Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 115367 |
| Name | oriT_pCL011-2  |
| Organism | Shigella flexneri 1c strain CL-011 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OR237794 (40020..40626 [+], 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) 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_pCL011-2
CTTTGTTTACCTGTTAAGTACATCGTTGTTTTGATAAAATCATTATTATCAAAAAACGTATTTATATCCTTACTGACAGCTTTACTTTTTAATAAAGCATTTGCTAAAAGTTTCATGCCTTTAGCTACTGTTAAAGCTGGTTCATCCGGATAAAGAGTTTTAAGGCAATCCAGCAAATCATCATGCTGATTTTCATCAATTCTGAATTGAACTTTTTTCATAAAATTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAATGTTGCGGAATGGCGTCAGAGACGTCATTTTGCAGTGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
CTTTGTTTACCTGTTAAGTACATCGTTGTTTTGATAAAATCATTATTATCAAAAAACGTATTTATATCCTTACTGACAGCTTTACTTTTTAATAAAGCATTTGCTAAAAGTTTCATGCCTTTAGCTACTGTTAAAGCTGGTTCATCCGGATAAAGAGTTTTAAGGCAATCCAGCAAATCATCATGCTGATTTTCATCAATTCTGAATTGAACTTTTTTCATAAAATTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAATGTTGCGGAATGGCGTCAGAGACGTCATTTTGCAGTGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9829 | GenBank | WP_001576909 |
| Name | mobP1_RI181_RS00250_pCL011-2 |
UniProt ID | A0A631M5V6 |
| Length | 388 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 388 a.a. Molecular weight: 44446.83 Da Isoelectric Point: 10.5067
>WP_001576909.1 MULTISPECIES: MobP1 family relaxase [Enterobacterales]
MGVYVDKEYRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKEHMIDRANDPQHVMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDIGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFLGL
MGVYVDKEYRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKEHMIDRANDPQHVMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDIGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFLGL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A631M5V6 |
T4CP
| ID | 11453 | GenBank | WP_000053829 |
| Name | t4cp2_RI181_RS00185_pCL011-2 |
UniProt ID | _ |
| Length | 611 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 611 a.a. Molecular weight: 69290.20 Da Isoelectric Point: 6.9121
>WP_000053829.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacterales]
MSLKLPDKGQWVFIGLVMCLVTYYAGSVAVYFLNGKTPLYIWKNFDSMLLWKIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFVIWQLNKMDVALYGDAKFASDNDLKKSKLLKWETENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVFSI
GSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAKIS
EKLGYITTTSKSTSKSRGRSASQGESESEARRALVLPQELGTLDFKEEFIILKGENPVKAEKALYYLDPY
FMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL
MSLKLPDKGQWVFIGLVMCLVTYYAGSVAVYFLNGKTPLYIWKNFDSMLLWKIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFVIWQLNKMDVALYGDAKFASDNDLKKSKLLKWETENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVFSI
GSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAKIS
EKLGYITTTSKSTSKSRGRSASQGESESEARRALVLPQELGTLDFKEEFIILKGENPVKAEKALYYLDPY
FMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 27520..37480
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RI181_RS00150 (pCL011-2_00030) | 22861..23181 | - | 321 | WP_001020837 | hypothetical protein | - |
| RI181_RS00155 (pCL011-2_00031) | 23241..23645 | - | 405 | WP_001576899 | hypothetical protein | - |
| RI181_RS00160 (pCL011-2_00032) | 23661..24197 | - | 537 | WP_001576898 | thermonuclease family protein | - |
| RI181_RS00165 (pCL011-2_00033) | 24194..24628 | - | 435 | WP_001579348 | hypothetical protein | - |
| RI181_RS00170 (pCL011-2_00034) | 24710..24967 | - | 258 | WP_001547185 | hypothetical protein | - |
| RI181_RS00175 (pCL011-2_00035) | 24973..25275 | - | 303 | WP_001576896 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| RI181_RS00180 (pCL011-2_00036) | 25272..25685 | - | 414 | WP_001579347 | cag pathogenicity island Cag12 family protein | - |
| RI181_RS00185 (pCL011-2_00037) | 25682..27517 | - | 1836 | WP_000053829 | type IV secretory system conjugative DNA transfer family protein | - |
| RI181_RS00190 (pCL011-2_00038) | 27520..28551 | - | 1032 | WP_001058476 | P-type DNA transfer ATPase VirB11 | virB11 |
| RI181_RS00195 (pCL011-2_00039) | 28553..29758 | - | 1206 | WP_001579345 | VirB10/TraB/TrbI family type IV secretion system protein | virB10 |
| RI181_RS00200 (pCL011-2_00040) | 29755..30684 | - | 930 | WP_000783381 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| RI181_RS00205 (pCL011-2_00041) | 30689..31402 | - | 714 | WP_000394613 | type IV secretion system protein | virB8 |
| RI181_RS00210 (pCL011-2_00042) | 31647..32780 | - | 1134 | WP_001576910 | type IV secretion system protein | virB6 |
| RI181_RS00215 (pCL011-2_00043) | 32790..33017 | - | 228 | WP_000835348 | EexN family lipoprotein | - |
| RI181_RS00220 (pCL011-2_00044) | 33018..33776 | - | 759 | WP_000744201 | type IV secretion system protein | - |
| RI181_RS00225 (pCL011-2_00045) | 33787..36540 | - | 2754 | WP_001363160 | VirB3 family type IV secretion system protein | virb4 |
| RI181_RS00230 (pCL011-2_00046) | 36559..36855 | - | 297 | WP_000040716 | TrbC/VirB2 family protein | virB2 |
| RI181_RS00235 (pCL011-2_00047) | 36833..37480 | - | 648 | WP_001579339 | lytic transglycosylase domain-containing protein | virB1 |
| RI181_RS00240 (pCL011-2_00048) | 37513..37725 | - | 213 | WP_000125172 | hypothetical protein | - |
| RI181_RS00245 | 37655..38173 | - | 519 | WP_001446885 | transcription termination/antitermination NusG family protein | - |
| RI181_RS00250 (pCL011-2_00049) | 38526..39692 | - | 1167 | WP_001576909 | MobP1 family relaxase | - |
| RI181_RS00255 (pCL011-2_00050) | 39695..40240 | - | 546 | WP_000757693 | DNA distortion polypeptide 1 | - |
| RI181_RS00260 (pCL011-2_00052) | 40566..40838 | - | 273 | WP_000160399 | hypothetical protein | - |
| RI181_RS00265 (pCL011-2_00053) | 40851..41048 | - | 198 | WP_001675595 | hypothetical protein | - |
| RI181_RS00270 (pCL011-2_00054) | 41070..41249 | - | 180 | WP_000439078 | hypothetical protein | - |
| RI181_RS00275 (pCL011-2_00055) | 41292..41621 | - | 330 | WP_000866648 | hypothetical protein | - |
| RI181_RS00280 (pCL011-2_00056) | 41714..41929 | - | 216 | WP_001180116 | hypothetical protein | - |
| RI181_RS00285 (pCL011-2_00057) | 41919..42164 | - | 246 | WP_000356546 | hypothetical protein | - |
Host bacterium
| ID | 15800 | GenBank | NZ_OR237794 |
| Plasmid name | pCL011-2 | Incompatibility group | IncX1 |
| Plasmid size | 44261 bp | Coordinate of oriT [Strand] | 40020..40626 [+] |
| Host baterium | Shigella flexneri 1c strain CL-011 |
Cargo genes
| Drug resistance gene | dfrA1, blaTEM-1B |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |