Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 121380 |
| Name | oriT_Sour cherry (Prunus cerasus) symptomatic leaf|p58T3  |
| Organism | Pseudomonas cerasi isolate Sour cherry (Prunus cerasus) symptomatic leaf |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_LT222315 (130151..130332 [-], 182 nt) |
| oriT length | 182 nt |
| IRs (inverted repeats) | 82..89, 93..100 (CAAAGGGG..CCCCTTTG) 44..49, 58..63 (AAAAAG..CTTTTT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 182 nt
>oriT_Sour cherry (Prunus cerasus) symptomatic leaf|p58T3
AAATCTCGAATTCGCTAAACAGGCACGTTACCGATTGTCTACAAAAAAGAGCTTCGCCTTTTTCGTATCCAATCGACGTGCCAAAGGGGATACCCCTTTGAAACCCCGCAGAGCGGGAAAGCGTTGTTGTTGTCGTTGTTGGTTGTCGTCATTCAGGTGCCCTCAGGAGGTGATCTTGTGGC
AAATCTCGAATTCGCTAAACAGGCACGTTACCGATTGTCTACAAAAAAGAGCTTCGCCTTTTTCGTATCCAATCGACGTGCCAAAGGGGATACCCCTTTGAAACCCCGCAGAGCGGGAAAGCGTTGTTGTTGTCGTTGTTGGTTGTCGTCATTCAGGTGCCCTCAGGAGGTGATCTTGTGGC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 15790 | GenBank | WP_065348621 |
| Name | t4cp2_PCPL58_RS00985_Sour cherry (Prunus cerasus) symptomatic leaf|p58T3 |
UniProt ID | _ |
| Length | 550 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 550 a.a. Molecular weight: 61523.12 Da Isoelectric Point: 6.1471
>WP_065348621.1 type IV secretory system conjugative DNA transfer family protein [Pseudomonas cerasi]
MAKAKPQPISPDNPQERIEEHPAFLLGKHPTKDVFLASYGQQFVMLAAPPGSMKGVSAVIPNLLSYPDSM
VVNDPKFENWDVTSGFRASAGHKVYRFSPERLETHRWNPVSAISRDPLYRLGDIRTLARVLFVSDNPKNQ
EWYNKAGNVFSSILLYLMETPAMPCTLPQAYEIGSLGTGMGAWAQQIIELRSTGPNALTVETLRELNGVY
EASKNKSSGWSTTVDIVRDVLSVYAEKTVAWAVSDDDIDFAKMREEKTTVYFSVTERNLKKYGPLMNLFF
TQAIRLNSTVIPEQGGHCADGTLRYKYQLALMMDEFAIMGRMEIMETAPALTRGAGLRFFLIFQGKDQVR
AIYGETAGNAIMKAIHNEIVFAPGDIELAKEYSTRLGNTTVRVHNQSLNRQKHEVGARGQTDSYSEQPRP
LLLPQEVNELPFDKQLIFVQGNRQTEPMKILARKIIYFEEDVFKARQKMTPPPLPVGDATKIDALTVPVR
TVEAKVAVADTKPMQAEQRQRWNPKDTASNPAQVEADKAQPPEVEPDPEPAQADDTPETM
MAKAKPQPISPDNPQERIEEHPAFLLGKHPTKDVFLASYGQQFVMLAAPPGSMKGVSAVIPNLLSYPDSM
VVNDPKFENWDVTSGFRASAGHKVYRFSPERLETHRWNPVSAISRDPLYRLGDIRTLARVLFVSDNPKNQ
EWYNKAGNVFSSILLYLMETPAMPCTLPQAYEIGSLGTGMGAWAQQIIELRSTGPNALTVETLRELNGVY
EASKNKSSGWSTTVDIVRDVLSVYAEKTVAWAVSDDDIDFAKMREEKTTVYFSVTERNLKKYGPLMNLFF
TQAIRLNSTVIPEQGGHCADGTLRYKYQLALMMDEFAIMGRMEIMETAPALTRGAGLRFFLIFQGKDQVR
AIYGETAGNAIMKAIHNEIVFAPGDIELAKEYSTRLGNTTVRVHNQSLNRQKHEVGARGQTDSYSEQPRP
LLLPQEVNELPFDKQLIFVQGNRQTEPMKILARKIIYFEEDVFKARQKMTPPPLPVGDATKIDALTVPVR
TVEAKVAVADTKPMQAEQRQRWNPKDTASNPAQVEADKAQPPEVEPDPEPAQADDTPETM
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 15791 | GenBank | WP_065348673 |
| Name | t4cp2_PCPL58_RS01665_Sour cherry (Prunus cerasus) symptomatic leaf|p58T3 |
UniProt ID | _ |
| Length | 557 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 557 a.a. Molecular weight: 61750.41 Da Isoelectric Point: 6.4345
>WP_065348673.1 type IV secretory system conjugative DNA transfer family protein [Pseudomonas cerasi]
MGKAKSKPISPDNPQERIEEHPAILIGKHPTKDTFLASYGQTFVMLAAPPGTGKTVGVVTPNLLSYPDSV
VVNDPKFENWRDTAGFRAAAGHKVYRFSPELLETHRWNPLSALSRDPLYRLGQIRTLAGVLFVSDNPKNQ
EWYNKAANVFAAILLYLMEMEAMKLNGMKLTLPQAYEVASLGTGLGVWAQQAIEQHSTGPNALSVETLRE
LNGVFEASKNKSSGWSTTVDILRGALSMYAEKTVAWAVSDTDIDFTKLRKEKISIYFCVTGNAIKKYGPL
MNLFFTQAIQQNTDVMPEQGGHCADGTLILKYQVLFVIDEIAVMGRIEIMEMAPALTRGAGLRYIIIFQG
KDQLRSERTYGREAGNGIMQAFHIEIVYGTGNVELAKEYSTRLGNTTVRVHNQSLNRQKHEIGARGQTDS
YSEQPRPLLLPQEVSALPYGEELIFVEATKTTPAANIRARKIFWYEEPVFKERAGMPTPDVPIGDASKID
ALTVPVRTVEAKVAVADAKPMQAEQRQRWNPRDTTSKPVQVEADKAQPPEVEPDPEPAQADDTPETM
MGKAKSKPISPDNPQERIEEHPAILIGKHPTKDTFLASYGQTFVMLAAPPGTGKTVGVVTPNLLSYPDSV
VVNDPKFENWRDTAGFRAAAGHKVYRFSPELLETHRWNPLSALSRDPLYRLGQIRTLAGVLFVSDNPKNQ
EWYNKAANVFAAILLYLMEMEAMKLNGMKLTLPQAYEVASLGTGLGVWAQQAIEQHSTGPNALSVETLRE
LNGVFEASKNKSSGWSTTVDILRGALSMYAEKTVAWAVSDTDIDFTKLRKEKISIYFCVTGNAIKKYGPL
MNLFFTQAIQQNTDVMPEQGGHCADGTLILKYQVLFVIDEIAVMGRIEIMEMAPALTRGAGLRYIIIFQG
KDQLRSERTYGREAGNGIMQAFHIEIVYGTGNVELAKEYSTRLGNTTVRVHNQSLNRQKHEIGARGQTDS
YSEQPRPLLLPQEVSALPYGEELIFVEATKTTPAANIRARKIFWYEEPVFKERAGMPTPDVPIGDASKID
ALTVPVRTVEAKVAVADAKPMQAEQRQRWNPRDTTSKPVQVEADKAQPPEVEPDPEPAQADDTPETM
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 19937..30316
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PCPL58_RS00990 (PCPL58_p3018) | 15529..15762 | - | 234 | WP_044422741 | hypothetical protein | - |
| PCPL58_RS00995 (PCPL58_p3019) | 15780..15977 | - | 198 | Protein_19 | type IV secretory system conjugative DNA transfer family protein | - |
| PCPL58_RS01000 (PCPL58_p3020) | 15977..16207 | - | 231 | WP_065348622 | hypothetical protein | - |
| PCPL58_RS01005 (PCPL58_p3021) | 16325..18742 | - | 2418 | WP_065348623 | ATP-binding protein | - |
| PCPL58_RS01010 (PCPL58_p3022) | 18868..19140 | - | 273 | WP_044324439 | hypothetical protein | - |
| PCPL58_RS01015 (PCPL58_p3023) | 19187..19552 | - | 366 | WP_004667995 | hypothetical protein | - |
| PCPL58_RS01020 (PCPL58_p3024) | 19537..19923 | - | 387 | WP_065348624 | hypothetical protein | - |
| PCPL58_RS01025 (PCPL58_p3025) | 19937..20989 | - | 1053 | WP_065348625 | P-type DNA transfer ATPase VirB11 | virB11 |
| PCPL58_RS01030 (PCPL58_p3026) | 20999..22378 | - | 1380 | WP_065348626 | TrbI/VirB10 family protein | virB10 |
| PCPL58_RS01035 (PCPL58_p3027) | 22365..23174 | - | 810 | WP_065348627 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| PCPL58_RS01040 (PCPL58_p3028) | 23164..23952 | - | 789 | WP_065348628 | virB8 family protein | virB8 |
| PCPL58_RS01045 (PCPL58_p3030) | 24360..25292 | - | 933 | WP_065348629 | type IV secretion system protein | virB6 |
| PCPL58_RS01050 (PCPL58_p3031) | 25303..25656 | - | 354 | WP_065348630 | hypothetical protein | - |
| PCPL58_RS01055 (PCPL58_p3032) | 25689..26375 | - | 687 | WP_065348631 | P-type DNA transfer protein VirB5 | - |
| PCPL58_RS01060 (PCPL58_p3033) | 26372..28870 | - | 2499 | WP_232002778 | VirB4 family type IV secretion system protein | virb4 |
| PCPL58_RS01065 (PCPL58_p3034) | 28773..29261 | - | 489 | WP_060404295 | VirB3 family type IV secretion system protein | virB3 |
| PCPL58_RS01070 (PCPL58_p3035) | 29274..29609 | - | 336 | WP_020325459 | hypothetical protein | - |
| PCPL58_RS01075 (PCPL58_p3036) | 29609..30316 | - | 708 | WP_065348633 | lytic transglycosylase domain-containing protein | virB1 |
| PCPL58_RS01080 (PCPL58_p3037) | 30344..30556 | - | 213 | WP_031599400 | hypothetical protein | - |
| PCPL58_RS01085 (PCPL58_p3038) | 30645..31178 | - | 534 | WP_031598405 | transcription termination/antitermination NusG family protein | - |
| PCPL58_RS30430 | 31250..31417 | + | 168 | WP_157893872 | hypothetical protein | - |
| PCPL58_RS01090 (PCPL58_p3039) | 31421..31774 | + | 354 | WP_003319387 | helix-turn-helix domain-containing protein | - |
| PCPL58_RS31825 (PCPL58_p3040) | 31791..31976 | - | 186 | WP_065348634 | hypothetical protein | - |
| PCPL58_RS01100 (PCPL58_p3041) | 32032..33378 | - | 1347 | WP_083188280 | MFS transporter | - |
| PCPL58_RS01105 (PCPL58_p3042) | 33420..34616 | - | 1197 | WP_065348636 | L-2-hydroxyglutarate oxidase | - |
Region 2: 85593..95993
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PCPL58_RS01340 (PCPL58_p3094) | 81253..81486 | - | 234 | WP_053486459 | hypothetical protein | - |
| PCPL58_RS28715 | 81504..81702 | - | 199 | Protein_94 | type IV secretory system conjugative DNA transfer family protein | - |
| PCPL58_RS01345 (PCPL58_p3095) | 81702..81932 | - | 231 | WP_065348622 | hypothetical protein | - |
| PCPL58_RS01350 (PCPL58_p3096) | 82019..84409 | - | 2391 | WP_065348648 | ATP-binding protein | - |
| PCPL58_RS01355 (PCPL58_p3097) | 84534..84800 | - | 267 | WP_060402382 | hypothetical protein | - |
| PCPL58_RS01360 (PCPL58_p3098) | 84847..85212 | - | 366 | WP_002556101 | hypothetical protein | - |
| PCPL58_RS01365 (PCPL58_p3099) | 85197..85583 | - | 387 | WP_065348649 | hypothetical protein | - |
| PCPL58_RS01370 (PCPL58_p3100) | 85593..86651 | - | 1059 | WP_065348650 | P-type DNA transfer ATPase VirB11 | virB11 |
| PCPL58_RS01375 (PCPL58_p3101) | 86661..88043 | - | 1383 | WP_065348651 | TrbI/VirB10 family protein | virB10 |
| PCPL58_RS01380 (PCPL58_p3102) | 88030..88839 | - | 810 | WP_065348627 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| PCPL58_RS01385 (PCPL58_p3103) | 88829..89617 | - | 789 | WP_065348628 | virB8 family protein | virB8 |
| PCPL58_RS01390 (PCPL58_p3105) | 90025..90957 | - | 933 | WP_065348629 | type IV secretion system protein | virB6 |
| PCPL58_RS01395 (PCPL58_p3106) | 90968..91333 | - | 366 | WP_065348652 | hypothetical protein | - |
| PCPL58_RS01400 (PCPL58_p3107) | 91366..92052 | - | 687 | WP_057424700 | P-type DNA transfer protein VirB5 | - |
| PCPL58_RS01405 (PCPL58_p3108) | 92049..94547 | - | 2499 | WP_232002781 | VirB4 family type IV secretion system protein | virb4 |
| PCPL58_RS01410 (PCPL58_p3109) | 94450..94938 | - | 489 | WP_060404295 | VirB3 family type IV secretion system protein | virB3 |
| PCPL58_RS01415 (PCPL58_p3110) | 94951..95286 | - | 336 | WP_020325459 | hypothetical protein | - |
| PCPL58_RS01420 (PCPL58_p3111) | 95286..95993 | - | 708 | WP_065348654 | lytic transglycosylase domain-containing protein | virB1 |
| PCPL58_RS01425 (PCPL58_p3112) | 96006..96248 | - | 243 | WP_057443007 | hypothetical protein | - |
| PCPL58_RS01430 (PCPL58_p3113) | 96337..96870 | - | 534 | WP_057443006 | transcription termination/antitermination NusG family protein | - |
| PCPL58_RS01435 | 97125..97454 | + | 330 | WP_044424053 | helix-turn-helix domain-containing protein | - |
| PCPL58_RS30470 (PCPL58_p3114) | 97461..97865 | - | 405 | WP_162273802 | hypothetical protein | - |
| PCPL58_RS01440 (PCPL58_p3115) | 97923..99269 | - | 1347 | WP_065348655 | MFS transporter | - |
| PCPL58_RS01445 (PCPL58_p3116) | 99310..100506 | - | 1197 | WP_065348656 | L-2-hydroxyglutarate oxidase | - |
Host bacterium
| ID | 21807 | GenBank | NZ_LT222315 |
| Plasmid name | Sour cherry (Prunus cerasus) symptomatic leaf|p58T3 | Incompatibility group | - |
| Plasmid size | 143614 bp | Coordinate of oriT [Strand] | 130151..130332 [-] |
| Host baterium | Pseudomonas cerasi isolate Sour cherry (Prunus cerasus) symptomatic leaf |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |