Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115461
Name   oriT_pPJM1 in_silico
Organism   Salmonella sp. strain PJM1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MN539017 (188626..188879 [-], 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_pPJM1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9902 GenBank   WP_001011151
Name   mobH_H5E24_RS00980_pPJM1 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   11542 GenBank   WP_001284076
Name   traD_H5E24_RS00985_pPJM1 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: 28990..38197

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5E24_RS00100 (NPGAP_22530) 24099..24815 - 717 WP_000838218 zinc finger-like domain-containing protein -
H5E24_RS00105 (NPGAP_22535) 24812..25012 - 201 WP_000594931 hypothetical protein -
H5E24_RS00110 (NPGAP_22540) 25030..26085 - 1056 WP_065311103 hypothetical protein -
H5E24_RS00115 (NPGAP_22545) 26562..27437 + 876 WP_000594612 RepB family plasmid replication initiator protein -
H5E24_RS00120 (NPGAP_22555) 28586..28939 + 354 WP_000423602 hypothetical protein -
H5E24_RS00125 (NPGAP_22560) 28990..29307 + 318 WP_000043356 type IV conjugative transfer system protein TraL traL
H5E24_RS00130 (NPGAP_22565) 29319..30107 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
H5E24_RS00135 (NPGAP_22570) 30107..31378 + 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
H5E24_RS00140 (NPGAP_22575) 31380..31841 + 462 WP_000521240 plasmid transfer protein HtdO -
H5E24_RS00145 (NPGAP_22580) 31831..33186 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
H5E24_RS00150 (NPGAP_22585) 33194..33676 + 483 WP_065311104 transcriptional regulator -
H5E24_RS00155 (NPGAP_22590) 33795..34547 + 753 WP_183079335 protein-disulfide isomerase HtdT -
H5E24_RS00160 (NPGAP_22595) 34557..35507 + 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
H5E24_RS00165 (NPGAP_22600) 35516..38197 + 2682 WP_000387412 TraC family protein virb4
H5E24_RS01270 38820..38975 + 156 WP_220182447 hypothetical protein -
H5E24_RS01275 39069..39230 + 162 WP_001426357 hypothetical protein -
H5E24_RS01280 39576..39731 + 156 WP_220182447 hypothetical protein -
H5E24_RS01285 39825..39986 + 162 WP_001426357 hypothetical protein -
H5E24_RS01290 40332..40478 + 147 WP_172692801 hypothetical protein -
H5E24_RS01295 40571..40726 + 156 WP_181710366 hypothetical protein -
H5E24_RS01300 41780..41935 + 156 WP_181710363 hypothetical protein -
H5E24_RS01310 42029..42154 + 126 WP_258558355 hypothetical protein -

Host bacterium

ID   15894 GenBank   NZ_MN539017
Plasmid name   pPJM1 Incompatibility group   IncHI2
Plasmid size   236068 bp Coordinate of oriT [Strand]   188626..188879 [-]
Host baterium   Salmonella sp. strain PJM1

Cargo genes

Drug resistance gene   aph(3')-Ia, 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   -