Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107424 |
| Name | oriT_pP6VIM-11  |
| Organism | Pseudomonas aeruginosa strain C6 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_MW300275 (48487..48583 [+], 97 nt) |
| oriT length | 97 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: 97 nt
>oriT_pP6VIM-11
GAATAAGGGACAGCGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCGCCTATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTA
GAATAAGGGACAGCGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCGCCTATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4961 | GenBank | WP_031943002 |
| Name | Relaxase_JYH28_RS00240_pP6VIM-11 |
UniProt ID | _ |
| Length | 752 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 752 a.a. Molecular weight: 83052.85 Da Isoelectric Point: 10.7938
>WP_031943002.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIVKHVPMRSLGKSDFAGLVNYVTDAQSKDHRLGQVQITNCDAVSVQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSVDTLRAIEERICAGLGFAEHQRVSAVHNDTDNLHIHIAINKIHPTRHTMHEPFGQHRT
LAELCVALERDYGLERDNHEPRQRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARFGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTVTRGQALEQARRRKDRLVEAAKRSNRLRRATIKVIGESGPNKKLLYAQASKALRDE
IQAINKQYQQDRQALYDSHSRRTWADWLKKEATHGNAEALTALRAREAAQGLQGNTIQGRGDARPGHAPV
TDNITKKGTIIFRAGLSAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFKAQVIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTERADQRPAEHRGRTGRGPGGPGQRAAAHDDAARPVAVA
RAGFGRPGAGRTDAAGVHAGAVHRKPDVGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVPRHL
EQQGTQPDHQLRRGISRPGTGVAAAPQGLAAVDKYIAEREAKRSKGFDIPKHARYTDGDGALAFQGVRNI
EGQALALLKRGDEVMVMPIDQATARRLSRIAVGDAVTITPKGSIKTSKGRSR
MIVKHVPMRSLGKSDFAGLVNYVTDAQSKDHRLGQVQITNCDAVSVQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSVDTLRAIEERICAGLGFAEHQRVSAVHNDTDNLHIHIAINKIHPTRHTMHEPFGQHRT
LAELCVALERDYGLERDNHEPRQRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARFGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTVTRGQALEQARRRKDRLVEAAKRSNRLRRATIKVIGESGPNKKLLYAQASKALRDE
IQAINKQYQQDRQALYDSHSRRTWADWLKKEATHGNAEALTALRAREAAQGLQGNTIQGRGDARPGHAPV
TDNITKKGTIIFRAGLSAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFKAQVIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTERADQRPAEHRGRTGRGPGGPGQRAAAHDDAARPVAVA
RAGFGRPGAGRTDAAGVHAGAVHRKPDVGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVPRHL
EQQGTQPDHQLRRGISRPGTGVAAAPQGLAAVDKYIAEREAKRSKGFDIPKHARYTDGDGALAFQGVRNI
EGQALALLKRGDEVMVMPIDQATARRLSRIAVGDAVTITPKGSIKTSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 2275 | GenBank | WP_011013290 |
| Name | WP_011013290_pP6VIM-11 |
UniProt ID | A0A7T2VWC8 |
| Length | 123 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 123 a.a. Molecular weight: 13936.01 Da Isoelectric Point: 8.4443
>WP_011013290.1 MULTISPECIES: conjugal transfer transcriptional regulator TraJ [Pseudomonadota]
MEADEQPTAKRRQHLRVPVFPEEKELIEANAKRAGVSVARYLRDVGQGYQIKGVMDYEYVRELVRVNGDL
GRLGGLLKLWLTDDPRTARFGDATILALLGRIEATQDEMSRLMKSVVQPRAEP
MEADEQPTAKRRQHLRVPVFPEEKELIEANAKRAGVSVARYLRDVGQGYQIKGVMDYEYVRELVRVNGDL
GRLGGLLKLWLTDDPRTARFGDATILALLGRIEATQDEMSRLMKSVVQPRAEP
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A7T2VWC8 |
T4CP
| ID | 5163 | GenBank | WP_031942981 |
| Name | t4cp2_JYH28_RS00020_pP6VIM-11 |
UniProt ID | _ |
| Length | 852 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 852 a.a. Molecular weight: 94169.09 Da Isoelectric Point: 6.3231
>WP_031942981.1 VirB4 family type IV secretion/conjugal transfer ATPase [Pseudomonas aeruginosa]
MIEAIAIGIAVLGAVLLLILFARIRQVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YQGDDNASSTEEQREMVSFRINQALAGLGSGWMVHVDAVRRPAPNYSERGVSTFTDPVSAAIDEERRRLF
EGLGTMYEGHFVFAVTWFPPVLAQRKFVELMFDDDAVTPDHTARTVGLIEQFKREIRSLESRLSSAVKLT
RLQGHKMATEEGREVTHDDFLSWLQFCVTGNYHPVQLPSNPMYLDAVIGGQELWGGVVPKIGRKFIQVVS
LEGFPLESTPGLLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSVNQD
AATMVADAEAAIAEVNSGLVAAGYFTSVVVLMDEDRERLAASALSVEKAINRLAFAARIETINTMDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLAPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAAINAGSKGKTGLHFTVAADDDRLAFC
PLQFLETKADRAWAMEWIDTILALNGVDTTPGQRNEIGHAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERGLRGQPAVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMG
LNKRQIEILATAVPKRQYYYVSENGRRLYDLALGPLALAFVGASDKESVAAIKSLQAKFGHEWVDHWLAG
RNLNLNDYLEAA
MIEAIAIGIAVLGAVLLLILFARIRQVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YQGDDNASSTEEQREMVSFRINQALAGLGSGWMVHVDAVRRPAPNYSERGVSTFTDPVSAAIDEERRRLF
EGLGTMYEGHFVFAVTWFPPVLAQRKFVELMFDDDAVTPDHTARTVGLIEQFKREIRSLESRLSSAVKLT
RLQGHKMATEEGREVTHDDFLSWLQFCVTGNYHPVQLPSNPMYLDAVIGGQELWGGVVPKIGRKFIQVVS
LEGFPLESTPGLLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSVNQD
AATMVADAEAAIAEVNSGLVAAGYFTSVVVLMDEDRERLAASALSVEKAINRLAFAARIETINTMDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLAPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAAINAGSKGKTGLHFTVAADDDRLAFC
PLQFLETKADRAWAMEWIDTILALNGVDTTPGQRNEIGHAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERGLRGQPAVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMG
LNKRQIEILATAVPKRQYYYVSENGRRLYDLALGPLALAFVGASDKESVAAIKSLQAKFGHEWVDHWLAG
RNLNLNDYLEAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 5164 | GenBank | WP_031943001 |
| Name | t4cp2_JYH28_RS00235_pP6VIM-11 |
UniProt ID | _ |
| Length | 634 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 634 a.a. Molecular weight: 69614.63 Da Isoelectric Point: 8.5000
>WP_031943001.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKIKMNNAVGPQVRSAKPKTPKLLPILGGVSLVGGLQAATQFFAYTFQYHASLGANLGHVYAPWSILNWS
AKWYSQYPDEIMRAGSIGMVTATVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKDAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSSGGVCWNPLDEIRVGTEAEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKARNDGGTATLPSVDAMLADPNRDIGELWMEMTTYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARSVSRSDFRIKDLMHSDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLRSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNDKGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFQARASIPAPKATDRLRQVVEAGE
GITI
MKIKMNNAVGPQVRSAKPKTPKLLPILGGVSLVGGLQAATQFFAYTFQYHASLGANLGHVYAPWSILNWS
AKWYSQYPDEIMRAGSIGMVTATVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKDAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSSGGVCWNPLDEIRVGTEAEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKARNDGGTATLPSVDAMLADPNRDIGELWMEMTTYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARSVSRSDFRIKDLMHSDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLRSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNDKGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFQARASIPAPKATDRLRQVVEAGE
GITI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 152..10767
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| JYH28_RS00005 | 152..1117 | + | 966 | WP_031942980 | P-type conjugative transfer ATPase TrbB | virB11 |
| JYH28_RS00010 | 1139..1603 | + | 465 | WP_011013262 | conjugal transfer system pilin TrbC | virB2 |
| JYH28_RS00015 | 1607..1918 | + | 312 | WP_011013263 | conjugal transfer protein TrbD | virB3 |
| JYH28_RS00020 | 1915..4473 | + | 2559 | WP_031942981 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| JYH28_RS00025 | 4470..5258 | + | 789 | WP_031942982 | conjugal transfer protein TrbF | virB8 |
| JYH28_RS00030 | 5276..6169 | + | 894 | WP_014386236 | P-type conjugative transfer protein TrbG | virB9 |
| JYH28_RS00035 | 6172..6633 | + | 462 | WP_031942983 | lipoprotein | - |
| JYH28_RS00040 | 6637..8022 | + | 1386 | WP_031942984 | TrbI/VirB10 family protein | virB10 |
| JYH28_RS00045 | 8039..8812 | + | 774 | WP_031942985 | P-type conjugative transfer protein TrbJ | virB5 |
| JYH28_RS00050 | 8822..9043 | + | 222 | WP_011255136 | entry exclusion lipoprotein TrbK | - |
| JYH28_RS00055 | 9055..10767 | + | 1713 | WP_031942986 | P-type conjugative transfer protein TrbL | virB6 |
| JYH28_RS00060 | 10786..11364 | + | 579 | WP_031942987 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| JYH28_RS00065 | 11366..12001 | + | 636 | WP_031942988 | transglycosylase SLT domain-containing protein | - |
| JYH28_RS00070 | 12031..12300 | + | 270 | WP_031942989 | hypothetical protein | - |
| JYH28_RS00075 | 12297..12995 | + | 699 | WP_031942990 | TraX family protein | - |
| JYH28_RS00080 | 13010..13477 | + | 468 | WP_031942991 | OmpA family protein | - |
| JYH28_RS00085 | 13580..13996 | + | 417 | WP_204884856 | hypothetical protein | - |
| JYH28_RS00090 | 14125..14799 | + | 675 | WP_031942993 | DNA methylase | - |
| JYH28_RS00095 | 14890..15399 | + | 510 | WP_031942994 | hypothetical protein | - |
Host bacterium
| ID | 7859 | GenBank | NZ_MW300275 |
| Plasmid name | pP6VIM-11 | Incompatibility group | IncP1 |
| Plasmid size | 61183 bp | Coordinate of oriT [Strand] | 48487..48583 [+] |
| Host baterium | Pseudomonas aeruginosa strain C6 |
Cargo genes
| Drug resistance gene | blaVIM-11, aadA1, sul1 |
| Virulence gene | - |
| Metal resistance gene | merE, merD, merA, merP, merT, merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |