Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113789
Name   oriT_pR13.1986_50k in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain R13.1986
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP129388 (13611..13962 [+], 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_pR13.1986_50k
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8830 GenBank   WP_000986962
Name   traI_ETE97_RS24605_pR13.1986_50k 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   5217 GenBank   WP_001151524
Name   WP_001151524_pR13.1986_50k 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   5218 GenBank   WP_001369361
Name   WP_001369361_pR13.1986_50k 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   10243 GenBank   WP_001064245
Name   traC_ETE97_RS24500_pR13.1986_50k 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   10244 GenBank   WP_000009324
Name   traD_ETE97_RS24590_pR13.1986_50k 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: 13040..39413

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ETE97_RS24375 (ETE97_24375) 8495..8728 + 234 WP_000005987 DUF905 family protein -
ETE97_RS24380 (ETE97_24380) 8756..8953 + 198 Protein_13 hypothetical protein -
ETE97_RS24385 (ETE97_24385) 9008..9442 + 435 WP_000845936 conjugation system SOS inhibitor PsiB -
ETE97_RS24390 (ETE97_24390) 9439..10201 + 763 Protein_15 plasmid SOS inhibition protein A -
ETE97_RS24395 (ETE97_24395) 10380..10529 + 150 Protein_16 plasmid maintenance protein Mok -
ETE97_RS24400 (ETE97_24400) 10471..10596 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
ETE97_RS24405 (ETE97_24405) 10816..11046 + 231 WP_071586998 hypothetical protein -
ETE97_RS24410 (ETE97_24410) 11044..11216 - 173 Protein_19 hypothetical protein -
ETE97_RS24415 (ETE97_24415) 11286..11492 + 207 WP_000547968 hypothetical protein -
ETE97_RS24420 (ETE97_24420) 11517..11804 + 288 WP_000107535 hypothetical protein -
ETE97_RS24425 (ETE97_24425) 11922..12743 + 822 WP_001234426 DUF932 domain-containing protein -
ETE97_RS24430 (ETE97_24430) 13040..13630 - 591 WP_001376243 transglycosylase SLT domain-containing protein virB1
ETE97_RS24435 (ETE97_24435) 13963..14346 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
ETE97_RS24440 (ETE97_24440) 14533..15222 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
ETE97_RS24445 (ETE97_24445) 15321..15716 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
ETE97_RS24450 (ETE97_24450) 15749..16114 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
ETE97_RS24455 (ETE97_24455) 16129..16440 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
ETE97_RS24460 (ETE97_24460) 16462..17028 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
ETE97_RS24465 (ETE97_24465) 17015..17743 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ETE97_RS24470 (ETE97_24470) 17743..19170 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
ETE97_RS24475 (ETE97_24475) 19160..19750 + 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
ETE97_RS24480 (ETE97_24480) 19737..19934 + 198 WP_001324648 conjugal transfer protein TrbD -
ETE97_RS24485 (ETE97_24485) 19946..20197 + 252 WP_001038342 conjugal transfer protein TrbG -
ETE97_RS24490 (ETE97_24490) 20194..20709 + 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
ETE97_RS24495 (ETE97_24495) 20844..21065 + 222 WP_001278689 conjugal transfer protein TraR -
ETE97_RS24500 (ETE97_24500) 21225..23852 + 2628 WP_001064245 type IV secretion system protein TraC virb4
ETE97_RS24505 (ETE97_24505) 23849..24235 + 387 WP_000099686 type-F conjugative transfer system protein TrbI -
ETE97_RS24510 (ETE97_24510) 24232..24864 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
ETE97_RS24515 (ETE97_24515) 24861..25853 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
ETE97_RS24520 (ETE97_24520) 25862..26500 + 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
ETE97_RS24525 (ETE97_24525) 26497..28305 + 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ETE97_RS24530 (ETE97_24530) 28332..28589 + 258 WP_000864318 conjugal transfer protein TrbE -
ETE97_RS24535 (ETE97_24535) 28582..29325 + 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
ETE97_RS24540 (ETE97_24540) 29341..29688 + 348 WP_001287910 conjugal transfer protein TrbA -
ETE97_RS24545 (ETE97_24545) 29690..30004 - 315 WP_001324103 hypothetical protein -
ETE97_RS24550 (ETE97_24550) 30085..30369 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
ETE97_RS24555 (ETE97_24555) 30356..30901 + 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ETE97_RS24560 (ETE97_24560) 30831..31172 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
ETE97_RS24565 (ETE97_24565) 31159..31539 + 381 WP_001389370 F-type conjugal transfer protein TrbF -
ETE97_RS24570 (ETE97_24570) 31536..32912 + 1377 WP_000982840 conjugal transfer pilus assembly protein TraH traH
ETE97_RS24575 (ETE97_24575) 32909..35731 + 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
ETE97_RS24580 (ETE97_24580) 35747..36244 + 498 WP_000605857 entry exclusion protein -
ETE97_RS24585 (ETE97_24585) 36276..37007 + 732 WP_023565183 conjugal transfer complement resistance protein TraT -
ETE97_RS24590 (ETE97_24590) 37260..39413 + 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
ETE97_RS24595 (ETE97_24595) 39422..39820 - 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
ETE97_RS24600 (ETE97_24600) 39820..40047 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   14224 GenBank   NZ_CP129388
Plasmid name   pR13.1986_50k Incompatibility group   IncFIC
Plasmid size   50239 bp Coordinate of oriT [Strand]   13611..13962 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain R13.1986

Cargo genes

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