Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106711
Name   oriT_pEtSC002-3 in_silico
Organism   Edwardsiella tarda strain SC002
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP116678 (73817..73852 [+], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAACT..AGTTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_pEtSC002-3
AAATCAGCAAAACTTTAGTTTTGCGTAGTGTGTGGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4434 GenBank   WP_279509896
Name   traI_PHA77_RS18495_pEtSC002-3 insolico UniProt ID   _
Length   1745 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1745 a.a.        Molecular weight: 188086.16 Da        Isoelectric Point: 6.9341

>WP_279509896.1 conjugative transfer relaxase/helicase TraI [Edwardsiella tarda]
MMSFSQVKSAGNASGYYTDKDNYYVLGSMDDHWYGEGAKQLGLSGAVDKAVFTQLLHGRLPDGADLSRLE
NGVNKHRPGYDLTFSAPKSVSMMAMLGGDRRLIDAHNRAVDVALKQAEALASTRIMRDGVSETVLTGNLI
IARFNHDTSRDQDPQLHTHSVVLNATRKSDKWQALSSDTVGKTGFSENILANRIAIGKIYNQALRSDVEA
MGYQVEVVGKHGLWEMKSVPVEAFSHRSQAIQEAVGADASLKSRDVAALDTRKAKTAIDPTEKMAEWMAT
LKSTGFDIQGYREAAAQRVTQGHVPAPAEPVVVDMAKTVRQAISQLSERKVQFTYSDMLAATVSLLPTTD
GVIAQARAGIDHAIEQQQLIPLDREKGVFTSDIHVLDELSVRTLGQSLGEQGHVTVGAMALSASRHDYSP
LVQQVMTERPPLAMLASPGGAGVQRQRVSELVQATQALGREVQILASDAKSQRFLQQDAVLGQAAIFPQR
VLNDGMAFTPNSTLIVTEGEKLTLKETVTLLDGALRNNVQLLILDTAQRQATGNALSVLRESGIDTLHYA
QTAPVETQILSEPDKPSRFARLADDYVAARQAGDPVVAQVSGPTDQQHLTRAIRSAMKTQGALGQNDTTL
MALEPVWLDSKNRLSRDTYRAGMVMERWDAESKTATRYVIDRVTARSHTLTLRDEQGATQTLRLSSLDSR
WSLYQPQTLAVSSGEQLRVLGKMEGLAWRAGDSLQVQQADEAGIQVERQGQMQRLAVGKTPFTAIKVAYG
YVEGLGRSVNDKAQVLAAVAHNDLNQGTLNRLARSGSRIRLYSAQAEDKVAARLGRHPAFSTVTTHLKQV
AGQAGLEEALTRQRAALHTPAQQALHLAVPVLEREGGSLAFSRVSLLAQAQEVAGGQVPLSVLADTIQTQ
IREGALISVDSAPGHGNDLLVSRATFEAEKSILRHIAEGKAAVTPLMGNVPESHLAGLTAGQQAATRMIL
ETPDRFTVVQGYAGVGKTTQFRAVMSAIATLPETARPRVVGLGPTHRAVGEMQAAGVEAQTLASFLFDTR
QAQQQGDVADFSNTLFLIDESSMLGNSDMASAYALIARGGGRAVASGDTDQLQAIAPGQPFHLQQTRSAA
DVAIMKEIVRQTPALRPAVYSLIARDVAGALETVERISPQQVPRQAQAWFPPSSVMEIKKEPDASPDGVD
AVSATLSPPVPATLHDAIVADYLGRTPQARDNTLIITHLNQDRRAVNALIHDARVASGELSREERPLPIL
VSANIPEGALRRISTWKTHQDTRPLLENTYHRIVEVDEKNQRVTLQDETGRQRVLSPQEAVREGVTLYRS
DTITVSVGDRMRFSKSDSERGFVANSTWTISAIEGDSVTLTNGNATRVVHPATEPADRHIDLAYAITAHG
AQGASESFAIALEGAAGKRRSMVNHASAYVALSRAKQHVQVYTDNREAWVTAIQKADRGATAHEILQPRG
ERTADNAARLLAQAVPLSAVAAGRAVLKQDGLEAGTSLARFVAPGRKYPQPHVAFPAFDENGKAAGAWLS
PLSQGDKPAAVVLPREGRLFGSTAARFVALQASRNGESRLAAGIEEGVKLAARFPDAGIVVRLQGEGVPW
NPGAMTGGRVWADAGETGQGTSGEAARLPPEILALRQSEEAARVALEKQAEKTAREMLGQKEKPSPDDVA
PEKMRQIVDEVVKGGAEQVPHPADTLPTLPDHQQSAVEQVAERLQRERLQQMERELVCDKTLAGD

  Protein domains


Predicted by InterproScan.

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

(632-711)

TrwC relaxase (TrwC)

(10-282)

AAA domain (AAA_30)

(968-1154)

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

(574-625)

DNA helicase TraI (TraI_C)

(1430-1546)


  Protein structure



No available structure.




Auxiliary protein

ID   1968 GenBank   WP_279509814
Name   WP_279509814_pEtSC002-3 insolico UniProt ID   _
Length   128 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 128 a.a.        Molecular weight: 14836.99 Da        Isoelectric Point: 4.8382

>WP_279509814.1 conjugal transfer relaxosome DNA-binding protein TraM [Edwardsiella tarda]
MAKIQAYVSDEVTNKINAIVEARRLEGAKERDVSFSSISTMLLELGLRVYEAQMERKESAFNQMEFNKVL
LESVLKTKRAVDKVMSMESLSPHVQGDPRWVYKNMTQDILQDVNPIIERFFPIEHDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure



No available structure.




T4CP

ID   4464 GenBank   WP_279509902
Name   traD_PHA77_RS18510_pEtSC002-3 insolico UniProt ID   _
Length   734 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 734 a.a.        Molecular weight: 82237.44 Da        Isoelectric Point: 5.2141

>WP_279509902.1 type IV conjugative transfer system coupling protein TraD [Edwardsiella tarda]
MSFNAKDMTQGGQIASMRFRMFGQIANIIFYCLFLLFWVIAALTLMARLSWQTFVNGCVYWWCQTLAPMR
SLLRSQPVYHIEYYGRKLAYNAEQILQDKYTIWCGEQLWSSFVLAAIIGGITCLITFFVASWILGHQGKK
QSEDEITGGRQLTDNPKEVAAMLKRDGRQSDIRIEKLPLIKDSEIQNFCLHGTVGTGKSEFYRRLMNHAR
QRGDIAIVYDRSCEYVKSYYDPAKDKILNPLDVRCANWDLWRECLTQPDFDNVANTLIPMGSSEDPFWQG
SGRTIFAEAAYRMRKDDDRSYAKLVDTLLSIKIDKLRAYLQSSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIERNGESFTIRDWMRSVREDGQNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRQRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVLGFQSYAQLEDIYGIKGAATLFDVLNTRAFFRSPSKQIA
EFAAGEIGEKEIQKASEQYSYGADPVRDGVSVGKDMERVTLVSYSDIQTLPDLTCFVTLPGPYPAIKLAL
KYQSRPRIAQEFIPRVIDTDAEARLSAVLAAREEEGRSIDGLFETDSQADAGVQPSQPTPVDSQPITVVP
RHTPATTAAAAAVAAVQGGADTVSAMGGGVERDLQELLPSVQSEKQEAALPPGIDAQGEIVDPDAYAAWQ
ADQSSHALRDKQRQEEVNVNHSHVVSDEELGDDY

  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: 49499..74417

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PHA77_RS18500 (PHA77_18500) 48796..49023 + 228 WP_279509898 toxin-antitoxin system antitoxin VapB -
PHA77_RS18505 (PHA77_18505) 49023..49421 + 399 WP_279509900 tRNA(fMet)-specific endonuclease VapC -
PHA77_RS18510 (PHA77_18510) 49499..51703 - 2205 WP_279509902 type IV conjugative transfer system coupling protein TraD virb4
PHA77_RS18515 (PHA77_18515) 51790..52287 - 498 WP_279509904 conjugal transfer protein TraS -
PHA77_RS18520 (PHA77_18520) 52296..55148 - 2853 WP_279509905 conjugal transfer mating-pair stabilization protein TraG traG
PHA77_RS18525 (PHA77_18525) 55148..56524 - 1377 WP_279509906 conjugal transfer pilus assembly protein TraH traH
PHA77_RS18530 (PHA77_18530) 56502..57251 - 750 WP_279509908 hypothetical protein -
PHA77_RS18535 (PHA77_18535) 57244..57621 - 378 WP_279509910 hypothetical protein -
PHA77_RS18540 (PHA77_18540) 57587..58144 - 558 WP_279509972 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
PHA77_RS18545 (PHA77_18545) 58137..58370 - 234 WP_279509912 type-F conjugative transfer system pilin chaperone TraQ -
PHA77_RS18550 (PHA77_18550) 58381..59133 - 753 WP_097364771 type-F conjugative transfer system pilin assembly protein TraF traF
PHA77_RS18555 (PHA77_18555) 59164..60939 - 1776 WP_279509973 type-F conjugative transfer system mating-pair stabilization protein TraN traN
PHA77_RS18560 (PHA77_18560) 60992..61657 - 666 WP_236893448 type-F conjugative transfer system pilin assembly protein TrbC trbC
PHA77_RS18565 (PHA77_18565) 61668..62678 - 1011 WP_279509914 conjugal transfer pilus assembly protein TraU traU
PHA77_RS18570 (PHA77_18570) 62675..63310 - 636 WP_097364773 type-F conjugative transfer system protein TraW traW
PHA77_RS18575 (PHA77_18575) 63312..63665 - 354 WP_279509974 type-F conjugative transfer system protein TrbI -
PHA77_RS18580 (PHA77_18580) 63680..66307 - 2628 WP_279509916 type IV secretion system protein TraC virb4
PHA77_RS18585 (PHA77_18585) 66436..67002 - 567 WP_279509917 type IV conjugative transfer system lipoprotein TraV traV
PHA77_RS18590 (PHA77_18590) 67014..67226 - 213 WP_279509918 hypothetical protein -
PHA77_RS18595 (PHA77_18595) 67301..67591 - 291 WP_279509919 hypothetical protein -
PHA77_RS18600 (PHA77_18600) 67594..68994 - 1401 WP_279509975 F-type conjugal transfer pilus assembly protein TraB traB
PHA77_RS18605 (PHA77_18605) 68991..69722 - 732 WP_279509920 type-F conjugative transfer system secretin TraK traK
PHA77_RS18610 (PHA77_18610) 69709..70275 - 567 WP_236893460 type IV conjugative transfer system protein TraE traE
PHA77_RS18615 (PHA77_18615) 70293..70598 - 306 WP_035599570 type IV conjugative transfer system protein TraL traL
PHA77_RS18620 (PHA77_18620) 70614..70961 - 348 WP_279509921 type IV conjugative transfer system pilin TraA -
PHA77_RS18625 (PHA77_18625) 71033..71245 - 213 WP_279509923 TraY domain-containing protein -
PHA77_RS18630 (PHA77_18630) 71375..72079 - 705 WP_279509925 hypothetical protein -
PHA77_RS18635 (PHA77_18635) 72322..73062 - 741 Protein_79 complement resistance protein TraT -
PHA77_RS18640 (PHA77_18640) 73119..73505 - 387 WP_279509814 conjugal transfer relaxosome DNA-binding protein TraM -
PHA77_RS18645 (PHA77_18645) 73944..74417 + 474 WP_279509813 transglycosylase SLT domain-containing protein virB1
PHA77_RS18650 (PHA77_18650) 74921..75803 - 883 Protein_82 ArdC-like ssDNA-binding domain-containing protein -
PHA77_RS18655 (PHA77_18655) 76614..78233 - 1620 WP_279509927 ISL3 family transposase -

Host bacterium

ID   7148 GenBank   NZ_CP116678
Plasmid name   pEtSC002-3 Incompatibility group   -
Plasmid size   154848 bp Coordinate of oriT [Strand]   73817..73852 [+]
Host baterium   Edwardsiella tarda strain SC002

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -