Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101579
Name   oriT_pMFDS1016228 in_silico
Organism   Escherichia coli strain MFDS1016228
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMVG010000002 (81067..81190 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 41..48, 61..68  (AAAAACAA..TTGTTTTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pMFDS1016228
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1400 GenBank   WP_096136349
Name   traI_V6M01_RS24530_pMFDS1016228 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192263.11 Da        Isoelectric Point: 5.9188

>WP_096136349.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGRNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIEAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLGERKVQFTYTDVLARTVGILPPE
NGVIERVRAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYETEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVELPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLQ
DGRTEQAVREIAGQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)

TrwC relaxase (TrwC)

(10-283)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   535 GenBank   WP_001254386
Name   WP_001254386_pMFDS1016228 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5

ID   536 GenBank   WP_040073112
Name   WP_040073112_pMFDS1016228 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14556.62 Da        Isoelectric Point: 5.0278

>WP_040073112.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSIEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.




T4CP

ID   1047 GenBank   WP_062873762
Name   traD_V6M01_RS24545_pMFDS1016228 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81434.90 Da        Isoelectric Point: 5.0485

>WP_062873762.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPDMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

  Protein structure



No available structure.



ID   1048 GenBank   WP_001064245
Name   traC_V6M01_RS24635_pMFDS1016228 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 55624..81762

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6M01_RS24535 54990..55217 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
V6M01_RS24540 55217..55615 + 399 WP_000911317 type II toxin-antitoxin system VapC family toxin -
V6M01_RS24545 55624..57777 - 2154 WP_062873762 type IV conjugative transfer system coupling protein TraD virb4
V6M01_RS24550 58029..58760 - 732 WP_024187508 conjugal transfer complement resistance protein TraT -
V6M01_RS24555 58774..59283 - 510 WP_032082913 conjugal transfer entry exclusion protein TraS -
V6M01_RS24560 59280..62105 - 2826 WP_062873763 conjugal transfer mating-pair stabilization protein TraG traG
V6M01_RS24565 62102..63475 - 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
V6M01_RS24570 63462..63854 - 393 WP_032082924 F-type conjugal transfer protein TrbF -
V6M01_RS24575 63841..64182 - 342 WP_001442101 P-type conjugative transfer protein TrbJ -
V6M01_RS24580 64112..64657 - 546 WP_032082911 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6M01_RS24585 64644..64928 - 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
V6M01_RS24590 65009..65284 + 276 WP_074430089 toxin ArtA -
V6M01_RS24595 65286..65633 - 348 WP_032082949 conjugal transfer protein TrbA -
V6M01_RS24600 65649..66392 - 744 WP_135460420 type-F conjugative transfer system pilin assembly protein TraF traF
V6M01_RS24605 66385..66642 - 258 WP_000864318 conjugal transfer protein TrbE -
V6M01_RS24610 66669..68477 - 1809 WP_032082947 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6M01_RS24615 68474..69112 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6M01_RS24620 69121..70113 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
V6M01_RS24625 70110..70742 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
V6M01_RS24630 70739..71125 - 387 WP_032082946 type-F conjugative transfer system protein TrbI -
V6M01_RS24635 71122..73749 - 2628 WP_001064245 type IV secretion system protein TraC virb4
V6M01_RS24640 73909..74130 - 222 WP_001278689 conjugal transfer protein TraR -
V6M01_RS24645 74265..74780 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
V6M01_RS24650 74777..75027 - 251 Protein_98 conjugal transfer protein TrbG -
V6M01_RS24655 75039..75236 - 198 WP_001324648 conjugal transfer protein TrbD -
V6M01_RS24660 75223..75813 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6M01_RS24665 75803..77230 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
V6M01_RS24670 77230..77958 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
V6M01_RS24675 77945..78511 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6M01_RS24680 78533..78844 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6M01_RS24685 78859..79224 - 366 WP_000340270 type IV conjugative transfer system pilin TraA -
V6M01_RS24690 79258..79485 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6M01_RS24695 79579..80265 - 687 WP_000332492 PAS domain-containing protein -
V6M01_RS24700 80455..80838 - 384 WP_040073112 conjugal transfer relaxosome DNA-binding protein TraM -
V6M01_RS24705 81115..81762 + 648 WP_241363796 transglycosylase SLT domain-containing protein virB1
V6M01_RS24710 82059..82880 - 822 WP_074014913 DUF932 domain-containing protein -
V6M01_RS24715 82999..83285 - 287 Protein_111 hypothetical protein -
V6M01_RS24720 83310..83516 - 207 WP_000547968 hypothetical protein -
V6M01_RS24725 83586..83759 + 174 Protein_113 hypothetical protein -
V6M01_RS24730 83757..83987 - 231 WP_074014914 hypothetical protein -
V6M01_RS24735 84207..84332 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6M01_RS24740 84274..84423 - 150 Protein_116 plasmid maintenance protein Mok -
V6M01_RS24745 84647..86218 - 1572 WP_332833059 IS66-like element ISCro1 family transposase -
V6M01_RS24750 86238..86585 - 348 WP_000624622 IS66 family insertion sequence element accessory protein TnpB -

Host bacterium

ID   2023 GenBank   NZ_JAQMVG010000002
Plasmid name   pMFDS1016228 Incompatibility group   IncFII
Plasmid size   89809 bp Coordinate of oriT [Strand]   81067..81190 [-]
Host baterium   Escherichia coli strain MFDS1016228

Cargo genes

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