Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101586
Name   oriT_pMFDS1016416 in_silico
Organism   Escherichia coli strain MFDS1016416
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMVK010000002 (53116..53239 [+], 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_pMFDS1016416
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1407 GenBank   WP_096124000
Name   traI_V6L93_RS24805_pMFDS1016416 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: 192290.18 Da        Isoelectric Point: 5.9188

>WP_096124000.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGRNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIEAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGVVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERVRAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYETEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVELPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   548 GenBank   WP_032083503
Name   WP_032083503_pMFDS1016416 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: 14584.63 Da        Isoelectric Point: 5.0278

>WP_032083503.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MARVNLYISNEVHEKINMIVERRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSIEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   549 GenBank   WP_001254386
Name   WP_001254386_pMFDS1016416 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


T4CP

ID   1061 GenBank   WP_001064245
Name   traC_V6L93_RS24700_pMFDS1016416 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: 52544..75026

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6L93_RS24580 48511..48945 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
V6L93_RS24585 48942..49704 + 763 Protein_63 plasmid SOS inhibition protein A -
V6L93_RS24590 49673..49861 - 189 WP_032084246 hypothetical protein -
V6L93_RS24595 49883..50032 + 150 Protein_65 plasmid maintenance protein Mok -
V6L93_RS24600 49974..50099 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6L93_RS24605 50319..50549 + 231 WP_074014914 hypothetical protein -
V6L93_RS24610 50547..50720 - 174 Protein_68 hypothetical protein -
V6L93_RS24615 50790..50996 + 207 WP_000547968 hypothetical protein -
V6L93_RS24620 51021..51307 + 287 Protein_70 hypothetical protein -
V6L93_RS24625 51426..52247 + 822 WP_074014913 DUF932 domain-containing protein -
V6L93_RS24630 52544..53191 - 648 WP_123007297 transglycosylase SLT domain-containing protein virB1
V6L93_RS24635 53468..53851 + 384 WP_032083503 conjugal transfer relaxosome DNA-binding protein TraM -
V6L93_RS24640 54041..54727 + 687 WP_000332492 PAS domain-containing protein -
V6L93_RS24645 54821..55048 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6L93_RS24650 55082..55447 + 366 WP_000340270 type IV conjugative transfer system pilin TraA -
V6L93_RS24655 55462..55773 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6L93_RS24660 55795..56361 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6L93_RS24665 56348..57076 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
V6L93_RS24670 57076..58503 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
V6L93_RS24675 58493..59083 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6L93_RS24680 59070..59267 + 198 WP_001324648 conjugal transfer protein TrbD -
V6L93_RS24685 59279..59529 + 251 Protein_83 conjugal transfer protein TrbG -
V6L93_RS24690 59526..60041 + 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
V6L93_RS24695 60176..60397 + 222 WP_001278689 conjugal transfer protein TraR -
V6L93_RS24700 60557..63184 + 2628 WP_001064245 type IV secretion system protein TraC virb4
V6L93_RS24705 63181..63567 + 387 WP_032082946 type-F conjugative transfer system protein TrbI -
V6L93_RS24710 63564..64196 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
V6L93_RS24715 64193..65185 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
V6L93_RS24720 65194..65832 + 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6L93_RS24725 65829..67637 + 1809 WP_096111975 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6L93_RS24730 67664..67921 + 258 WP_000864318 conjugal transfer protein TrbE -
V6L93_RS24735 67914..68657 + 744 WP_123010632 type-F conjugative transfer system pilin assembly protein TraF traF
V6L93_RS24740 68673..69020 + 348 WP_032082949 conjugal transfer protein TrbA -
V6L93_RS24745 69022..69297 - 276 WP_001513501 hypothetical protein -
V6L93_RS24750 69378..69662 + 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
V6L93_RS24755 69649..70194 + 546 WP_000059818 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6L93_RS24760 70124..70465 + 342 WP_001442101 P-type conjugative transfer protein TrbJ -
V6L93_RS24765 70452..70844 + 393 WP_282868770 F-type conjugal transfer protein TrbF -
V6L93_RS24770 70831..72204 + 1374 WP_021532658 conjugal transfer pilus assembly protein TraH traH
V6L93_RS24775 72201..75026 + 2826 WP_032082912 conjugal transfer mating-pair stabilization protein TraG traG
V6L93_RS24780 75023..75532 + 510 WP_032082913 conjugal transfer entry exclusion protein TraS -
V6L93_RS24785 75546..76277 + 732 WP_024187508 conjugal transfer complement resistance protein TraT -
V6L93_RS24790 76529..78682 + 2154 Protein_104 type IV conjugative transfer system coupling protein TraD -
V6L93_RS24795 78691..79089 - 399 WP_000911317 type II toxin-antitoxin system VapC family toxin -
V6L93_RS24800 79089..79316 - 228 WP_000450532 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   2030 GenBank   NZ_JAQMVK010000002
Plasmid name   pMFDS1016416 Incompatibility group   IncFII
Plasmid size   108906 bp Coordinate of oriT [Strand]   53116..53239 [+]
Host baterium   Escherichia coli strain MFDS1016416

Cargo genes

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