Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100396 |
| Name | oriT_pI2  |
| Organism | Comamonas testosteroni |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_016978 (56292..56664 [+], 373 nt) |
| oriT length | 373 nt |
| IRs (inverted repeats) | IR1: 64..68, 72..76 (GCGCC..GGCGC) IR2: 89..107, 110..128 (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC) |
| Location of nic site | 136..137 |
| Conserved sequence flanking the nic site |
CATCCTG|C |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 373 nt
>oriT_pI2
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 467 | GenBank | YP_005352128 |
| Name | TraI_pI2 |
UniProt ID | G9C9Y0 |
| Length | 348 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 348 a.a. Molecular weight: 38822.89 Da Isoelectric Point: 9.4403
>YP_005352128.1 TraI (plasmid) [Comamonas testosteroni]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRVSAVHNDTDNLHIHIAINKIHPTRNTMHEPYYSHRA
LAELCTALERDYGLERDNHEPRQRGAEGRAADMEQHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARLGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRGQALALLKRGDEVMVMPIDQATARRMSRIAVGDAVTITPKGSIKTSKGRSR
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRVSAVHNDTDNLHIHIAINKIHPTRNTMHEPYYSHRA
LAELCTALERDYGLERDNHEPRQRGAEGRAADMEQHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARLGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRGQALALLKRGDEVMVMPIDQATARRMSRIAVGDAVTITPKGSIKTSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | G9C9Y0 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2395..13017
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS872_RS00005 (PI2_p01) | 1..1221 | - | 1221 | WP_011114072 | plasmid replication initiator TrfA | - |
| HS872_RS00010 (PI2_p02) | 1268..1609 | - | 342 | WP_000019167 | single-stranded DNA-binding protein | - |
| HS872_RS00015 (PI2_p03) | 1723..2085 | + | 363 | WP_011114045 | transcriptional regulator | - |
| HS872_RS00020 (PI2_p04) | 2395..3357 | + | 963 | WP_000132020 | P-type conjugative transfer ATPase TrbB | virB11 |
| HS872_RS00025 (PI2_p05) | 3374..3838 | + | 465 | WP_014386436 | conjugal transfer system pilin TrbC | virB2 |
| HS872_RS00030 (PI2_p06) | 3842..4153 | + | 312 | WP_011013263 | conjugal transfer protein TrbD | virB3 |
| HS872_RS00035 (PI2_p07) | 4150..6708 | + | 2559 | WP_014386438 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HS872_RS00040 (PI2_p08) | 6705..7493 | + | 789 | WP_011013265 | conjugal transfer protein TrbF | virB8 |
| HS872_RS00045 (PI2_p09) | 7511..8404 | + | 894 | WP_014386236 | P-type conjugative transfer protein TrbG | virB9 |
| HS872_RS00050 (PI2_p10) | 8407..8868 | + | 462 | WP_011013267 | lipoprotein | - |
| HS872_RS00055 (PI2_p11) | 8872..10251 | + | 1380 | WP_012478192 | TrbI/VirB10 family protein | virB10 |
| HS872_RS00060 (PI2_p12) | 10268..11041 | + | 774 | WP_011255135 | P-type conjugative transfer protein TrbJ | virB5 |
| HS872_RS00065 (PI2_p13) | 11051..11272 | + | 222 | WP_011255136 | entry exclusion lipoprotein TrbK | - |
| HS872_RS00070 (PI2_p14) | 11284..13017 | + | 1734 | WP_014386439 | P-type conjugative transfer protein TrbL | virB6 |
| HS872_RS00075 (PI2_p15) | 13036..13614 | + | 579 | WP_011255138 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HS872_RS00080 (PI2_p16) | 13616..14251 | + | 636 | WP_014386440 | TrbN | - |
| HS872_RS00085 (PI2_p17) | 14281..14550 | + | 270 | WP_011255140 | hypothetical protein | - |
| HS872_RS00090 (PI2_p18) | 14547..15245 | + | 699 | WP_012478194 | TraX family protein | - |
| HS872_RS00095 (PI2_p19) | 15320..15703 | + | 384 | WP_014386441 | OmpA family protein | - |
| HS872_RS00100 (PI2_p20) | 15806..16222 | + | 417 | WP_012478195 | hypothetical protein | - |
Host bacterium
| ID | 857 | GenBank | NC_016978 |
| Plasmid name | pI2 | Incompatibility group | IncP1 |
| Plasmid size | 84204 bp | Coordinate of oriT [Strand] | 56292..56664 [+] |
| Host baterium | Comamonas testosteroni |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | merE, merD, merA, merP, merT, merR |
| Degradation gene | nahI, nahN, bphX2(BphK), bphX3(BphK) |
| Symbiosis gene | - |
| Anti-CRISPR | - |