Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 104558 |
| Name | oriT_STLIN_4|unnamed3  |
| Organism | Shigella flexneri strain STLIN_4 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP058789 (42337..42952 [+], 616 nt) |
| oriT length | 616 nt |
| IRs (inverted repeats) | 599..604, 609..614 (ATGCCC..GGGCAT) 526..532, 538..544 (CCTCCCG..CGGGAGG) 462..467, 471..476 (GTTCGC..GCGAAC) 52..58, 62..68 (CATTATC..GATAATG) 40..45, 54..59 (TGATAA..TTATCA) |
| Location of nic site | 322..323 |
| Conserved sequence flanking the nic site |
TCCTGCATCG |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 616 nt
>oriT_STLIN_4|unnamed3
TCTTACTTCTTTGCGTAGCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
TCTTACTTCTTTGCGTAGCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 3222 | GenBank | WP_000053826 |
| Name | t4cp2_HZT07_RS24210_STLIN_4|unnamed3 |
UniProt ID | _ |
| Length | 611 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 611 a.a. Molecular weight: 69231.07 Da Isoelectric Point: 8.0208
>WP_000053826.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWAFIILVMCLIAYYTGSVAIYFFNHKTPLYIWKHYDSLLLWRVIIDSSIKSEVRFTALPS
LLSGALASLAAPAFIIWKLNQKDAPLFGDAKFASDSDLKKSKLLKWEKENDTDILVGRYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNMLVKKHSIIALDPKQELWKITSKVREQILGNKVYLLDPFNTKTHKCNPLF
YVDLKSESGAKDLLKLVEILFPSFGLTGAEAHFNNLAGQYWTGLAKLLHFFINFAPEWIEELRVKPVFSI
GTVVDLYSNIDREQVLSNRETFEELAQGNETALFHLKDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQMRREDITVYVGVNAEDMILAYDFLNLFFNLVVEVTLRENPDFDPTLKHDCLLFL
DEFPSIGYMPIIKKGSGYIAGYKLKLLTIYQNISQLNEIYGTEGAKTLLSAHPCRVIYAVSEEDDAKKIS
EKLGYITARSKGSSKTSGKATSRSNSENEAQRALVLPQELGTLDFSEEMIILKGEHPVKAEKALYYLDNY
FMERLMLVSPKLTALTASINRSNKIFGVKGIKYPSKEKMLSVGELESEVLL
MSLKLPDKGQWAFIILVMCLIAYYTGSVAIYFFNHKTPLYIWKHYDSLLLWRVIIDSSIKSEVRFTALPS
LLSGALASLAAPAFIIWKLNQKDAPLFGDAKFASDSDLKKSKLLKWEKENDTDILVGRYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNMLVKKHSIIALDPKQELWKITSKVREQILGNKVYLLDPFNTKTHKCNPLF
YVDLKSESGAKDLLKLVEILFPSFGLTGAEAHFNNLAGQYWTGLAKLLHFFINFAPEWIEELRVKPVFSI
GTVVDLYSNIDREQVLSNRETFEELAQGNETALFHLKDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQMRREDITVYVGVNAEDMILAYDFLNLFFNLVVEVTLRENPDFDPTLKHDCLLFL
DEFPSIGYMPIIKKGSGYIAGYKLKLLTIYQNISQLNEIYGTEGAKTLLSAHPCRVIYAVSEEDDAKKIS
EKLGYITARSKGSSKTSGKATSRSNSENEAQRALVLPQELGTLDFSEEMIILKGEHPVKAEKALYYLDNY
FMERLMLVSPKLTALTASINRSNKIFGVKGIKYPSKEKMLSVGELESEVLL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 3223 | GenBank | WP_000108725 |
| Name | t4cp2_HZT07_RS24250_STLIN_4|unnamed3 |
UniProt ID | _ |
| Length | 919 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 919 a.a. Molecular weight: 104758.78 Da Isoelectric Point: 6.1962
>WP_000108725.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacteriaceae]
MSTVFKGLTRPALIRGLGVPLYPFLAMCVLVVLLGVWIDDLMYFLILPGWFAIKRVTKIDERFFDLLYLR
AVVKGHPLANKRFSAVHYAGSQYDEVDISKVDNFMKLKDQASIEALIPYSSHITDDLVVTKNRDLLATWQ
VDGAYFECVDDEDLTLLTDQLNTLIRSFEGRAITFYTHRVRVRKEVKVGFNSKIPFVNRVMNDYYSSLSE
PEYFENRLYLTICYKPFNIEDKVSHFISKNKKENNIFDEPINDMNEICGRLDTYLSRFHAHRLGLVEENG
RVFSDQLSLFQYLLSGKWQKVRVTNSPFYTYLGGKDLFFGNDAGQITASQNARYFRSIEIKDYFQETDAG
IFDALMYLPVEYVFTSSFTSMDKQAAVKALDDQIDKLELTDDAAKSLLADLRVGLDMVSSGYNSFGKCHQ
TLIVFADTPERLVKDTNIVTTTLEDLGLIVTYSTLSLGAAFFSQLPGNYNLRPRLSMLSSLNFAEMESFH
NFFHGKATGNTWGNSLMALRGSGNDVYHLNYHMTTENINFFGKNPTLGHCEILGTSNVGKTVLMMIMSYA
AQQFGTPESFPENRKVRKLTTVFFDKDRAGEVGIRAMGGAYFRVKGGEPTGWNPAALPPTKRNIAFVKDI
IRLICKLNGNTVDDYQHSLISSAVDRLMQREDRSFPISKLIPLIMEPDDTETKRHGLKARLRAWKQGGEY
GWLLDNASDSFDVAHLDVFGIDGTEFLDDKVVAPVASFYLIYRVTMLADGRRLLIYMDEFWQWINNDAFK
DFVYNKLKTGRKLDMVLVPATQSPDELIKSPIAAAVREQCATHIYLANPKAKRNEYVDELQVRDLYFDKI
KAIDPLSRQFLVVKNPQRQGERDDFAAFAKLDLGKAAYYLPILSASAEQLELFDEIWSEGMAPEEWIDTY
LERANRGVK
MSTVFKGLTRPALIRGLGVPLYPFLAMCVLVVLLGVWIDDLMYFLILPGWFAIKRVTKIDERFFDLLYLR
AVVKGHPLANKRFSAVHYAGSQYDEVDISKVDNFMKLKDQASIEALIPYSSHITDDLVVTKNRDLLATWQ
VDGAYFECVDDEDLTLLTDQLNTLIRSFEGRAITFYTHRVRVRKEVKVGFNSKIPFVNRVMNDYYSSLSE
PEYFENRLYLTICYKPFNIEDKVSHFISKNKKENNIFDEPINDMNEICGRLDTYLSRFHAHRLGLVEENG
RVFSDQLSLFQYLLSGKWQKVRVTNSPFYTYLGGKDLFFGNDAGQITASQNARYFRSIEIKDYFQETDAG
IFDALMYLPVEYVFTSSFTSMDKQAAVKALDDQIDKLELTDDAAKSLLADLRVGLDMVSSGYNSFGKCHQ
TLIVFADTPERLVKDTNIVTTTLEDLGLIVTYSTLSLGAAFFSQLPGNYNLRPRLSMLSSLNFAEMESFH
NFFHGKATGNTWGNSLMALRGSGNDVYHLNYHMTTENINFFGKNPTLGHCEILGTSNVGKTVLMMIMSYA
AQQFGTPESFPENRKVRKLTTVFFDKDRAGEVGIRAMGGAYFRVKGGEPTGWNPAALPPTKRNIAFVKDI
IRLICKLNGNTVDDYQHSLISSAVDRLMQREDRSFPISKLIPLIMEPDDTETKRHGLKARLRAWKQGGEY
GWLLDNASDSFDVAHLDVFGIDGTEFLDDKVVAPVASFYLIYRVTMLADGRRLLIYMDEFWQWINNDAFK
DFVYNKLKTGRKLDMVLVPATQSPDELIKSPIAAAVREQCATHIYLANPKAKRNEYVDELQVRDLYFDKI
KAIDPLSRQFLVVKNPQRQGERDDFAAFAKLDLGKAAYYLPILSASAEQLELFDEIWSEGMAPEEWIDTY
LERANRGVK
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 29893..39783
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HZT07_RS24185 | 24973..25059 | - | 87 | Protein_25 | micrococcal nuclease | - |
| HZT07_RS24190 (HZT07_24020) | 25206..26114 | + | 909 | WP_000174819 | C45 family peptidase | - |
| HZT07_RS24195 (HZT07_24025) | 26268..27083 | - | 816 | WP_000018321 | aminoglycoside O-phosphotransferase APH(3')-Ia | - |
| HZT07_RS24200 | 27326..27658 | - | 333 | WP_000699980 | hypothetical protein | - |
| HZT07_RS24205 (HZT07_24035) | 27661..28056 | - | 396 | WP_000733627 | cag pathogenicity island Cag12 family protein | - |
| HZT07_RS24210 (HZT07_24040) | 28053..29888 | - | 1836 | WP_000053826 | type IV secretory system conjugative DNA transfer family protein | - |
| HZT07_RS24215 (HZT07_24045) | 29893..30930 | - | 1038 | WP_000217791 | P-type DNA transfer ATPase VirB11 | virB11 |
| HZT07_RS24220 (HZT07_24050) | 30948..32162 | - | 1215 | WP_001295061 | VirB10/TraB/TrbI family type IV secretion system protein | virB10 |
| HZT07_RS24225 (HZT07_24055) | 32159..33088 | - | 930 | WP_000776689 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HZT07_RS24230 (HZT07_24060) | 33094..33816 | - | 723 | WP_000394570 | type IV secretion system protein | virB8 |
| HZT07_RS24235 (HZT07_24065) | 34006..35061 | - | 1056 | WP_000235774 | type IV secretion system protein | virB6 |
| HZT07_RS24240 (HZT07_24070) | 35073..35333 | - | 261 | WP_001228869 | EexN family lipoprotein | - |
| HZT07_RS24245 (HZT07_24075) | 35343..36080 | - | 738 | WP_000737859 | type IV secretion system protein | - |
| HZT07_RS24250 (HZT07_24080) | 36082..38841 | - | 2760 | WP_000108725 | VirB3 family type IV secretion system protein | virb4 |
| HZT07_RS24255 (HZT07_24085) | 38865..39155 | - | 291 | WP_000921916 | TrbC/VirB2 family protein | virB2 |
| HZT07_RS24260 (HZT07_24090) | 39139..39783 | - | 645 | WP_000953539 | lytic transglycosylase domain-containing protein | virB1 |
| HZT07_RS24265 (HZT07_24095) | 40008..40499 | - | 492 | WP_000872475 | transcription termination/antitermination NusG family protein | - |
| HZT07_RS24270 (HZT07_24100) | 40860..42017 | - | 1158 | WP_000538023 | DNA distortion polypeptide 2 | - |
| HZT07_RS24275 (HZT07_24105) | 42020..42565 | - | 546 | WP_038976855 | DNA distortion polypeptide 1 | - |
| HZT07_RS24280 (HZT07_24110) | 42892..43164 | - | 273 | WP_000160399 | hypothetical protein | - |
| HZT07_RS24285 (HZT07_24115) | 43177..43326 | - | 150 | WP_000003880 | hypothetical protein | - |
| HZT07_RS24290 (HZT07_24120) | 43613..43942 | - | 330 | WP_000866648 | hypothetical protein | - |
| HZT07_RS24295 (HZT07_24125) | 44035..44250 | - | 216 | WP_001180116 | hypothetical protein | - |
| HZT07_RS24300 (HZT07_24130) | 44240..44485 | - | 246 | WP_000356546 | hypothetical protein | - |
Host bacterium
| ID | 4997 | GenBank | NZ_CP058789 |
| Plasmid name | STLIN_4|unnamed3 | Incompatibility group | IncX1 |
| Plasmid size | 45031 bp | Coordinate of oriT [Strand] | 42337..42952 [+] |
| Host baterium | Shigella flexneri strain STLIN_4 |
Cargo genes
| Drug resistance gene | blaTEM-1B, qnrS1, blaCTX-M-55, aph(3')-Ia |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |