Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102416
Name   oriT_SMG002F9|unnamed1 in_silico
Organism   Escherichia coli strain SMG002F9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKVSS010000023 (39920..40008 [-], 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_SMG002F9|unnamed1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1809 GenBank   WP_001474686
Name   nikB_ML382_RS19295_SMG002F9|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   728 GenBank   WP_001283947
Name   WP_001283947_SMG002F9|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   1393 GenBank   WP_001289271
Name   trbC_ML382_RS19300_SMG002F9|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: 45386..75092

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ML382_RS19300 (ML382_19295) 43102..45393 - 2292 WP_001289271 F-type conjugative transfer protein TrbC -
ML382_RS19305 (ML382_19300) 45386..46456 - 1071 WP_000151576 IncI1-type conjugal transfer protein TrbB trbB
ML382_RS19310 (ML382_19305) 46475..47683 - 1209 WP_242426024 IncI1-type conjugal transfer protein TrbA trbA
ML382_RS19315 (ML382_19310) 47975..48127 + 153 WP_001303307 Hok/Gef family protein -
ML382_RS19320 (ML382_19315) 48199..48450 - 252 WP_001291965 hypothetical protein -
ML382_RS19325 (ML382_19320) 49374..49550 - 177 WP_001054900 hypothetical protein -
ML382_RS19330 (ML382_19325) 49942..50151 + 210 WP_000062603 HEAT repeat domain-containing protein -
ML382_RS19335 (ML382_19330) 50223..50885 - 663 WP_000644794 plasmid IncI1-type surface exclusion protein ExcA -
ML382_RS19340 (ML382_19335) 50956..53124 - 2169 WP_000698368 DotA/TraY family protein traY
ML382_RS19345 (ML382_19340) 53221..53805 - 585 WP_001037985 IncI1-type conjugal transfer protein TraX -
ML382_RS19350 (ML382_19345) 53834..55036 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
ML382_RS19355 (ML382_19350) 55003..55617 - 615 WP_000337400 IncI1-type conjugal transfer protein TraV traV
ML382_RS19360 (ML382_19355) 55617..58661 - 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
ML382_RS19365 (ML382_19360) 58751..59551 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
ML382_RS19370 (ML382_19365) 59535..59723 - 189 WP_001277255 putative conjugal transfer protein TraS -
ML382_RS19375 (ML382_19370) 59787..60191 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
ML382_RS19380 (ML382_19375) 60242..60769 - 528 WP_001055569 conjugal transfer protein TraQ traQ
ML382_RS19385 (ML382_19380) 60769..61473 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
ML382_RS19390 (ML382_19385) 61473..62762 - 1290 WP_001271997 conjugal transfer protein TraO traO
ML382_RS19395 (ML382_19390) 62765..63748 - 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
ML382_RS19400 (ML382_19395) 63759..64451 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
ML382_RS19405 (ML382_19400) 64448..64795 - 348 WP_001055900 conjugal transfer protein traL
ML382_RS19410 (ML382_19405) 64813..68580 - 3768 WP_001141542 LPD7 domain-containing protein -
ML382_RS19415 (ML382_19410) 68670..69221 - 552 WP_000014584 phospholipase D family protein -
ML382_RS19420 (ML382_19415) 69236..69526 - 291 WP_001372180 hypothetical protein traK
ML382_RS19425 (ML382_19420) 69523..70671 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
ML382_RS19430 (ML382_19425) 70668..71486 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
ML382_RS19435 (ML382_19430) 71483..71941 - 459 WP_242426025 IncI1-type conjugal transfer lipoprotein TraH -
ML382_RS19440 (ML382_19435) 72336..72920 - 585 WP_242426026 histidine phosphatase family protein -
ML382_RS19445 (ML382_19440) 72980..74182 - 1203 WP_080217891 conjugal transfer protein TraF -
ML382_RS19450 (ML382_19445) 74268..75092 - 825 WP_001238932 conjugal transfer protein TraE traE
ML382_RS19455 (ML382_19450) 75243..76397 - 1155 WP_001139955 site-specific integrase -

Host bacterium

ID   2860 GenBank   NZ_JAKVSS010000023
Plasmid name   SMG002F9|unnamed1 Incompatibility group   IncI1
Plasmid size   77075 bp Coordinate of oriT [Strand]   39920..40008 [-]
Host baterium   Escherichia coli strain SMG002F9

Cargo genes

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