Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119253
Name   oriT_pET-ATCC-159-1 in_silico
Organism   Edwardsiella tarda ATCC 15947 = NBRC 105688 strain ATCC 15947
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084508 (124871..124906 [+], 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_pET-ATCC-159-1
AAATCAGCAAAACTTTAGTTTTGCGTAGTGTGTGGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12178 GenBank   WP_035599333
Name   traI_DCL27_RS17400_pET-ATCC-159-1 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: 188197.94 Da        Isoelectric Point: 6.6461

>WP_035599333.1 conjugative transfer relaxase/helicase TraI [Edwardsiella tarda]
MMSFSQVKSASNASGYYTDKDNYYVLGSMDDHWYGEGAKQLGLSGAVDKAVFTQLLHGRLPDGADLSRLE
NGVNKHRPGYDLTFSAPKSVSMMAMLGGDRRLIDAHNRAVDVALRQAEALASTRSMRDGVSETVLTGNLI
IARFNHDTSRDQDPQLHTHSVVLNATRNGDKWQALSSDTVGKTGFSENILANRIAIGKIYNQALRSEVEA
MGYQVEVVGKHGLWEMKNVPVEAFSHRSQAIQEAVGADASLKSRDVAALDTRKAKTAIDPTEKMAEWMAT
LKSTGFDIQGYREAAAQRVTQGQVPAPADPAAVDMAKTVRQAISQLSERKVQFTYSDMLAATVSLLPAND
GVIARARAGIDHAIEQQQLIPLDREKGVFTSDIHVLDELSVRTLGQSLGEQGHVTVGAMASSASRHDYSP
LAQQVMTERPPLAMLASPGGAGVQRQRVSELVQATQALGREVQILVSDAKSQRFLQQDAELGQAAIFPQR
VLNDGMAFTPNSTLIVTEGEKLTLKETVTLLDGALRNNVQLLILDTAQRQATGNALSVLRESGIDTLHYA
QTAPVETQILSEPDKPSRFARLADDYVAARQAGDPVVAQVSGPTDQQHLTRAIRSAMKTQGALGQNDTTL
MALEPVWLDSKNRLSRDTYRAGMVMERWDAESKTATRYVIDRVTARSHTLTLRDEQGEMQTLRLSSLDSR
WSLYQPQTLAVSSGEQLRVLGKMEGLTWRAGDSLQVQQADEAGIQVERQGQMQRLAVGKTPFTAIKVAYG
YVEGLGRSVNDKAQVLAAVAHNDLNQGTLNRLARSGSRIRLYSAQAEDKVAARLGRHPAFSTVTTHLKQV
AGQAGLEEALTRQRVALHTPVQQALHLAVPVLEREGGSLAFSRVSLLAQAQEVAGGQVPLSVLADTIQTQ
IREGALISVDSAPGHGNDLLVSRATFEAEKSILRHIAEGKAAVTPLMANVPESHLAGLTAGQQAATRMIL
ETPDRFTVVQGYAGVGKTTQFRAVMSAIATLPETARPRVVGLGPTHRAVGEMLAAGVESQTLASFLFDTR
QAQQQGEVADFSNTLFLIDESSMLGNSDMASAYALIAAGGGRAVASGDTDQLQAIAPGQPFHLQQTRSAA
DVAIMKEIVRQTPELRPAVYSLIARDVAGALETVERVSPQQVPRQAQAWFPPSSVMEIKKEPDASPDGVD
VVSATLSPTVPATLHDAIVADYLGRTPQARDNTLIITHLNQDRRAVNALIHDARVASGELSGGERTLPIL
VSANIPEGALRRLSTWKTHQDTRPLLDNTYHRIVEVDEKNQLVTLQDETGRQRVLSPQEAVREGVTLYRS
DTITVSVGDRMRFSKSDSERGFVANSTWTISAIEGDSVTLTNGNATRVVHPAIDQAERHIDLAYAITAHG
AQGASESFAIALEGTAGGRRQMVNHASAYVALSRAKQHVQVYTDNREAWVTAIQKADRGATAHEILQPRG
ERTADNAARLLAQAVPLSAGAAGRAVLKQDGLDAGTSLARFVAPGRKYPQPHVAFPAFDENGKAAGAWLS
SLSQGDKPAAVVLPREGRLFGSTAARFVALQASRNGESRLAAGIEEGVKLAARFPDDGIVVRLQGEGVPW
NPGAMTGGRVWADAGETGQGISGEAARLAPEILALRQSEEAARVALEKQAEKTAREMLGQKEKPTPDDVA
PEKMRQIVDEVVKGGVEQERHPADTLPTLPDHQQSAVERVAENLQRERLQQMERELVRDKTLAGD

  Protein domains


Predicted by InterproScan.

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

(574-625)

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

(632-711)

AAA domain (AAA_30)

(968-1154)

DNA helicase TraI (TraI_C)

(1430-1546)

TrwC relaxase (TrwC)

(11-282)


  Protein structure



No available structure.




Auxiliary protein

ID   6951 GenBank   WP_035599580
Name   WP_035599580_pET-ATCC-159-1 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: 14737.95 Da        Isoelectric Point: 4.8329

>WP_035599580.1 conjugal transfer relaxosome DNA-binding protein TraM [Edwardsiella tarda]
MAKIQAYVSDEVTNKINAIVEARRLEGAKERDVSFSSISTMLLELGLRVYEAQMERKESAFNQMEFNKIL
LENVLKTQFGICKVMGMASLSPYVQGKEKFVYSNMKSDILEDVRQIIEKFFPSEHDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   14264 GenBank   WP_050979619
Name   traD_DCL27_RS17415_pET-ATCC-159-1 insolico UniProt ID   _
Length   736 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 736 a.a.        Molecular weight: 82279.65 Da        Isoelectric Point: 5.0782

>WP_050979619.1 type IV conjugative transfer system coupling protein TraD [Edwardsiella tarda]
MSFNAKDMTQGGQIASMRFRMFGQIANIIFYCLFLLFWVIAALTLMARLSWQTFVNGCVYWWCQTLAPMR
SLLRSQPVYHIEYYGRKLAYNAEQILQDKYTIWCGEQLWSSFVLAAIIGGITCLITFFVASWILGHQGKK
QSEDEVTGGRQLTDNPKEVAAMLKRDGRQSDIRIEKLPLIKDSEIQNFCLHGTVGSGKSEFIRRLMNHAR
QRGDMVIVYDRSCEFVKSYYDPAKDKILNPLDVRCANWDLWRECLTQPDFDNVANTLIPMGSSEDPFWQG
SGRTIFAEAAYRMRKDDDRSYAKLVDTLLSIKIDKLRAYLQSSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIECNGESFTIRDWMRSVREDGQNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRQRRV
WIFADELPTLYKLPDLVEILPEARKFGGCYVLGFQSYAQLEDIYGVKGAATLFDVLNTRAFFRSPSKQIA
EFAAGEIGEKEIQKASEQYSYGADPVRDGVSVGKDMERVTLVSYSDIQTLPDLTCFVTLPGPYPAIKLAL
KYQPRPRIAQEFIPRVIDTDAEARLSAVLAAREEEGRSIDGLFESDSQAAAGVQPSQPAVTPVDSQPVNT
VSRKMAATTAAAAVVAAVQGGTDAVAAMGGGVERDLQELQVSAQPEQQDQEDVLPPGIDVQGEVVDPDAY
AAWQAGSHTLRDKQRQEEVNVNHSHVVSDEELGDGF

  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: 101661..125471

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DCL27_RS17405 (DCL27_17430) 100958..101185 + 228 WP_035599335 type II toxin-antitoxin system VapB family antitoxin -
DCL27_RS17410 (DCL27_17435) 101185..101583 + 399 WP_035599338 tRNA(fMet)-specific endonuclease VapC -
DCL27_RS17415 (DCL27_17440) 101661..103871 - 2211 WP_050979619 type IV conjugative transfer system coupling protein TraD virb4
DCL27_RS17420 (DCL27_17445) 103958..104476 - 519 WP_109691577 conjugal transfer protein TraS -
DCL27_RS17425 (DCL27_17450) 104473..107325 - 2853 WP_035599532 conjugal transfer mating-pair stabilization protein TraG traG
DCL27_RS17430 (DCL27_17455) 107325..108692 - 1368 WP_035599543 conjugal transfer pilus assembly protein TraH traH
DCL27_RS17435 (DCL27_17460) 108689..109228 - 540 WP_035599587 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
DCL27_RS17440 (DCL27_17465) 109209..109442 - 234 WP_035599544 type-F conjugative transfer system pilin chaperone TraQ -
DCL27_RS17445 (DCL27_17470) 109453..110205 - 753 WP_035599547 type-F conjugative transfer system pilin assembly protein TraF traF
DCL27_RS17450 (DCL27_17475) 110236..112011 - 1776 WP_050979625 type-F conjugative transfer system mating-pair stabilization protein TraN traN
DCL27_RS17455 (DCL27_17480) 112064..112636 - 573 WP_035599590 type-F conjugative transfer system pilin assembly protein TrbC trbC
DCL27_RS17460 (DCL27_17485) 112740..113750 - 1011 WP_050979623 conjugal transfer pilus assembly protein TraU traU
DCL27_RS17465 (DCL27_17490) 113747..114382 - 636 WP_035599550 type-F conjugative transfer system protein TraW traW
DCL27_RS17470 (DCL27_17495) 114384..114755 - 372 WP_035599552 type-F conjugative transfer system protein TrbI -
DCL27_RS17475 (DCL27_17500) 114752..117379 - 2628 WP_035599553 type IV secretion system protein TraC virb4
DCL27_RS17480 (DCL27_17505) 117508..118074 - 567 WP_035599554 type IV conjugative transfer system lipoprotein TraV traV
DCL27_RS17485 (DCL27_17510) 118086..118298 - 213 WP_035599555 hypothetical protein -
DCL27_RS17490 (DCL27_17515) 118295..118666 - 372 WP_146196432 hypothetical protein -
DCL27_RS17495 (DCL27_17520) 118666..120051 - 1386 WP_035599560 F-type conjugal transfer pilus assembly protein TraB traB
DCL27_RS17500 (DCL27_17525) 120048..120779 - 732 WP_035599563 type-F conjugative transfer system secretin TraK traK
DCL27_RS17505 (DCL27_17530) 120766..121332 - 567 WP_035599565 type IV conjugative transfer system protein TraE traE
DCL27_RS17510 (DCL27_17535) 121350..121655 - 306 WP_035599570 type IV conjugative transfer system protein TraL traL
DCL27_RS17515 (DCL27_17540) 121671..122018 - 348 WP_035599572 type IV conjugative transfer system pilin TraA -
DCL27_RS17520 (DCL27_17545) 122090..122302 - 213 WP_071526360 TraY domain-containing protein -
DCL27_RS17525 (DCL27_17550) 122434..123129 - 696 WP_146196433 hypothetical protein -
DCL27_RS17530 (DCL27_17555) 123376..124116 - 741 WP_035599577 complement resistance protein TraT -
DCL27_RS17535 (DCL27_17560) 124173..124559 - 387 WP_035599580 conjugal transfer relaxosome DNA-binding protein TraM -
DCL27_RS17540 (DCL27_17565) 124998..125471 + 474 WP_035599583 transglycosylase SLT domain-containing protein virB1
DCL27_RS17545 (DCL27_17570) 125976..126881 - 906 WP_035599585 ArdC family protein -
DCL27_RS17550 (DCL27_17575) 127550..128278 - 729 WP_035601205 plasmid SOS inhibition protein A -
DCL27_RS17555 (DCL27_17580) 128275..128706 - 432 WP_035601208 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   19683 GenBank   NZ_CP084508
Plasmid name   pET-ATCC-159-1 Incompatibility group   -
Plasmid size   145764 bp Coordinate of oriT [Strand]   124871..124906 [+]
Host baterium   Edwardsiella tarda ATCC 15947 = NBRC 105688 strain ATCC 15947

Cargo genes

Drug resistance gene   -
Virulence gene   faeC, faeD, faeE, faeF, faeH, faeI
Metal resistance gene   cusR/ylcA, silC, silB, silA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -