Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111547
Name   oriT_pSE109-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Enteritidis strain SE109
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050710 (53022..53145 [+], 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_pSE109-1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7501 GenBank   WP_072648275
Name   traI_HEC98_RS23155_pSE109-1 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   4133 GenBank   WP_000124981
Name   WP_000124981_pSE109-1 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   4134 GenBank   WP_001254386
Name   WP_001254386_pSE109-1 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   8543 GenBank   WP_015059012
Name   traC_HEC98_RS23045_pSE109-1 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   8544 GenBank   WP_072646483
Name   traD_HEC98_RS23150_pSE109-1 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: 52450..80656

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HEC98_RS22940 (HEC98_22940) 48422..48856 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HEC98_RS22945 (HEC98_22945) 48853..49572 + 720 WP_001276217 plasmid SOS inhibition protein A -
HEC98_RS23960 49794..49943 + 150 Protein_64 plasmid maintenance protein Mok -
HEC98_RS22950 (HEC98_22950) 49885..50010 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HEC98_RS23660 50329..50625 - 297 Protein_66 hypothetical protein -
HEC98_RS22965 (HEC98_22965) 50925..51221 + 297 WP_001272251 hypothetical protein -
HEC98_RS22970 (HEC98_22970) 51332..52153 + 822 WP_001234445 DUF932 domain-containing protein -
HEC98_RS22975 (HEC98_22975) 52450..53097 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
HEC98_RS22980 (HEC98_22980) 53374..53757 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HEC98_RS22985 (HEC98_22985) 53948..54634 + 687 WP_015059009 PAS domain-containing protein -
HEC98_RS22990 (HEC98_22990) 54728..54955 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HEC98_RS22995 (HEC98_22995) 54989..55354 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
HEC98_RS23000 (HEC98_23000) 55369..55680 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HEC98_RS23005 (HEC98_23005) 55702..56268 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
HEC98_RS23010 (HEC98_23010) 56255..56983 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HEC98_RS23015 (HEC98_23015) 56983..58410 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
HEC98_RS23020 (HEC98_23020) 58400..58990 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HEC98_RS23025 (HEC98_23025) 58977..59174 + 198 WP_001324648 conjugal transfer protein TrbD -
HEC98_RS23030 (HEC98_23030) 59186..59437 + 252 WP_001038341 conjugal transfer protein TrbG -
HEC98_RS23035 (HEC98_23035) 59434..59949 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
HEC98_RS23040 (HEC98_23040) 60084..60305 + 222 WP_001278692 conjugal transfer protein TraR -
HEC98_RS23045 (HEC98_23045) 60465..63092 + 2628 WP_015059012 type IV secretion system protein TraC virb4
HEC98_RS23050 (HEC98_23050) 63089..63475 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HEC98_RS23055 (HEC98_23055) 63472..64104 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
HEC98_RS23060 (HEC98_23060) 64101..65093 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HEC98_RS23065 (HEC98_23065) 65120..65428 + 309 WP_000412447 hypothetical protein -
HEC98_RS23070 (HEC98_23070) 65491..66012 + 522 WP_015059014 hypothetical protein -
HEC98_RS23075 (HEC98_23075) 66039..66677 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
HEC98_RS23080 (HEC98_23080) 66674..67045 + 372 WP_000056336 hypothetical protein -
HEC98_RS23085 (HEC98_23085) 67071..67493 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
HEC98_RS23090 (HEC98_23090) 67490..69340 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HEC98_RS23095 (HEC98_23095) 69367..69624 + 258 WP_053913405 conjugal transfer protein TrbE -
HEC98_RS23100 (HEC98_23100) 69617..70360 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
HEC98_RS23105 (HEC98_23105) 70476..70757 + 282 WP_000549793 type-F conjugative transfer system pilin chaperone TraQ -
HEC98_RS23110 (HEC98_23110) 70744..71289 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HEC98_RS23115 (HEC98_23115) 71279..71593 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
HEC98_RS23120 (HEC98_23120) 71547..71939 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
HEC98_RS23125 (HEC98_23125) 71926..73299 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
HEC98_RS23130 (HEC98_23130) 73296..76112 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
HEC98_RS23135 (HEC98_23135) 76145..76666 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
HEC98_RS23140 (HEC98_23140) 76691..77422 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
HEC98_RS23145 (HEC98_23145) 77625..78362 + 738 WP_015059020 hypothetical protein -
HEC98_RS23150 (HEC98_23150) 78413..80656 + 2244 WP_072646483 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   11982 GenBank   NZ_CP050710
Plasmid name   pSE109-1 Incompatibility group   IncX1
Plasmid size   90315 bp Coordinate of oriT [Strand]   53022..53145 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Enteritidis strain SE109

Cargo genes

Drug resistance gene   aph(3')-IIa, oqxB, oqxA, blaTEM-1B, blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -