Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103804 |
| Name | oriT_pYU39_IncX  |
| Organism | Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 isolate YUHS 05-78 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP011431 (38650..39256 [+], 607 nt) |
| oriT length | 607 nt |
| IRs (inverted repeats) | 590..595, 600..605 (ATGCCC..GGGCAT) 517..523, 529..535 (CCTCCCG..CGGGAGG) 453..458, 462..467 (GTTCGC..GCGAAC) 196..202, 204..210 (TCAATTC..GAATTGA) 175..180, 187..192 (AAATCA..TGATTT) 170..175, 184..189 (TCAGCA..TGCTGA) 103..108, 120..125 (GCTAAA..TTTAGC) 79..84, 93..98 (GCTTTA..TAAAGC) 29..37, 46..54 (TTTTGATAA..TTATCAAAA) |
| Location of nic site | 313..314 |
| Conserved sequence flanking the nic site |
TCCTGCATCG |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 607 nt
>oriT_pYU39_IncX
CTTTGTTTACCTGTTAAGTACATCGTTGTTTTGATAAAATCATTATTATCAAAAAACGTATTTATATCCTTACTGACAGCTTTACTTTTTAATAAAGCATTTGCTAAAAGTTTCATGCCTTTAGCTACTGTTAAAGCTGGTTCATCCGGATAAAGAGTTTTAAGGCAATTCAGCAAATCATCATGCTGATTTTCATCAATTCTGAATTGAACTTTTTTCATAAAATTCTCCGACAAGAACCGACTGTAGGTCACCGGGCAAATGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTGCGTCTGCGACCAGAAACTCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
CTTTGTTTACCTGTTAAGTACATCGTTGTTTTGATAAAATCATTATTATCAAAAAACGTATTTATATCCTTACTGACAGCTTTACTTTTTAATAAAGCATTTGCTAAAAGTTTCATGCCTTTAGCTACTGTTAAAGCTGGTTCATCCGGATAAAGAGTTTTAAGGCAATTCAGCAAATCATCATGCTGATTTTCATCAATTCTGAATTGAACTTTTTTCATAAAATTCTCCGACAAGAACCGACTGTAGGTCACCGGGCAAATGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTGCGTCTGCGACCAGAAACTCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 2825 | GenBank | WP_000539529 |
| Name | Relaxase_SE14_RS25420_pYU39_IncX |
UniProt ID | A0A0F7JE92 |
| Length | 388 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 388 a.a. Molecular weight: 44493.85 Da Isoelectric Point: 10.5286
>WP_000539529.1 MULTISPECIES: MobP1 family relaxase [Enterobacteriaceae]
MGVYVDKEHRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKEHMIDRANDPQHVMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDIGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFWGL
MGVYVDKEHRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKEHMIDRANDPQHVMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDIGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFWGL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A0F7JE92 |
T4CP
| ID | 2649 | GenBank | WP_000053818 |
| Name | t4cp2_SE14_RS25360_pYU39_IncX |
UniProt ID | _ |
| Length | 611 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 611 a.a. Molecular weight: 69331.19 Da Isoelectric Point: 7.4339
>WP_000053818.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWAFIGLVMCLVTYYTGSVAVYFLNGKTPLYIWKNFDSMLLWRIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFIIWQLNKTDVALYGDAKFASDNDLRKSKLLKWEKENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVFSI
GSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAKIS
EKLGYITTTSKSTSKSRGRSTSQGESESEARRALVLPQELGTLDFKEEFIILKGANPVKAEKALYYLDPY
FMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL
MSLKLPDKGQWAFIGLVMCLVTYYTGSVAVYFLNGKTPLYIWKNFDSMLLWRIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFIIWQLNKTDVALYGDAKFASDNDLRKSKLLKWEKENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVFSI
GSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAKIS
EKLGYITTTSKSTSKSRGRSTSQGESESEARRALVLPQELGTLDFKEEFIILKGANPVKAEKALYYLDPY
FMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 26094..36110
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SE14_RS25355 (SE14_05172) | 22509..23432 | + | 924 | WP_000902514 | SMEK domain-containing protein | - |
| SE14_RS27385 (SE14_05173) | 23547..23849 | - | 303 | WP_000717624 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| SE14_RS27390 (SE14_05174) | 23846..24259 | - | 414 | WP_071844337 | cag pathogenicity island Cag12 family protein | - |
| SE14_RS25360 (SE14_05175) | 24256..26091 | - | 1836 | WP_000053818 | type IV secretory system conjugative DNA transfer family protein | - |
| SE14_RS25365 (SE14_05176) | 26094..27125 | - | 1032 | WP_001058465 | P-type DNA transfer ATPase VirB11 | virB11 |
| SE14_RS25370 (SE14_05177) | 27127..28332 | - | 1206 | WP_000139139 | VirB10/TraB/TrbI family type IV secretion system protein | virB10 |
| SE14_RS25375 (SE14_05178) | 28329..29258 | - | 930 | WP_000783379 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| SE14_RS25380 (SE14_05179) | 29263..29976 | - | 714 | WP_000394613 | type IV secretion system protein | virB8 |
| SE14_RS25385 (SE14_05180) | 30221..31351 | - | 1131 | WP_000524912 | type IV secretion system protein | virB6 |
| SE14_RS25390 (SE14_05181) | 31360..31647 | - | 288 | WP_000835347 | EexN family lipoprotein | - |
| SE14_RS25395 (SE14_05182) | 31648..32406 | - | 759 | WP_000744200 | type IV secretion system protein | - |
| SE14_RS25400 (SE14_05183) | 32417..35170 | - | 2754 | WP_016731577 | VirB3 family type IV secretion system protein | virb4 |
| SE14_RS25405 (SE14_05184) | 35189..35485 | - | 297 | WP_000916182 | TrbC/VirB2 family protein | virB2 |
| SE14_RS25410 (SE14_05185) | 35463..36110 | - | 648 | WP_000953525 | lytic transglycosylase domain-containing protein | virB1 |
| SE14_RS25415 | 36143..36355 | - | 213 | WP_000125172 | hypothetical protein | - |
| SE14_RS27395 (SE14_05186) | 36285..36803 | - | 519 | WP_001446885 | transcription termination/antitermination NusG family protein | - |
| SE14_RS25420 (SE14_05187) | 37156..38322 | - | 1167 | WP_000539529 | MobP1 family relaxase | - |
| SE14_RS25425 (SE14_05188) | 38325..38870 | - | 546 | WP_001436753 | DNA distortion polypeptide 1 | - |
| SE14_RS27400 (SE14_05190) | 39196..39468 | - | 273 | WP_000160399 | hypothetical protein | - |
| SE14_RS28525 | 39481..39678 | - | 198 | WP_077626006 | hypothetical protein | - |
| SE14_RS25435 | 39700..39879 | - | 180 | WP_000439078 | hypothetical protein | - |
| SE14_RS25440 (SE14_05192) | 39922..40251 | - | 330 | WP_046891377 | hypothetical protein | - |
| SE14_RS25445 (SE14_05193) | 40344..40559 | - | 216 | WP_001180118 | hypothetical protein | - |
| SE14_RS25450 (SE14_05194) | 40549..40794 | - | 246 | WP_000356542 | hypothetical protein | - |
Host bacterium
| ID | 4244 | GenBank | NZ_CP011431 |
| Plasmid name | pYU39_IncX | Incompatibility group | IncX3 |
| Plasmid size | 42199 bp | Coordinate of oriT [Strand] | 38650..39256 [+] |
| Host baterium | Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 isolate YUHS 05-78 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |