Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101561
Name   oriT_pMFDS1009760 in_silico
Organism   Escherichia coli strain MFDS1009760
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMUK010000004 (67118..67241 [-], 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_pMFDS1009760
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1384 GenBank   WP_332829301
Name   traI_V6L99_RS25980_pMFDS1009760 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: 192260.20 Da        Isoelectric Point: 5.9737

>WP_332829301.1 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
LYTPDTIRVGTGDRMRFTKSDRVRGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVELPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   504 GenBank   WP_001254386
Name   WP_001254386_pMFDS1009760 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   505 GenBank   WP_032083503
Name   WP_032083503_pMFDS1009760 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.




T4CP

ID   1017 GenBank   WP_001064245
Name   traC_V6L99_RS26085_pMFDS1009760 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: 45331..67813

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6L99_RS25985 41041..41268 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
V6L99_RS25990 41268..41666 + 399 WP_000911317 type II toxin-antitoxin system VapC family toxin -
V6L99_RS25995 41675..43828 - 2154 Protein_51 type IV conjugative transfer system coupling protein TraD -
V6L99_RS26000 44080..44811 - 732 WP_024187508 conjugal transfer complement resistance protein TraT -
V6L99_RS26005 44825..45334 - 510 WP_032082913 conjugal transfer entry exclusion protein TraS -
V6L99_RS26010 45331..48156 - 2826 WP_032082912 conjugal transfer mating-pair stabilization protein TraG traG
V6L99_RS26015 48153..49526 - 1374 WP_021532658 conjugal transfer pilus assembly protein TraH traH
V6L99_RS26020 49513..49905 - 393 WP_282868770 F-type conjugal transfer protein TrbF -
V6L99_RS26025 49892..50233 - 342 WP_001442101 P-type conjugative transfer protein TrbJ -
V6L99_RS26030 50163..50708 - 546 WP_000059818 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6L99_RS26035 50695..50979 - 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
V6L99_RS26040 51060..51335 + 276 WP_001513501 hypothetical protein -
V6L99_RS26045 51337..51684 - 348 WP_032082949 conjugal transfer protein TrbA -
V6L99_RS26050 51700..52443 - 744 WP_123010632 type-F conjugative transfer system pilin assembly protein TraF traF
V6L99_RS26055 52436..52693 - 258 WP_000864318 conjugal transfer protein TrbE -
V6L99_RS26060 52720..54528 - 1809 WP_096111975 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6L99_RS26065 54525..55163 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6L99_RS26070 55172..56164 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
V6L99_RS26075 56161..56793 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
V6L99_RS26080 56790..57176 - 387 WP_032082946 type-F conjugative transfer system protein TrbI -
V6L99_RS26085 57173..59800 - 2628 WP_001064245 type IV secretion system protein TraC virb4
V6L99_RS26090 59960..60181 - 222 WP_001278689 conjugal transfer protein TraR -
V6L99_RS26095 60316..60831 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
V6L99_RS26100 60828..61078 - 251 Protein_72 conjugal transfer protein TrbG -
V6L99_RS26105 61090..61287 - 198 WP_001324648 conjugal transfer protein TrbD -
V6L99_RS26110 61274..61864 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6L99_RS26115 61854..63281 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
V6L99_RS26120 63281..64009 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
V6L99_RS26125 63996..64562 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6L99_RS26130 64584..64895 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6L99_RS26135 64910..65275 - 366 WP_000340270 type IV conjugative transfer system pilin TraA -
V6L99_RS26140 65309..65536 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6L99_RS26145 65630..66316 - 687 WP_000332492 PAS domain-containing protein -
V6L99_RS26150 66506..66889 - 384 WP_032083503 conjugal transfer relaxosome DNA-binding protein TraM -
V6L99_RS26155 67166..67813 + 648 WP_123007297 transglycosylase SLT domain-containing protein virB1
V6L99_RS26160 68110..68931 - 822 WP_074014913 DUF932 domain-containing protein -
V6L99_RS26165 69050..69336 - 287 Protein_85 hypothetical protein -
V6L99_RS26170 69361..69567 - 207 WP_000547968 hypothetical protein -
V6L99_RS26175 69637..69810 + 174 Protein_87 hypothetical protein -
V6L99_RS26180 69808..70038 - 231 WP_074014914 hypothetical protein -
V6L99_RS26185 70258..70383 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6L99_RS26190 70325..70474 - 150 Protein_90 plasmid maintenance protein Mok -
V6L99_RS26195 70496..70684 + 189 WP_032084246 hypothetical protein -
V6L99_RS26200 70653..71415 - 763 Protein_92 plasmid SOS inhibition protein A -
V6L99_RS26205 71412..71846 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   2005 GenBank   NZ_JAQMUK010000004
Plasmid name   pMFDS1009760 Incompatibility group   IncFII
Plasmid size   87036 bp Coordinate of oriT [Strand]   67118..67241 [-]
Host baterium   Escherichia coli strain MFDS1009760

Cargo genes

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