Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113588
Name   oriT_pC32_2 in_silico
Organism   Shigella flexneri strain C32
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP041621 (28737..28823 [+], 87 nt)
oriT length   87 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 87 nt

>oriT_pC32_2
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8704 GenBank   WP_021520371
Name   nikB_FNL95_RS25115_pC32_2 insolico UniProt ID   A0A446GKR4
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103939.37 Da        Isoelectric Point: 7.3426

>WP_021520371.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRNERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A446GKR4


Auxiliary protein

ID   5089 GenBank   WP_001281051
Name   WP_001281051_pC32_2 insolico UniProt ID   A0A3U8I0C6
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12646.44 Da        Isoelectric Point: 10.4030

>WP_001281051.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSDKRQRSGSERRQKTILRAVRFSPDEDETICKNAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A3U8I0C6


T4CP

ID   10074 GenBank   WP_021520372
Name   trbC_FNL95_RS25110_pC32_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: 86911.08 Da        Isoelectric Point: 6.7713

>WP_021520372.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2743..23358

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FNL95_RS25005 2743..3090 + 348 WP_001055900 conjugal transfer protein traL
FNL95_RS25010 3087..3779 + 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
FNL95_RS25015 3790..4773 + 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
FNL95_RS25020 4776..6065 + 1290 WP_042004726 conjugal transfer protein TraO traO
FNL95_RS25025 6065..6769 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
FNL95_RS25030 6769..7296 + 528 WP_001055569 conjugal transfer protein TraQ traQ
FNL95_RS25035 7347..7751 + 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
FNL95_RS25040 7815..8003 + 189 WP_001277253 putative conjugal transfer protein TraS -
FNL95_RS25045 7987..8787 + 801 WP_001164784 IncI1-type conjugal transfer protein TraT traT
FNL95_RS25050 8877..11921 + 3045 WP_001024789 IncI1-type conjugal transfer protein TraU traU
FNL95_RS25055 11921..12535 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
FNL95_RS25060 12502..13703 + 1202 Protein_12 IncI1-type conjugal transfer protein TraW -
FNL95_RS25065 13732..14316 + 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
FNL95_RS25070 14413..16581 + 2169 WP_000698357 DotA/TraY family protein traY
FNL95_RS25075 16655..17305 + 651 WP_001178506 plasmid IncI1-type surface exclusion protein ExcA -
FNL95_RS25080 17377..17586 - 210 WP_000062603 HEAT repeat domain-containing protein -
FNL95_RS25745 17978..18154 + 177 WP_001054898 hypothetical protein -
FNL95_RS26295 18219..18314 - 96 WP_001303310 DinQ-like type I toxin DqlB -
FNL95_RS25085 18813..19064 + 252 WP_001291964 hypothetical protein -
FNL95_RS25090 19136..19288 - 153 WP_001331364 Hok/Gef family protein -
FNL95_RS25095 19857..20843 + 987 WP_001257838 hypothetical protein -
FNL95_RS25100 21061..22269 + 1209 WP_154832363 IncI1-type conjugal transfer protein TrbA trbA
FNL95_RS25105 22288..23358 + 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
FNL95_RS25110 23351..25642 + 2292 WP_021520372 F-type conjugative transfer protein TrbC -

Region 2: 71657..86380

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FNL95_RS25475 66720..67786 + 1067 Protein_78 type IV pilus biogenesis lipoprotein PilL -
FNL95_RS25480 67786..68223 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
FNL95_RS25485 68237..69919 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
FNL95_RS25490 69912..71207 + 1296 WP_001388364 type 4b pilus protein PilO2 -
FNL95_RS25495 71194..71646 + 453 WP_001247870 type IV pilus biogenesis protein PilP -
FNL95_RS25500 71657..73210 + 1554 WP_001492932 GspE/PulE family protein virB11
FNL95_RS25505 73223..74320 + 1098 WP_001492931 type II secretion system F family protein -
FNL95_RS25510 74338..74952 + 615 WP_001542527 type 4 pilus major pilin -
FNL95_RS25515 74962..75522 + 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
FNL95_RS25520 75507..76163 + 657 WP_001193553 prepilin peptidase -
FNL95_RS25525 76163..77587 + 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
FNL95_RS26415 77584..77805 - 222 Protein_89 prepilin -
FNL95_RS25560 79221..80375 + 1155 WP_001139955 tyrosine-type recombinase/integrase -
FNL95_RS25565 80526..81350 + 825 WP_001238932 conjugal transfer protein TraE traE
FNL95_RS25570 81436..82638 + 1203 WP_000976353 conjugal transfer protein TraF -
FNL95_RS25575 82697..83281 + 585 WP_000977522 histidine phosphatase family protein -
FNL95_RS25580 83675..84133 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
FNL95_RS25585 84130..84948 + 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
FNL95_RS25590 84945..86093 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
FNL95_RS25595 86090..86380 + 291 WP_001299214 hypothetical protein traK
FNL95_RS25600 86395..86946 + 552 WP_000014583 phospholipase D family protein -

Host bacterium

ID   14023 GenBank   NZ_CP041621
Plasmid name   pC32_2 Incompatibility group   IncI1
Plasmid size   88076 bp Coordinate of oriT [Strand]   28737..28823 [+]
Host baterium   Shigella flexneri strain C32

Cargo genes

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