Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113916 |
| Name | oriT_pPHE101  |
| Organism | Pseudomonas thivervalensis strain P101 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_MH061178 (26203..26629 [-], 427 nt) |
| oriT length | 427 nt |
| IRs (inverted repeats) | 164..170, 174..180 (GCCGCGC..GCGCGGC) 123..128, 142..147 (GCAATT..AATTGC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 427 nt
>oriT_pPHE101
GGTGGTCCTCTCTGAGCCGAAATTGACGCATTTTCACAGATACAATATCGGTCCGAACCGCGTATAGCAAATGTAATACAAAAAAAGCTTGATTTTGCTGGTCTAGATGGTACTTTTGTATAGCAATTGTATAGCGTAAGAAATTGCATGGATTTCGCTGTAGGCCGCGCTCTGCGCGGCTTGCGCCTCCCGCTAGGGGGGTGCGTGATGTGTATTGAGATTTTGACCCTGTTAAGGGGAAAAATCGAAGCTCTTGTTAAGGGCGTATCCACTGTTTAGGCCGAAGGCCGTAGGGTGGTATGCAGAAAGGGTGCAGGAAGGGTGCAGGAAGGGTGCTACAAGAGTGCAAGAGCAGTGCAACTTGACTACAGGTAGGGGGCAGGTAAGATGCACATAGAGTGCAACAGGGGTGCAGGTAGGGTGCAAA
GGTGGTCCTCTCTGAGCCGAAATTGACGCATTTTCACAGATACAATATCGGTCCGAACCGCGTATAGCAAATGTAATACAAAAAAAGCTTGATTTTGCTGGTCTAGATGGTACTTTTGTATAGCAATTGTATAGCGTAAGAAATTGCATGGATTTCGCTGTAGGCCGCGCTCTGCGCGGCTTGCGCCTCCCGCTAGGGGGGTGCGTGATGTGTATTGAGATTTTGACCCTGTTAAGGGGAAAAATCGAAGCTCTTGTTAAGGGCGTATCCACTGTTTAGGCCGAAGGCCGTAGGGTGGTATGCAGAAAGGGTGCAGGAAGGGTGCAGGAAGGGTGCTACAAGAGTGCAAGAGCAGTGCAACTTGACTACAGGTAGGGGGCAGGTAAGATGCACATAGAGTGCAACAGGGGTGCAGGTAGGGTGCAAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8934 | GenBank | WP_172693479 |
| Name | mobF_HTS55_RS00190_pPHE101 |
UniProt ID | _ |
| Length | 981 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 981 a.a. Molecular weight: 109227.09 Da Isoelectric Point: 9.9333
>WP_172693479.1 MobF family relaxase [Pseudomonas thivervalensis]
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLEGPIDQQELAKLFDGKLPNGEMMPKP
VNKETGEIVTRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQTRRKEHGKSMLER
TGNLIIGKFRHELSRAKDPQLHTHAVVMNATRRADGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGY
EIRVLDKDGNFELAHISRDQIEAFSSRAKVIEDALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVK
EYWVTKARELGIEFGGRSQLDNREYGRRSESIHAEHNLPEGISAGQAVVQYAINHLTEREQVVGESDLRT
AALRRAVGLASPTEVDDEIKRLVKQGSLIESPPAYRMATAPDGAALSPAGWRALLKEQKGWSEKEAQQYV
KKAIDRGSLVEVEKRYTTQRALKREKAILAIERTGRGQVTPLLTKEQVAKALEGSTLSAGQYQAVEVIVS
TSNRFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERSTTTDATFRVVALAPYGNQVTALKNEGLDAHTL
ASFFHTKDKKLDERTIVVLDEAGVVGARQMEQLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGM
ETARIKEIQRQKNQELKIAVQHAAEGNPGKSLAHVNHVEEFRDPALRHEAIVRDYISLTPEERKEVLIVA
GTNKDRKQINTMTREALGLVGKGLELPTLNRVDTTQAERRYAPSYKKGLIVQPEKDYIRAGLTRGELYTV
DQALPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNVNG
VIELASVKERDGKPERVVTLPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSRTTSQNLWYVAISRA
RYEARIYTDKIAHLPAAIANRYDKTTALSLQQERERQRKEPIKPRTVLDGKAMEKKQRTALDGASAGKSG
V
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLEGPIDQQELAKLFDGKLPNGEMMPKP
VNKETGEIVTRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQTRRKEHGKSMLER
TGNLIIGKFRHELSRAKDPQLHTHAVVMNATRRADGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGY
EIRVLDKDGNFELAHISRDQIEAFSSRAKVIEDALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVK
EYWVTKARELGIEFGGRSQLDNREYGRRSESIHAEHNLPEGISAGQAVVQYAINHLTEREQVVGESDLRT
AALRRAVGLASPTEVDDEIKRLVKQGSLIESPPAYRMATAPDGAALSPAGWRALLKEQKGWSEKEAQQYV
KKAIDRGSLVEVEKRYTTQRALKREKAILAIERTGRGQVTPLLTKEQVAKALEGSTLSAGQYQAVEVIVS
TSNRFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERSTTTDATFRVVALAPYGNQVTALKNEGLDAHTL
ASFFHTKDKKLDERTIVVLDEAGVVGARQMEQLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGM
ETARIKEIQRQKNQELKIAVQHAAEGNPGKSLAHVNHVEEFRDPALRHEAIVRDYISLTPEERKEVLIVA
GTNKDRKQINTMTREALGLVGKGLELPTLNRVDTTQAERRYAPSYKKGLIVQPEKDYIRAGLTRGELYTV
DQALPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNVNG
VIELASVKERDGKPERVVTLPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSRTTSQNLWYVAISRA
RYEARIYTDKIAHLPAAIANRYDKTTALSLQQERERQRKEPIKPRTVLDGKAMEKKQRTALDGASAGKSG
V
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 10375 | GenBank | WP_017124988 |
| Name | t4cp2_HTS55_RS00185_pPHE101 |
UniProt ID | _ |
| Length | 518 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 518 a.a. Molecular weight: 58205.54 Da Isoelectric Point: 8.9125
>WP_017124988.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Pseudomonas]
MHKREVDSATMTAGFGLPIAGWGAGVYLAQMPLTPFPAAFKETLHNGWHNPIVLGATIATSVAAASLVYY
LQEYCDDGFRGEQYQEFLRGSQIKNWHTVKAKVNRRNAQTNRERKKKGLAKSDPIMIGKLPMPLHLEDRN
TMICASIGAGKSVTMEGMIASALKRGDRMAVVDPNGTFYSKFSFKGDYILNPFDVRSAGWTIFNEIRGIH
DFNRMAKSIIPPQVDPSDEQWCAYARDVLSDTMRKLKETNNPNQDTLVNLLVREDGDTIRAFLANTDSEG
YFRDNAEKAIASIQFMMNKYIRPLRYMSKGEFSIYQWVNDPNAGNLFITWREDMRDTMKPLVATWIDTIC
ATILSSEPMTGKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF
RNYVILAAANAKNAGMASEILGSHDVKRWRKSHTAGKLTRTEEVTRDEPVVQASEISNLPDLVAYVKFGE
DFPITKVKTPYIDYKERAQAIMITGQAA
MHKREVDSATMTAGFGLPIAGWGAGVYLAQMPLTPFPAAFKETLHNGWHNPIVLGATIATSVAAASLVYY
LQEYCDDGFRGEQYQEFLRGSQIKNWHTVKAKVNRRNAQTNRERKKKGLAKSDPIMIGKLPMPLHLEDRN
TMICASIGAGKSVTMEGMIASALKRGDRMAVVDPNGTFYSKFSFKGDYILNPFDVRSAGWTIFNEIRGIH
DFNRMAKSIIPPQVDPSDEQWCAYARDVLSDTMRKLKETNNPNQDTLVNLLVREDGDTIRAFLANTDSEG
YFRDNAEKAIASIQFMMNKYIRPLRYMSKGEFSIYQWVNDPNAGNLFITWREDMRDTMKPLVATWIDTIC
ATILSSEPMTGKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF
RNYVILAAANAKNAGMASEILGSHDVKRWRKSHTAGKLTRTEEVTRDEPVVQASEISNLPDLVAYVKFGE
DFPITKVKTPYIDYKERAQAIMITGQAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 27015..48675
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTS55_RS00145 | 22176..22448 | + | 273 | WP_054076656 | hypothetical protein | - |
| HTS55_RS00150 | 22462..22668 | + | 207 | WP_054076657 | hypothetical protein | - |
| HTS55_RS00155 | 22703..22966 | + | 264 | WP_081003825 | antirestriction protein ArdR | - |
| HTS55_RS00160 | 23705..24508 | - | 804 | WP_054076658 | SprT-like domain-containing protein | - |
| HTS55_RS00165 | 24641..25027 | - | 387 | WP_172693477 | hypothetical protein | - |
| HTS55_RS00170 | 25031..25750 | - | 720 | WP_054076660 | StbB family protein | - |
| HTS55_RS00175 | 25747..26202 | - | 456 | WP_172693478 | conjugal transfer protein TraD | - |
| HTS55_RS00180 | 26654..27022 | + | 369 | WP_042934865 | hypothetical protein | - |
| HTS55_RS00185 | 27015..28571 | + | 1557 | WP_017124988 | type IV secretion system DNA-binding domain-containing protein | virb4 |
| HTS55_RS00190 | 28582..31527 | + | 2946 | WP_172693479 | MobF family relaxase | - |
| HTS55_RS00195 | 31681..33441 | + | 1761 | WP_172693480 | ATP-dependent endonuclease | - |
| HTS55_RS00200 | 33438..34952 | + | 1515 | WP_172693481 | UvrD-helicase domain-containing protein | - |
| HTS55_RS00205 | 35169..35924 | + | 756 | WP_254170384 | hypothetical protein | - |
| HTS55_RS00210 | 36247..36885 | - | 639 | WP_172693482 | hypothetical protein | - |
| HTS55_RS00215 | 36931..37413 | - | 483 | WP_172693483 | hypothetical protein | - |
| HTS55_RS00220 | 37428..38015 | - | 588 | WP_254170385 | phospholipase D family protein | - |
| HTS55_RS00225 | 38023..38352 | - | 330 | WP_017124984 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HTS55_RS00230 | 38382..39284 | - | 903 | WP_172693484 | lytic transglycosylase domain-containing protein | virB1 |
| HTS55_RS00235 | 39268..40296 | - | 1029 | WP_017124982 | P-type DNA transfer ATPase VirB11 | virB11 |
| HTS55_RS00240 | 40306..41589 | - | 1284 | WP_017124981 | TrbI/VirB10 family protein | virB10 |
| HTS55_RS00245 | 41592..42383 | - | 792 | WP_172693485 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HTS55_RS00250 | 42410..43075 | - | 666 | WP_017124979 | type IV secretion system protein | virB8 |
| HTS55_RS00255 | 43075..43938 | - | 864 | WP_017124978 | type IV secretion system protein | virB6 |
| HTS55_RS00260 | 43926..44330 | - | 405 | WP_172693486 | hypothetical protein | - |
| HTS55_RS00265 | 44323..44535 | - | 213 | WP_017124976 | hypothetical protein | - |
| HTS55_RS00270 | 44563..45246 | - | 684 | WP_042934861 | type IV secretion system protein | virB5 |
| HTS55_RS00275 | 45246..47888 | - | 2643 | WP_172693487 | type VI secretion protein | virb4 |
| HTS55_RS00280 | 47917..48210 | - | 294 | WP_054076673 | VirB3 family type IV secretion system protein | virB3 |
| HTS55_RS00285 | 48214..48675 | - | 462 | WP_172693488 | TrbC/VirB2 family protein | virB2 |
| HTS55_RS00290 | 48692..48967 | - | 276 | WP_054076675 | hypothetical protein | - |
| HTS55_RS00295 | 49614..50387 | + | 774 | WP_254170386 | ParA family protein | - |
| HTS55_RS00300 | 50398..51321 | + | 924 | WP_172693489 | ParB/RepB/Spo0J family partition protein | - |
| HTS55_RS00305 | 51330..51668 | + | 339 | WP_172693490 | TrfB-related DNA-binding protein | - |
| HTS55_RS00310 | 51665..52081 | + | 417 | WP_172693491 | hypothetical protein | - |
| HTS55_RS00315 | 52348..52977 | + | 630 | WP_172693492 | recombinase family protein | - |
Host bacterium
| ID | 14351 | GenBank | NZ_MH061178 |
| Plasmid name | pPHE101 | Incompatibility group | - |
| Plasmid size | 60958 bp | Coordinate of oriT [Strand] | 26203..26629 [-] |
| Host baterium | Pseudomonas thivervalensis strain P101 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |