Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107746
Name   oriT_pLYYSPS2-3 in_silico
Organism   Citrobacter werkmanii strain LYYSPS2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MZ342958 (49966..50089 [+], 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_pLYYSPS2-3
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5204 GenBank   WP_015059021
Name   traI_MZV96_RS00500_pLYYSPS2-3 insolico UniProt ID   A0A0X8XR69
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192132.90 Da        Isoelectric Point: 6.0788

>WP_015059021.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Gammaproteobacteria]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAENRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
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.

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   2370 GenBank   WP_000124981
Name   WP_000124981_pLYYSPS2-3 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   2371 GenBank   WP_001254386
Name   WP_001254386_pLYYSPS2-3 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   5451 GenBank   WP_015059012
Name   traC_MZV96_RS00390_pLYYSPS2-3 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   5452 GenBank   WP_059274178
Name   traD_MZV96_RS00495_pLYYSPS2-3 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83906.57 Da        Isoelectric Point: 5.0504

>WP_059274178.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 49394..77573

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MZV96_RS00285 45366..45800 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
MZV96_RS00290 45797..46516 + 720 WP_001276217 plasmid SOS inhibition protein A -
MZV96_RS00295 46738..46887 + 150 Protein_59 plasmid maintenance protein Mok -
MZV96_RS00300 46829..46954 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
MZV96_RS00305 47273..47569 - 297 Protein_61 hypothetical protein -
MZV96_RS00310 47869..48165 + 297 WP_001272251 hypothetical protein -
MZV96_RS00315 48276..49097 + 822 WP_001234445 DUF932 domain-containing protein -
MZV96_RS00320 49394..50041 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
MZV96_RS00325 50318..50701 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
MZV96_RS00330 50892..51578 + 687 WP_015059009 PAS domain-containing protein -
MZV96_RS00335 51672..51899 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
MZV96_RS00340 51933..52298 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
MZV96_RS00345 52313..52624 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
MZV96_RS00350 52646..53212 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
MZV96_RS00355 53199..53927 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
MZV96_RS00360 53927..55354 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
MZV96_RS00365 55344..55934 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
MZV96_RS00370 55921..56118 + 198 WP_001324648 conjugal transfer protein TrbD -
MZV96_RS00375 56130..56381 + 252 WP_001038341 conjugal transfer protein TrbG -
MZV96_RS00380 56378..56893 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
MZV96_RS00385 57028..57249 + 222 WP_001278692 conjugal transfer protein TraR -
MZV96_RS00390 57409..60036 + 2628 WP_015059012 type IV secretion system protein TraC virb4
MZV96_RS00395 60033..60419 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
MZV96_RS00400 60416..61048 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
MZV96_RS00405 61045..62037 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
MZV96_RS00410 62064..62372 + 309 WP_000412447 hypothetical protein -
MZV96_RS00415 62435..62956 + 522 WP_015059014 hypothetical protein -
MZV96_RS00420 62983..63621 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
MZV96_RS00425 63618..63989 + 372 WP_000056336 hypothetical protein -
MZV96_RS00430 64015..64437 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
MZV96_RS00435 64434..66284 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MZV96_RS00440 66311..66568 + 258 WP_053913405 conjugal transfer protein TrbE -
MZV96_RS00445 66561..67304 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
MZV96_RS00450 67465..67701 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
MZV96_RS00455 67688..68233 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MZV96_RS00460 68223..68537 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
MZV96_RS00465 68491..68883 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
MZV96_RS00470 68870..70243 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
MZV96_RS00475 70240..73056 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
MZV96_RS00480 73089..73610 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
MZV96_RS00485 73635..74366 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
MZV96_RS00490 74569..75306 + 738 WP_015059020 hypothetical protein -
MZV96_RS00495 75357..77573 + 2217 WP_059274178 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   8181 GenBank   NZ_MZ342958
Plasmid name   pLYYSPS2-3 Incompatibility group   IncFII
Plasmid size   87232 bp Coordinate of oriT [Strand]   49966..50089 [+]
Host baterium   Citrobacter werkmanii strain LYYSPS2

Cargo genes

Drug resistance gene   aph(3')-VI, blaNDM-1, fosA3, blaTEM-1B, rmtB
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -