Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116832
Name   oriT_JXY0409-18|unnamed1 in_silico
Organism   Salmonella sp. JXY0409-18
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084217 (208545..208798 [+], 254 nt)
oriT length   254 nt
IRs (inverted repeats)      152..157, 159..164  (AAAAGT..ACTTTT)
 121..129, 134..142  (TTAAGGCTT..AAGCCTTAA)
 50..55, 59..64  (AATTTT..AAAATT)
Location of nic site      77..78
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 254 nt

>oriT_JXY0409-18|unnamed1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10733 GenBank   WP_001011151
Name   mobH_LDB27_RS23415_JXY0409-18|unnamed1 insolico UniProt ID   A0A1P8VU63
Length   1048 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1048 a.a.        Molecular weight: 117773.04 Da        Isoelectric Point: 4.6054

>WP_001011151.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPTGI
QTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGGLL
SHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWTPS
SQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYTDG
NDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGEVY
LNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFRNG
IGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDTVE
TAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESEDE
SAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGSLD
GMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLELP
PPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVGSC
ATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAAAT
SVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPASPV
SGHNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTLYL
TQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(106-302)


  Protein structure


Source ID Structure
AlphaFold DB A0A1P8VU63


T4CP

ID   12535 GenBank   WP_001284076
Name   traD_LDB27_RS23410_JXY0409-18|unnamed1 insolico UniProt ID   _
Length   694 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 694 a.a.        Molecular weight: 78137.93 Da        Isoelectric Point: 8.0177

>WP_001284076.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANETLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH

  Protein domains


Predicted by InterproScan.

AAA-like domain (AAA_10)

(199-249)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(406-609)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 123159..132366

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDB27_RS22970 (LDB27_22970) 123159..125840 - 2682 WP_000387412 TraC family protein virb4
LDB27_RS22975 (LDB27_22975) 125849..126799 - 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
LDB27_RS22980 (LDB27_22980) 126809..127561 - 753 WP_183079335 protein-disulfide isomerase HtdT -
LDB27_RS22985 (LDB27_22985) 127680..128162 - 483 WP_065311104 transcriptional regulator -
LDB27_RS22990 (LDB27_22990) 128170..129525 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
LDB27_RS22995 (LDB27_22995) 129515..129976 - 462 WP_000521240 plasmid transfer protein HtdO -
LDB27_RS23000 (LDB27_23000) 129978..131249 - 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
LDB27_RS23005 (LDB27_23005) 131249..132037 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
LDB27_RS23010 (LDB27_23010) 132049..132366 - 318 WP_000043356 type IV conjugative transfer system protein TraL traL
LDB27_RS23015 (LDB27_23015) 132417..132770 - 354 WP_000423602 hypothetical protein -
LDB27_RS23020 (LDB27_23020) 133919..134794 - 876 WP_000594612 RepB family plasmid replication initiator protein -
LDB27_RS23025 (LDB27_23025) 135271..136326 + 1056 WP_065311103 hypothetical protein -
LDB27_RS23030 (LDB27_23030) 136344..136544 + 201 WP_000594931 hypothetical protein -
LDB27_RS23035 (LDB27_23035) 136541..137257 + 717 WP_000838218 zinc finger-like domain-containing protein -

Host bacterium

ID   17265 GenBank   NZ_CP084217
Plasmid name   JXY0409-18|unnamed1 Incompatibility group   IncHI2A
Plasmid size   263947 bp Coordinate of oriT [Strand]   208545..208798 [+]
Host baterium   Salmonella sp. JXY0409-18

Cargo genes

Drug resistance gene   tet(A), aph(6)-Id, floR, aph(3')-Ia, dfrA14, ARR-3, mph(A), qnrS1, blaCTX-M-55, blaTEM-1B, blaLAP-2, aac(3)-IId, ant(3'')-Ia, lnu(F)
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -