Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101125
Name   oriT_p288_18 in_silico
Organism   Salmonella enterica subsp. enterica serovar Agona strain SAL 288_18
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAODHS010000007 (30007..30130 [+], 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)
 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_p288_18
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1137 GenBank   WP_061093447
Name   traI_N5P38_RS24385_p288_18 insolico UniProt ID   A0A2Z4I1F4
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192119.90 Da        Isoelectric Point: 6.0788

>WP_061093447.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

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

(633-712)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   412 GenBank   WP_000124981
Name   WP_000124981_p288_18 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   413 GenBank   WP_001254386
Name   WP_001254386_p288_18 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


T4CP

ID   698 GenBank   WP_015059012
Name   traC_N5P38_RS24275_p288_18 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: 99393.22 Da        Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   699 GenBank   WP_021573169
Name   traD_N5P38_RS24380_p288_18 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83553.19 Da        Isoelectric Point: 5.0504

>WP_021573169.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 29435..57603

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N5P38_RS24170 (N5P38_24125) 25406..25842 + 437 Protein_34 conjugation system SOS inhibitor PsiB -
N5P38_RS24175 (N5P38_24130) 25839..26558 + 720 WP_001276217 plasmid SOS inhibition protein A -
N5P38_RS24180 (N5P38_24135) 26780..26929 + 150 Protein_36 plasmid maintenance protein Mok -
N5P38_RS24185 (N5P38_24140) 26871..26996 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
N5P38_RS24190 (N5P38_24145) 27315..27610 - 296 Protein_38 hypothetical protein -
N5P38_RS24195 (N5P38_24150) 27910..28206 + 297 WP_001272251 hypothetical protein -
N5P38_RS24200 (N5P38_24155) 28317..29138 + 822 WP_001234445 DUF932 domain-containing protein -
N5P38_RS24205 (N5P38_24160) 29435..30082 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
N5P38_RS24210 (N5P38_24165) 30357..30740 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
N5P38_RS24215 (N5P38_24170) 30931..31617 + 687 WP_015059009 PAS domain-containing protein -
N5P38_RS24220 (N5P38_24175) 31711..31938 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
N5P38_RS24225 (N5P38_24180) 31972..32337 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
N5P38_RS24230 (N5P38_24185) 32352..32663 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
N5P38_RS24235 (N5P38_24190) 32685..33251 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
N5P38_RS24240 (N5P38_24195) 33238..33966 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
N5P38_RS24245 (N5P38_24200) 33966..35393 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
N5P38_RS24250 (N5P38_24205) 35383..35973 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
N5P38_RS24255 (N5P38_24210) 35960..36157 + 198 WP_001324648 conjugal transfer protein TrbD -
N5P38_RS24260 (N5P38_24215) 36169..36420 + 252 WP_001038341 conjugal transfer protein TrbG -
N5P38_RS24265 (N5P38_24220) 36417..36932 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
N5P38_RS24270 (N5P38_24225) 37067..37288 + 222 WP_001278692 conjugal transfer protein TraR -
N5P38_RS24275 (N5P38_24230) 37448..40075 + 2628 WP_015059012 type IV secretion system protein TraC virb4
N5P38_RS24280 (N5P38_24235) 40072..40458 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
N5P38_RS24285 (N5P38_24240) 40455..41087 + 633 WP_099098220 type-F conjugative transfer system protein TraW traW
N5P38_RS24290 (N5P38_24245) 41084..42076 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
N5P38_RS24295 (N5P38_24250) 42103..42411 + 309 WP_000412447 hypothetical protein -
N5P38_RS24300 (N5P38_24255) 42474..42995 + 522 WP_015059014 hypothetical protein -
N5P38_RS24305 (N5P38_24260) 43022..43660 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
N5P38_RS24310 (N5P38_24265) 43657..44028 + 372 WP_000056336 hypothetical protein -
N5P38_RS24315 (N5P38_24270) 44054..44476 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
N5P38_RS24320 (N5P38_24275) 44473..46323 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
N5P38_RS24325 (N5P38_24280) 46350..46607 + 258 WP_053913405 conjugal transfer protein TrbE -
N5P38_RS24330 (N5P38_24285) 46600..47343 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
N5P38_RS24335 (N5P38_24290) 47459..47740 + 282 WP_000549793 type-F conjugative transfer system pilin chaperone TraQ -
N5P38_RS24340 (N5P38_24295) 47727..48272 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
N5P38_RS24345 (N5P38_24300) 48262..48576 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
N5P38_RS24350 (N5P38_24305) 48530..48922 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
N5P38_RS24355 (N5P38_24310) 48909..50282 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
N5P38_RS24360 (N5P38_24315) 50279..53095 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
N5P38_RS24365 (N5P38_24320) 53128..53649 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
N5P38_RS24370 (N5P38_24325) 53674..54405 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
N5P38_RS24375 (N5P38_24330) 54608..55345 + 738 WP_015059020 hypothetical protein -
N5P38_RS24380 (N5P38_24335) 55396..57603 + 2208 WP_021573169 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1569 GenBank   NZ_JAODHS010000007
Plasmid name   p288_18 Incompatibility group   IncFII
Plasmid size   67262 bp Coordinate of oriT [Strand]   30007..30130 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Agona strain SAL 288_18

Cargo genes

Drug resistance gene   blaTEM-1B, blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -