Detailed information of oriT
oriT
The information of the oriT region
oriTDB ID | 107523 |
Name | oriT_pPJ-T16-250kb |
Organism | Salmonella sp. strain PJM1 |
Sequence Completeness | - |
NCBI accession of oriT (coordinates [strand]) | NZ_OL598601 (84941..85194 [-], 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-T16-250kb
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure fileRelaxase
ID | 5047 | GenBank | WP_000980119 |
Name | mobH_MM051_RS00515_pPJ-T16-250kb | 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
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDT
VETAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVG
SCATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL
Protein domains
Predicted by InterproScan.
Protein structure
Source | ID | Structure |
---|---|---|
AlphaFold DB | A0A0H3VVI8 |
T4CP
ID | 5266 | GenBank | WP_001284076 |
Name | traD_MM051_RS00520_pPJ-T16-250kb | 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
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANETLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 161369..170576
Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
---|---|---|---|---|---|---|
MM051_RS00900 | 156478..157194 | - | 717 | WP_000838218 | zinc finger-like domain-containing protein | - |
MM051_RS00905 | 157191..157391 | - | 201 | WP_000594931 | hypothetical protein | - |
MM051_RS00910 | 157409..158464 | - | 1056 | WP_065311103 | hypothetical protein | - |
MM051_RS00915 | 158941..159816 | + | 876 | WP_000594612 | RepB family plasmid replication initiator protein | - |
MM051_RS00920 | 160965..161318 | + | 354 | WP_000423602 | hypothetical protein | - |
MM051_RS00925 | 161369..161686 | + | 318 | WP_000043356 | type IV conjugative transfer system protein TraL | traL |
MM051_RS00930 | 161698..162486 | + | 789 | WP_000783153 | TraE/TraK family type IV conjugative transfer system protein | traE |
MM051_RS00935 | 162486..163757 | + | 1272 | WP_000592090 | type-F conjugative transfer system secretin TraK | traK |
MM051_RS00940 | 163759..164220 | + | 462 | WP_000521240 | plasmid transfer protein HtdO | - |
MM051_RS00945 | 164210..165565 | + | 1356 | WP_000351841 | IncHI-type conjugal transfer protein TrhB | traB |
MM051_RS00950 | 165573..166055 | + | 483 | WP_065311104 | transcriptional regulator | - |
MM051_RS00955 | 166174..166926 | + | 753 | WP_183079335 | protein-disulfide isomerase HtdT | - |
MM051_RS00960 | 166936..167886 | + | 951 | WP_001022587 | IncHI-type conjugal transfer lipoprotein TrhV | traV |
MM051_RS00965 | 167895..170576 | + | 2682 | WP_000387412 | TraC family protein | virb4 |
Host bacterium
ID | 7958 | GenBank | NZ_OL598601 |
Plasmid name | pPJ-T16-250kb | Incompatibility group | IncHI2 |
Plasmid size | 247473 bp | Coordinate of oriT [Strand] | 84941..85194 [-] |
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 | - |