Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103271
Name   oriT_pECM13 in_silico
Organism   Escherichia coli strain SY286M
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY865323 (56301..56389 [-], 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_pECM13
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2444 GenBank   WP_001493820
Name   nikB_HTT53_RS00365_pECM13 insolico UniProt ID   A0A229B7S1
Length   900 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 900 a.a.        Molecular weight: 104037.65 Da        Isoelectric Point: 7.3321

>WP_001493820.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVDFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHCTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLNGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRIVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
YNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKLWEPPSPMR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A229B7S1


Auxiliary protein

ID   1043 GenBank   WP_001283947
Name   WP_001283947_pECM13 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   2214 GenBank   WP_001289272
Name   trbC_HTT53_RS00375_pECM13 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: 86924.04 Da        Isoelectric Point: 6.6402

>WP_001289272.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPIVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETNEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 62747..100842

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTT53_RS00370 59572..60390 + 819 WP_000106196 DUF2971 domain-containing protein -
HTT53_RS00375 60463..62754 - 2292 WP_001289272 F-type conjugative transfer protein TrbC -
HTT53_RS00380 62747..63817 - 1071 WP_001535705 IncI1-type conjugal transfer protein TrbB trbB
HTT53_RS00385 63836..65044 - 1209 WP_001535704 IncI1-type conjugal transfer protein TrbA trbA
HTT53_RS00390 65336..65488 + 153 WP_001331364 Hok/Gef family protein -
HTT53_RS00395 65560..65811 - 252 WP_001535703 hypothetical protein -
HTT53_RS00650 66312..66407 + 96 WP_000609148 DinQ-like type I toxin DqlB -
HTT53_RS00405 66472..66756 - 285 WP_024129996 hypothetical protein -
HTT53_RS00410 66857..67066 - 210 WP_001140545 hemolysin expression modulator Hha -
HTT53_RS00415 67164..67778 - 615 WP_000578649 plasmid IncI1-type surface exclusion protein ExcA -
HTT53_RS00420 67854..70022 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
HTT53_RS00425 70119..70703 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
HTT53_RS00430 70732..71934 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
HTT53_RS00435 71901..72515 - 615 WP_000337400 IncI1-type conjugal transfer protein TraV traV
HTT53_RS00440 72515..75559 - 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
HTT53_RS00445 75649..76449 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HTT53_RS00450 76433..76621 - 189 WP_001277255 putative conjugal transfer protein TraS -
HTT53_RS00455 76685..77089 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
HTT53_RS00460 77140..77667 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HTT53_RS00465 77667..78371 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HTT53_RS00470 78371..79660 - 1290 WP_001535701 conjugal transfer protein TraO traO
HTT53_RS00475 79663..80646 - 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
HTT53_RS00480 80657..81349 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HTT53_RS00485 81346..81693 - 348 WP_001055900 conjugal transfer protein traL
HTT53_RS00490 81711..85478 - 3768 WP_001141542 LPD7 domain-containing protein -
HTT53_RS00495 85568..86119 - 552 WP_000014584 phospholipase D family protein -
HTT53_RS00500 86134..86424 - 291 WP_001372180 hypothetical protein traK
HTT53_RS00505 86421..87569 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HTT53_RS00510 87566..88384 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
HTT53_RS00515 88381..88839 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HTT53_RS00520 89234..89818 - 585 WP_000977522 histidine phosphatase family protein -
HTT53_RS00525 89878..91080 - 1203 WP_000976351 conjugal transfer protein TraF -
HTT53_RS00530 91165..91989 - 825 WP_001238939 conjugal transfer protein TraE traE
HTT53_RS00535 92140..93294 - 1155 WP_172693847 site-specific integrase -
HTT53_RS00540 93293..93610 + 318 WP_001558195 hypothetical protein -
HTT53_RS00545 94822..94989 + 168 WP_236918907 hypothetical protein -
HTT53_RS00550 95052..96336 - 1285 Protein_108 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HTT53_RS00555 96336..96992 - 657 WP_001193553 prepilin peptidase -
HTT53_RS00560 96977..97537 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HTT53_RS00565 97547..98161 - 615 WP_000959785 type 4 pilus major pilin -
HTT53_RS00570 98179..99276 - 1098 WP_001208805 type II secretion system F family protein -
HTT53_RS00575 99289..100842 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
HTT53_RS00580 100853..101254 - 402 WP_172693848 type IV pilus biogenesis protein PilP -
HTT53_RS00590 102628..103923 - 1296 WP_000752774 type 4b pilus protein PilO2 -
HTT53_RS00595 103916..105598 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -

Host bacterium

ID   3714 GenBank   NZ_KY865323
Plasmid name   pECM13 Incompatibility group   IncI1
Plasmid size   113006 bp Coordinate of oriT [Strand]   56301..56389 [-]
Host baterium   Escherichia coli strain SY286M

Cargo genes

Drug resistance gene   blaCTX-M-14, fosA3, aac(3)-IId, blaTEM-1B, rmtB, sul1, qacE, aadA2, dfrA12
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -