Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107518
Name   oriT_pPJ-T7-250kb in_silico
Organism   Salmonella sp. strain PJM1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OL598600 (134243..134496 [-], 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_pPJ-T7-250kb
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5042 GenBank   WP_000980119
Name   mobH_MM000_RS00795_pPJ-T7-250kb insolico UniProt ID   A0A0H3VVI8
Length   1050 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1050 a.a.        Molecular weight: 118035.42 Da        Isoelectric Point: 4.6054

>WP_000980119.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDT
VETAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVG
SCATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(108-304)


  Protein structure


Source ID Structure
AlphaFold DB A0A0H3VVI8


T4CP

ID   5257 GenBank   WP_001284076
Name   traD_MM000_RS00800_pPJ-T7-250kb 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: 210675..219882

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MM000_RS01185 205784..206500 - 717 WP_000838218 zinc finger-like domain-containing protein -
MM000_RS01190 206497..206697 - 201 WP_000594931 hypothetical protein -
MM000_RS01195 206715..207770 - 1056 WP_065311103 hypothetical protein -
MM000_RS01200 208247..209122 + 876 WP_000594612 RepB family plasmid replication initiator protein -
MM000_RS01205 210271..210624 + 354 WP_000423602 hypothetical protein -
MM000_RS01210 210675..210992 + 318 WP_000043356 type IV conjugative transfer system protein TraL traL
MM000_RS01215 211004..211792 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
MM000_RS01220 211792..213063 + 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
MM000_RS01225 213065..213526 + 462 WP_000521240 plasmid transfer protein HtdO -
MM000_RS01230 213516..214871 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
MM000_RS01235 214879..215361 + 483 WP_065311104 transcriptional regulator -
MM000_RS01240 215480..216232 + 753 WP_183079335 protein-disulfide isomerase HtdT -
MM000_RS01245 216242..217192 + 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
MM000_RS01250 217201..219882 + 2682 WP_000387412 TraC family protein virb4

Host bacterium

ID   7953 GenBank   NZ_OL598600
Plasmid name   pPJ-T7-250kb Incompatibility group   IncHI2
Plasmid size   247477 bp Coordinate of oriT [Strand]   134243..134496 [-]
Host baterium   Salmonella sp. strain PJM1

Cargo genes

Drug resistance gene   floR, aph(6)-Id, tet(A), sul3, aac(3)-IId, blaLAP-2, blaTEM-1B, blaCTX-M-55, qnrS1, mph(A), ARR-3, dfrA14
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -