Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103857 |
| Name | oriT_USDA1021|accessoryA  |
| Organism | Sinorhizobium meliloti strain USDA1021 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP021803 (102455..102511 [+], 57 nt) |
| oriT length | 57 nt |
| IRs (inverted repeats) | 4..9, 23..28 (GGAAAA..TTTTCC) |
| Location of nic site | 36..37 |
| Conserved sequence flanking the nic site |
TCCTGCCTCT |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 57 nt
>oriT_USDA1021|accessoryA
GCAGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTAAGGGGA
GCAGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTAAGGGGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 2705 | GenBank | WP_088204060 |
| Name | t4cp2_CDO29_RS34920_USDA1021|accessoryA |
UniProt ID | _ |
| Length | 699 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 699 a.a. Molecular weight: 77864.76 Da Isoelectric Point: 9.6664
>WP_088204060.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium meliloti]
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQFWHYKTSPALQKVALGS
LVPAMLVAGLVAYIGLKPTSSPLGDAAFQDMASLRRGKWFRKQGHIFGRVGRNILRTRDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRENGSQVFLFAPGSEKTSSYNPLDFIRPERGNRT
TDIQNIASILVPENTASENSVWQATAQQVLAGAISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPRVPEVDYLSPKPVPATTP
EYAKGGEPSVEIPSPAIEKEEKPVAAAAIQSAAVKEEPAADDMPSTTAKRTVNRKALRPSAKATAANTGG
AEASPSLDAMEARIRAIEEGLKPKAAQLREVVEMKAEKLGDKSPTKRRNIMDIFSATVPDPVEVGVAAE
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQFWHYKTSPALQKVALGS
LVPAMLVAGLVAYIGLKPTSSPLGDAAFQDMASLRRGKWFRKQGHIFGRVGRNILRTRDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRENGSQVFLFAPGSEKTSSYNPLDFIRPERGNRT
TDIQNIASILVPENTASENSVWQATAQQVLAGAISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPRVPEVDYLSPKPVPATTP
EYAKGGEPSVEIPSPAIEKEEKPVAAAAIQSAAVKEEPAADDMPSTTAKRTVNRKALRPSAKATAANTGG
AEASPSLDAMEARIRAIEEGLKPKAAQLREVVEMKAEKLGDKSPTKRRNIMDIFSATVPDPVEVGVAAE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 79920..89843
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CDO29_RS34825 (CDO29_34810) | 75088..75423 | + | 336 | Protein_66 | hypothetical protein | - |
| CDO29_RS34830 (CDO29_34815) | 75501..75916 | - | 416 | Protein_67 | hypothetical protein | - |
| CDO29_RS34835 (CDO29_34820) | 75938..76531 | - | 594 | WP_088204051 | hypothetical protein | - |
| CDO29_RS34845 (CDO29_34830) | 76938..77636 | - | 699 | WP_088204052 | thermonuclease family protein | - |
| CDO29_RS34850 (CDO29_34835) | 77633..78169 | - | 537 | WP_088204053 | succinoglycan biosynthesis protein exoi | - |
| CDO29_RS34855 (CDO29_34840) | 78166..78774 | - | 609 | WP_088204054 | hypothetical protein | - |
| CDO29_RS34860 (CDO29_34845) | 78997..79908 | + | 912 | WP_153497611 | lytic transglycosylase domain-containing protein | - |
| CDO29_RS34865 (CDO29_34850) | 79920..80258 | + | 339 | WP_013845316 | TrbC/VirB2 family protein | virB2 |
| CDO29_RS34870 (CDO29_34855) | 80262..80561 | + | 300 | WP_088204055 | VirB3 family type IV secretion system protein | virB3 |
| CDO29_RS34875 (CDO29_34860) | 80564..83023 | + | 2460 | WP_088204056 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| CDO29_RS34880 (CDO29_34865) | 83020..84108 | + | 1089 | WP_088204057 | lytic transglycosylase domain-containing protein | - |
| CDO29_RS34885 (CDO29_34870) | 84120..84821 | + | 702 | WP_088204058 | type IV secretion system protein | - |
| CDO29_RS34890 (CDO29_34875) | 84811..85038 | + | 228 | WP_014531073 | hypothetical protein | - |
| CDO29_RS34895 (CDO29_34880) | 85054..86082 | + | 1029 | WP_014531072 | type IV secretion system protein | virB6 |
| CDO29_RS34900 (CDO29_34885) | 86122..86817 | + | 696 | WP_017266187 | type IV secretion system protein | virB8 |
| CDO29_RS34905 (CDO29_34890) | 86814..87623 | + | 810 | WP_017266188 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| CDO29_RS34910 (CDO29_34895) | 87623..88834 | + | 1212 | WP_088204059 | type IV secretion system protein VirB10 | virB10 |
| CDO29_RS34915 (CDO29_34900) | 88815..89843 | + | 1029 | WP_014531068 | P-type DNA transfer ATPase VirB11 | virB11 |
| CDO29_RS34920 (CDO29_34905) | 89840..91939 | + | 2100 | WP_088204060 | type IV secretory system conjugative DNA transfer family protein | - |
| CDO29_RS34925 (CDO29_34910) | 92727..94571 | + | 1845 | WP_088204061 | DUF3604 domain-containing protein | - |
Host bacterium
| ID | 4297 | GenBank | NZ_CP021803 |
| Plasmid name | USDA1021|accessoryA | Incompatibility group | - |
| Plasmid size | 297816 bp | Coordinate of oriT [Strand] | 102455..102511 [+] |
| Host baterium | Sinorhizobium meliloti strain USDA1021 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | htpB |
| Metal resistance gene | - |
| Degradation gene | LinG, dxnH |
| Symbiosis gene | - |
| Anti-CRISPR | - |