Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 106323 |
| Name | oriT_Ery-6A|unnamed1  |
| Organism | Delftia tsuruhatensis strain Ery-6A |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP120957 (32806..32904 [+], 99 nt) |
| oriT length | 99 nt |
| IRs (inverted repeats) | 24..31, 34..41 (TAACCGGC..GCCGGTTA) |
| Location of nic site | 60..61 |
| Conserved sequence flanking the nic site |
TCCTGCCCGC |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 99 nt
>oriT_Ery-6A|unnamed1
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4229 | GenBank | WP_011222100 |
| Name | Relaxase_PYR84_RS30085_Ery-6A|unnamed1 |
UniProt ID | A0A0K6ICB3 |
| Length | 746 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 746 a.a. Molecular weight: 82170.86 Da Isoelectric Point: 10.7900
>WP_011222100.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMREN
GLELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTVKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARGQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGSADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPPADQHATGAAAVARAGDGRPA
AGRGDRADAGIHAANVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVVAADKYIAEREAKRLKGFDIPKHSRYTAGEGALTFQGTRNVEGQPLA
LLKRGEEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMREN
GLELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTVKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARGQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGSADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPPADQHATGAAAVARAGDGRPA
AGRGDRADAGIHAANVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVVAADKYIAEREAKRLKGFDIPKHSRYTAGEGALTFQGTRNVEGQPLA
LLKRGEEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A0K6ICB3 |
T4CP
| ID | 4250 | GenBank | WP_011114047 |
| Name | t4cp2_PYR84_RS29950_Ery-6A|unnamed1 |
UniProt ID | _ |
| Length | 852 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 852 a.a. Molecular weight: 93980.15 Da Isoelectric Point: 6.3901
>WP_011114047.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Bacteria]
MIEAIAIAIAVLGAVLLLILFARIRAVDAELKLKKHRAKDAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YKGDDNASSTEEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERGVSSFPDSVSFAIDEERRRLF
EGLGAMFEGYFVLTVTWFPPVLAQRKFVELMFDDDAVAPDHTARTTGLIAQFKREITSLESRLSSAVKMT
RLRGQKVVSEEGREVTHDDFLSWLQFCVTGLHHPVMLPSNPMYLDAVIGGQELWGGVVPKIGRKFIQVVA
IEGFPLESTPGVLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSINQD
AAAMVGDAEAAIAEVNSGLVAAGYYTSVVVLMDEDRERLAASALLVEKAVNRLAFAARIETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLSPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAGIRAATKGKSGLHFTVAADDDRLAFC
PLQFLETKGDRAWAMEWIDTILALNGVNTTPAQRNEIGNAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERALKGQPSVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMG
LNARQIEILATAIPKRQYYYVSENGRRLYDLALGPMALAFVGASDKESVATIKSLEAKFGHEWVHEWLAG
RGLNLNDYLEAA
MIEAIAIAIAVLGAVLLLILFARIRAVDAELKLKKHRAKDAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YKGDDNASSTEEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERGVSSFPDSVSFAIDEERRRLF
EGLGAMFEGYFVLTVTWFPPVLAQRKFVELMFDDDAVAPDHTARTTGLIAQFKREITSLESRLSSAVKMT
RLRGQKVVSEEGREVTHDDFLSWLQFCVTGLHHPVMLPSNPMYLDAVIGGQELWGGVVPKIGRKFIQVVA
IEGFPLESTPGVLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSINQD
AAAMVGDAEAAIAEVNSGLVAAGYYTSVVVLMDEDRERLAASALLVEKAVNRLAFAARIETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLSPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAGIRAATKGKSGLHFTVAADDDRLAFC
PLQFLETKGDRAWAMEWIDTILALNGVNTTPAQRNEIGNAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERALKGQPSVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMG
LNARQIEILATAIPKRQYYYVSENGRRLYDLALGPMALAFVGASDKESVATIKSLEAKFGHEWVHEWLAG
RGLNLNDYLEAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 4251 | GenBank | WP_011222099 |
| Name | t4cp2_PYR84_RS30080_Ery-6A|unnamed1 |
UniProt ID | _ |
| Length | 637 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 637 a.a. Molecular weight: 69911.12 Da Isoelectric Point: 8.2993
>WP_011222099.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDEGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQAET
EGEGITI
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDEGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQAET
EGEGITI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 1..10690
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PYR84_RS29935 (PYR84_29935) | 1..963 | + | 963 | WP_000132020 | P-type conjugative transfer ATPase TrbB | virB11 |
| PYR84_RS29940 (PYR84_29940) | 980..1444 | + | 465 | WP_011114046 | conjugal transfer system pilin TrbC | virB2 |
| PYR84_RS29945 (PYR84_29945) | 1448..1759 | + | 312 | WP_001207961 | conjugal transfer protein TrbD | virB3 |
| PYR84_RS29950 (PYR84_29950) | 1756..4314 | + | 2559 | WP_011114047 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| PYR84_RS29955 (PYR84_29955) | 4311..5093 | + | 783 | WP_006122481 | conjugal transfer protein TrbF | virB8 |
| PYR84_RS29960 (PYR84_29960) | 5111..6010 | + | 900 | WP_006122480 | P-type conjugative transfer protein TrbG | virB9 |
| PYR84_RS29965 (PYR84_29965) | 6013..6501 | + | 489 | WP_006122479 | conjugal transfer protein TrbH | - |
| PYR84_RS29970 (PYR84_29970) | 6506..7927 | + | 1422 | WP_087864351 | TrbI/VirB10 family protein | virB10 |
| PYR84_RS29975 (PYR84_29975) | 7948..8712 | + | 765 | WP_011222084 | P-type conjugative transfer protein TrbJ | virB5 |
| PYR84_RS29980 (PYR84_29980) | 8722..8949 | + | 228 | WP_011222085 | entry exclusion lipoprotein TrbK | - |
| PYR84_RS29985 (PYR84_29985) | 8960..10690 | + | 1731 | WP_011222086 | P-type conjugative transfer protein TrbL | virB6 |
| PYR84_RS29990 (PYR84_29990) | 10708..11295 | + | 588 | WP_011222087 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| PYR84_RS29995 (PYR84_29995) | 11309..11944 | + | 636 | WP_011222088 | transglycosylase SLT domain-containing protein | - |
| PYR84_RS30000 (PYR84_30000) | 11973..12239 | + | 267 | WP_010890140 | hypothetical protein | - |
| PYR84_RS30005 (PYR84_30005) | 12239..12937 | + | 699 | WP_011222089 | TraX family protein | - |
| PYR84_RS30010 (PYR84_30010) | 12953..13384 | + | 432 | WP_011222090 | OmpA family protein | - |
| PYR84_RS30015 (PYR84_30015) | 13539..14213 | + | 675 | WP_011222091 | site-specific DNA-methyltransferase | - |
| PYR84_RS30020 (PYR84_30020) | 14215..14970 | - | 756 | WP_277849950 | recombinase family protein | - |
| PYR84_RS30025 (PYR84_30025) | 15091..15339 | + | 249 | WP_011191340 | type II toxin-antitoxin system YafQ family toxin | - |
Host bacterium
| ID | 6760 | GenBank | NZ_CP120957 |
| Plasmid name | Ery-6A|unnamed1 | Incompatibility group | IncP1 |
| Plasmid size | 51319 bp | Coordinate of oriT [Strand] | 32806..32904 [+] |
| Host baterium | Delftia tsuruhatensis strain Ery-6A |
Cargo genes
| Drug resistance gene | mph(F) |
| Virulence gene | - |
| Metal resistance gene | merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |