   7326 GenBank   NZ_CP094989
Plasmid name   pS3160_2 Incompatibility group   IncI1
Plasmid size   101193 bp Coordinate of oriT [Strand]   47771..47859 [-]
Host baterium   Shigella flexneri strain 3160_NCHU22

Cargo genes

Drug resistance gene   dfrA12, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -