Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103738
Name   oriT_pBU53M1 in_silico
Organism   Shigella dysenteriae strain BU53M1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP024468 (96909..96997 [+], 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_pBU53M1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCCTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2768 GenBank   WP_069896299
Name   nikB_CPZ97_RS25180_pBU53M1 insolico UniProt ID   A0A142CMC3
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103891.35 Da        Isoelectric Point: 7.4288

>WP_069896299.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKHTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
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 A0A142CMC3


Auxiliary protein

ID   983 GenBank   WP_001283947
Name   WP_001283947_pBU53M1 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   2597 GenBank   WP_072121498
Name   trbC_CPZ97_RS25175_pBU53M1 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: 86896.07 Da        Isoelectric Point: 6.7712

>WP_072121498.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTAKTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 50701..91531

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CPZ97_RS24915 45763..46830 + 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -
CPZ97_RS24920 46830..47267 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
CPZ97_RS24925 47281..48963 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
CPZ97_RS24930 48956..50251 + 1296 WP_050197975 type 4b pilus protein PilO2 -
CPZ97_RS24935 50238..50690 + 453 WP_001247337 type IV pilus biogenesis protein PilP -
CPZ97_RS24940 50701..52254 + 1554 WP_032220709 ATPase, T2SS/T4P/T4SS family virB11
CPZ97_RS24945 52267..53352 + 1086 WP_001208802 type II secretion system F family protein -
CPZ97_RS24950 53369..53983 + 615 WP_000908226 type 4 pilus major pilin -
CPZ97_RS24955 53993..54553 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
CPZ97_RS24960 54538..55194 + 657 WP_001193549 A24 family peptidase -
CPZ97_RS24965 55194..56486 + 1293 WP_134802185 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
CPZ97_RS25005 58252..59406 + 1155 WP_001139955 site-specific integrase -
CPZ97_RS25010 59557..60381 + 825 WP_001690630 conjugal transfer protein TraE traE
CPZ97_RS25015 60467..61669 + 1203 WP_000976353 conjugal transfer protein TraF -
CPZ97_RS25020 61729..62313 + 585 WP_000977525 histidine phosphatase family protein -
CPZ97_RS25025 62708..63166 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
CPZ97_RS25030 63163..63981 + 819 WP_032220737 IncI1-type conjugal transfer lipoprotein TraI traI
CPZ97_RS25035 63978..65126 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
CPZ97_RS25040 65123..65413 + 291 WP_001299214 hypothetical protein traK
CPZ97_RS25045 65428..65979 + 552 WP_000014586 phospholipase D family protein -
CPZ97_RS25050 66069..69836 + 3768 WP_050197986 LPD7 domain-containing protein -
CPZ97_RS25055 69854..70201 + 348 WP_001055900 conjugal transfer protein traL
CPZ97_RS25060 70198..70890 + 693 WP_000138551 DotI/IcmL family type IV secretion protein traM
CPZ97_RS25065 70901..71884 + 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
CPZ97_RS25070 71887..73176 + 1290 WP_050197985 conjugal transfer protein TraO traO
CPZ97_RS25075 73176..73880 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
CPZ97_RS25080 73880..74407 + 528 WP_001055569 conjugal transfer protein TraQ traQ
CPZ97_RS25085 74458..74862 + 405 WP_025769131 IncI1-type conjugal transfer protein TraR traR
CPZ97_RS25090 74926..75114 + 189 WP_001277255 putative conjugal transfer protein TraS -
CPZ97_RS25095 75098..75898 + 801 WP_001493813 IncI1-type conjugal transfer protein TraT traT
CPZ97_RS25100 75988..79032 + 3045 WP_050197984 IncI1-type conjugal transfer protein TraU traU
CPZ97_RS25105 79032..79646 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
CPZ97_RS25110 79613..80815 + 1203 WP_012783938 IncI1-type conjugal transfer protein TraW traW
CPZ97_RS25115 80844..81428 + 585 WP_050197983 IncI1-type conjugal transfer protein TraX -
CPZ97_RS25120 81525..83693 + 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
CPZ97_RS25125 83769..84383 + 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
CPZ97_RS25130 84481..84690 + 210 WP_001140543 hemolysin expression modulator Hha -
CPZ97_RS25135 84934..85596 + 663 WP_042078443 plasmid IncI1-type surface exclusion protein ExcA -
CPZ97_RS25140 85668..85877 - 210 WP_000062603 HEAT repeat domain-containing protein -
CPZ97_RS27885 86209..86385 + 177 WP_001054900 hypothetical protein -
CPZ97_RS28985 86450..86545 - 96 WP_000609148 DinQ-like type I toxin DqlB -
CPZ97_RS25150 87046..87297 + 252 WP_001291964 hypothetical protein -
CPZ97_RS25155 87369..87521 - 153 WP_001387489 Hok/Gef family protein -
CPZ97_RS25160 88148..88927 + 780 WP_275450201 protein FinQ -
CPZ97_RS25165 89234..90442 + 1209 WP_000121263 IncI1-type conjugal transfer protein TrbA trbA
CPZ97_RS25170 90461..91531 + 1071 WP_050197982 IncI1-type conjugal transfer protein TrbB trbB
CPZ97_RS25175 91524..93815 + 2292 WP_072121498 F-type conjugative transfer protein TrbC -

Host bacterium

ID   4178 GenBank   NZ_CP024468
Plasmid name   pBU53M1 Incompatibility group   IncI1
Plasmid size   115922 bp Coordinate of oriT [Strand]   96909..96997 [+]
Host baterium   Shigella dysenteriae strain BU53M1

Cargo genes

Drug resistance gene   catA1, dfrA1, ant(3'')-Ia, qacE, sul1, tet(A)
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2