Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104684
Name   oriT_XNC1_p in_silico
Organism   Xenorhabdus nematophila ATCC 19061
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_014170 (136059..136162 [+], 104 nt)
oriT length   104 nt
IRs (inverted repeats)      55..60, 73..78  (TGGAAT..ATTCCA)
 45..50, 55..60  (ATTCCA..TGGAAT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 104 nt

>oriT_XNC1_p
ATTTGACAAATTCCAAAGATGGGGTAGCCTAGTAACAGGACTAGATTCCAGTATTGGAATAATCAGCTTTAAATTCCAGATAGATAGTTATGTGGATAGGAATT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   3291 GenBank   WP_013141552
Name   traC_XNC1_RS19725_XNC1_p insolico UniProt ID   _
Length   814 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 814 a.a.        Molecular weight: 92347.53 Da        Isoelectric Point: 6.0244

>WP_013141552.1 type IV secretion system protein TraC [Xenorhabdus nematophila]
MIVTIKKKLQETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGTYDNGLIQ
DLKLFVTCKVPINNNNPSESELQNLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
AVDWEMDKPICEQIFDYGTDVEVSKNGLRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKISYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWD
EKGKEMKVDDIAERCLEGEDVRLRDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHLR
QVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLYE
NAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRLI
VGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRNRKQAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(449-808)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11978..34727

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
XNC1_RS19635 7120..7353 - 234 WP_013184414 hypothetical protein -
XNC1_RS19640 (XNC1_p0011) 7335..7952 - 618 WP_013184413 hypothetical protein -
XNC1_RS24460 (XNC1_p0012) 8257..8886 + 630 WP_231858625 MobH family relaxase -
XNC1_RS24465 (XNC1_p0013) 8873..9982 + 1110 WP_231858624 hypothetical protein -
XNC1_RS19650 (XNC1_p0014) 9979..10509 + 531 WP_013141538 hypothetical protein -
XNC1_RS19655 (XNC1_p0015) 10543..11583 - 1041 WP_013141539 IS481 family transposase -
XNC1_RS23785 11696..11992 + 297 Protein_15 ATP-binding protein -
XNC1_RS23140 11999..12382 + 384 Protein_16 DUF4400 domain-containing protein -
XNC1_RS19665 12391..12837 + 447 WP_013184411 hypothetical protein -
XNC1_RS19670 (XNC1_p0017) 12847..13224 + 378 WP_013141541 hypothetical protein -
XNC1_RS19675 (XNC1_p0018) 13254..13886 + 633 WP_231858623 hypothetical protein -
XNC1_RS23710 14067..14210 + 144 WP_021326607 hypothetical protein -
XNC1_RS19680 (XNC1_p0019) 14222..14569 + 348 WP_013141543 TraE/TraK family type IV conjugative transfer system protein traE
XNC1_RS19685 (XNC1_p0020) 14553..15470 + 918 WP_013141544 type-F conjugative transfer system secretin TraK traK
XNC1_RS19690 (XNC1_p0021) 15470..16783 + 1314 WP_041573865 TraB/VirB10 family protein traB
XNC1_RS19695 (XNC1_p0022) 16780..17358 + 579 WP_013141546 type IV conjugative transfer system lipoprotein TraV traV
XNC1_RS19700 (XNC1_p0023) 17371..17754 + 384 WP_013184407 TraA family conjugative transfer protein -
XNC1_RS19710 (XNC1_p0025) 17874..19042 + 1169 Protein_26 IS3 family transposase -
XNC1_RS19715 (XNC1_p0026) 19265..24751 + 5487 WP_041573977 DUF4165 domain-containing protein -
XNC1_RS19720 (XNC1_p0027) 24900..25607 + 708 WP_013141551 DsbC family protein trbB
XNC1_RS19725 (XNC1_p0028) 25604..28048 + 2445 WP_013141552 type IV secretion system protein TraC virb4
XNC1_RS19730 (XNC1_p0029) 28063..28380 + 318 WP_013141553 hypothetical protein -
XNC1_RS19735 (XNC1_p0030) 28377..28907 + 531 WP_013141554 S26 family signal peptidase -
XNC1_RS19740 (XNC1_p0031) 28870..30135 + 1266 WP_013141555 TrbC family F-type conjugative pilus assembly protein traW
XNC1_RS19745 (XNC1_p0032) 30132..30803 + 672 WP_013141556 EAL domain-containing protein -
XNC1_RS19750 (XNC1_p0033) 30824..31807 + 984 WP_231858734 TraU family protein traU
XNC1_RS19755 (XNC1_p0034) 31923..34727 + 2805 WP_041573978 conjugal transfer mating pair stabilization protein TraN traN
XNC1_RS19760 (XNC1_p0035) 34765..35628 - 864 WP_013141559 hypothetical protein -
XNC1_RS19765 (XNC1_p0036) 35750..36391 - 642 WP_041979271 hypothetical protein -
XNC1_RS19770 (XNC1_p0037) 36684..37004 + 321 WP_013141561 hypothetical protein -
XNC1_RS19775 (XNC1_p0039) 37309..37494 + 186 WP_231858731 hypothetical protein -
XNC1_RS19780 (XNC1_p0040) 37713..38681 + 969 WP_013141564 AAA family ATPase -
XNC1_RS19785 (XNC1_p0041) 38692..39597 + 906 WP_013141565 hypothetical protein -

Host bacterium

ID   5123 GenBank   NC_014170
Plasmid name   XNC1_p Incompatibility group   IncA/C2
Plasmid size   155327 bp Coordinate of oriT [Strand]   136059..136162 [+]
Host baterium   Xenorhabdus nematophila ATCC 19061

Cargo genes

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