Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100618 |
| Name | oriT_pTKS  |
| Organism | Sphingobium sp. TKS |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP005089 (26685..26875 [-], 191 nt) |
| oriT length | 191 nt |
| IRs (inverted repeats) | IR1: 19..38, 39..58 (AACCGTGAAGCGCGATCCGA..TAGGATTGAGCGTATCGGTT) IR2: 119..128, 131..140 (AGCGGTGGCA..TGCCACCGCT) |
| Location of nic site | 86..87 |
| Conserved sequence flanking the nic site |
TATCCTG|C |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 191 nt
>oriT_pTKS
GTGGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCGATAGGATTGAGCGTATCGGTTAACATTAGCCGCCGCAAGGCTTATCCTGCCATAAAGTAGATACCTACCCCACAAACAAAAAGCGGTGGCAACTGCCACCGCTTCAAAATTCCACGCCGCCTCAATGCTGAGTGAACGTGGACGGTAAAAGCTA
GTGGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCGATAGGATTGAGCGTATCGGTTAACATTAGCCGCCGCAAGGCTTATCCTGCCATAAAGTAGATACCTACCCCACAAACAAAAAGCGGTGGCAACTGCCACCGCTTCAAAATTCCACGCCGCCTCAATGCTGAGTGAACGTGGACGGTAAAAGCTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 690 | GenBank | WP_021245546 |
| Name | PutativerelaxaseofpTKS |
UniProt ID | A0A126RXL4 |
| Length | 347 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 347 a.a. Molecular weight: 38451.18 Da Isoelectric Point: 11.4070
>WP_021245546.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Sphingomonadaceae]
MSDFDSSFEAGQLAALFKPKLTSDPNRRGADMLLRSLSSRRAGQGGSTRARLARIVSRAPEVMVKVTGRP
KGKNHAAAHFDYIGRKGDVPLETRDGDILTDKEDRAALARDWGDPVYWRDNSTVAAVSMVFSMPAGTDPD
KVLSAVREVARSEIGHEWDYVLALHTDTPRPHVHVTVAARGDTGKRFNPRPQTLHHYRERFAEELRARGV
TAEATPRAARGVGRAGQSMALNRMRQRYMAGTAPAPFANQKITAAARDQLAGRSTAPDFVVRGRQAWTET
QHRYLAAAKRLEASSDPADRQLADQVRQFVGAGRTPTIHERSVAAMERKRQSERSRNRDRSREGPGR
MSDFDSSFEAGQLAALFKPKLTSDPNRRGADMLLRSLSSRRAGQGGSTRARLARIVSRAPEVMVKVTGRP
KGKNHAAAHFDYIGRKGDVPLETRDGDILTDKEDRAALARDWGDPVYWRDNSTVAAVSMVFSMPAGTDPD
KVLSAVREVARSEIGHEWDYVLALHTDTPRPHVHVTVAARGDTGKRFNPRPQTLHHYRERFAEELRARGV
TAEATPRAARGVGRAGQSMALNRMRQRYMAGTAPAPFANQKITAAARDQLAGRSTAPDFVVRGRQAWTET
QHRYLAAAKRLEASSDPADRQLADQVRQFVGAGRTPTIHERSVAAMERKRQSERSRNRDRSREGPGR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A126RXL4 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 32290..42256
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| K426_RS29510 (K426_29805) | 27414..28457 | + | 1044 | WP_021245546 | relaxase/mobilization nuclease domain-containing protein | - |
| K426_RS29515 (K426_29810) | 28458..28688 | - | 231 | WP_020819802 | hypothetical protein | - |
| K426_RS29520 (K426_29815) | 28748..29197 | - | 450 | WP_021245547 | hypothetical protein | - |
| K426_RS29525 (K426_29820) | 29237..30421 | - | 1185 | WP_020819804 | LPD7 domain-containing protein | - |
| K426_RS29530 (K426_29825) | 30411..32312 | - | 1902 | WP_059153602 | type IV secretory system conjugative DNA transfer family protein | - |
| K426_RS29535 (K426_29830) | 32290..33282 | - | 993 | WP_011627746 | P-type DNA transfer ATPase VirB11 | virB11 |
| K426_RS29540 (K426_29835) | 33279..34547 | - | 1269 | WP_059153601 | type IV secretion system protein VirB10 | virB10 |
| K426_RS29545 (K426_29840) | 34549..35391 | - | 843 | WP_059153600 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| K426_RS29550 (K426_29845) | 35388..36071 | - | 684 | WP_059153599 | VirB8/TrbF family protein | virB8 |
| K426_RS31030 (K426_29846) | 36081..36401 | - | 321 | WP_022684495 | hypothetical protein | - |
| K426_RS29555 (K426_29850) | 36412..37428 | - | 1017 | WP_059153598 | type IV secretion system protein | virB6 |
| K426_RS29560 (K426_29855) | 37472..37777 | - | 306 | WP_059153597 | hypothetical protein | - |
| K426_RS29565 (K426_29860) | 37779..38492 | - | 714 | WP_059153596 | type IV secretion system protein | virB5 |
| K426_RS29570 (K426_29865) | 38506..40890 | - | 2385 | WP_006949654 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| K426_RS29575 (K426_29870) | 40877..41221 | - | 345 | WP_006949650 | VirB3 family type IV secretion system protein | virB3 |
| K426_RS29580 (K426_29875) | 41228..41569 | - | 342 | WP_059153595 | TrbC/VirB2 family protein | virB2 |
| K426_RS29585 (K426_29880) | 41591..42256 | - | 666 | WP_059153594 | lytic transglycosylase domain-containing protein | virB1 |
| K426_RS29590 (K426_29885) | 42654..42962 | - | 309 | WP_020819813 | hypothetical protein | - |
| K426_RS31990 | 43218..43370 | + | 153 | WP_006949649 | hypothetical protein | - |
| K426_RS29600 (K426_29895) | 43451..44317 | - | 867 | WP_006953933 | recombinase family protein | - |
| K426_RS32900 (K426_29900) | 44460..44861 | - | 402 | WP_066564853 | DUF4158 domain-containing protein | - |
| K426_RS29615 (K426_29910) | 45216..45491 | + | 276 | WP_059153592 | AbrB/MazE/SpoVT family DNA-binding domain-containing protein | - |
| K426_RS29620 (K426_29915) | 45488..45886 | + | 399 | WP_059153591 | type II toxin-antitoxin system VapC family toxin | - |
| K426_RS29625 | 45889..46508 | + | 620 | Protein_65 | histidine phosphatase family protein | - |
| K426_RS31040 (K426_29930) | 46885..47043 | + | 159 | Protein_66 | transcriptional regulator | - |
| K426_RS32780 | 47061..47171 | + | 111 | Protein_67 | type II toxin-antitoxin system antitoxin, RelB/DinJ family | - |
Host bacterium
| ID | 1078 | GenBank | NZ_CP005089 |
| Plasmid name | pTKS | Incompatibility group | _ |
| Plasmid size | 53908 bp | Coordinate of oriT [Strand] | 26685..26875 [-] |
| Host baterium | Sphingobium sp. TKS |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |