Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101603
Name   oriT_L3M1-CTX07|unnamed in_silico
Organism   Escherichia coli strain L3M1-CTX07
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQFWM010000065 (4484..4572 [-], 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_L3M1-CTX07|unnamed
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1419 GenBank   WP_024143648
Name   nikB_PDQ35_RS23865_L3M1-CTX07|unnamed 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   553 GenBank   WP_001283947
Name   WP_001283947_L3M1-CTX07|unnamed 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   1077 GenBank   WP_001289276
Name   trbC_PDQ35_RS23870_L3M1-CTX07|unnamed 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: 9950..50928

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PDQ35_RS23870 (PDQ35_23870) 7666..9957 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
PDQ35_RS23875 (PDQ35_23875) 9950..11020 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
PDQ35_RS23880 (PDQ35_23880) 11039..12247 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
PDQ35_RS23885 (PDQ35_23885) 12539..12691 + 153 WP_001331364 Hok/Gef family protein -
PDQ35_RS23890 (PDQ35_23890) 12763..13014 - 252 WP_001291964 hypothetical protein -
PDQ35_RS26660 13513..13608 + 96 WP_001303310 DinQ-like type I toxin DqlB -
PDQ35_RS23900 (PDQ35_23900) 13673..13849 - 177 WP_001054904 hypothetical protein -
PDQ35_RS23905 (PDQ35_23905) 14241..14450 + 210 WP_000062603 HEAT repeat domain-containing protein -
PDQ35_RS23910 (PDQ35_23910) 14522..15172 - 651 WP_001178506 plasmid IncI1-type surface exclusion protein ExcA -
PDQ35_RS23915 (PDQ35_23915) 15246..17414 - 2169 WP_021537350 DotA/TraY family protein traY
PDQ35_RS23920 (PDQ35_23920) 17511..18095 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
PDQ35_RS23925 (PDQ35_23925) 18124..19326 - 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
PDQ35_RS23930 (PDQ35_23930) 19293..19907 - 615 WP_000337398 IncI1-type conjugal transfer protein TraV traV
PDQ35_RS23935 (PDQ35_23935) 19907..22951 - 3045 WP_021265678 IncI1-type conjugal transfer protein TraU traU
PDQ35_RS23940 (PDQ35_23940) 23041..23841 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
PDQ35_RS23945 (PDQ35_23945) 23825..24013 - 189 WP_001277255 putative conjugal transfer protein TraS -
PDQ35_RS23950 (PDQ35_23950) 24077..24481 - 405 WP_000086958 IncI1-type conjugal transfer protein TraR traR
PDQ35_RS23955 (PDQ35_23955) 24532..25059 - 528 WP_001055569 conjugal transfer protein TraQ traQ
PDQ35_RS23960 (PDQ35_23960) 25059..25763 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
PDQ35_RS23965 (PDQ35_23965) 25763..27052 - 1290 WP_001272003 conjugal transfer protein TraO traO
PDQ35_RS23970 (PDQ35_23970) 27055..28038 - 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
PDQ35_RS23975 (PDQ35_23975) 28049..28741 - 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
PDQ35_RS23980 (PDQ35_23980) 28738..29085 - 348 WP_001055900 conjugal transfer protein traL
PDQ35_RS23985 (PDQ35_23985) 29103..32870 - 3768 WP_001141527 LPD7 domain-containing protein -
PDQ35_RS23990 (PDQ35_23990) 32959..33510 - 552 WP_000014583 phospholipase D family protein -
PDQ35_RS23995 (PDQ35_23995) 33525..33815 - 291 WP_001299214 hypothetical protein traK
PDQ35_RS24000 (PDQ35_24000) 33812..34960 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
PDQ35_RS24005 (PDQ35_24005) 34957..35775 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
PDQ35_RS24010 (PDQ35_24010) 35772..36230 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
PDQ35_RS24015 (PDQ35_24015) 36625..37209 - 585 WP_000977522 histidine phosphatase family protein -
PDQ35_RS24020 (PDQ35_24020) 37269..38471 - 1203 WP_000976351 conjugal transfer protein TraF -
PDQ35_RS24025 (PDQ35_24025) 38556..39380 - 825 WP_001238939 conjugal transfer protein TraE traE
PDQ35_RS24030 (PDQ35_24030) 39531..40685 - 1155 WP_001139957 site-specific integrase -
PDQ35_RS24035 (PDQ35_24035) 40979..42241 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
PDQ35_RS24040 (PDQ35_24040) 42529..43404 + 876 WP_013188473 extended-spectrum class A beta-lactamase CTX-M-1 -
PDQ35_RS24045 (PDQ35_24045) 43451..43795 - 345 Protein_46 WbuC family cupin fold metalloprotein -
PDQ35_RS24050 (PDQ35_24050) 43795..44004 + 210 Protein_47 hypothetical protein -
PDQ35_RS26665 44780..45001 + 222 Protein_48 prepilin -
PDQ35_RS24055 (PDQ35_24055) 44998..46422 - 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
PDQ35_RS24060 (PDQ35_24060) 46422..47078 - 657 WP_001193553 prepilin peptidase -
PDQ35_RS24065 (PDQ35_24065) 47063..47623 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
PDQ35_RS24070 (PDQ35_24070) 47633..48247 - 615 WP_000959785 type 4 pilus major pilin -
PDQ35_RS24075 (PDQ35_24075) 48265..49362 - 1098 WP_001208805 type II secretion system F family protein -
PDQ35_RS24080 (PDQ35_24080) 49375..50928 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
PDQ35_RS24085 (PDQ35_24085) 50939..51391 - 453 WP_001247336 type IV pilus biogenesis protein PilP -
PDQ35_RS24090 (PDQ35_24090) 51378..52673 - 1296 WP_000752774 type 4b pilus protein PilO2 -
PDQ35_RS24095 (PDQ35_24095) 52666..54348 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
PDQ35_RS24100 (PDQ35_24100) 54362..54799 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
PDQ35_RS24105 (PDQ35_24105) 54799..55866 - 1068 WP_000742600 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   2047 GenBank   NZ_JAQFWM010000065
Plasmid name   L3M1-CTX07|unnamed Incompatibility group   IncI1
Plasmid size   76248 bp Coordinate of oriT [Strand]   4484..4572 [-]
Host baterium   Escherichia coli strain L3M1-CTX07

Cargo genes

Drug resistance gene   blaCTX-M-1, tet(A), sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -