Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101565
Name   oriT_pMFDS1016233 in_silico
Organism   Escherichia coli strain MFDS1016233
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMVI010000003 (79687..79810 [-], 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_pMFDS1016233
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1387 GenBank   WP_064578954
Name   traI_V6M13_RS28015_pMFDS1016233 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: 192244.09 Da        Isoelectric Point: 5.9188

>WP_064578954.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGRNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIEAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERVRAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMIAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
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)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   510 GenBank   WP_001254386
Name   WP_001254386_pMFDS1016233 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   511 GenBank   WP_040073112
Name   WP_040073112_pMFDS1016233 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   1022 GenBank   WP_062873762
Name   traD_V6M13_RS28030_pMFDS1016233 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   1023 GenBank   WP_001064245
Name   traC_V6M13_RS28120_pMFDS1016233 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: 54245..80382

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6M13_RS28020 53611..53838 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
V6M13_RS28025 53838..54236 + 399 WP_000911317 type II toxin-antitoxin system VapC family toxin -
V6M13_RS28030 54245..56398 - 2154 WP_062873762 type IV conjugative transfer system coupling protein TraD virb4
V6M13_RS28035 56650..57381 - 732 WP_024187508 conjugal transfer complement resistance protein TraT -
V6M13_RS28040 57395..57904 - 510 WP_032082913 conjugal transfer entry exclusion protein TraS -
V6M13_RS28045 57901..60726 - 2826 WP_032082912 conjugal transfer mating-pair stabilization protein TraG traG
V6M13_RS28050 60723..62096 - 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
V6M13_RS28055 62083..62475 - 393 WP_032082924 F-type conjugal transfer protein TrbF -
V6M13_RS28060 62462..62803 - 342 WP_001442101 P-type conjugative transfer protein TrbJ -
V6M13_RS28065 62733..63278 - 546 WP_032082911 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6M13_RS28070 63265..63549 - 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
V6M13_RS28075 63630..63905 + 276 WP_001513501 hypothetical protein -
V6M13_RS28080 63907..64254 - 348 WP_032082949 conjugal transfer protein TrbA -
V6M13_RS28085 64270..65013 - 744 WP_032082948 type-F conjugative transfer system pilin assembly protein TraF traF
V6M13_RS28090 65006..65263 - 258 WP_000864318 conjugal transfer protein TrbE -
V6M13_RS28095 65290..67098 - 1809 WP_032082947 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6M13_RS28100 67095..67733 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6M13_RS28105 67742..68734 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
V6M13_RS28110 68731..69363 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
V6M13_RS28115 69360..69746 - 387 WP_032082946 type-F conjugative transfer system protein TrbI -
V6M13_RS28120 69743..72370 - 2628 WP_001064245 type IV secretion system protein TraC virb4
V6M13_RS28125 72530..72751 - 222 WP_001278689 conjugal transfer protein TraR -
V6M13_RS28130 72886..73401 - 516 WP_332829757 type IV conjugative transfer system lipoprotein TraV traV
V6M13_RS28135 73398..73648 - 251 Protein_87 conjugal transfer protein TrbG -
V6M13_RS28140 73660..73857 - 198 WP_001324648 conjugal transfer protein TrbD -
V6M13_RS28145 73844..74434 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6M13_RS28150 74424..75851 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
V6M13_RS28155 75851..76578 - 728 Protein_91 type-F conjugative transfer system secretin TraK -
V6M13_RS28160 76565..77131 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6M13_RS28165 77153..77464 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6M13_RS28170 77479..77844 - 366 WP_000340270 type IV conjugative transfer system pilin TraA -
V6M13_RS28175 77878..78105 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6M13_RS28180 78199..78885 - 687 WP_000332492 PAS domain-containing protein -
V6M13_RS28185 79075..79458 - 384 WP_040073112 conjugal transfer relaxosome DNA-binding protein TraM -
V6M13_RS28190 79735..80382 + 648 WP_123007297 transglycosylase SLT domain-containing protein virB1
V6M13_RS28195 80679..81500 - 822 WP_074014913 DUF932 domain-containing protein -
V6M13_RS28200 81619..81905 - 287 Protein_100 hypothetical protein -
V6M13_RS28205 81930..82136 - 207 WP_000547968 hypothetical protein -
V6M13_RS28210 82206..82379 + 174 Protein_102 hypothetical protein -
V6M13_RS28215 82377..82607 - 231 WP_074014914 hypothetical protein -
V6M13_RS28220 82827..82952 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6M13_RS28225 82894..83043 - 150 Protein_105 plasmid maintenance protein Mok -
V6M13_RS28230 83065..83253 + 189 WP_032084246 hypothetical protein -
V6M13_RS28235 83222..83984 - 763 Protein_107 plasmid SOS inhibition protein A -
V6M13_RS28240 83981..84415 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   2009 GenBank   NZ_JAQMVI010000003
Plasmid name   pMFDS1016233 Incompatibility group   IncFII
Plasmid size   116352 bp Coordinate of oriT [Strand]   79687..79810 [-]
Host baterium   Escherichia coli strain MFDS1016233

Cargo genes

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