Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102419
Name   oriT_SMG002F4|unnamed1 in_silico
Organism   Escherichia coli strain SMG002F4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKVSO010000024 (36456..36544 [+], 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_SMG002F4|unnamed1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1811 GenBank   WP_001474686
Name   nikB_ML367_RS18800_SMG002F4|unnamed1 insolico UniProt ID   A0A2J0RB70
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103834.33 Da        Isoelectric Point: 7.3473

>WP_001474686.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
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 A0A2J0RB70


Auxiliary protein

ID   731 GenBank   WP_001283947
Name   WP_001283947_SMG002F4|unnamed1 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   1396 GenBank   WP_001289271
Name   trbC_ML367_RS18795_SMG002F4|unnamed1 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: 86927.12 Da        Isoelectric Point: 6.7713

>WP_001289271.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1372..31078

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ML367_RS18640 (ML367_18635) 67..1221 + 1155 WP_001139955 site-specific integrase -
ML367_RS18645 (ML367_18640) 1372..2196 + 825 WP_001238932 conjugal transfer protein TraE traE
ML367_RS18650 (ML367_18645) 2282..3484 + 1203 WP_080217891 conjugal transfer protein TraF -
ML367_RS18655 (ML367_18650) 3544..4128 + 585 WP_242426026 histidine phosphatase family protein -
ML367_RS18660 (ML367_18655) 4523..4981 + 459 WP_242426025 IncI1-type conjugal transfer lipoprotein TraH -
ML367_RS18665 (ML367_18660) 4978..5796 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
ML367_RS18670 (ML367_18665) 5793..6941 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
ML367_RS18675 (ML367_18670) 6938..7228 + 291 WP_001372180 hypothetical protein traK
ML367_RS18680 (ML367_18675) 7243..7794 + 552 WP_000014584 phospholipase D family protein -
ML367_RS18685 (ML367_18680) 7884..11651 + 3768 WP_001141542 LPD7 domain-containing protein -
ML367_RS18690 (ML367_18685) 11669..12016 + 348 WP_001055900 conjugal transfer protein traL
ML367_RS18695 (ML367_18690) 12013..12705 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
ML367_RS18700 (ML367_18695) 12716..13699 + 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
ML367_RS18705 (ML367_18700) 13702..14991 + 1290 WP_001271997 conjugal transfer protein TraO traO
ML367_RS18710 (ML367_18705) 14991..15695 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
ML367_RS18715 (ML367_18710) 15695..16222 + 528 WP_001055569 conjugal transfer protein TraQ traQ
ML367_RS18720 (ML367_18715) 16273..16677 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
ML367_RS18725 (ML367_18720) 16741..16929 + 189 WP_001277255 putative conjugal transfer protein TraS -
ML367_RS18730 (ML367_18725) 16913..17713 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
ML367_RS18735 (ML367_18730) 17803..20847 + 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
ML367_RS18740 (ML367_18735) 20847..21461 + 615 WP_000337400 IncI1-type conjugal transfer protein TraV traV
ML367_RS18745 (ML367_18740) 21428..22630 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
ML367_RS18750 (ML367_18745) 22659..23243 + 585 WP_001037985 IncI1-type conjugal transfer protein TraX -
ML367_RS18755 (ML367_18750) 23340..25508 + 2169 WP_000698368 DotA/TraY family protein traY
ML367_RS18760 (ML367_18755) 25579..26241 + 663 WP_000644794 plasmid IncI1-type surface exclusion protein ExcA -
ML367_RS18765 (ML367_18760) 26313..26522 - 210 WP_000062603 HEAT repeat domain-containing protein -
ML367_RS18770 (ML367_18765) 26914..27090 + 177 WP_001054900 hypothetical protein -
ML367_RS18775 (ML367_18770) 28014..28265 + 252 WP_001291965 hypothetical protein -
ML367_RS18780 (ML367_18775) 28337..28489 - 153 WP_001303307 Hok/Gef family protein -
ML367_RS18785 (ML367_18780) 28781..29989 + 1209 WP_242426024 IncI1-type conjugal transfer protein TrbA trbA
ML367_RS18790 (ML367_18785) 30008..31078 + 1071 WP_000151576 IncI1-type conjugal transfer protein TrbB trbB
ML367_RS18795 (ML367_18790) 31071..33362 + 2292 WP_001289271 F-type conjugative transfer protein TrbC -

Host bacterium

ID   2863 GenBank   NZ_JAKVSO010000024
Plasmid name   SMG002F4|unnamed1 Incompatibility group   IncI1
Plasmid size   84091 bp Coordinate of oriT [Strand]   36456..36544 [+]
Host baterium   Escherichia coli strain SMG002F4

Cargo genes

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