Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107443 |
| Name | oriT_pP9014  |
| Organism | Photobacterium damselae subsp. piscicida |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NC_012919 (15524..15629 [+], 106 nt) |
| oriT length | 106 nt |
| IRs (inverted repeats) | 66..73, 76..83 (CCACCAAC..GTTGGTGG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 106 nt
>oriT_pP9014
AGCCTCGCAGAGCAGGATTCCCGTTGAGCCCGAAGGCGCGAATAAGGGTTAGAGTGAAGTAGCATCCACCAACTTGTTGGTGGGGCTACTTCACCTATCCTGCCCG
AGCCTCGCAGAGCAGGATTCCCGTTGAGCCCGAAGGCGCGAATAAGGGTTAGAGTGAAGTAGCATCCACCAACTTGTTGGTGGGGCTACTTCACCTATCCTGCCCG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4979 | GenBank | WP_086959614 |
| Name | Relaxase_HXC42_RS00060_pP9014 |
UniProt ID | _ |
| Length | 798 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 798 a.a. Molecular weight: 88946.81 Da Isoelectric Point: 10.7477
>WP_086959614.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Gammaproteobacteria]
MIIKHVPMRSAKKSDFSGLVKYITDEQSKTERLGLVNVTNCHANTMQAVIGEVLATQHTNTRATGDKTYH
LIVSFRPGEKPDSDVLKAIEERVCAGLGFSEHQRVSAVHHDTDNVHIHIAINKIHPTNKTMHEPFQAYRK
FGSLSDILENEYGLEKDNHQGFKTVSEGRASDMEKHAGIESLVSWVKRECLEEIRAAENWQQLHQVLSEN
SLEIRKQGNGFVVESADGTQVKASTLARDLSKQKLEKKLGEFEQINNPVPPQDKRRRYEKRPTKFKVNTT
ELYAKYQEEQKQLTAARKIEWINAKGRKDSRIEAAKRKNRLRRAAIKLMGESRLNKKILYSQAHKALKAD
IQAINKANKLERQALYEKYKRRAWADWLKQESLKGNKTALEALRARDKAKALKGDVISGKQKKSSPVNLE
GLNKPNVAPIGKKPPAFAKNRLRSMSSLGAVHFEHKPGYAPVMDNITKKGTIIYRAGKSAIRDDGEKLQI
SREATNEALKNALLLAKERYGSRITVNGSAQFKAQVIFTAATLNLPITFADAGMERRRQDLLNQENNHDR
REQTTGRTERGRSDRPSTSRLGRGITEHTDSGTRTTIANDDRSNTNGADSAPSTSNSVGGANAGNDGGNV
LRKPKPNVTGIGRNPPSIAKNRLRTLSSLSVVRFARRSEMLLPSDVSGQLEHQGTKPDNQLRWGVSGGGR
LNPGEVAVNKYLSERESKRAKGFDIPKHSRYNNQPGAFTYGGIRNVEGQALALLNRGDEVLVLPIDKATA
QRMKRVRIGEAVTVTPQGSLNKSKGRSR
MIIKHVPMRSAKKSDFSGLVKYITDEQSKTERLGLVNVTNCHANTMQAVIGEVLATQHTNTRATGDKTYH
LIVSFRPGEKPDSDVLKAIEERVCAGLGFSEHQRVSAVHHDTDNVHIHIAINKIHPTNKTMHEPFQAYRK
FGSLSDILENEYGLEKDNHQGFKTVSEGRASDMEKHAGIESLVSWVKRECLEEIRAAENWQQLHQVLSEN
SLEIRKQGNGFVVESADGTQVKASTLARDLSKQKLEKKLGEFEQINNPVPPQDKRRRYEKRPTKFKVNTT
ELYAKYQEEQKQLTAARKIEWINAKGRKDSRIEAAKRKNRLRRAAIKLMGESRLNKKILYSQAHKALKAD
IQAINKANKLERQALYEKYKRRAWADWLKQESLKGNKTALEALRARDKAKALKGDVISGKQKKSSPVNLE
GLNKPNVAPIGKKPPAFAKNRLRSMSSLGAVHFEHKPGYAPVMDNITKKGTIIYRAGKSAIRDDGEKLQI
SREATNEALKNALLLAKERYGSRITVNGSAQFKAQVIFTAATLNLPITFADAGMERRRQDLLNQENNHDR
REQTTGRTERGRSDRPSTSRLGRGITEHTDSGTRTTIANDDRSNTNGADSAPSTSNSVGGANAGNDGGNV
LRKPKPNVTGIGRNPPSIAKNRLRTLSSLSVVRFARRSEMLLPSDVSGQLEHQGTKPDNQLRWGVSGGGR
LNPGEVAVNKYLSERESKRAKGFDIPKHSRYNNQPGAFTYGGIRNVEGQALALLNRGDEVLVLPIDKATA
QRMKRVRIGEAVTVTPQGSLNKSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 2281 | GenBank | WP_012774829 |
| Name | WP_012774829_pP9014 |
UniProt ID | A0A510BQP9 |
| Length | 123 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 123 a.a. Molecular weight: 13720.78 Da Isoelectric Point: 7.1664
>WP_012774829.1 MULTISPECIES: conjugal transfer transcriptional regulator TraJ [Pseudomonadota]
MTEEKKVTRKNSTPIKVYCLPDEKELIEAQAARAGMSAARYLREVGQGYHIQGVVDYDQVHELAKINGDL
GRLGGLLKLWLTNDVRTAQFGESTIRAVLSKIEATQEEMGAVMTKIVMPRSEQ
MTEEKKVTRKNSTPIKVYCLPDEKELIEAQAARAGMSAARYLREVGQGYHIQGVVDYDQVHELAKINGDL
GRLGGLLKLWLTNDVRTAQFGESTIRAVLSKIEATQEEMGAVMTKIVMPRSEQ
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A510BQP9 |
T4CP
| ID | 5183 | GenBank | WP_012774826 |
| Name | t4cp2_HXC42_RS00055_pP9014 |
UniProt ID | _ |
| Length | 634 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 634 a.a. Molecular weight: 69997.69 Da Isoelectric Point: 6.8647
>WP_012774826.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Gammaproteobacteria]
MNPKINNAVGPQVRAKKTSKNRTLPALGAVSIAVGLQSATQYFAHSFNYQESLGANINNVYAPWKILNWA
SDWYSNYPNQFMEAASVGMVVTSVGLLGVTITKVVTNNSSKANEYLHGSARWAGKKDIQSAGLLPRNRNL
LEVVTGKDAPSSTGVYVGGWEDEEGNFYYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWAQSAVITDLK
GELWALTAGWRQQYANNKVLRFEPASNYGGIHWNPLDEIRIGTEYEVGDVQNLATLIVDPDGKGMESHWQ
KTAFALLVGVILHALYKAKNEGTPATLPAVDAMLADPERDTGELWMEMATYGHVDGQNHPAVGSAARDMM
DRPEEEGGSVLSTAKSYLALYRDPVVARNVSESEFKIRDLMNHDNPVSLYIVTQPNDKARLRPLVRILVN
MIIRLLADEMTFEKGRPVAHYKHRLLAMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDLNQLKSRET
GYGPDETITSNCHVQNAYPPNRIETAEHLSRLTGQTTVVKEQITTSGRRTSALLGQVSRTIQEVQRPLLT
PDECLRMPGPVKNAKGDIDTAGDMVVYVAGYPAVYGKQPLYFKDPIFLARAQIEAPKVCDKLRVVEQVEE
GIQI
MNPKINNAVGPQVRAKKTSKNRTLPALGAVSIAVGLQSATQYFAHSFNYQESLGANINNVYAPWKILNWA
SDWYSNYPNQFMEAASVGMVVTSVGLLGVTITKVVTNNSSKANEYLHGSARWAGKKDIQSAGLLPRNRNL
LEVVTGKDAPSSTGVYVGGWEDEEGNFYYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWAQSAVITDLK
GELWALTAGWRQQYANNKVLRFEPASNYGGIHWNPLDEIRIGTEYEVGDVQNLATLIVDPDGKGMESHWQ
KTAFALLVGVILHALYKAKNEGTPATLPAVDAMLADPERDTGELWMEMATYGHVDGQNHPAVGSAARDMM
DRPEEEGGSVLSTAKSYLALYRDPVVARNVSESEFKIRDLMNHDNPVSLYIVTQPNDKARLRPLVRILVN
MIIRLLADEMTFEKGRPVAHYKHRLLAMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDLNQLKSRET
GYGPDETITSNCHVQNAYPPNRIETAEHLSRLTGQTTVVKEQITTSGRRTSALLGQVSRTIQEVQRPLLT
PDECLRMPGPVKNAKGDIDTAGDMVVYVAGYPAVYGKQPLYFKDPIFLARAQIEAPKVCDKLRVVEQVEE
GIQI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 5184 | GenBank | WP_012774849 |
| Name | t4cp2_HXC42_RS00165_pP9014 |
UniProt ID | _ |
| Length | 845 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 845 a.a. Molecular weight: 94316.92 Da Isoelectric Point: 6.1869
>WP_012774849.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Gammaproteobacteria]
MIQSISFAIAGFGALLLLILFSRVRAVDAELKLKKHRSKDAGLADLLNYAAVVDDGVVVCKNGAFMASWL
YKGEDNASSTDAQREMVSFRINQALSGLGSGWMVHVDAVRRPSPKYSDRNLSEFPDKISAAIDEERRQLF
EGLGTMYEGYFVLTLTWFPPVLAQRKFVELMFDDDAEIVGKKEQTKGLINQFKREITAIENRLSSAVNLS
RLRGNKITNEDGKTITHDDFLGWLQFCITGLNHPVTLPSNPMYLDAYLGGQEMWGGVVPKVGRKFVQVVA
IEGFPMESYPGVLSALAELPVEYRWSSRFIFMDQHESLRHLDKFRKKWRQKIRGFFDQVFNTNNGTVDQD
ALSMVQDAEAAIAEISSGVVAAGYYTSVVVLMDENRDRLEQSARQVEKSVNRLGFAARTETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTVWTGSNKAPCPMYPSLAPALMNCVTSGSTPFRLNLHVRDLGH
TFMFGPTGAGKSTHLALIAAQLRRYKGMSIYAFDKGMSMYPLTKAVNGLHFSVGADDDRLAFCPLQFLDS
KSDRAWAMEWIDTILALNGVNTTPAQRNEIGNAIQSMYESGARTLSEFSLTIQDENIREAMRQYTVDGAM
GHLLDSEQDGLSLTDFTTFEIEELMNLGEKFALPVLLYLFRRIECSLKGQPSVIILDEAWLMLGHPAFRE
KIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMGLNSRQID
ILATAVPKRQYYYVSENGRRLYDLALGPLALSFVGASDKESVAIIKQLEAKHGETWVDEWLASRGININN
YLEAA
MIQSISFAIAGFGALLLLILFSRVRAVDAELKLKKHRSKDAGLADLLNYAAVVDDGVVVCKNGAFMASWL
YKGEDNASSTDAQREMVSFRINQALSGLGSGWMVHVDAVRRPSPKYSDRNLSEFPDKISAAIDEERRQLF
EGLGTMYEGYFVLTLTWFPPVLAQRKFVELMFDDDAEIVGKKEQTKGLINQFKREITAIENRLSSAVNLS
RLRGNKITNEDGKTITHDDFLGWLQFCITGLNHPVTLPSNPMYLDAYLGGQEMWGGVVPKVGRKFVQVVA
IEGFPMESYPGVLSALAELPVEYRWSSRFIFMDQHESLRHLDKFRKKWRQKIRGFFDQVFNTNNGTVDQD
ALSMVQDAEAAIAEISSGVVAAGYYTSVVVLMDENRDRLEQSARQVEKSVNRLGFAARTETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTVWTGSNKAPCPMYPSLAPALMNCVTSGSTPFRLNLHVRDLGH
TFMFGPTGAGKSTHLALIAAQLRRYKGMSIYAFDKGMSMYPLTKAVNGLHFSVGADDDRLAFCPLQFLDS
KSDRAWAMEWIDTILALNGVNTTPAQRNEIGNAIQSMYESGARTLSEFSLTIQDENIREAMRQYTVDGAM
GHLLDSEQDGLSLTDFTTFEIEELMNLGEKFALPVLLYLFRRIECSLKGQPSVIILDEAWLMLGHPAFRE
KIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMGLNSRQID
ILATAVPKRQYYYVSENGRRLYDLALGPLALSFVGASDKESVAIIKQLEAKHGETWVDEWLASRGININN
YLEAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 28002..38634
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HXC42_RS00125 (pP9014_p23) | 23694..24128 | - | 435 | WP_012774840 | antirestriction protein | - |
| HXC42_RS00130 (pP9014_p24) | 24851..25615 | + | 765 | WP_012774841 | replication initiation protein | - |
| HXC42_RS00135 (pP9014_p25) | 25972..26304 | - | 333 | WP_012774842 | hypothetical protein | - |
| HXC42_RS00140 (pP9014_p26) | 26291..26707 | - | 417 | WP_012774843 | hypothetical protein | - |
| HXC42_RS00145 (pP9014_p28) | 27351..27728 | + | 378 | WP_012774845 | transcriptional regulator | - |
| HXC42_RS00150 (pP9014_p29) | 28002..28991 | + | 990 | WP_012774846 | P-type conjugative transfer ATPase TrbB | virB11 |
| HXC42_RS00155 (pP9014_p30) | 29003..29428 | + | 426 | WP_012774847 | conjugal transfer system pilin TrbC | virB2 |
| HXC42_RS00160 (pP9014_p31) | 29431..29742 | + | 312 | WP_012774848 | conjugal transfer protein TrbD | virB3 |
| HXC42_RS00165 (pP9014_p32) | 29742..32279 | + | 2538 | WP_012774849 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HXC42_RS00170 (pP9014_p33) | 32279..33055 | + | 777 | WP_012774850 | conjugal transfer protein TrbF | virB8 |
| HXC42_RS00175 (pP9014_p34) | 33073..33978 | + | 906 | WP_012774851 | P-type conjugative transfer protein TrbG | virB9 |
| HXC42_RS00180 (pP9014_p35) | 33981..34481 | + | 501 | WP_012774852 | TrbH protein | - |
| HXC42_RS00185 (pP9014_p36) | 34488..35909 | + | 1422 | WP_012774853 | TrbI/VirB10 family protein | virB10 |
| HXC42_RS00190 (pP9014_p37) | 35927..36709 | + | 783 | WP_012774854 | P-type conjugative transfer protein TrbJ | virB5 |
| HXC42_RS00195 (pP9014_p38) | 36715..36942 | + | 228 | WP_086959606 | entry exclusion lipoprotein TrbK | - |
| HXC42_RS00200 (pP9014_p39) | 36952..38634 | + | 1683 | WP_012774856 | P-type conjugative transfer protein TrbL | virB6 |
| HXC42_RS00205 | 38651..39148 | + | 498 | WP_086959604 | conjugal transfer protein TraL | - |
| HXC42_RS00210 (pP9014_p40) | 39160..39774 | + | 615 | WP_012774857 | transglycosylase SLT domain-containing protein | - |
| HXC42_RS00215 (pP9014_p41) | 39785..40513 | + | 729 | WP_165761827 | TraX family protein | - |
| HXC42_RS00220 (pP9014_p42) | 40591..40983 | + | 393 | WP_237306416 | OmpA family protein | - |
| HXC42_RS00225 (pP9014_p43) | 41003..41245 | + | 243 | WP_012774860 | hypothetical protein | - |
| HXC42_RS00230 (pP9014_p44) | 41330..41755 | - | 426 | Protein_45 | Tn3 family transposase | - |
| HXC42_RS00235 (pP9014_p45) | 41811..42515 | - | 705 | WP_001067855 | IS6-like element IS26 family transposase | - |
| HXC42_RS00240 (pP9014_p46) | 42527..43183 | - | 657 | WP_000113282 | tetracycline resistance transcriptional repressor TetR(D) | - |
Host bacterium
| ID | 7878 | GenBank | NC_012919 |
| Plasmid name | pP9014 | Incompatibility group | - |
| Plasmid size | 55851 bp | Coordinate of oriT [Strand] | 15524..15629 [+] |
| Host baterium | Photobacterium damselae subsp. piscicida |
Cargo genes
| Drug resistance gene | tet(D), catA2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |