Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101887
Name   oriT_pIncFIC_FII in_silico
Organism   Escherichia coli strain CM22_Ec
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKKDE010000032 (49..241 [+], 193 nt)
oriT length   193 nt
IRs (inverted repeats)      96..103, 112..119  (ACCGCTAG..CTAGCGGT)
 33..39, 47..53  (TATAAAA..TTTTATA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 193 nt

>oriT_pIncFIC_FII
CACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1548 GenBank   WP_000986962
Name   traI_L4I77_RS19600_pIncFIC_FII insolico UniProt ID   A0A0K2B7B9
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192018.92 Da        Isoelectric Point: 5.8722

>WP_000986962.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQDETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQIRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

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

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


T4CP

ID   1221 GenBank   WP_001064245
Name   traC_L4I77_RS19495_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: 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   1222 GenBank   WP_000009324
Name   traD_L4I77_RS19585_pIncFIC_FII 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: 81528.14 Da        Isoelectric Point: 5.1126

>WP_000009324.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2408..25692

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L4I77_RS19430 (L4I77_19380) 242..625 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
L4I77_RS19435 (L4I77_19385) 812..1501 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
L4I77_RS19440 (L4I77_19390) 1600..1995 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
L4I77_RS19445 (L4I77_19395) 2028..2393 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
L4I77_RS19450 (L4I77_19400) 2408..2719 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
L4I77_RS19455 (L4I77_19405) 2741..3307 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
L4I77_RS19460 (L4I77_19410) 3294..4022 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
L4I77_RS19465 (L4I77_19415) 4022..5449 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
L4I77_RS19470 (L4I77_19420) 5439..6029 + 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
L4I77_RS19475 (L4I77_19425) 6016..6213 + 198 WP_001324648 conjugal transfer protein TrbD -
L4I77_RS19480 (L4I77_19430) 6225..6476 + 252 WP_001038342 conjugal transfer protein TrbG -
L4I77_RS19485 (L4I77_19435) 6473..6988 + 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
L4I77_RS19490 (L4I77_19440) 7123..7344 + 222 WP_001278689 conjugal transfer protein TraR -
L4I77_RS19495 (L4I77_19445) 7504..10131 + 2628 WP_001064245 type IV secretion system protein TraC virb4
L4I77_RS19500 (L4I77_19450) 10128..10514 + 387 WP_000099686 type-F conjugative transfer system protein TrbI -
L4I77_RS19505 (L4I77_19455) 10511..11143 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
L4I77_RS19510 (L4I77_19460) 11140..12132 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
L4I77_RS19515 (L4I77_19465) 12141..12779 + 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
L4I77_RS19520 (L4I77_19470) 12776..14584 + 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L4I77_RS19525 (L4I77_19475) 14611..14868 + 258 WP_000864318 conjugal transfer protein TrbE -
L4I77_RS19530 (L4I77_19480) 14861..15604 + 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
L4I77_RS19535 (L4I77_19485) 15620..15967 + 348 WP_180234160 conjugal transfer protein TrbA -
L4I77_RS19540 (L4I77_19490) 15969..16283 - 315 WP_001324103 hypothetical protein -
L4I77_RS19545 (L4I77_19495) 16364..16648 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
L4I77_RS19550 (L4I77_19500) 16635..17180 + 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L4I77_RS19555 (L4I77_19505) 17110..17451 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
L4I77_RS19560 (L4I77_19510) 17438..17818 + 381 WP_001389370 F-type conjugal transfer protein TrbF -
L4I77_RS19565 (L4I77_19515) 17818..19191 + 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
L4I77_RS19570 (L4I77_19520) 19188..22010 + 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
L4I77_RS19575 (L4I77_19525) 22026..22523 + 498 WP_000605857 entry exclusion protein -
L4I77_RS19580 (L4I77_19530) 22555..23286 + 732 WP_023565183 conjugal transfer complement resistance protein TraT -
L4I77_RS19585 (L4I77_19535) 23539..25692 + 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
L4I77_RS19590 (L4I77_19540) 25701..26099 - 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
L4I77_RS19595 (L4I77_19545) 26099..26326 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   2331 GenBank   NZ_JAKKDE010000032
Plasmid name   pIncFIC_FII Incompatibility group   IncFIC
Plasmid size   50109 bp Coordinate of oriT [Strand]   49..241 [+]
Host baterium   Escherichia coli strain CM22_Ec

Cargo genes

Drug resistance gene   tet(A), blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -