Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103944
Name   oriT_pSE104-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Enteritidis strain SE104
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050713 (69359..69482 [+], 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_pSE104-1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2936 GenBank   WP_072648275
Name   traI_HEC97_RS23270_pSE104-1 insolico UniProt ID   A0A647AQ34
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192066.85 Da        Isoelectric Point: 6.0285

>WP_072648275.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLACSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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)


  Protein structure



No available structure.




Auxiliary protein

ID   1211 GenBank   WP_000124981
Name   WP_000124981_pSE104-1 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   1212 GenBank   WP_001254386
Name   WP_001254386_pSE104-1 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   2790 GenBank   WP_015059012
Name   traC_HEC97_RS23160_pSE104-1 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   2791 GenBank   WP_072646483
Name   traD_HEC97_RS23265_pSE104-1 insolico UniProt ID   _
Length   747 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 747 a.a.        Molecular weight: 84966.71 Da        Isoelectric Point: 5.0504

>WP_072646483.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESG
EVVDMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 68787..96993

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HEC97_RS23055 (HEC97_23055) 64759..65193 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HEC97_RS23060 (HEC97_23060) 65190..65909 + 720 WP_001276217 plasmid SOS inhibition protein A -
HEC97_RS24095 66131..66280 + 150 Protein_85 plasmid maintenance protein Mok -
HEC97_RS23065 (HEC97_23065) 66222..66347 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HEC97_RS23800 66666..66962 - 297 Protein_87 hypothetical protein -
HEC97_RS23080 (HEC97_23080) 67262..67558 + 297 WP_001272251 hypothetical protein -
HEC97_RS23085 (HEC97_23085) 67669..68490 + 822 WP_001234445 DUF932 domain-containing protein -
HEC97_RS23090 (HEC97_23090) 68787..69434 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
HEC97_RS23095 (HEC97_23095) 69711..70094 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HEC97_RS23100 (HEC97_23100) 70285..70971 + 687 WP_015059009 PAS domain-containing protein -
HEC97_RS23105 (HEC97_23105) 71065..71292 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HEC97_RS23110 (HEC97_23110) 71326..71691 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
HEC97_RS23115 (HEC97_23115) 71706..72017 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HEC97_RS23120 (HEC97_23120) 72039..72605 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
HEC97_RS23125 (HEC97_23125) 72592..73320 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HEC97_RS23130 (HEC97_23130) 73320..74747 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
HEC97_RS23135 (HEC97_23135) 74737..75327 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HEC97_RS23140 (HEC97_23140) 75314..75511 + 198 WP_001324648 conjugal transfer protein TrbD -
HEC97_RS23145 (HEC97_23145) 75523..75774 + 252 WP_001038341 conjugal transfer protein TrbG -
HEC97_RS23150 (HEC97_23150) 75771..76286 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
HEC97_RS23155 (HEC97_23155) 76421..76642 + 222 WP_001278692 conjugal transfer protein TraR -
HEC97_RS23160 (HEC97_23160) 76802..79429 + 2628 WP_015059012 type IV secretion system protein TraC virb4
HEC97_RS23165 (HEC97_23165) 79426..79812 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HEC97_RS23170 (HEC97_23170) 79809..80441 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
HEC97_RS23175 (HEC97_23175) 80438..81430 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HEC97_RS23180 (HEC97_23180) 81457..81765 + 309 WP_000412447 hypothetical protein -
HEC97_RS23185 (HEC97_23185) 81828..82349 + 522 WP_015059014 hypothetical protein -
HEC97_RS23190 (HEC97_23190) 82376..83014 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
HEC97_RS23195 (HEC97_23195) 83011..83382 + 372 WP_000056336 hypothetical protein -
HEC97_RS23200 (HEC97_23200) 83408..83830 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
HEC97_RS23205 (HEC97_23205) 83827..85677 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HEC97_RS23210 (HEC97_23210) 85704..85961 + 258 WP_053913405 conjugal transfer protein TrbE -
HEC97_RS23215 (HEC97_23215) 85954..86697 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
HEC97_RS23220 (HEC97_23220) 86813..87094 + 282 WP_000549793 type-F conjugative transfer system pilin chaperone TraQ -
HEC97_RS23225 (HEC97_23225) 87081..87626 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HEC97_RS23230 (HEC97_23230) 87616..87930 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
HEC97_RS23235 (HEC97_23235) 87884..88276 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
HEC97_RS23240 (HEC97_23240) 88263..89636 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
HEC97_RS23245 (HEC97_23245) 89633..92449 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
HEC97_RS23250 (HEC97_23250) 92482..93003 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
HEC97_RS23255 (HEC97_23255) 93028..93759 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
HEC97_RS23260 (HEC97_23260) 93962..94699 + 738 WP_015059020 hypothetical protein -
HEC97_RS23265 (HEC97_23265) 94750..96993 + 2244 WP_072646483 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4384 GenBank   NZ_CP050713
Plasmid name   pSE104-1 Incompatibility group   IncX1
Plasmid size   106652 bp Coordinate of oriT [Strand]   69359..69482 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Enteritidis strain SE104

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, tet(A), oqxA, oqxB, aph(3')-IIa, fosA3, blaTEM-1B, blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -