Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101884
Name   oriT_pIncFIC_FII in_silico
Organism   Escherichia coli strain CI17_E
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKKDD010000026 (53945..54296 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_pIncFIC_FII
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGAGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1546 GenBank   WP_001611029
Name   traI_L3V76_RS16030_pIncFIC_FII insolico UniProt ID   A0A075MCD1
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191983.83 Da        Isoelectric Point: 5.9594

>WP_001611029.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFIDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRECGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMTGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(575-625)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   621 GenBank   WP_001369361
Name   WP_001369361_pIncFIC_FII insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   622 GenBank   WP_001151524
Name   WP_001151524_pIncFIC_FII insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   1217 GenBank   WP_068862939
Name   traD_L3V76_RS16045_pIncFIC_FII insolico UniProt ID   _
Length   723 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 723 a.a.        Molecular weight: 82234.90 Da        Isoelectric Point: 5.1126

>WP_068862939.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PVSPAINDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQ
RREEVNINVHRERGEDVEPGDDF

  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   1218 GenBank   WP_277494181
Name   traC_L3V76_RS16135_pIncFIC_FII 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: 99269.97 Da        Isoelectric Point: 6.1582

>WP_277494181.1 type IV secretion system protein TraC [Escherichia coli]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTAHILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 28476..54867

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L3V76_RS16035 (L3V76_15940) 27842..28069 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
L3V76_RS16040 (L3V76_15945) 28069..28467 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
L3V76_RS16045 (L3V76_15950) 28476..30647 - 2172 WP_068862939 type IV conjugative transfer system coupling protein TraD virb4
L3V76_RS16050 (L3V76_15955) 30900..31631 - 732 WP_021499552 conjugal transfer complement resistance protein TraT -
L3V76_RS16055 (L3V76_15960) 31663..32160 - 498 WP_000605858 hypothetical protein -
L3V76_RS16060 (L3V76_15965) 32176..34998 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
L3V76_RS16065 (L3V76_15970) 34995..36368 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
L3V76_RS16070 (L3V76_15975) 36368..36748 - 381 WP_001680290 F-type conjugal transfer protein TrbF -
L3V76_RS16075 (L3V76_15980) 36735..37076 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
L3V76_RS16080 (L3V76_15985) 37006..37551 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L3V76_RS16085 (L3V76_15990) 37538..37822 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
L3V76_RS16090 (L3V76_15995) 37903..38217 + 315 WP_000415566 protein ArtA -
L3V76_RS16095 (L3V76_16000) 38219..38566 - 348 WP_001287910 conjugal transfer protein TrbA -
L3V76_RS16100 (L3V76_16005) 38582..39325 - 744 WP_001030377 type-F conjugative transfer system pilin assembly protein TraF traF
L3V76_RS16105 (L3V76_16010) 39318..39575 - 258 WP_000864318 conjugal transfer protein TrbE -
L3V76_RS16110 (L3V76_16015) 39602..41410 - 1809 WP_000821849 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L3V76_RS16115 (L3V76_16020) 41407..42045 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
L3V76_RS16120 (L3V76_16025) 42054..43046 - 993 WP_000830180 conjugal transfer pilus assembly protein TraU traU
L3V76_RS16125 (L3V76_16030) 43043..43675 - 633 WP_032072880 type-F conjugative transfer system protein TraW traW
L3V76_RS16130 (L3V76_16035) 43672..44058 - 387 WP_000214098 type-F conjugative transfer system protein TrbI -
L3V76_RS16135 (L3V76_16040) 44055..46682 - 2628 WP_277494181 type IV secretion system protein TraC virb4
L3V76_RS16140 (L3V76_16045) 46842..47063 - 222 WP_001278692 conjugal transfer protein TraR -
L3V76_RS16145 (L3V76_16050) 47198..47713 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
L3V76_RS16150 (L3V76_16055) 47710..47961 - 252 WP_001038342 conjugal transfer protein TrbG -
L3V76_RS16155 (L3V76_16060) 47973..48170 - 198 WP_001324648 conjugal transfer protein TrbD -
L3V76_RS16160 (L3V76_16065) 48157..48747 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
L3V76_RS16165 (L3V76_16070) 48737..50164 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
L3V76_RS16170 (L3V76_16075) 50164..50892 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
L3V76_RS16175 (L3V76_16080) 50879..51445 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
L3V76_RS16180 (L3V76_16085) 51467..51778 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
L3V76_RS16185 (L3V76_16090) 51793..52158 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
L3V76_RS16190 (L3V76_16095) 52191..52586 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
L3V76_RS16195 (L3V76_16100) 52685..53374 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
L3V76_RS16200 (L3V76_16105) 53561..53944 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
L3V76_RS16205 (L3V76_16110) 54265..54867 + 603 WP_000243712 transglycosylase SLT domain-containing protein virB1
L3V76_RS16210 (L3V76_16115) 55164..55985 - 822 WP_001234487 DUF932 domain-containing protein -
L3V76_RS16215 (L3V76_16120) 56096..56392 - 297 WP_001272245 hypothetical protein -
L3V76_RS16220 (L3V76_16125) 56444..56717 + 274 Protein_65 hypothetical protein -
L3V76_RS16225 (L3V76_16130) 57018..57143 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
L3V76_RS16230 (L3V76_16135) 57085..57234 - 150 Protein_67 plasmid maintenance protein Mok -
L3V76_RS16235 (L3V76_16140) 57413..58175 - 763 Protein_68 plasmid SOS inhibition protein A -
L3V76_RS16240 (L3V76_16145) 58172..58606 - 435 WP_000845962 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   2328 GenBank   NZ_JAKKDD010000026
Plasmid name   pIncFIC_FII Incompatibility group   IncFIC
Plasmid size   72690 bp Coordinate of oriT [Strand]   53945..54296 [-]
Host baterium   Escherichia coli strain CI17_E

Cargo genes

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