Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121171
Name   oriT_pS13F in_silico
Organism   Salmonella sp. S13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT742153 (36300..36423 [+], 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_pS13F
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13365 GenBank   WP_061093447
Name   traI_I5Z92_RS00405_pS13F 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   7392 GenBank   WP_000124981
Name   WP_000124981_pS13F 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   7393 GenBank   WP_001254386
Name   WP_001254386_pS13F 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   15662 GenBank   WP_015059012
Name   traC_I5Z92_RS00295_pS13F 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   15663 GenBank   WP_000009363
Name   traD_I5Z92_RS00400_pS13F insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84259.95 Da        Isoelectric Point: 5.0504

>WP_000009363.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 35728..63916

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I5Z92_RS00195 31700..32134 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
I5Z92_RS00200 32131..32850 + 720 WP_001276217 plasmid SOS inhibition protein A -
I5Z92_RS00780 33072..33221 + 150 Protein_42 plasmid maintenance protein Mok -
I5Z92_RS00205 33163..33288 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
I5Z92_RS00210 33607..33903 - 297 Protein_44 hypothetical protein -
I5Z92_RS00215 34203..34499 + 297 WP_001272251 hypothetical protein -
I5Z92_RS00220 34610..35431 + 822 WP_001234445 DUF932 domain-containing protein -
I5Z92_RS00225 35728..36375 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
I5Z92_RS00230 36652..37035 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
I5Z92_RS00235 37226..37912 + 687 WP_015059009 PAS domain-containing protein -
I5Z92_RS00240 38006..38233 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
I5Z92_RS00245 38267..38632 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
I5Z92_RS00250 38647..38958 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
I5Z92_RS00255 38980..39546 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
I5Z92_RS00260 39533..40261 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
I5Z92_RS00265 40261..41688 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
I5Z92_RS00270 41678..42268 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
I5Z92_RS00275 42255..42452 + 198 WP_001324648 conjugal transfer protein TrbD -
I5Z92_RS00280 42464..42715 + 252 WP_001038341 conjugal transfer protein TrbG -
I5Z92_RS00285 42712..43227 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
I5Z92_RS00290 43362..43583 + 222 WP_001278692 conjugal transfer protein TraR -
I5Z92_RS00295 43743..46370 + 2628 WP_015059012 type IV secretion system protein TraC virb4
I5Z92_RS00300 46367..46753 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
I5Z92_RS00305 46750..47382 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
I5Z92_RS00310 47379..48371 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
I5Z92_RS00315 48398..48706 + 309 WP_000412447 hypothetical protein -
I5Z92_RS00320 48769..49290 + 522 WP_015059014 hypothetical protein -
I5Z92_RS00325 49317..49955 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
I5Z92_RS00330 49952..50323 + 372 WP_000056336 hypothetical protein -
I5Z92_RS00335 50349..50771 + 423 WP_001229309 HNH endonuclease -
I5Z92_RS00340 50768..52618 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
I5Z92_RS00345 52645..52902 + 258 WP_053913405 conjugal transfer protein TrbE -
I5Z92_RS00350 52895..53638 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
I5Z92_RS00355 53754..54035 + 282 WP_000549793 type-F conjugative transfer system pilin chaperone TraQ -
I5Z92_RS00360 54022..54567 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
I5Z92_RS00365 54557..54871 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
I5Z92_RS00370 54825..55217 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
I5Z92_RS00375 55204..56577 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
I5Z92_RS00380 56574..59390 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
I5Z92_RS00385 59423..59944 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
I5Z92_RS00390 59969..60700 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
I5Z92_RS00395 60903..61640 + 738 WP_015059020 hypothetical protein -
I5Z92_RS00400 61691..63916 + 2226 WP_000009363 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21599 GenBank   NZ_MT742153
Plasmid name   pS13F Incompatibility group   ColE10
Plasmid size   128223 bp Coordinate of oriT [Strand]   36300..36423 [+]
Host baterium   Salmonella sp. S13

Cargo genes

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