Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 122589 |
| Name | oriT1_pR39-1-B  |
| Organism | Enterococcus faecium strain R39-1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP116519 (39573..39776 [+], 204 nt) |
| oriT length | 204 nt |
| IRs (inverted repeats) | 125..130, 143..148 (AAATCC..GGATTT) 66..72, 83..89 (ACCCCCC..GGGGGGT) |
| Location of nic site | 135..136 |
| Conserved sequence flanking the nic site |
TTTGGTTACA |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 204 nt
>oriT1_pR39-1-B
AAGCGGAAGTCGCAGGTGTGGACTGATCTTGCTGGCTGGTGTGGCAATAGCCACGCCAGCACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATACGCCTTTTTGAT
AAGCGGAAGTCGCAGGTGTGGACTGATCTTGCTGGCTGGTGTGGCAATAGCCACGCCAGCACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATACGCCTTTTTGAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 14251 | GenBank | WP_000398284 |
| Name | mobT_PML88_RS13140_pR39-1-B |
UniProt ID | A0A3P3PY43 |
| Length | 401 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 401 a.a. Molecular weight: 47398.10 Da Isoelectric Point: 6.5091
>WP_000398284.1 MULTISPECIES: MobT family relaxase [Bacteria]
MEGFLLNEQTWLQHLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLWEALERFNPDAP
LEMLFDYVRIRFPTTDVQQVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKK
MEGFLLNEQTWLQHLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLWEALERFNPDAP
LEMLFDYVRIRFPTTDVQQVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A3P3PY43 |
T4CP
| ID | 16493 | GenBank | WP_000813488 |
| Name | tcpA_PML88_RS13130_pR39-1-B |
UniProt ID | _ |
| Length | 461 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 461 a.a. Molecular weight: 53370.27 Da Isoelectric Point: 9.0687
>WP_000813488.1 MULTISPECIES: FtsK/SpoIIIE domain-containing protein [Bacteria]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 16494 | GenBank | WP_159373489 |
| Name | t4cp2_PML88_RS13295_pR39-1-B |
UniProt ID | _ |
| Length | 508 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 508 a.a. Molecular weight: 56880.09 Da Isoelectric Point: 4.6922
>WP_159373489.1 MULTISPECIES: VirD4-like conjugal transfer protein, CD1115 family [Enterococcus]
MNGTILGMVDKQIIYQNNSTKPNRNVFVVGGPGSYKTQSVVITNLFNETQNSIVVTDPKGELYEKTAGVK
VAQGYQVHVVNFANMIHSDRYNPFDYIDRDIQAENVATKIVQSENKEGKKDVWFSTQRQLLKALILFVMN
HREPKQRNLAGVTNVLQKFDVEPGEDETDSPLDSLFLDLDMSDPARRAYELGFKKAKGEMKASIIESLLA
TVSKFVDAEVADFTGFSDFDLKDIGSTKTVLYVIIPVMDDTYESFINLFFSQLFDELYKLASDHGAKLPV
SVDFILDEFVNLGKFPKYEEFLATCRGYGIGVTTICQTLTQLQALYGKEKAESILGNHAVKICLNAANDV
TAKYFSDLLGKSTVKVETGSESTSRSKETSTSKSDSYSYTSRSLMTSDEIMRMPDTQSLLIFSNQRPIKA
TKAFQFKLFPGADHLVELKQNDYTSEPTGSQLTKFNEANEKWEAELAKAKATKAKNDVKPEEEEDMQDEM
DLAVAKQQASSENEDVDF
MNGTILGMVDKQIIYQNNSTKPNRNVFVVGGPGSYKTQSVVITNLFNETQNSIVVTDPKGELYEKTAGVK
VAQGYQVHVVNFANMIHSDRYNPFDYIDRDIQAENVATKIVQSENKEGKKDVWFSTQRQLLKALILFVMN
HREPKQRNLAGVTNVLQKFDVEPGEDETDSPLDSLFLDLDMSDPARRAYELGFKKAKGEMKASIIESLLA
TVSKFVDAEVADFTGFSDFDLKDIGSTKTVLYVIIPVMDDTYESFINLFFSQLFDELYKLASDHGAKLPV
SVDFILDEFVNLGKFPKYEEFLATCRGYGIGVTTICQTLTQLQALYGKEKAESILGNHAVKICLNAANDV
TAKYFSDLLGKSTVKVETGSESTSRSKETSTSKSDSYSYTSRSLMTSDEIMRMPDTQSLLIFSNQRPIKA
TKAFQFKLFPGADHLVELKQNDYTSEPTGSQLTKFNEANEKWEAELAKAKATKAKNDVKPEEEEDMQDEM
DLAVAKQQASSENEDVDF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 37468..48877
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PML88_RS13095 (PML88_13095) | 32773..33138 | - | 366 | Protein_42 | DNA topoisomerase | - |
| PML88_RS13100 (PML88_13100) | 33237..35123 | - | 1887 | WP_010718345 | group II intron reverse transcriptase/maturase | - |
| PML88_RS13105 (PML88_13105) | 35860..36222 | - | 363 | WP_002333457 | toprim domain-containing protein | - |
| PML88_RS13110 (PML88_13110) | 36238..36840 | - | 603 | WP_001062586 | recombinase family protein | - |
| PML88_RS13115 (PML88_13115) | 36854..37024 | - | 171 | WP_000713595 | hypothetical protein | - |
| PML88_RS13120 (PML88_13120) | 37468..37782 | + | 315 | WP_000420682 | YdcP family protein | orf23 |
| PML88_RS13125 (PML88_13125) | 37798..38184 | + | 387 | WP_000985015 | YdcP family protein | orf23 |
| PML88_RS13130 (PML88_13130) | 38213..39598 | + | 1386 | WP_000813488 | FtsK/SpoIIIE domain-containing protein | virb4 |
| PML88_RS13135 (PML88_13135) | 39601..39753 | + | 153 | WP_000879507 | hypothetical protein | - |
| PML88_RS13140 (PML88_13140) | 39776..40981 | + | 1206 | WP_000398284 | MobT family relaxase | - |
| PML88_RS13145 (PML88_13145) | 41024..41245 | + | 222 | WP_001009056 | hypothetical protein | orf19 |
| PML88_RS13150 (PML88_13150) | 41362..41859 | + | 498 | WP_000342539 | antirestriction protein ArdA | - |
| PML88_RS13155 (PML88_13155) | 41948..42340 | + | 393 | WP_000723888 | conjugal transfer protein | orf17a |
| PML88_RS13160 (PML88_13160) | 42324..44771 | + | 2448 | WP_000331160 | ATP-binding protein | virb4 |
| PML88_RS13165 (PML88_13165) | 44774..46933 | + | 2160 | Protein_56 | YtxH domain-containing protein | - |
| PML88_RS13170 (PML88_13170) | 46947..47948 | + | 1002 | WP_001574272 | lysozyme family protein | orf14 |
| PML88_RS13175 (PML88_13175) | 47945..48877 | + | 933 | WP_001224319 | conjugal transfer protein | orf13 |
| PML88_RS13180 (PML88_13180) | 49122..49238 | + | 117 | WP_001791010 | tetracycline resistance determinant leader peptide | - |
| PML88_RS13185 (PML88_13185) | 49254..51173 | + | 1920 | WP_001574275 | tetracycline resistance ribosomal protection protein Tet(M) | - |
| PML88_RS13190 (PML88_13190) | 51367..52743 | + | 1377 | WP_112080982 | tetracycline efflux MFS transporter Tet(L) | - |
Host bacterium
| ID | 23015 | GenBank | NZ_CP116519 |
| Plasmid name | pR39-1-B | Incompatibility group | - |
| Plasmid size | 77238 bp | Coordinate of oriT [Strand] | 39573..39776 [+]; 53200..53237 [+] |
| Host baterium | Enterococcus faecium strain R39-1 |
Cargo genes
| Drug resistance gene | erm(B), lnu(B), lsa(E), ant(6)-Ia, tet(M), tet(L), fexB, poxtA |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |