Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100489 |
| Name | oriT_pC1-1  |
| Organism | Delftia acidovorans |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019283 (61641..62231 [+], 591 nt) |
| oriT length | 591 nt |
| IRs (inverted repeats) | 148..160, 166..178 (AGGCGCTGCCGGT..ACCGGAAGCGCCT) 250..255, 260..265 (GCCGGC..GCCGGC) 318..336, 339..357 (GCGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCGC) |
| Location of nic site | 365..366 |
| Conserved sequence flanking the nic site |
CATCCTG|C |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 591 nt
>oriT_pC1-1
TGTCGCTACCCCTTGAGCGCGTGCGCCGTGTGTCGCGCGTAGGTCGCCACGGCTCGCCAGTAGGCGGCCATCGGCCCCTTGCGGCGTGCCCATGCCTTTTCCGCCTCGTCGTTGGCCTGCGTGCGCAGCTCGCGCAGCACGCGGGCAAGGCGCTGCCGGTCGGCAACCGGAAGCGCCTGGAGTTCGCGGCCTGCTGGAAGCTCCAGCAGCGGATTGATGTAGCCCATGTCGTTCGTCTCTCGCTTCTTGGCCGGCGGTAGCCGGCAGCCTCGCAGAGCAGGATGCCCGTTGAGTGCCGCAGGCGCGAATAAGGGACAGCGAAGATAGATAACCGGCCCGCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTATACCGAAACCTTCGCATCTGTCTGCATTTAGCGCGAAAAGATGGCGGATATATCGAATGAAGGCGTACAATGCCCGGAAAGCGCGCTAGATGCAGCGGTGTCAAGCTGCTATCCACGCGCTTTACATAGACTTTCCACGGGTCGATACATGAAAATGACGGCTATTTACAAACCACGGAAGCGAGGCGA
TGTCGCTACCCCTTGAGCGCGTGCGCCGTGTGTCGCGCGTAGGTCGCCACGGCTCGCCAGTAGGCGGCCATCGGCCCCTTGCGGCGTGCCCATGCCTTTTCCGCCTCGTCGTTGGCCTGCGTGCGCAGCTCGCGCAGCACGCGGGCAAGGCGCTGCCGGTCGGCAACCGGAAGCGCCTGGAGTTCGCGGCCTGCTGGAAGCTCCAGCAGCGGATTGATGTAGCCCATGTCGTTCGTCTCTCGCTTCTTGGCCGGCGGTAGCCGGCAGCCTCGCAGAGCAGGATGCCCGTTGAGTGCCGCAGGCGCGAATAAGGGACAGCGAAGATAGATAACCGGCCCGCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTATACCGAAACCTTCGCATCTGTCTGCATTTAGCGCGAAAAGATGGCGGATATATCGAATGAAGGCGTACAATGCCCGGAAAGCGCGCTAGATGCAGCGGTGTCAAGCTGCTATCCACGCGCTTTACATAGACTTTCCACGGGTCGATACATGAAAATGACGGCTATTTACAAACCACGGAAGCGAGGCGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 560 | GenBank | YP_006961897 |
| Name | TraI_pC1-1 |
UniProt ID | G9CA54 |
| Length | 752 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 752 a.a. Molecular weight: 82867.55 Da Isoelectric Point: 10.6815
>YP_006961897.1 TraI (plasmid) [Delftia acidovorans]
MIAKHVPMRSLGKSDFAGLVNYVTDAQSKDHRLGQVQITNCDAVSVQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRVSAVHNDTDNLHIHIAINKIHPTRNTMHEPYYSHRA
LAELCTALERDYGLERDNHEPRQRGAEGRAADMEQHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARLGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRGQALEQARRRKDRLVEAAKRSGRLRRATIKVIGESGPNKKLLYAQASKALRDE
IQAINKQYQQDRQALYDSHSRRTWADWLKKEATHGNAEALTALRAREAAQGLKGNTIQGRGDPRPGHAPV
TDNITKKGTIIFRAGLTAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFQAQIIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTERADQRPAEHRGRAGRGPGGPGQRAATHDDAARPIAVA
RAGFGRPGGGRAGTAGVHAGAVHRKPDIGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVPRHL
EQQGTQPDHQLRRDISRPGSGVAAAPPGLAAADKYIAERESKRSKGFDIPKHARYTAGEGGLAFEGVRNI
EGQALALLKRGDEVMVMPIDQATARRMSRIAVGDAVTITPKGSIKTSKGRSR
MIAKHVPMRSLGKSDFAGLVNYVTDAQSKDHRLGQVQITNCDAVSVQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRVSAVHNDTDNLHIHIAINKIHPTRNTMHEPYYSHRA
LAELCTALERDYGLERDNHEPRQRGAEGRAADMEQHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARLGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRGQALEQARRRKDRLVEAAKRSGRLRRATIKVIGESGPNKKLLYAQASKALRDE
IQAINKQYQQDRQALYDSHSRRTWADWLKKEATHGNAEALTALRAREAAQGLKGNTIQGRGDPRPGHAPV
TDNITKKGTIIFRAGLTAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFQAQIIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTERADQRPAEHRGRAGRGPGGPGQRAATHDDAARPIAVA
RAGFGRPGGGRAGTAGVHAGAVHRKPDIGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVPRHL
EQQGTQPDHQLRRDISRPGSGVAAAPPGLAAADKYIAERESKRSKGFDIPKHARYTAGEGGLAFEGVRNI
EGQALALLKRGDEVMVMPIDQATARRMSRIAVGDAVTITPKGSIKTSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | G9CA54 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2395..13018
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS903_RS00005 (D764_p2068) | 1..1224 | - | 1224 | WP_011013257 | plasmid replication initiator TrfA | - |
| HS903_RS00010 (D764_p2067) | 1273..1611 | - | 339 | WP_011013259 | single-stranded DNA-binding protein | - |
| HS903_RS00015 (D764_p2066) | 1721..2080 | + | 360 | WP_011013260 | transcriptional regulator | - |
| HS903_RS00020 (D764_p2065) | 2395..3360 | + | 966 | WP_011013261 | P-type conjugative transfer ATPase TrbB | virB11 |
| HS903_RS00025 (D764_p2064) | 3390..3854 | + | 465 | WP_011013262 | conjugal transfer system pilin TrbC | virB2 |
| HS903_RS00030 (D764_p2063) | 3858..4169 | + | 312 | WP_011013263 | conjugal transfer protein TrbD | virB3 |
| HS903_RS00035 (D764_p2062) | 4166..6724 | + | 2559 | WP_011013264 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HS903_RS00040 (D764_p2061) | 6721..7509 | + | 789 | WP_011013265 | conjugal transfer protein TrbF | virB8 |
| HS903_RS00045 (D764_p2060) | 7527..8420 | + | 894 | WP_014386236 | P-type conjugative transfer protein TrbG | virB9 |
| HS903_RS00050 (D764_p2059) | 8423..8884 | + | 462 | WP_011013267 | lipoprotein | - |
| HS903_RS00055 (D764_p2058) | 8888..10267 | + | 1380 | WP_012478192 | TrbI/VirB10 family protein | virB10 |
| HS903_RS00060 (D764_p2057) | 10284..11057 | + | 774 | WP_011255135 | P-type conjugative transfer protein TrbJ | virB5 |
| HS903_RS00065 (D764_p2056) | 11067..11288 | + | 222 | WP_011255136 | entry exclusion lipoprotein TrbK | - |
| HS903_RS00070 (D764_p2055) | 11300..13018 | + | 1719 | WP_012478193 | P-type conjugative transfer protein TrbL | virB6 |
| HS903_RS00075 (D764_p2054) | 13037..13615 | + | 579 | WP_011255138 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HS903_RS00080 (D764_p2053) | 13617..14252 | + | 636 | WP_011255139 | transglycosylase SLT domain-containing protein | - |
| HS903_RS00085 (D764_p2052) | 14282..14551 | + | 270 | WP_011255140 | hypothetical protein | - |
| HS903_RS00090 (D764_p2051) | 14548..15246 | + | 699 | WP_012478194 | TraX family protein | - |
| HS903_RS00095 (D764_p2050) | 15262..15705 | + | 444 | WP_011255142 | OmpA family protein | - |
| HS903_RS00100 (D764_p2049) | 15808..16224 | + | 417 | WP_012478195 | hypothetical protein | - |
Host bacterium
| ID | 950 | GenBank | NC_019283 |
| Plasmid name | pC1-1 | Incompatibility group | IncP(Beta) |
| Plasmid size | 74280 bp | Coordinate of oriT [Strand] | 61641..62231 [+] |
| Host baterium | Delftia acidovorans |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | chloroaniline degradation plasmid |
| Symbiosis gene | - |
| Anti-CRISPR | - |