Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101626
Name   oriT_FEX675|unnamed4 in_silico
Organism   Escherichia coli strain FEX675
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_PSNU01000036 (5258..5609 [+], 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_FEX675|unnamed4
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGAGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1428 GenBank   WP_064237180
Name   traI_C4M77_RS22060_FEX675|unnamed4 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: 192011.89 Da        Isoelectric Point: 6.0139

>WP_064237180.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFIDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLRQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRECGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMTGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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

(633-712)

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   559 GenBank   WP_001151524
Name   WP_001151524_FEX675|unnamed4 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

ID   560 GenBank   WP_001369361
Name   WP_001369361_FEX675|unnamed4 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


T4CP

ID   1090 GenBank   WP_001064245
Name   traC_C4M77_RS21955_FEX675|unnamed4 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.



ID   1091 GenBank   WP_072666843
Name   traD_C4M77_RS22045_FEX675|unnamed4 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 84001.79 Da        Isoelectric Point: 5.1126

>WP_072666843.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYE
AWQREQNPDIQQKMQRREEVNINVHRERGEDVEPGDDF

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 4687..31123

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C4M77_RS21850 (C4M77_21850) 1..879 + 879 Protein_0 hypothetical protein -
C4M77_RS21855 (C4M77_21855) 948..1382 + 435 WP_000845962 conjugation system SOS inhibitor PsiB -
C4M77_RS21860 (C4M77_21860) 1379..2141 + 763 Protein_2 plasmid SOS inhibition protein A -
C4M77_RS29535 2320..2469 + 150 Protein_3 plasmid maintenance protein Mok -
C4M77_RS21865 (C4M77_21865) 2411..2536 + 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
C4M77_RS29540 2837..3110 - 274 Protein_5 hypothetical protein -
C4M77_RS21875 (C4M77_21875) 3162..3458 + 297 WP_001272245 hypothetical protein -
C4M77_RS21880 (C4M77_21880) 3569..4390 + 822 WP_001234487 DUF932 domain-containing protein -
C4M77_RS21885 (C4M77_21885) 4687..5277 - 591 WP_001376243 transglycosylase SLT domain-containing protein virB1
C4M77_RS21890 (C4M77_21890) 5610..5993 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
C4M77_RS21895 (C4M77_21895) 6180..6869 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
C4M77_RS21900 (C4M77_21900) 6968..7363 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
C4M77_RS21905 (C4M77_21905) 7396..7761 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
C4M77_RS21910 (C4M77_21910) 7776..8087 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
C4M77_RS21915 (C4M77_21915) 8109..8675 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
C4M77_RS21920 (C4M77_21920) 8662..9390 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
C4M77_RS21925 (C4M77_21925) 9390..10817 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
C4M77_RS21930 (C4M77_21930) 10807..11397 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
C4M77_RS21935 (C4M77_21935) 11384..11581 + 198 WP_001324648 conjugal transfer protein TrbD -
C4M77_RS21940 (C4M77_21940) 11593..11844 + 252 WP_001038342 conjugal transfer protein TrbG -
C4M77_RS21945 (C4M77_21945) 11841..12356 + 516 WP_033803052 type IV conjugative transfer system lipoprotein TraV traV
C4M77_RS21950 (C4M77_21950) 12491..12712 + 222 WP_001278689 conjugal transfer protein TraR -
C4M77_RS21955 (C4M77_21955) 12872..15499 + 2628 WP_001064245 type IV secretion system protein TraC virb4
C4M77_RS21960 (C4M77_21960) 15496..15882 + 387 WP_000099686 type-F conjugative transfer system protein TrbI -
C4M77_RS21965 (C4M77_21965) 15879..16511 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
C4M77_RS21970 (C4M77_21970) 16508..17500 + 993 WP_000830180 conjugal transfer pilus assembly protein TraU traU
C4M77_RS21975 (C4M77_21975) 17509..18147 + 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
C4M77_RS21980 (C4M77_21980) 18144..19952 + 1809 WP_000821849 type-F conjugative transfer system mating-pair stabilization protein TraN traN
C4M77_RS21985 (C4M77_21985) 19979..20236 + 258 WP_000864318 conjugal transfer protein TrbE -
C4M77_RS21990 (C4M77_21990) 20229..20972 + 744 WP_001030377 type-F conjugative transfer system pilin assembly protein TraF traF
C4M77_RS21995 (C4M77_21995) 20988..21335 + 348 WP_001287910 conjugal transfer protein TrbA -
C4M77_RS22000 (C4M77_22000) 21337..21651 - 315 WP_000415566 protein ArtA -
C4M77_RS22005 (C4M77_22005) 21732..22016 + 285 WP_050009059 type-F conjugative transfer system pilin chaperone TraQ -
C4M77_RS22010 (C4M77_22010) 22003..22548 + 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
C4M77_RS22015 (C4M77_22015) 22478..22819 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
C4M77_RS22020 (C4M77_22020) 22806..23186 + 381 WP_001680290 F-type conjugal transfer protein TrbF -
C4M77_RS22025 (C4M77_22025) 23186..24559 + 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
C4M77_RS22030 (C4M77_22030) 24556..27378 + 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
C4M77_RS22035 (C4M77_22035) 27394..27891 + 498 WP_000605857 entry exclusion protein -
C4M77_RS22040 (C4M77_22040) 27923..28654 + 732 WP_023565183 conjugal transfer complement resistance protein TraT -
C4M77_RS22045 (C4M77_22045) 28907..31123 + 2217 WP_072666843 type IV conjugative transfer system coupling protein TraD virb4
C4M77_RS22050 (C4M77_22050) 31132..31530 - 399 WP_064237181 tRNA(fMet)-specific endonuclease VapC -
C4M77_RS22055 (C4M77_22055) 31530..31757 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   2070 GenBank   NZ_PSNU01000036
Plasmid name   FEX675|unnamed4 Incompatibility group   IncFIC
Plasmid size   42979 bp Coordinate of oriT [Strand]   5258..5609 [+]
Host baterium   Escherichia coli strain FEX675

Cargo genes

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