Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 116776 |
| Name | oriT_pENK22  |
| Organism | Pseudomonas umsongensis strain GO16 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP044408 (36591..37020 [-], 430 nt) |
| oriT length | 430 nt |
| IRs (inverted repeats) | 164..170, 174..180 (GCCGCGC..GCGCGGC) 60..65, 76..81 (GTGTAT..ATACAC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 430 nt
>oriT_pENK22
GGTGTTCCTCTCTGAGCCCAAAATGGGACATATTCAGGCTAACGATAACTGCCGAAACAGTGTATAGCAAATGTAATACACAAAAAGCTTGATTTTGCTGATCTAGACTGTACTTTTGTAATACATATGTATAGCGCATAAAAACACCACTTTTTCTCTGCAGGCCGCGCACAGCGCGGCTGTCACCTCCCGCTAGGGGGGTGCGTATTGTGTATTGAGACTTTGAATTGAGACTTTGACCCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGCCAGGCCGAAGGCCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCTAGAAGAGAGCAGGAAGAGTGCAACTTGACTACAGGTAGGGGGCGAGTAAGATGCACATAGAGTGCAATAGGGGTGCAGATAGGGTGCAAA
GGTGTTCCTCTCTGAGCCCAAAATGGGACATATTCAGGCTAACGATAACTGCCGAAACAGTGTATAGCAAATGTAATACACAAAAAGCTTGATTTTGCTGATCTAGACTGTACTTTTGTAATACATATGTATAGCGCATAAAAACACCACTTTTTCTCTGCAGGCCGCGCACAGCGCGGCTGTCACCTCCCGCTAGGGGGGTGCGTATTGTGTATTGAGACTTTGAATTGAGACTTTGACCCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGCCAGGCCGAAGGCCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCTAGAAGAGAGCAGGAAGAGTGCAACTTGACTACAGGTAGGGGGCGAGTAAGATGCACATAGAGTGCAATAGGGGTGCAGATAGGGTGCAAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 10703 | GenBank | WP_011475370 |
| Name | mobF_F6476_RS00255_pENK22 |
UniProt ID | Q1XGM7 |
| Length | 978 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 978 a.a. Molecular weight: 108592.12 Da Isoelectric Point: 9.9224
>WP_011475370.1 MULTISPECIES: MobF family relaxase [Pseudomonas]
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLAGPIDQKELAKLFDGKLPNGEVMPKT
FDKETGNRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQARRKEHGKSMLERTGN
LIIGKFRHELSRAKDPQLHTHAVVMNATRREDGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGYEIR
VLDKDGNFELAHISRDQIEAFSSRAKVIEEALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVKEYW
VTKARDLGIEFGGRSQLDNQEYGRRSESIHAEHNLPEGITAGQAVVQYAINHLTEREQVVGESDLRTAAL
RRAVGLASPSEVDDEIKRLVKQGTLIESPPTYRMATGKDGAALSPAGWRALLKEQKGWSEKEAQQYVKMA
INRGSLVEAEKRYTTQRALKREKAILAIERSGRGQVAPLLSKEQVAKALESSTLSAGQYQAVEVIVSTSN
RFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERSTTTDAVFRVVALAPYGNQVTALKNEGLDAHTLASF
FHTKDKKLDERTIVVLDEAGVVGARQMEQLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGMQTA
RIKEIQRQKNQELKIAVQHAADGNPGKSLEHVNHVEELREPGQRHQAIVRDYMSLTPQERKEVLIVAGTN
KDRKQINAMTRESLGLVGNGKELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRAGLSRGELYTVDQA
LPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNANGVIE
LASLKEKDGTPERVVALPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSLTTSQNLWYVAISRARHE
ARIYTDSIAGLPAAIANRYDKTTALSLQQARERQRNESIKPRTVLDGKELERKQRSALDGAGLGKSGV
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLAGPIDQKELAKLFDGKLPNGEVMPKT
FDKETGNRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQARRKEHGKSMLERTGN
LIIGKFRHELSRAKDPQLHTHAVVMNATRREDGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGYEIR
VLDKDGNFELAHISRDQIEAFSSRAKVIEEALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVKEYW
VTKARDLGIEFGGRSQLDNQEYGRRSESIHAEHNLPEGITAGQAVVQYAINHLTEREQVVGESDLRTAAL
RRAVGLASPSEVDDEIKRLVKQGTLIESPPTYRMATGKDGAALSPAGWRALLKEQKGWSEKEAQQYVKMA
INRGSLVEAEKRYTTQRALKREKAILAIERSGRGQVAPLLSKEQVAKALESSTLSAGQYQAVEVIVSTSN
RFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERSTTTDAVFRVVALAPYGNQVTALKNEGLDAHTLASF
FHTKDKKLDERTIVVLDEAGVVGARQMEQLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGMQTA
RIKEIQRQKNQELKIAVQHAADGNPGKSLEHVNHVEELREPGQRHQAIVRDYMSLTPQERKEVLIVAGTN
KDRKQINAMTRESLGLVGNGKELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRAGLSRGELYTVDQA
LPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNANGVIE
LASLKEKDGTPERVVALPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSLTTSQNLWYVAISRARHE
ARIYTDSIAGLPAAIANRYDKTTALSLQQARERQRNESIKPRTVLDGKELERKQRSALDGAGLGKSGV
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q1XGM7 |
T4CP
| ID | 12503 | GenBank | WP_011475369 |
| Name | t4cp2_F6476_RS00250_pENK22 |
UniProt ID | _ |
| Length | 519 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 519 a.a. Molecular weight: 58521.92 Da Isoelectric Point: 8.5125
>WP_011475369.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Pseudomonas]
MHKREVDSAVMTAGFGLPIAGWAAGVYFAQMPLTPFPAAFKETLHNGWHNPIVLGATIATSAVAASLVYY
LYEYCDDGFRGEQYQEFLRGSEIKNWHTVKAKVRRRNEKTNRERKKWGLAKSEPIMIGKLPMPLHLEDRN
TMICASIGAGKSVTMEGMIASALKRGDRLAVVDPNGTFYSKFSFKGDSILNPFDERSVGWTIFNEIRGIH
DFNRMAKSIIPPQVDPSDEQWCAYARDVLSDTMRKLKETNNPDQDTLVNLLVREDGDTIRAFLANTDSEG
YFRDNAEKAIASIQFMMNKYIRPLRYMSKGEFSIYKWVNDPNAGNLFITWREDMRDTMKPLVATWIDTIC
ATILSSEPMTGKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF
RNYVILAAANAKNAGMASEILGSHDVKRWRKSYTAGKLTRTEEVTRDEPVVQASEISNLPDLVAYVKFGE
DFPITKVKTPYIDYKERAQAIMLTGQAAA
MHKREVDSAVMTAGFGLPIAGWAAGVYFAQMPLTPFPAAFKETLHNGWHNPIVLGATIATSAVAASLVYY
LYEYCDDGFRGEQYQEFLRGSEIKNWHTVKAKVRRRNEKTNRERKKWGLAKSEPIMIGKLPMPLHLEDRN
TMICASIGAGKSVTMEGMIASALKRGDRLAVVDPNGTFYSKFSFKGDSILNPFDERSVGWTIFNEIRGIH
DFNRMAKSIIPPQVDPSDEQWCAYARDVLSDTMRKLKETNNPDQDTLVNLLVREDGDTIRAFLANTDSEG
YFRDNAEKAIASIQFMMNKYIRPLRYMSKGEFSIYKWVNDPNAGNLFITWREDMRDTMKPLVATWIDTIC
ATILSSEPMTGKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF
RNYVILAAANAKNAGMASEILGSHDVKRWRKSYTAGKLTRTEEVTRDEPVVQASEISNLPDLVAYVKFGE
DFPITKVKTPYIDYKERAQAIMLTGQAAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 5898..16196
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| F6476_RS00015 (F6476_00015) | 1445..2932 | - | 1488 | WP_011475407 | SulP family inorganic anion transporter | - |
| F6476_RS00025 (F6476_00025) | 3451..3747 | - | 297 | WP_011475408 | hypothetical protein | - |
| F6476_RS00030 (F6476_00030) | 3761..4399 | - | 639 | WP_011475409 | hypothetical protein | - |
| F6476_RS00035 (F6476_00035) | 4447..4929 | - | 483 | WP_011475410 | hypothetical protein | - |
| F6476_RS00040 (F6476_00040) | 4944..5549 | - | 606 | WP_011475411 | phospholipase D family protein | - |
| F6476_RS00045 (F6476_00045) | 5539..5868 | - | 330 | WP_011475412 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| F6476_RS00050 (F6476_00050) | 5898..6803 | - | 906 | WP_011475413 | lytic transglycosylase domain-containing protein | virB1 |
| F6476_RS00055 (F6476_00055) | 6787..7815 | - | 1029 | WP_011475414 | P-type DNA transfer ATPase VirB11 | virB11 |
| F6476_RS00060 (F6476_00060) | 7825..9108 | - | 1284 | WP_011475415 | TrbI/VirB10 family protein | virB10 |
| F6476_RS00065 (F6476_00065) | 9111..9902 | - | 792 | WP_011475416 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| F6476_RS00070 (F6476_00070) | 9927..10592 | - | 666 | WP_011475417 | type IV secretion system protein | virB8 |
| F6476_RS00075 (F6476_00075) | 10596..11459 | - | 864 | WP_011475418 | type IV secretion system protein | virB6 |
| F6476_RS00080 (F6476_00080) | 11447..11851 | - | 405 | WP_011475419 | hypothetical protein | - |
| F6476_RS00085 (F6476_00085) | 11844..12056 | - | 213 | WP_011475420 | hypothetical protein | - |
| F6476_RS00090 (F6476_00090) | 12084..12767 | - | 684 | WP_011475421 | type IV secretion system protein | virB5 |
| F6476_RS00095 (F6476_00095) | 12767..15451 | - | 2685 | WP_011475422 | mating pair formation protein MpfC | virb4 |
| F6476_RS00100 (F6476_00100) | 15438..15731 | - | 294 | WP_011475423 | VirB3 family type IV secretion system protein | virB3 |
| F6476_RS00105 (F6476_00105) | 15735..16196 | - | 462 | WP_011475424 | TrbC/VirB2 family protein | virB2 |
| F6476_RS00115 (F6476_00115) | 17134..17907 | + | 774 | WP_011475342 | ParA family protein | - |
| F6476_RS00120 (F6476_00120) | 17918..18844 | + | 927 | WP_011475343 | ParB/RepB/Spo0J family partition protein | - |
| F6476_RS00125 (F6476_00125) | 18841..19188 | + | 348 | WP_011475344 | TrfB-related DNA-binding protein | - |
| F6476_RS00130 (F6476_00130) | 19185..19601 | + | 417 | WP_011475345 | hypothetical protein | - |
| F6476_RS00135 (F6476_00135) | 19869..20516 | + | 648 | WP_011475346 | recombinase family protein | - |
Host bacterium
| ID | 17209 | GenBank | NZ_CP044408 |
| Plasmid name | pENK22 | Incompatibility group | - |
| Plasmid size | 81914 bp | Coordinate of oriT [Strand] | 36591..37020 [-] |
| Host baterium | Pseudomonas umsongensis strain GO16 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | nahAa, nahAb, nahAc, nahAd, nahB, nahF, nahC, nahE, nahD, nahG, nahH, nahI, nahN, nahL, nahO, nahM, nahK, nahJ |
| Symbiosis gene | - |
| Anti-CRISPR | - |