Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100571 |
| Name | oriT_pYD626E  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_024967 (59368..59994 [+], 627 nt) |
| oriT length | 627 nt |
| IRs (inverted repeats) | IR1: 198..207, 211..220 (ATTGGGTGTT..AATACCTAAT) IR2:319..324, 330..335 (AAAAAA..TTTTTT) IR3: 393..402, 405..414 (GTATTCATGC..GCATGAATAC) |
| Location of nic site | 301..302 |
| Conserved sequence flanking the nic site |
GGTGT|ATAGC |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 627 nt
>oriT_pYD626E
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 643 | GenBank | YP_009060593 |
| Name | TraI_pYD626E |
UniProt ID | _ |
| Length | 1078 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 1078 a.a. Molecular weight: 120141.30 Da Isoelectric Point: 6.5229
>YP_009060593.1 TraI (plasmid) [Escherichia coli]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 11620..21945
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTD23_RS00040 (D616_p121010) | 7634..8254 | + | 621 | WP_002210516 | aldolase | - |
| HTD23_RS00045 (D616_p121011) | 8259..9041 | + | 783 | WP_004179747 | HPr family phosphocarrier protein | - |
| HTD23_RS00050 (D616_p121012) | 9174..9359 | + | 186 | Protein_9 | transposase | - |
| HTD23_RS00055 (D616_p121013) | 9411..10115 | - | 705 | WP_001067855 | IS6-like element IS26 family transposase | - |
| HTD23_RS00060 (D616_p121014) | 10180..10359 | - | 180 | Protein_11 | helix-turn-helix domain-containing protein | - |
| HTD23_RS00070 | 10785..10913 | + | 129 | WP_002210551 | DUF6710 family protein | - |
| HTD23_RS00075 (D616_p121017) | 11087..11620 | - | 534 | WP_000792636 | phospholipase D family protein | - |
| HTD23_RS00080 (D616_p121018) | 11620..12615 | - | 996 | WP_000128596 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HTD23_RS00085 (D616_p121019) | 12657..13817 | - | 1161 | WP_000101710 | type IV secretion system protein VirB10 | virB10 |
| HTD23_RS00090 (D616_p121020) | 13817..14701 | - | 885 | WP_000735066 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HTD23_RS00095 (D616_p121021) | 14712..15410 | - | 699 | WP_000646594 | type IV secretion system protein | virB8 |
| HTD23_RS00100 (D616_p121022) | 15400..15558 | - | 159 | WP_012561180 | hypothetical protein | - |
| HTD23_RS00105 (D616_p121023) | 15629..16669 | - | 1041 | WP_001749958 | type IV secretion system protein | virB6 |
| HTD23_RS00110 (D616_p121024) | 16685..16912 | - | 228 | WP_001749959 | IncN-type entry exclusion lipoprotein EexN | - |
| HTD23_RS00115 (D616_p121025) | 16920..17684 | - | 765 | WP_013149461 | type IV secretion system protein | virB5 |
| HTD23_RS00120 (D616_p121026) | 17651..20251 | - | 2601 | WP_001749961 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HTD23_RS00125 (D616_p121027) | 20251..20568 | - | 318 | WP_000496058 | VirB3 family type IV secretion system protein | virB3 |
| HTD23_RS00130 (D616_p121028) | 20618..20911 | - | 294 | WP_001749962 | hypothetical protein | virB2 |
| HTD23_RS00135 (D616_p121029) | 20921..21202 | - | 282 | WP_000440698 | transcriptional repressor KorA | - |
| HTD23_RS00140 (D616_p121030) | 21211..21945 | - | 735 | WP_001749963 | lytic transglycosylase domain-containing protein | virB1 |
| HTD23_RS00145 (D616_p121031) | 21988..22359 | + | 372 | WP_011867773 | H-NS family nucleoid-associated regulatory protein | - |
| HTD23_RS00150 (D616_p121032) | 22375..22719 | + | 345 | WP_001749964 | hypothetical protein | - |
| HTD23_RS00155 (D616_p121033) | 22716..23030 | + | 315 | WP_001749965 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HTD23_RS00160 (D616_p121034) | 23144..23377 | + | 234 | WP_001191790 | hypothetical protein | - |
| HTD23_RS00165 (D616_p121035) | 23427..24074 | + | 648 | WP_015344958 | restriction endonuclease | - |
| HTD23_RS00170 (D616_p121036) | 24079..24285 | + | 207 | WP_001749967 | hypothetical protein | - |
| HTD23_RS00175 (D616_p121037) | 24296..24568 | - | 273 | Protein_33 | IS1 family transposase | - |
| HTD23_RS00180 (D616_p121038) | 24667..26100 | + | 1434 | WP_001288432 | DNA cytosine methyltransferase | - |
Host bacterium
| ID | 1031 | GenBank | NC_024967 |
| Plasmid name | pYD626E | Incompatibility group | IncN |
| Plasmid size | 72800 bp | Coordinate of oriT [Strand] | 59368..59994 [+] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | blaSHV-187, dfrA14, qnrS1, blaLAP-1, blaTEM-1B, blaKPC-2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |