Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107823 |
| Name | oriT_pSCLE2  |
| Organism | Escherichia sp. SCLE84 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP051432 (27232..27847 [-], 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_pSCLE2
TCTTACTTCTTTGCGTATCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
TCTTACTTCTTTGCGTATCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 5494 | GenBank | WP_000108725 |
| Name | t4cp2_HGD79_RS25690_pSCLE2 |
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.
| ID | 5495 | GenBank | WP_168848546 |
| Name | t4cp2_HGD79_RS25730_pSCLE2 |
UniProt ID | _ |
| Length | 611 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 611 a.a. Molecular weight: 69192.03 Da Isoelectric Point: 7.7595
>WP_168848546.1 type IV secretory system conjugative DNA transfer family protein [Escherichia sp. SCLE84]
MSLKLPDKGQWAFIILVMCLIAYYTGSVAIYFFNHKTTLYIWKHYDSLLLWRVIIDSSIKSEVRFTALPS
LLSGALASLAAPAFIIWKLNQKDAPLFGDAKFASDSDLKKSKLLKWEKENDTDILVGRYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNMLVKKHSIIALDPKQELWKITSKVREQILGNKVYLLDPFNTKTHKCNPLF
YVDLKSESGAKDLLKLVEILFPSFGLTGAEAHFNNLAGQYWTGLAKLLHFFINFAPEWIEELRVKPVFSI
GTVVDLYSNIDLEQVLSNRETFEELAQGNETALFHLKDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQMRREDITVYVGVNAEDMILAYDFLNLFFNLVVEVTLRENPDFDPTLKHDCLLFL
DEFPSIGYMPIIKKGSGYIAGYKLKLLTIYQNISQLNEIYGTEGAKTLLSAHPCRVIYAVSEEDDAKKIS
EKLGYITARSKGSSKTSGKATSRSNSENEAQRALVLPQELGTLDFSEEMIILKGEHPVKAEKALYYLDNY
FMERLMLVSPKLTALTASINRSNKIFGVKGIKYPSKEKMLSVGELESEVLL
MSLKLPDKGQWAFIILVMCLIAYYTGSVAIYFFNHKTTLYIWKHYDSLLLWRVIIDSSIKSEVRFTALPS
LLSGALASLAAPAFIIWKLNQKDAPLFGDAKFASDSDLKKSKLLKWEKENDTDILVGRYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNMLVKKHSIIALDPKQELWKITSKVREQILGNKVYLLDPFNTKTHKCNPLF
YVDLKSESGAKDLLKLVEILFPSFGLTGAEAHFNNLAGQYWTGLAKLLHFFINFAPEWIEELRVKPVFSI
GTVVDLYSNIDLEQVLSNRETFEELAQGNETALFHLKDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQMRREDITVYVGVNAEDMILAYDFLNLFFNLVVEVTLRENPDFDPTLKHDCLLFL
DEFPSIGYMPIIKKGSGYIAGYKLKLLTIYQNISQLNEIYGTEGAKTLLSAHPCRVIYAVSEEDDAKKIS
EKLGYITARSKGSSKTSGKATSRSNSENEAQRALVLPQELGTLDFSEEMIILKGEHPVKAEKALYYLDNY
FMERLMLVSPKLTALTASINRSNKIFGVKGIKYPSKEKMLSVGELESEVLL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 30401..40291
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HGD79_RS25640 (HGD79_25660) | 25699..25944 | + | 246 | WP_000356546 | hypothetical protein | - |
| HGD79_RS25645 (HGD79_25665) | 25934..26149 | + | 216 | WP_001180116 | hypothetical protein | - |
| HGD79_RS25650 (HGD79_25670) | 26242..26571 | + | 330 | WP_000866648 | hypothetical protein | - |
| HGD79_RS25655 (HGD79_25675) | 26858..27007 | + | 150 | WP_000003880 | hypothetical protein | - |
| HGD79_RS25660 (HGD79_25680) | 27020..27292 | + | 273 | WP_000160399 | hypothetical protein | - |
| HGD79_RS25665 (HGD79_25685) | 27619..28164 | + | 546 | WP_025755763 | DNA distortion polypeptide 1 | - |
| HGD79_RS25670 (HGD79_25690) | 28167..29324 | + | 1158 | WP_000538023 | DNA distortion polypeptide 2 | - |
| HGD79_RS25675 (HGD79_25695) | 29685..30176 | + | 492 | WP_000872475 | transcription termination/antitermination NusG family protein | - |
| HGD79_RS25680 (HGD79_25700) | 30401..31045 | + | 645 | WP_000953539 | lytic transglycosylase domain-containing protein | virB1 |
| HGD79_RS25685 (HGD79_25705) | 31029..31319 | + | 291 | WP_000921916 | TrbC/VirB2 family protein | virB2 |
| HGD79_RS25690 (HGD79_25710) | 31343..34102 | + | 2760 | WP_000108725 | VirB3 family type IV secretion system protein | virb4 |
| HGD79_RS25695 (HGD79_25715) | 34104..34841 | + | 738 | WP_000737859 | type IV secretion system protein | - |
| HGD79_RS25700 (HGD79_25720) | 34851..35111 | + | 261 | WP_001228869 | EexN family lipoprotein | - |
| HGD79_RS25705 (HGD79_25725) | 35123..36178 | + | 1056 | WP_000235774 | type IV secretion system protein | virB6 |
| HGD79_RS25710 (HGD79_25730) | 36368..37090 | + | 723 | WP_000394570 | type IV secretion system protein | virB8 |
| HGD79_RS25715 (HGD79_25735) | 37096..38025 | + | 930 | WP_025755764 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HGD79_RS25720 (HGD79_25740) | 38022..39236 | + | 1215 | WP_025755765 | VirB10/TraB/TrbI family type IV secretion system protein | virB10 |
| HGD79_RS25725 (HGD79_25745) | 39254..40291 | + | 1038 | WP_000217791 | P-type DNA transfer ATPase VirB11 | virB11 |
| HGD79_RS25730 (HGD79_25750) | 40296..42131 | + | 1836 | WP_168848546 | type IV secretory system conjugative DNA transfer family protein | - |
| HGD79_RS25735 (HGD79_25755) | 42128..42523 | + | 396 | WP_000733627 | cag pathogenicity island Cag12 family protein | - |
| HGD79_RS26775 | 42526..42858 | + | 333 | WP_000699980 | hypothetical protein | - |
| HGD79_RS25745 (HGD79_25765) | 42941..43411 | + | 471 | WP_025755767 | thermonuclease family protein | - |
| HGD79_RS25750 (HGD79_25770) | 43826..44071 | + | 246 | WP_001243650 | hypothetical protein | - |
Host bacterium
| ID | 8258 | GenBank | NZ_CP051432 |
| Plasmid name | pSCLE2 | Incompatibility group | IncX1 |
| Plasmid size | 45814 bp | Coordinate of oriT [Strand] | 27232..27847 [-] |
| Host baterium | Escherichia sp. SCLE84 |
Cargo genes
| Drug resistance gene | floR |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |