Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 104468 |
| Name | oriT_STEFF_16|unnamed1  |
| Organism | Shigella flexneri strain STEFF_16 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP055185 (44385..45000 [+], 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_STEFF_16|unnamed1
TCTTACTTCTTTGCGTAGCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
TCTTACTTCTTTGCGTAGCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 3158 | GenBank | WP_000053826 |
| Name | t4cp2_HUZ44_RS22980_STEFF_16|unnamed1 |
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 | 3159 | GenBank | WP_000108725 |
| Name | t4cp2_HUZ44_RS23020_STEFF_16|unnamed1 |
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: 31941..41831
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HUZ44_RS22955 | 27021..27107 | - | 87 | Protein_34 | micrococcal nuclease | - |
| HUZ44_RS22960 (HUZ44_22825) | 27254..28162 | + | 909 | WP_239606674 | C45 family peptidase | - |
| HUZ44_RS22965 (HUZ44_22830) | 28316..29131 | - | 816 | WP_000018321 | aminoglycoside O-phosphotransferase APH(3')-Ia | - |
| HUZ44_RS22970 | 29374..29706 | - | 333 | WP_000699980 | hypothetical protein | - |
| HUZ44_RS22975 (HUZ44_22840) | 29709..30104 | - | 396 | WP_000733627 | cag pathogenicity island Cag12 family protein | - |
| HUZ44_RS22980 (HUZ44_22845) | 30101..31936 | - | 1836 | WP_000053826 | type IV secretory system conjugative DNA transfer family protein | - |
| HUZ44_RS22985 (HUZ44_22850) | 31941..32978 | - | 1038 | WP_000217791 | P-type DNA transfer ATPase VirB11 | virB11 |
| HUZ44_RS22990 (HUZ44_22855) | 32996..34210 | - | 1215 | WP_001295061 | VirB10/TraB/TrbI family type IV secretion system protein | virB10 |
| HUZ44_RS22995 (HUZ44_22860) | 34207..35136 | - | 930 | WP_000776689 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HUZ44_RS23000 (HUZ44_22865) | 35142..35864 | - | 723 | WP_000394570 | type IV secretion system protein | virB8 |
| HUZ44_RS23005 (HUZ44_22870) | 36054..37109 | - | 1056 | WP_000235774 | type IV secretion system protein | virB6 |
| HUZ44_RS23010 (HUZ44_22875) | 37121..37381 | - | 261 | WP_001228869 | EexN family lipoprotein | - |
| HUZ44_RS23015 (HUZ44_22880) | 37391..38128 | - | 738 | WP_000737859 | type IV secretion system protein | - |
| HUZ44_RS23020 (HUZ44_22885) | 38130..40889 | - | 2760 | WP_000108725 | VirB3 family type IV secretion system protein | virb4 |
| HUZ44_RS23025 (HUZ44_22890) | 40913..41203 | - | 291 | WP_000921916 | TrbC/VirB2 family protein | virB2 |
| HUZ44_RS23030 (HUZ44_22895) | 41187..41831 | - | 645 | WP_000953539 | lytic transglycosylase domain-containing protein | virB1 |
| HUZ44_RS23035 (HUZ44_22900) | 42056..42547 | - | 492 | WP_038976853 | transcription termination/antitermination NusG family protein | - |
| HUZ44_RS23040 (HUZ44_22905) | 42908..44065 | - | 1158 | WP_000538023 | DNA distortion polypeptide 2 | - |
| HUZ44_RS23045 (HUZ44_22910) | 44068..44613 | - | 546 | WP_038976855 | DNA distortion polypeptide 1 | - |
| HUZ44_RS23050 (HUZ44_22915) | 44940..45212 | - | 273 | WP_000160399 | hypothetical protein | - |
| HUZ44_RS23055 (HUZ44_22920) | 45225..45374 | - | 150 | WP_000003880 | hypothetical protein | - |
| HUZ44_RS23060 (HUZ44_22925) | 45661..45990 | - | 330 | WP_000866648 | hypothetical protein | - |
| HUZ44_RS23065 (HUZ44_22930) | 46083..46298 | - | 216 | WP_001180116 | hypothetical protein | - |
| HUZ44_RS23070 (HUZ44_22935) | 46288..46533 | - | 246 | WP_000356546 | hypothetical protein | - |
Host bacterium
| ID | 4907 | GenBank | NZ_CP055185 |
| Plasmid name | STEFF_16|unnamed1 | Incompatibility group | IncX1 |
| Plasmid size | 46569 bp | Coordinate of oriT [Strand] | 44385..45000 [+] |
| Host baterium | Shigella flexneri strain STEFF_16 |
Cargo genes
| Drug resistance gene | blaTEM-176, floR, tet(A), qnrS1, dfrA14, aph(3')-Ia |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |