Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103750
Name   oriT_R478 in_silico
Organism   Serratia marcescens
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_005211 (190388..190642 [-], 255 nt)
oriT length   255 nt
IRs (inverted repeats)      153..158, 160..165  (AAAAGT..ACTTTT)
 122..130, 135..143  (TTAAGGCTT..AAGCCTTAA)
 49..55, 60..66  (GAATTTT..AAAATTC)
Location of nic site      78..79
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 255 nt

>oriT_R478
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2782 GenBank   WP_001447828
Name   mobH_HXG62_RS00985_R478 insolico UniProt ID   Q6MXI7
Length   1050 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1050 a.a.        Molecular weight: 118097.49 Da        Isoelectric Point: 4.6347

>WP_001447828.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDVITKITDT
VETAVLKVNDLGRSSASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDTTMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEKEDEEHEIIDYTDFSQLSVSRPEVG
SCATSSSVHNEKLLSEPSELPELNREQNADPQGTNERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAT
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFASTESDQNGEFSLISEGDVTELEFVEIALVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(108-304)


  Protein structure


Source ID Structure
AlphaFold DB Q6MXI7


T4CP

ID   2610 GenBank   WP_001284073
Name   traD_HXG62_RS00990_R478 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: 78123.91 Da        Isoelectric Point: 8.0177

>WP_001284073.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANDTLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH

  Protein domains


Predicted by InterproScan.

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

(406-609)

AAA-like domain (AAA_10)

(199-249)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2429..11636

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXG62_RS00005 (SMR0001) 1..876 + 876 WP_000594611 RepB family plasmid replication initiator protein -
HXG62_RS00010 (SMR0004) 2025..2378 + 354 WP_000423602 hypothetical protein -
HXG62_RS00015 (SMR0005) 2396..2746 + 351 WP_001447770 type IV conjugative transfer system protein TraL -
HXG62_RS00020 (SMR0006) 2758..3546 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
HXG62_RS00025 (SMR0007) 3546..4817 + 1272 WP_000592092 type-F conjugative transfer system secretin TraK traK
HXG62_RS00030 (SMR0008) 4819..5280 + 462 WP_000521242 plasmid transfer protein HtdO -
HXG62_RS00035 (SMR0009) 5270..6625 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
HXG62_RS00040 (SMR0010) 6633..7115 + 483 WP_000377632 hypothetical protein -
HXG62_RS00045 (SMR0011) 7234..7986 + 753 WP_182911723 protein-disulfide isomerase HtdT -
HXG62_RS00050 (SMR0012) 7996..8946 + 951 WP_001022588 IncHI-type conjugal transfer lipoprotein TrhV traV
HXG62_RS00055 (SMR0013) 8955..11636 + 2682 WP_000387412 TraC family protein virb4

Host bacterium

ID   4190 GenBank   NC_005211
Plasmid name   R478 Incompatibility group   IncHI2A
Plasmid size   274762 bp Coordinate of oriT [Strand]   190388..190642 [-]
Host baterium   Serratia marcescens

Cargo genes

Drug resistance gene   catA1, aph(3')-Ia, tet(B)
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE, merE, merD, merA, merC, merP, merT, merR, silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsC, arsB, arsR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -