Detailed information of oriT
oriT
The information of the oriT region
oriTDB ID | 120467 |
Name | oriT_p565_1 |
Organism | Citrobacter freundii strain 565 |
Sequence Completeness | - |
NCBI accession of oriT (coordinates [strand]) | NZ_CP038657 (180713..180967 [+], 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_p565_1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure fileRelaxase
ID | 12889 | GenBank | WP_012477394 |
Name | mobH_E4177_RS26355_p565_1 | UniProt ID | A0A2Z2E7B6 |
Length | 1050 a.a. | PDB ID | |
Note | Predicted by oriTfinder 2.0 |
Relaxase protein sequence
Download Length: 1050 a.a. Molecular weight: 118067.47 Da Isoelectric Point: 4.6347
>WP_012477394.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDVITKITDT
VETAVLKVNDLGRSSASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDTTMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEKEDEEHEIIDYTDFSQLSVSRPEVG
SCATSSSVHNEKLLSEPSELPELNREQNADPQGTNERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFASTESDQNGEFSLISEGDVTELEFVEIALVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDVITKITDT
VETAVLKVNDLGRSSASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDTTMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEKEDEEHEIIDYTDFSQLSVSRPEVG
SCATSSSVHNEKLLSEPSELPELNREQNADPQGTNERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFASTESDQNGEFSLISEGDVTELEFVEIALVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL
Protein domains
Predicted by InterproScan.
Protein structure
Source | ID | Structure |
---|---|---|
AlphaFold DB | A0A2Z2E7B6 |
T4CP
ID | 15138 | GenBank | WP_001284073 |
Name | traD_E4177_RS26350_p565_1 | 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
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANDTLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 86351..95591
Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
---|---|---|---|---|---|---|
E4177_RS27035 | 83641..83802 | - | 162 | WP_001371949 | hypothetical protein | - |
E4177_RS25855 (E4177_26575) | 86351..89032 | - | 2682 | WP_000387412 | TraC family protein | virb4 |
E4177_RS25860 (E4177_26580) | 89041..89991 | - | 951 | WP_001022588 | IncHI-type conjugal transfer lipoprotein TrhV | traV |
E4177_RS25865 (E4177_26585) | 90001..90753 | - | 753 | WP_182911723 | protein-disulfide isomerase HtdT | - |
E4177_RS25870 (E4177_26590) | 90872..91354 | - | 483 | WP_000377632 | hypothetical protein | - |
E4177_RS25875 (E4177_26595) | 91362..92717 | - | 1356 | WP_000351841 | IncHI-type conjugal transfer protein TrhB | traB |
E4177_RS25880 (E4177_26600) | 92707..93168 | - | 462 | WP_000521242 | plasmid transfer protein HtdO | - |
E4177_RS25885 (E4177_26605) | 93170..94441 | - | 1272 | WP_000592092 | type-F conjugative transfer system secretin TraK | traK |
E4177_RS25890 (E4177_26610) | 94441..95229 | - | 789 | WP_000783153 | TraE/TraK family type IV conjugative transfer system protein | traE |
E4177_RS25895 (E4177_26615) | 95241..95591 | - | 351 | WP_001447770 | type IV conjugative transfer system protein TraL | traL |
E4177_RS25900 (E4177_26620) | 95609..95962 | - | 354 | WP_000423602 | hypothetical protein | - |
E4177_RS25905 (E4177_26630) | 97111..97986 | - | 876 | WP_000594611 | RepB family plasmid replication initiator protein | - |
E4177_RS25910 (E4177_26635) | 98463..99515 | + | 1053 | WP_001065778 | hypothetical protein | - |
E4177_RS25915 (E4177_26640) | 99535..99735 | + | 201 | WP_000594930 | hypothetical protein | - |
E4177_RS25920 (E4177_26645) | 99732..100448 | + | 717 | WP_000838219 | zinc finger-like domain-containing protein | - |
Host bacterium
ID | 20896 | GenBank | NZ_CP038657 |
Plasmid name | p565_1 | Incompatibility group | IncHI2A |
Plasmid size | 263189 bp | Coordinate of oriT [Strand] | 180713..180967 [+] |
Host baterium | Citrobacter freundii strain 565 |
Cargo genes
Drug resistance gene | sul1, qacE, ant(3'')-Ia, aac(6')-Ib-cr, blaVIM-1, mcr-9, blaCTX-M-9, aadA2, dfrA16, catA1, blaSHV-12, qnrA1 |
Virulence gene | - |
Metal resistance gene | terE, terD, terC, terB, terA, terZ, terW, arsH, arsR, arsB, arsC, rcnR/yohL, ncrC, pcoE, pcoS |
Degradation gene | - |
Symbiosis gene | - |
Anti-CRISPR | - |