Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121603
Name   oriT_pEh-Pc1 in_silico
Organism   Edwardsiella tarda strain KC-Pc-HB1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP023707 (65509..65559 [+], 51 nt)
oriT length   51 nt
IRs (inverted repeats)      22..27, 34..39  (GCAAAA..TTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 51 nt

>oriT_pEh-Pc1
ACTGTATTTACATGAAAATCAGCAAAATTTTAGTTTTGCGTGGGGTGTGGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13625 GenBank   WP_097364765
Name   traI_CPU03_RS17070_pEh-Pc1 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: 188399.57 Da        Isoelectric Point: 6.9356

>WP_097364765.1 conjugative transfer relaxase/helicase TraI [Edwardsiella tarda]
MMSFSQVKSAGNAGGYYTDKDNYYVLGSMDDHWYGEGAKQQGLSGAVDKAVFTQLLHGRLPDGADLSRLE
NGVNKHRPGYDLTFSAPKSVSMMAMLGGDRRLIDAHNRAVDVALKQAEALASTRTMREGVSETVLTGNLV
IARFNHDTSRDQDPQLHTHSVVLNATRKGDKWQALSSDTVGKTGFSENILANQIALGKIYRQALRSEVEA
MGYQVEVVGKHGLWEMKNVPVEAFSHRSQAIQEAVGPDASLKSRDVATLDTRKAKMAIDPTEKMAEWMAT
LKSTGFDIQGYREAAAQRVTQGHVPAPAEPAAVDMAKTVRQAISQLSERKVQFTYSDMLAATVSLLPATD
GVIARARAGIDHAIEQQQLIPLDREKGVFTSDIHVLDELSVRTLGQSLGEQGHVTVGAMALSASRHDYSP
LAQQVMTERPPLAMLASPGGAGVQRQRVSELVQATQALGREVQILVSDAKSQRFLQQDAELGQAAIFPQR
VLNDGMVFTPNSTLIVTEGEKLTLKETVTLLDGALRNNVQLLILDTAQRQATGNALSVLRESGIDTLHYV
QTAPVETQILSEPDKPSRFARLADDYVAARQAGDPVVAQVSGPTDQQHLTRAIRSAMKTQGALGQNDTAL
MALEPVWLDSKNRLSRDTYRAGMVMERWDAESKTATRYVIDRVTARSHTLTLRDEQGATQTLRLSSLDSR
WSLYQPQTLAVSSGEQLRVLGKMEGLTWRAGDSLQVQQADEAGIQVERQGQMQRLAVGKTPFTAIKVAYG
YVEGLGRSVNDKAQVLAAVAHNDLNQGTLNRLARSGSRIRLYSAQAEDKVAARLGRHPAFSTVITHLKQV
AGQTGLEEALTRQRVALHTPAQQALHLAVPVLEREGGSLAFSRVSLLAQAQEVAGGQVPLSVLADTIQTQ
IREGALISVDSAPGHGNDLLVSRATFEAEKSILRHIAEGKAAVTPLMGNVPESHLAGLTAGQQAATRMIL
ETPDRFTVVQGYAGVGKTTQFRAVMSAIATLPETARPRVVGLGPTHRAVGEMQAAGVEAQTLASFLFDTR
QAQQQGEVADFSNTLFLIDESSMLGNSDMASAYALIARGGGRAVASGDTDQLQAIAPGQPFHLQQTRSAA
DVAIMKEIVRQTPALRPAVYSLIARDVAGALETVERISPQQVPRQAQAWFPPSSVMEIKKEPDASPDGVD
AVSATLSPPVPATLHDAIVADYLGRTPQARDNTLIITHLNQDRRAVNALIHDARVASGELSREERPLPIL
VSANIPEGALRRISTWKTHQDTRPLLENTYHRIVEVDEKNQLVTLQDETGRQRVLSPQEAVREGVTLYRS
DTITVSVGDRMRFSKSDSERGFVANSTWTISAIEGDSVTLTNGNATRVVHPATDQADRHIDLAYAITAHG
AQGASESFAIALEGAAGKRRYMVNHASAYVALSRAKQHVQVYTDNREAWVTAIQKADRGATAHEILQPRG
ERTADNAARLLAQAVPLSAVAAGRAVLKQDGLEAGTSLARFVAPGRKYPQPHVAFPAFDENGKAAGAWLS
PLSQGDKPAAVVLPREGRLFGSTAARFVALQASRNGESRLAAGIEEGVKLAARFPDAGIVVRLQGEGVPW
NPGAMTGGRVWAEAGETGQGTSGEAARLPPEILALRQSEEAARVALEKQAEKTAREMLGQKEKPSPDDVA
PEKMRQIVDEVVKGGAEQVPHPADTLPTLPDHQQSAVEQVAERLQRERLQQMERELVRDKTLAGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(968-1154)

TrwC relaxase (TrwC)

(10-282)

DNA helicase TraI (TraI_C)

(1430-1546)

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

(632-711)

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

(574-625)


  Protein structure



No available structure.




T4CP

ID   15926 GenBank   WP_097364767
Name   traD_CPU03_RS17085_pEh-Pc1 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: 82167.58 Da        Isoelectric Point: 5.3878

>WP_097364767.1 type IV conjugative transfer system coupling protein TraD [Edwardsiella tarda]
MSFNAKDMTQGGQIASMRFRMFGQIANIIFYCLFLLFWVIAALTLMVRLSWQTFVNGCVYWWCQTLAPMR
SLLRSQPVYHIEYYGRKLAYNAEQILQDKYTIWCGEQLWSSFVLAAIIGGITCLITFFVASWILGHQGKK
QSEDEVTGGRQLTDNPKEVAAMLKRDGRQSDIRIEKLPLIKDSEIQNFCLHGTVGSGKSEFIRRLMNHAR
QRGDMVIVYDRSCEFVKSYYDPAKDKILNPLDVRCANWDLWRECLTQPDFDNVANTLIPMGSSEDPFWQG
SGRTIFAEAAYRMRKDDDRSYAKLVDTLLSIKIDKLRAYLQSSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIERNGESFTIRDWMRSVREDGQNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRQRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVLGFQSYAQLEDIYGVKGAATLFDVLNTRAFFRSPSKQIA
EFAAGEIGEKEIQKASEQYSYGADPVRDGVSVGKDMERVTLVSYSDIQTLPDLTCFVTLPGPYPAIKLAL
KYQSRPRIAQEFIPRVIDTDAEARLSAVLAVREEEGRSIDGLFESDSQADAGVRPSQPTPVDNQPITVVP
RHTPVTTAAAAAVAAVQGGADTVAAMGGGVERDLQELLPSAQSEKQEAALPPGIDAQGEIVDPDAYAAWQ
ADQSSHALRDKQRLEEVNVNHSHVVSDEELGDGF

  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: 42293..66124

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CPU03_RS17075 (CPU03_17075) 41590..41817 + 228 WP_068872245 type II toxin-antitoxin system VapB family antitoxin -
CPU03_RS17080 (CPU03_17080) 41817..42215 + 399 WP_097364766 tRNA(fMet)-specific endonuclease VapC -
CPU03_RS17085 (CPU03_17085) 42293..44497 - 2205 WP_097364767 type IV conjugative transfer system coupling protein TraD virb4
CPU03_RS17090 (CPU03_17090) 44584..45081 - 498 WP_097364768 conjugal transfer protein TraS -
CPU03_RS17095 (CPU03_17095) 45090..47942 - 2853 WP_097364769 conjugal transfer mating-pair stabilization protein TraG traG
CPU03_RS17100 (CPU03_17100) 47942..49309 - 1368 WP_097364770 conjugal transfer pilus assembly protein TraH traH
CPU03_RS17105 (CPU03_17105) 49306..49845 - 540 WP_035599587 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CPU03_RS17110 (CPU03_17110) 49826..50059 - 234 WP_068872072 type-F conjugative transfer system pilin chaperone TraQ -
CPU03_RS17115 (CPU03_17115) 50070..50822 - 753 WP_097364771 type-F conjugative transfer system pilin assembly protein TraF traF
CPU03_RS17120 (CPU03_17120) 50853..52628 - 1776 WP_097364801 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CPU03_RS17125 (CPU03_17125) 52681..53346 - 666 WP_157757888 type-F conjugative transfer system pilin assembly protein TrbC trbC
CPU03_RS17130 (CPU03_17130) 53357..54367 - 1011 WP_097364772 conjugal transfer pilus assembly protein TraU traU
CPU03_RS17135 (CPU03_17135) 54364..54999 - 636 WP_097364773 type-F conjugative transfer system protein TraW traW
CPU03_RS17140 (CPU03_17140) 55001..55372 - 372 WP_068872079 type-F conjugative transfer system protein TrbI -
CPU03_RS17145 (CPU03_17145) 55369..58002 - 2634 WP_097364774 type IV secretion system protein TraC virb4
CPU03_RS17150 (CPU03_17150) 58131..58697 - 567 WP_097364775 type IV conjugative transfer system lipoprotein TraV traV
CPU03_RS17155 (CPU03_17155) 58709..58921 - 213 WP_097364776 hypothetical protein -
CPU03_RS17160 (CPU03_17160) 58918..59286 - 369 WP_097364777 hypothetical protein -
CPU03_RS17165 (CPU03_17165) 59289..60689 - 1401 WP_068872089 F-type conjugal transfer pilus assembly protein TraB traB
CPU03_RS17170 (CPU03_17170) 60686..61417 - 732 WP_097364778 type-F conjugative transfer system secretin TraK traK
CPU03_RS17175 (CPU03_17175) 61404..61970 - 567 WP_068872092 type IV conjugative transfer system protein TraE traE
CPU03_RS17180 (CPU03_17180) 61988..62293 - 306 WP_035599570 type IV conjugative transfer system protein TraL traL
CPU03_RS17185 (CPU03_17185) 62309..62656 - 348 WP_035599572 type IV conjugative transfer system pilin TraA -
CPU03_RS17190 (CPU03_17190) 62728..62940 - 213 WP_097364779 TraY domain-containing protein -
CPU03_RS17505 63016..63705 - 690 WP_157757889 hypothetical protein -
CPU03_RS17195 (CPU03_17195) 63947..64687 - 741 WP_097364803 complement resistance protein TraT -
CPU03_RS17200 (CPU03_17200) 64744..65130 - 387 WP_068872098 conjugal transfer relaxosome DNA-binding protein TraM -
CPU03_RS17205 (CPU03_17205) 65651..66124 + 474 WP_097364780 transglycosylase SLT domain-containing protein virB1
CPU03_RS17210 (CPU03_17210) 66630..67535 - 906 WP_097364781 ArdC family protein -
CPU03_RS17215 (CPU03_17215) 68207..68575 - 369 WP_097364782 hypothetical protein -
CPU03_RS17220 (CPU03_17220) 69242..69970 - 729 WP_097364783 plasmid SOS inhibition protein A -
CPU03_RS17225 (CPU03_17225) 69967..70398 - 432 WP_097364784 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   22030 GenBank   NZ_CP023707
Plasmid name   pEh-Pc1 Incompatibility group   IncFII
Plasmid size   81404 bp Coordinate of oriT [Strand]   65509..65559 [+]
Host baterium   Edwardsiella tarda strain KC-Pc-HB1

Cargo genes

Drug resistance gene   -
Virulence gene   faeJ, faeI, faeH, faeG, faeF, faeE, faeD, faeC
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -