Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114178
Name   oriT_GT88|unnamed2 in_silico
Organism   Edwardsiella tarda strain GT88
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099741 (60715..60750 [-], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_GT88|unnamed2
AAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9103 GenBank   WP_302530042
Name   traI_NHU85_RS17375_GT88|unnamed2 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: 188180.11 Da        Isoelectric Point: 6.9356

>WP_302530042.1 conjugative transfer relaxase/helicase TraI [Edwardsiella tarda]
MMSFSQVKSAGNAGGYYTDKDNYYVLGSMDDHWYGEGAKQLGLSGAVDKAVFTQLLHGRLPDGADLSRLE
NGVNKHRPGYDLTFSAPKSVSMMAMLGGDRRLIDAHNRAVDVALKQAEALASTRTMRDGVSETVLTGNLI
IARFNHDTSRDQDPQLHTHSVVLNATRKGDKWQALSSDTVGKTGFSENILANQIALGKIYRQALRSEVEA
MGYQVEVVGKHGLWEMKNVPVEAFSHRSQAIQEAVGPDASLKSRDVATLDTRKAKTAIDPTEKMAEWMAT
LKSTGFDIQGYREAAAQRVTQGHVPAPAEPAAVDMAKTVRQAISQLSERKVQFTYSDMLAATVSLLPATD
GVIARARAGIDHAIEQQQLIPLDREKGVFTSDIHVLDELSVRMLGQSLGEQGHVTVGAMASSASRHDYSP
LAQQVMTERPPLAMLASSGGAGVQRQRVSELVQATQALGREVQILASDAKSQRFLQQDAVLGQAAIFPQR
VLNDGMAFTPNSTLIVTEGEKLTLKETVTLLDGALRNNVQLLILDTAQRQATGNALSVLRESGIDTLHYA
QTAPVETQILSEPDKPSRFARLADDYVAARQAGDPVVAQVSGPTDQQHLTRAIRSAMKTQGALGQNDTAL
MALEPVWLDSKNRLSRDTYRAGMVMERWDAESKTATRYVIDRVTARSHTLTLRDEQGATQTLRLSSLDSR
WSLYQPQTLAVSSGEQLRVLGKMEGLTWRAGDSLQVQQADEAGIQVERQGQMQRLAVGKTPFTAIKVAYG
YVEGLGRSVNDKAQVLAAVAHNDLNQGTLNRLSRSGSRIRLYSAQAEDKVAARLGRHPAFSTVTTHLKQV
AGQAGLEEALTRQRTALHTPAQQALHLAVPVLEREGGSLAFSRVSLLAQAQEVAGGQVPLSVLADTIQTQ
IREGALISVDSAPGHGNDLLVSRATFEAEKSILRHIAEGKAAVTPLMGNVPESHLAGLTAGQQAATRMIL
ETPDRFTVVQGYAGVGKTTQFRAVMSAIATLPETARPRVVGLGPTHRAVGEMQAAGVEAQTLASFLFDTR
QAQQQGEVADFSNTLFLIDESSMLGNSDMASAYALIARGGGRAVASGDTDQLQAISPGQPFHLQQTRSAA
DVAIMKEIVRQTPELRPAVYSLIARDVAGALETVERVSPQQVPRQAQAWFPPSSVMEIKKEPDASPDGVD
AVSATLSPPVPATIHDAIVADYLGRTPQARDNTLIITHLNQDRRAVNALIHDARVASGELSREERPLPIL
VSANIPEGALRRLSTWKTHQDTRPLLENTYHRIVEVDEKNQLVTLQDETGRQRVLSPQEAVREGVTLYRS
DTITVSVGDRMRFSKSDSERGFVANSTWTISAIEGDSVTLTNGNATRVVHPATDQADRHIDLAYAITAHG
AQGASESFAIALEGAAGKRRSMVNHASAYVALSRAKQHVQVYTDNREAWVTAIQKADRGATAHEILQPRG
ERTADNAARLLAQAVPLSAVAAGRAVLKQDGLEAGTSLARFVAPGRKYPQPHVAFPAFDENGKAAGAWLS
PLSQGDKPAAVVLPREGRLFGSTAARFVALQASRNGESRLAAGIEEGVKLAARFPDAGIVVRLQGEGVPW
NPGAMTGGRVWADAGETGQGTSGEAARLPPEILALRQSEEAARVALEKQAEKTAREMLGQKEKPSPDDVA
PEKMRQIVDEVVKGGAEQVPHPADTLPTLPDHQQSAVEQVAERLQRERLQQMERELVRDKTLAGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-282)

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

(632-711)

DNA helicase TraI (TraI_C)

(1430-1546)

AAA domain (AAA_30)

(968-1154)

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

(574-625)


  Protein structure



No available structure.




T4CP

ID   10549 GenBank   WP_302530041
Name   traD_NHU85_RS17370_GT88|unnamed2 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: 82046.36 Da        Isoelectric Point: 5.3878

>WP_302530041.1 type IV conjugative transfer system coupling protein TraD [Edwardsiella tarda]
MSFNAKDMTQGGQIASMRFRMFGQIANIIFYCLFLLFWVIAALTLMVRLSWQTFVNGCVYWWCQTLAPMR
SLLRSQPVYHIEYYGRKLAYNAEQILQDKYTIWCGEQLWSSFVLAAIIGGITCLITFFVASWILGHQGKK
QSEDEVTGGRQLTDNPKEVAAMLKRDGRQSDIRIEKLPLIKDSEIQNFCLHGTVGSGKSEFIRRLMNHAR
QRGDMVIVYDRSCEFVKSYYDPAKDKILNPLDVRCANWDLWRECLTQPDFDNVANTLIPMGSSEDPFWQG
SGRTIFAEAAYRMRKDDDRSYAKLVDTLLSIKIDKLRAYLQSSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIERNGESFTIRDWMRSVREDGQNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRQRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVLGFQSYAQLEDIYGVKGAATLFDVLNTRAFFRSPSKQIA
EFAAGEIGEKEIQKASEQYSYGADPVRDGVSVGKDMERVTLVSYSDIQTLPDLTCFVTLPGPYPAIKLAL
KYQSRPRIAQEFIPRVIDTDAEARLSAVLAAREEEGRSIDGLFESDSQADAGVRPSQPTSVDSQPITVAP
RHTPATTAAAAAVAAVQGGADTVAAMGGGVERDLQELLPSAQSEKQEAALPPGIDAQGEIVDPDAYAAWQ
ADQSSHALRDKQRLEEVNVNHSHVVSDEELGDGF

  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: 60150..84743

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHU85_RS17215 (NHU85_17205) 55909..56340 + 432 WP_236893473 conjugation system SOS inhibitor PsiB -
NHU85_RS17220 (NHU85_17210) 56337..57065 + 729 WP_236893471 plasmid SOS inhibition protein A -
NHU85_RS17225 (NHU85_17215) 57701..58069 + 369 WP_097364782 hypothetical protein -
NHU85_RS17230 (NHU85_17220) 58740..59645 + 906 WP_236893469 ArdC family protein -
NHU85_RS17235 (NHU85_17225) 60150..60623 - 474 WP_236893468 transglycosylase SLT domain-containing protein virB1
NHU85_RS17240 (NHU85_17230) 61144..61530 + 387 WP_302530025 conjugal transfer relaxosome DNA-binding protein TraM -
NHU85_RS17245 (NHU85_17235) 61587..62327 + 741 WP_097364803 complement resistance protein TraT -
NHU85_RS17250 (NHU85_17240) 62570..63259 + 690 WP_302530026 hypothetical protein -
NHU85_RS17255 63335..63547 + 213 WP_302530027 TraY domain-containing protein -
NHU85_RS17260 (NHU85_17250) 63619..63972 + 354 WP_302530028 type IV conjugative transfer system pilin TraA -
NHU85_RS17265 (NHU85_17255) 63988..64293 + 306 WP_035599570 type IV conjugative transfer system protein TraL traL
NHU85_RS17270 (NHU85_17260) 64311..64877 + 567 WP_068872092 type IV conjugative transfer system protein TraE traE
NHU85_RS17275 (NHU85_17265) 64864..65595 + 732 WP_302530029 type-F conjugative transfer system secretin TraK traK
NHU85_RS17280 (NHU85_17270) 65592..66992 + 1401 WP_302530059 F-type conjugal transfer pilus assembly protein TraB traB
NHU85_RS17285 (NHU85_17275) 66995..67363 + 369 WP_302530030 hypothetical protein -
NHU85_RS17290 (NHU85_17280) 67360..67563 + 204 WP_302530031 hypothetical protein -
NHU85_RS17295 (NHU85_17285) 67575..68141 + 567 WP_236893454 type IV conjugative transfer system lipoprotein TraV traV
NHU85_RS17300 (NHU85_17290) 68270..70897 + 2628 WP_302530032 type IV secretion system protein TraC virb4
NHU85_RS17305 (NHU85_17295) 70894..71265 + 372 WP_302530033 type-F conjugative transfer system protein TrbI -
NHU85_RS17310 (NHU85_17300) 71267..71902 + 636 WP_097364773 type-F conjugative transfer system protein TraW traW
NHU85_RS17315 (NHU85_17305) 71899..72909 + 1011 WP_302530034 conjugal transfer pilus assembly protein TraU traU
NHU85_RS17320 (NHU85_17310) 72945..73136 + 192 WP_302530035 hypothetical protein -
NHU85_RS17325 (NHU85_17315) 73139..73381 - 243 WP_302530036 hypothetical protein -
NHU85_RS17330 (NHU85_17320) 73780..74361 + 582 WP_302530060 type-F conjugative transfer system pilin assembly protein TrbC trbC
NHU85_RS17335 (NHU85_17325) 74414..76189 + 1776 WP_302530061 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NHU85_RS17340 (NHU85_17330) 76220..76972 + 753 WP_302530037 type-F conjugative transfer system pilin assembly protein TraF traF
NHU85_RS17345 (NHU85_17335) 76983..77216 + 234 WP_068872072 type-F conjugative transfer system pilin chaperone TraQ -
NHU85_RS17350 (NHU85_17340) 77197..77736 + 540 WP_141112598 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NHU85_RS17355 (NHU85_17345) 77733..79100 + 1368 WP_302530038 conjugal transfer pilus assembly protein TraH traH
NHU85_RS17360 (NHU85_17350) 79100..81952 + 2853 WP_302530039 conjugal transfer mating-pair stabilization protein TraG traG
NHU85_RS17365 (NHU85_17355) 81949..82452 + 504 WP_302530040 conjugal transfer protein TraS -
NHU85_RS17370 (NHU85_17360) 82539..84743 + 2205 WP_302530041 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   14613 GenBank   NZ_CP099741
Plasmid name   GT88|unnamed2 Incompatibility group   -
Plasmid size   95674 bp Coordinate of oriT [Strand]   60715..60750 [-]
Host baterium   Edwardsiella tarda strain GT88

Cargo genes

Drug resistance gene   tet(A)
Virulence gene   -
Metal resistance gene   arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9