Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116577
Name   oriT_FDAARGOS_1473|unnamed1 in_silico
Organism   Edwardsiella tarda strain FDAARGOS_1473
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP082940 (24..59 [-], 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_FDAARGOS_1473|unnamed1
AAATCAGCAAAACTTTAGTTTTGCGTAGTGTGTGGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10576 GenBank   WP_035599333
Name   traI_K8O98_RS17040_FDAARGOS_1473|unnamed1 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   6203 GenBank   WP_035599580
Name   WP_035599580_FDAARGOS_1473|unnamed1 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   12358 GenBank   WP_050979619
Name   traD_K8O98_RS17025_FDAARGOS_1473|unnamed1 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: 3275..23269

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
K8O98_RS16905 (K8O98_16855) 371..757 + 387 WP_035599580 conjugal transfer relaxosome DNA-binding protein TraM -
K8O98_RS16910 (K8O98_16860) 814..1554 + 741 WP_035599577 complement resistance protein TraT -
K8O98_RS16915 (K8O98_16865) 1801..2496 + 696 WP_146196433 hypothetical protein -
K8O98_RS16920 (K8O98_16870) 2628..2840 + 213 WP_071526360 TraY domain-containing protein -
K8O98_RS16925 (K8O98_16875) 2912..3259 + 348 WP_035599572 type IV conjugative transfer system pilin TraA -
K8O98_RS16930 (K8O98_16880) 3275..3580 + 306 WP_035599570 type IV conjugative transfer system protein TraL traL
K8O98_RS16935 (K8O98_16885) 3598..4164 + 567 WP_035599565 type IV conjugative transfer system protein TraE traE
K8O98_RS16940 (K8O98_16890) 4151..4882 + 732 WP_035599563 type-F conjugative transfer system secretin TraK traK
K8O98_RS16945 (K8O98_16895) 4879..6264 + 1386 WP_035599560 F-type conjugal transfer pilus assembly protein TraB traB
K8O98_RS16950 (K8O98_16900) 6264..6635 + 372 WP_146196432 hypothetical protein -
K8O98_RS16955 (K8O98_16905) 6632..6844 + 213 WP_035599555 hypothetical protein -
K8O98_RS16960 (K8O98_16910) 6856..7422 + 567 WP_035599554 type IV conjugative transfer system lipoprotein TraV traV
K8O98_RS16965 (K8O98_16915) 7551..10178 + 2628 WP_035599553 type IV secretion system protein TraC virb4
K8O98_RS16970 (K8O98_16920) 10175..10546 + 372 WP_035599552 type-F conjugative transfer system protein TrbI -
K8O98_RS16975 (K8O98_16925) 10548..11183 + 636 WP_035599550 type-F conjugative transfer system protein TraW traW
K8O98_RS16980 (K8O98_16930) 11180..12190 + 1011 WP_050979623 conjugal transfer pilus assembly protein TraU traU
K8O98_RS16985 (K8O98_16935) 12294..12866 + 573 WP_035599590 type-F conjugative transfer system pilin assembly protein TrbC trbC
K8O98_RS16990 (K8O98_16940) 12919..14694 + 1776 WP_050979625 type-F conjugative transfer system mating-pair stabilization protein TraN traN
K8O98_RS16995 (K8O98_16945) 14725..15477 + 753 WP_035599547 type-F conjugative transfer system pilin assembly protein TraF traF
K8O98_RS17000 (K8O98_16950) 15488..15721 + 234 WP_035599544 type-F conjugative transfer system pilin chaperone TraQ -
K8O98_RS17005 (K8O98_16955) 15702..16241 + 540 WP_035599587 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
K8O98_RS17010 (K8O98_16960) 16238..17605 + 1368 WP_035599543 conjugal transfer pilus assembly protein TraH traH
K8O98_RS17015 (K8O98_16965) 17605..20457 + 2853 WP_035599532 conjugal transfer mating-pair stabilization protein TraG traG
K8O98_RS17020 (K8O98_16970) 20454..20972 + 519 WP_109691577 conjugal transfer protein TraS -
K8O98_RS17025 (K8O98_16975) 21059..23269 + 2211 WP_050979619 type IV conjugative transfer system coupling protein TraD virb4
K8O98_RS17030 (K8O98_16980) 23347..23745 - 399 WP_035599338 tRNA(fMet)-specific endonuclease VapC -
K8O98_RS17035 (K8O98_16985) 23745..23972 - 228 WP_035599335 type II toxin-antitoxin system VapB family antitoxin -

Host bacterium

ID   17010 GenBank   NZ_CP082940
Plasmid name   FDAARGOS_1473|unnamed1 Incompatibility group   -
Plasmid size   145764 bp Coordinate of oriT [Strand]   24..59 [-]
Host baterium   Edwardsiella tarda strain FDAARGOS_1473

Cargo genes

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