Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100755
Name   oriT_PDM02 in_silico
Organism   Salmonella enterica subsp. enterica serovar Anatum strain GT-01
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP013221 (36168..36270 [+], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      IR1: 19..26, 30..37  (GTCGGGGC..GCCCTGAC)
 IR2: 44..58, 67..81  (GCAATTGTATAATCG..CGGTTATACAATTGC)
Location of nic site      89..90
Conserved sequence flanking the
  nic site    		  CATCCTG|T
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 103 nt

>oriT_PDM02
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   827 GenBank   WP_001354015
Name   NikB_PDM02 insolico UniProt ID   _
Length   899 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104018.47 Da        Isoelectric Point: 7.3526

>WP_001354015.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCLAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1372..30802

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AS587_RS00010 (AS587_23695) 67..1221 + 1155 WP_001139957 site-specific integrase -
AS587_RS00015 (AS587_23700) 1372..2196 + 825 WP_001238939 conjugal transfer protein TraE traE
AS587_RS00020 (AS587_23705) 2281..3483 + 1203 WP_000976351 conjugal transfer protein TraF -
AS587_RS00025 (AS587_23710) 3543..4127 + 585 WP_000977522 histidine phosphatase family protein -
AS587_RS00030 (AS587_23715) 4522..4980 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
AS587_RS00035 (AS587_23720) 4977..5795 + 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
AS587_RS00040 (AS587_23725) 5792..6940 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
AS587_RS24355 6937..7227 + 291 WP_001299214 hypothetical protein traK
AS587_RS00045 (AS587_23730) 7242..7793 + 552 WP_000014583 phospholipase D family protein -
AS587_RS00050 (AS587_23735) 7883..11650 + 3768 WP_001141529 LPD7 domain-containing protein -
AS587_RS00055 (AS587_23740) 11668..12015 + 348 WP_001055900 conjugal transfer protein traL
AS587_RS00060 (AS587_23745) 12012..12704 + 693 WP_000138548 DotI/IcmL family type IV secretion protein traM
AS587_RS00065 (AS587_23750) 12715..13698 + 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
AS587_RS00070 (AS587_23755) 13701..14990 + 1290 WP_001272005 conjugal transfer protein TraO traO
AS587_RS00075 (AS587_23760) 14990..15694 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
AS587_RS00080 (AS587_23765) 15694..16221 + 528 WP_001055569 conjugal transfer protein TraQ traQ
AS587_RS00085 (AS587_23770) 16272..16676 + 405 WP_000086957 IncI1-type conjugal transfer protein TraR traR
AS587_RS00090 (AS587_23775) 16740..16928 + 189 WP_001277255 putative conjugal transfer protein TraS -
AS587_RS00095 (AS587_23780) 16912..17712 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
AS587_RS00100 (AS587_23785) 17802..20846 + 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
AS587_RS24360 20846..21460 + 615 WP_000337398 IncI1-type conjugal transfer protein TraV traV
AS587_RS00105 (AS587_23790) 21427..22629 + 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
AS587_RS00110 (AS587_23795) 22658..23242 + 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
AS587_RS00115 (AS587_23800) 23339..25501 + 2163 WP_000698351 DotA/TraY family protein traY
AS587_RS00120 (AS587_23805) 25566..26228 + 663 WP_000653334 plasmid IncI1-type surface exclusion protein ExcA -
AS587_RS00125 (AS587_23810) 26300..26509 - 210 WP_000062603 HEAT repeat domain-containing protein -
AS587_RS26545 26901..27077 + 177 WP_001054904 hypothetical protein -
AS587_RS27035 27142..27237 - 96 WP_000609148 DinQ-like type I toxin DqlB -
AS587_RS27040 27798..27989 + 192 WP_174715448 hypothetical protein -
AS587_RS00135 (AS587_23820) 28061..28213 - 153 WP_001331364 Hok/Gef family protein -
AS587_RS00140 (AS587_23825) 28505..29713 + 1209 WP_000121274 IncI1-type conjugal transfer protein TrbA trbA
AS587_RS00145 (AS587_23830) 29732..30802 + 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
AS587_RS00150 (AS587_23835) 30795..33086 + 2292 WP_001289276 F-type conjugative transfer protein TrbC -

Host bacterium

ID   1215 GenBank   NZ_CP013221
Plasmid name   PDM02 Incompatibility group   IncI1
Plasmid size   112176 bp Coordinate of oriT [Strand]   36168..36270 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Anatum strain GT-01

Cargo genes

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